This page contains ASEs represented as a graph of the mRNA exonic structure mapped to the protein primary sequence. Exons are shown in white with black outline. The reference form is represented above the alternative form. Coding regions are shown with blue horizontal bars. These can be interrupted by red blocks for absent regions. Below are the domains in the protein obtained from NCBI's Conserved Domain Database. Domains that are affected by the ASE are outlined in red.

Further information can be obtained in the help page

FAS

• 113302 TNFRSF6-6 162 409
• NCBIGene 36.3 355
• Multiple exon skipping, size difference: 247
• Exclusion in the protein (no frameshift), Exclusion in the protein causing a frameshift
• Reference transcript: NM_000043

• Changed! cd TNFR 95aa 5e-16 in ref transcript
  • Tumor necrosis factor receptor (TNFR) domain; superfamily of TNF-like receptor domains. When bound to TNF-like cytokines, TNFRs trigger multiple signal transduction pathways, they are involved in inflammation response, apoptosis, autoimmunity and organogenesis. TNFRs domains are elongated with generally three tandem repeats of cysteine-rich domains (CRDs). They fit in the grooves between protomers within the ligand trimer. Some TNFRs, such as NGFR and HveA, bind ligands with no structural similarity to TNF and do not bind ligand trimers.
• Changed! smart DEATH 88aa 2e-16 in ref transcript
  • DEATH domain, found in proteins involved in cell death (apoptosis). Alpha-helical domain present in a variety of proteins with apoptotic functions. Some (but not all) of these domains form homotypic and heterotypic dimers.
• Changed! pfam TNFR_c6 37aa 4e-05 in ref transcript
  • TNFR/NGFR cysteine-rich region.

BCL2L11

• 113317 BCL2L11-4 130 220
• NCBIGene 36.2 10018
• Single exon skipping, size difference: 90
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_006538

• Changed! pfam Bclx_interact 36aa 3e-12 in ref transcript
  • Bcl-x interacting. This domain is a long alpha helix, required for interaction with Bcl-x. It is found in BAM, Bim and Bcl2-like protein 11.
• pfam Bim_N 37aa 9e-05 in ref transcript
  • Bim protein N-terminus. This family represents the N-terminal region of several mammal specific Bim proteins. The Bim protein is one of the BH3-only proteins, members of the Bcl-2 family that have only one of the Bcl-2 homology regions, BH3. BH3-only proteins are essential initiators of apoptotic cell death.
• Changed! pfam Bclx_interact 35aa 9e-11 in modified transcript

ACACA

• ACACA.F4 rs.ACACA.R1 208 319
• NCBIGene 36.3 31
• Single exon skipping, size difference: 111
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_198837

• Changed! cd biotinyl_domain 64aa 5e-11 in ref transcript
  • The biotinyl-domain or biotin carboxyl carrier protein (BCCP) domain is present in all biotin-dependent enzymes, such as acetyl-CoA carboxylase, pyruvate carboxylase, propionyl-CoA carboxylase, methylcrotonyl-CoA carboxylase, geranyl-CoA carboxylase, oxaloacetate decarboxylase, methylmalonyl-CoA decarboxylase, transcarboxylase and urea amidolyase. This domain functions in transferring CO2 from one subsite to another, allowing carboxylation, decarboxylation, or transcarboxylation. During this process, biotin is covalently attached to a specific lysine.
• Changed! pfam ACC_central 751aa 0.0 in ref transcript
  • Acetyl-CoA carboxylase, central region. The region featured in this family is found in various eukaryotic acetyl-CoA carboxylases, N-terminal to the catalytic domain (pfam01039). This enzyme (EC:6.4.1.2) is involved in the synthesis of long-chain fatty acids, as it catalyses the rate-limiting step in this process.
• Changed! pfam Carboxyl_trans 560aa 1e-163 in ref transcript
  • Carboxyl transferase domain. All of the members in this family are biotin dependent carboxylases. The carboxyl transferase domain carries out the following reaction; transcarboxylation from biotin to an acceptor molecule. There are two recognised types of carboxyl transferase. One of them uses acyl-CoA and the other uses 2-oxoacid as the acceptor molecule of carbon dioxide. All of the members in this family utilise acyl-CoA as the acceptor molecule.
• Changed! TIGR accC 502aa 2e-89 in ref transcript
  • This model represents the biotin carboxylase subunit found usually as a component of acetyl-CoA carboxylase. Acetyl-CoA carboxylase is designated EC 6.4.1.2 and this component, biotin carboxylase, has its own designation, EC 6.3.4.14. Homologous domains are found in eukaryotic forms of acetyl-CoA carboxylase and in a number of other carboxylases (e.g. pyruvate carboxylase), but seed members and trusted cutoff are selected so as to exclude these. In some systems, the biotin carboxyl carrier protein and this protein (biotin carboxylase) may be shared by different carboxyltransferases. However, this model is not intended to identify the biotin carboxylase domain of propionyl-coA carboxylase. The model should hit the full length of proteins, except for chloroplast transit peptides in plants. If it hits a domain only of a longer protein, there may be a problem with the identification.
• Changed! pfam Biotin_lipoyl 66aa 3e-13 in ref transcript
  • Biotin-requiring enzyme. This family covers two Prosite entries, the conserved lysine residue binds biotin in one group and lipoic acid in the other. May not recognise the Glycine cleavage system H proteins.
• Changed! COG AccC 503aa 1e-112 in ref transcript
  • Biotin carboxylase [Lipid metabolism].
• Changed! COG COG4799 561aa 2e-88 in ref transcript
  • Acetyl-CoA carboxylase, carboxyltransferase component (subunits alpha and beta) [Lipid metabolism].
• Changed! COG AccB 75aa 1e-07 in ref transcript
  • Biotin carboxyl carrier protein [Lipid metabolism].

AFF3

• AFF3.F2 AFF3.R31 380 455
• NCBIGene 36.3 3899
• Single exon skipping, size difference: 75
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001025108

• pfam AF-4 1204aa 0.0 in ref transcript
  • AF-4 proto-oncoprotein. This family consists of AF4 (Proto-oncogene AF4) and FMR2 (Fragile X E mental retardation syndrome) nuclear proteins. These proteins have been linked to human diseases such as acute lymphoblastic leukaemia and mental retardation. The family also contains a Drosophila AF4 protein homologue Lilliputian which contains an AT-hook domain. Lilliputian represents a novel pair-rule gene that acts in cytoskeleton regulation, segmentation and morphogenesis in Drosophila.

AKAP13

• AKAP13.u.f.21 AKAP13.u.r.24 286 352
• AceView 36.Apr07 AKAP13
• Single exon skipping, size difference: 66
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: AKAP13.bApr07

• cd RhoGEF 195aa 5e-37 in ref transcript
  • Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.
• cd PH 91aa 2e-05 in ref transcript
  • Pleckstrin homology (PH) domain. PH domains are only found in eukaryotes. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes.
• smart RhoGEF 192aa 5e-40 in ref transcript
  • Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases. Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains. Improved coverage.
• smart PH 102aa 5e-07 in ref transcript
  • Pleckstrin homology domain. Domain commonly found in eukaryotic signalling proteins. The domain family possesses multiple functions including the abilities to bind inositol phosphates, and various proteins. PH domains have been found to possess inserted domains (such as in PLC gamma, syntrophins) and to be inserted within other domains. Mutations in Brutons tyrosine kinase (Btk) within its PH domain cause X-linked agammaglobulinaemia (XLA) in patients. Point mutations cluster into the positively charged end of the molecule around the predicted binding site for phosphatidylinositol lipids.
• COG ROM1 305aa 5e-06 in ref transcript
  • RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms].

APAF1

• APAF1.F8 APAF1.R8 138 267
• NCBIGene 36.3 317
• Single exon skipping, size difference: 129
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_181861

• Changed! cd WD40 304aa 4e-60 in ref transcript
  • WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.
• cd WD40 274aa 5e-47 in ref transcript
• pfam NB-ARC 286aa 5e-73 in ref transcript
  • NB-ARC domain.
• pfam CARD 85aa 4e-14 in ref transcript
  • Caspase recruitment domain. Motif contained in proteins involved in apoptotic signaling. Predicted to possess a DEATH (pfam00531) domain-like fold.
• smart WD40 40aa 8e-08 in ref transcript
  • WD40 repeats. Note that these repeats are permuted with respect to the structural repeats (blades) of the beta propeller domain.
• smart WD40 40aa 2e-06 in ref transcript
• smart WD40 40aa 8e-05 in ref transcript
• smart WD40 42aa 1e-04 in ref transcript
• smart WD40 37aa 1e-04 in ref transcript
• Changed! pfam eIF2A 114aa 0.003 in ref transcript
  • Eukaryotic translation initiation factor eIF2A. This is a family of eukaryotic translation initiation factors.
• smart WD40 28aa 0.006 in ref transcript
• smart WD40 34aa 0.008 in ref transcript
• Changed! COG COG2319 398aa 4e-33 in ref transcript
  • FOG: WD40 repeat [General function prediction only].
• Changed! COG COG2319 408aa 5e-25 in ref transcript
• Changed! cd WD40 264aa 1e-55 in modified transcript
• Changed! COG COG2319 390aa 1e-33 in modified transcript

APCandSRP19andZRSR1

• APC.F16 APC.R14 232 344
• AceView 36.Apr07 APCandSRP19andZRSR1
• Single exon skipping, size difference: 112
• Inclusion in the protein causing a frameshift
• Reference transcript: APCandSRP19andZRSR1.eApr07

• Changed! cd RRM 61aa 5e-08 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• Changed! smart RRM_1 72aa 7e-16 in ref transcript
  • RNA recognition motif.
• Changed! pfam zf-CCCH 25aa 7e-04 in ref transcript
  • Zinc finger C-x8-C-x5-C-x3-H type (and similar).

ATG5

• APG5L.u.f.9 APG5L.u.r.5 148 276
• AceView 36.Apr07 ATG5
• Single exon skipping, size difference: 128
• Exclusion in the protein causing a frameshift
• Reference transcript: ATG5.bApr07

• Changed! pfam APG5 194aa 9e-71 in ref transcript
  • Autophagy protein Apg5. Apg5 is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway.

APP

• APP.F9 APP.R1 118 286
• NCBIGene 36.3 351
• Single exon skipping, size difference: 168
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_201413

• Changed! cd KU 52aa 1e-17 in ref transcript
  • BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
• pfam A4_EXTRA 165aa 1e-88 in ref transcript
  • Amyloid A4 extracellular domain.
• Changed! pfam Kunitz_BPTI 52aa 8e-19 in ref transcript
  • Kunitz/Bovine pancreatic trypsin inhibitor domain. Indicative of a protease inhibitor, usually a serine protease inhibitor. Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure. Certain family members are similar to the tick anticoagulant peptide (TAP). This is a highly selective inhibitor of factor Xa in the blood coagulation pathways. TAP molecules are highly dipolar, and are arranged to form a twisted two- stranded antiparallel beta-sheet followed by an alpha helix.
• pfam APP_amyloid 43aa 4e-18 in ref transcript
  • beta-amyloid precursor protein C-terminus. This is the amyloid, C-terminal, protein of the beta-Amyloid precursor protein (APP) which is a conserved and ubiquitous transmembrane glycoprotein strongly implicated in the pathogenesis of Alzheimer's disease but whose normal biological function is unknown. The C-terminal 100 residues are released and aggregate into amyloid deposits which are strongly implicated in the pathology of Alzheimer's disease plaque-formation. The domain is associated with family A4_EXTRA, pfam02177, further towards the N-terminus.
• pfam Beta-APP 34aa 1e-06 in ref transcript
  • Beta-amyloid peptide (beta-APP).
• pfam OmpH 81aa 0.004 in ref transcript
  • Outer membrane protein (OmpH-like). This family includes outer membrane proteins such as OmpH among others. Skp (OmpH) has been characterised as a molecular chaperone that interacts with unfolded proteins as they emerge in the periplasm from the Sec translocation machinery.
• Changed! PRK xseA 173aa 0.001 in ref transcript
  • exodeoxyribonuclease VII large subunit; Reviewed.

AXIN1

• AXIN1.u.f.11 AXIN1.R5 312 420
• NCBIGene 36.3 8312
• Single exon skipping, size difference: 108
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_003502

• pfam RGS 123aa 2e-31 in ref transcript
  • Regulator of G protein signaling domain. RGS family members are GTPase-activating proteins for heterotrimeric G-protein alpha-subunits.
• smart DAX 83aa 4e-27 in ref transcript
  • Domain present in Dishevelled and axin. Domain of unknown function.
• pfam Axin_b-cat_bind 33aa 2e-08 in ref transcript
  • Axin beta-catenin binding domain. This domain is found on the scaffolding protein Axin which is a component of the beta-catenin destruction complex. It competes with the tumour suppressor adenomatous polyposis coli protein (APC) for binding to beta-catenin.

AXL

• AXL_x151_x133_f AXL_x151_x133_r 178 205
• NCBIGene 36.3 558
• Single exon skipping, size difference: 27
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_021913

• cd PTKc_Axl 272aa 1e-167 in ref transcript
  • Catalytic Domain of the Protein Tyrosine Kinase, Axl. Protein Tyrosine Kinase (PTK) family; Axl; catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Axl is a member of the Axl subfamily, which is composed of receptor tyr kinases (RTKs) containing an extracellular ligand-binding region with two immunoglobulin-like domains followed by two fibronectin type III repeats, a transmembrane segment, and an intracellular catalytic domain. Binding to their ligands, Gas6 and protein S, leads to receptor dimerization, autophosphorylation, activation, and intracellular signaling. Axl is widely expressed in a variety of organs and cells including epithelial, mesenchymal, hematopoietic, as well as non-transformed cells. Axl signaling is important in many cellular functions such as survival, anti-apoptosis, proliferation, migration, and adhesion. Axl was originally isolated from patients with chronic myelogenous leukemia and a chronic myeloproliferative disorder. Axl is overexpressed in many human cancers including colon, squamous cell, thyroid, breast, and lung carcinomas.
• cd FN3 104aa 2e-06 in ref transcript
  • Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.
• cd IG 77aa 2e-05 in ref transcript
  • Immunoglobulin domain family; members are components of immunoglobulins, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• cd IGcam 84aa 0.006 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• cd FN3 88aa 0.009 in ref transcript
• smart TyrKc 266aa 1e-105 in ref transcript
  • Tyrosine kinase, catalytic domain. Phosphotransferases. Tyrosine-specific kinase subfamily.
• pfam fn3 85aa 2e-06 in ref transcript
  • Fibronectin type III domain.
• smart IG_like 83aa 2e-05 in ref transcript
  • Immunoglobulin like. IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
• pfam fn3 97aa 1e-04 in ref transcript
• pfam I-set 85aa 0.008 in ref transcript
  • Immunoglobulin I-set domain.
• COG SPS1 280aa 7e-23 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].

BCAS1

• BCAS1.F9 BCAS1.R4 226 292
• AceView 36.Apr07 BCAS1
• Single exon skipping, size difference: 66
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: BCAS1.aApr07

BCL2L1

• BCL2L1.u.f.5 BCL2L1.b.r.24 169 187
• AceView 36.Apr07 BCL2L1
• Alternative 3-prime, size difference: 18
• Inclusion in 5'UTR
• Reference transcript: BCL2L1.cApr07

• cd Bcl-2_like 114aa 2e-40 in ref transcript
  • Apoptosis regulator proteins of the Bcl-2 family, named after B-cell lymphoma 2. This alignment model spans what have been described as Bcl-2 homology regions BH1, BH2, BH3, and BH4. Many members of this family have an additional C-terminal transmembrane segment. Some homologous proteins, which are not included in this model, may miss either the BH4 (Bax, Bak) or the BH2 (Bcl-X(S)) region, and some appear to only share the BH3 region (Bik, Bim, Bad, Bid, Egl-1). This family is involved in the regulation of the outer mitochondrial membrane's permeability and in promoting or preventing the release of apoptogenic factors, which in turn may trigger apoptosis by activating caspases. Bcl-2 and the closely related Bcl-X(L) are anti-apoptotic key regulators of programmed cell death. They are assumed to function via heterodimeric protein-protein interactions, binding pro-apoptotic proteins such as Bad (BCL2-antagonist of cell death), Bid, and Bim, by specifically interacting with their BH3 regions. Interfering with this heterodimeric interaction via small-molecule inhibitors may prove effective in targeting various cancers. This family also includes the Caenorhabditis elegans Bcl-2 homolog CED-9, which binds to CED-4, the C. Elegans homolog of mammalian Apaf-1. Apaf-1, however, does not seem to be inhibited by Bcl-2 directly.
• TIGR bcl-2 233aa 1e-89 in ref transcript
  • in artificial membranes at acidic pH, proapoptotic Bcl-2 family proteins (including Bax and Bak) probably induce the mitochondrial permeability transition and cytochrome c release by interacting with permeability transition pores, the most important component for pore fomation of which is VDAC.

BCL2L12

• BCL2L12-3 BCL2L12-4 187 330
• AceView 36.Apr07 BCL2L12
• Single exon skipping, size difference: 143
• Exclusion in the protein causing a frameshift
• Reference transcript: BCL2L12.aApr07

AGR3

• BCMP11.F2 BCMP11.R2 119 255
• AceView 36.Apr07 AGR3
• Single exon skipping, size difference: 136
• Exclusion of the protein initiation site
• Reference transcript: AGR3.aApr07

• Changed! cd AGR 130aa 2e-67 in ref transcript
  • Anterior Gradient (AGR) family; members of this family are similar to secreted proteins encoded by the cement gland-specific genes XAG-1 and XAG-2, expressed in the anterior region of dorsal ectoderm of Xenopus. They are implicated in the formation of the cement gland and the induction of forebrain fate. The human homologs, hAG-2 and hAG-3, are secreted proteins associated with estrogen-positive breast tumors. Yeast two-hybrid studies identified the metastasis-associated C4.4a protein and dystroglycan as binding partners, indicating possible roles in the development and progression of breast cancer. hAG-2 has also been implicated in prostate cancer. Its gene was cloned as an androgen-inducible gene and it was shown to be overexpressed in prostate cancer cells at the mRNA and protein levels. AGR proteins contain one conserved cysteine corresponding to the first cysteine in the CXXC motif of TRX. They show high sequence similarity to ERp19.
• Changed! cd AGR 104aa 1e-51 in modified transcript

BMP4

• BMP4.u.f.4 BMP4.u.r.5 128 337
• NCBIGene 36.3 652
• Alternative 5-prime, size difference: 209
• Exclusion in 5'UTR
• Reference transcript: NM_001202

• pfam TGFb_propeptide 236aa 9e-62 in ref transcript
  • TGF-beta propeptide. This propeptide is known as latency associated peptide (LAP) in TGF-beta. LAP is a homodimer which is disulfide linked to TGF-beta binding protein.
• smart TGFB 101aa 9e-48 in ref transcript
  • Transforming growth factor-beta (TGF-beta) family. Family members are active as disulphide-linked homo- or heterodimers. TGFB is a multifunctional peptide that controls proliferation, differentiation, and other functions in many cell types.

BTC

• BTC.F1 BTC.R1 137 284
• AceView 36.Apr07 BTC
• Single exon skipping, size difference: 147
• Exclusion in the protein (no frameshift)
• Reference transcript: BTC.aApr07

C11orf17

• C11orf17-F1 C11orf17-R1 252 333
• AceView 36.Apr07 C11orf17
• Single exon skipping, size difference: 81
• Exclusion in the protein (no frameshift)
• Reference transcript: C11orf17.bApr07

SMG7

• C1orf16.F8 C1orf16.R8 99 249
• AceView 36.Apr07 SMG7
• Single exon skipping, size difference: 150
• Exclusion in the protein (no frameshift)
• Reference transcript: SMG7.aApr07

• cd TPR 79aa 0.003 in ref transcript
  • Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here.
• pfam EST1 119aa 1e-24 in ref transcript
  • Telomerase activating protein Est1. Est1 is a protein which recruits or activates telomerase at the site of polymerisation.

CAPN3

• CAPN3.u.f.38 CAPN3.u.r.40 153 297
• NCBIGene 36.3 825
• Single exon skipping, size difference: 144
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000070

• Changed! cd CysPc 353aa 1e-106 in ref transcript
  • Calpains, domains IIa, IIb; calcium-dependent cytoplasmic cysteine proteinases, papain-like. Functions in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction.
• cd Calpain_III 158aa 1e-54 in ref transcript
  • Calpain, subdomain III. Calpains are calcium-activated cytoplasmic cysteine proteinases, participate in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction. Catalytic domain and the two calmodulin-like domains are separated by C2-like domain III. Domain III plays an important role in calcium-induced activation of calpain involving electrostatic interactions with subdomain II. Proposed to mediate calpain's interaction with phospholipids and translocation to cytoplasmic/nuclear membranes. CD includes subdomain III of typical and atypical calpains.
• cd EFh 55aa 2e-06 in ref transcript
  • EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers.
• cd EFh 68aa 0.004 in ref transcript
• cd EFh 56aa 0.008 in ref transcript
• Changed! pfam Peptidase_C2 343aa 1e-158 in ref transcript
  • Calpain family cysteine protease.
• pfam Calpain_III 155aa 8e-65 in ref transcript
  • Calpain large subunit, domain III. The function of the domain III and I are currently unknown. Domain II is a cysteine protease and domain IV is a calcium binding domain. Calpains are believed to participate in intracellular signaling pathways mediated by calcium ions.
• COG FRQ1 99aa 6e-06 in ref transcript
  • Ca2+-binding protein (EF-Hand superfamily) [Signal transduction mechanisms / Cytoskeleton / Cell division and chromosome partitioning / General function prediction only].
• Changed! cd CysPc 305aa 1e-111 in modified transcript
• Changed! pfam Peptidase_C2 295aa 1e-165 in modified transcript

CASC4

• CASC4.F1 NM_177974-R1 127 295
• NCBIGene 36.3 113201
• Single exon skipping, size difference: 168
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_138423

• TIGR SMC_prok_B 159aa 3e-06 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• COG Smc 157aa 9e-05 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].
• COG FlaD 98aa 0.003 in ref transcript
  • Putative archaeal flagellar protein D/E [Cell motility and secretion].

CCL4

• CCL4.F1 CCL4.R1 259 372
• AceView 36.Apr07 CCL4
• Single exon skipping, size difference: 115
• Inclusion in the protein causing a new stop codon
• Reference transcript: CCL4.dApr07

• Changed! cd Chemokine_CC 26aa 1e-04 in ref transcript
  • Chemokine_CC: 1 of 4 subgroup designations based on the arrangement of the two N-terminal cysteine residues; includes a number of secreted growth factors and interferons involved in mitogenic, chemotactic, and inflammatory activity; some members (e.g. 2HCC) contain an additional disulfide bond which is thought to compensate for the highly conserved Trp missing in these; chemotatic for monocytes, macrophages, eosinophils, basophils, and T cells, but not neutrophils; exist as monomers and dimers, but are believed to be functional as monomers; found only in vertebrates and a few viruses; a subgroup of CC, identified by an N-terminal DCCL motif (Exodus-1, Exodus-2, and Exodus-3), has been shown to inhibit specific types of human cancer cell growth in a mouse model. See CDs: Chemokine (cd00169) for the general alignment of chemokines, or Chemokine_CXC (cd00273), Chemokine_C (cd00271), and Chemokine_CX3C (cd00274) for the additional chemokine subgroups, and Chemokine_CC_DCCL for the DCCL subgroup of this CD.
• Changed! pfam IL8 22aa 6e-05 in ref transcript
  • Small cytokines (intecrine/chemokine), interleukin-8 like. Includes a number of secreted growth factors and interferons involved in mitogenic, chemotactic, and inflammatory activity. Structure contains two highly conserved disulfide bonds.

CCNE1

• CCNE1.F14 CCNE1.R3 260 395
• AceView 36.Apr07 CCNE1
• Single exon skipping, size difference: 135
• Exclusion in the protein (no frameshift)
• Reference transcript: CCNE1.cApr07

• cd CYCLIN 91aa 1e-14 in ref transcript
  • Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain.
• Changed! pfam Cyclin_N 128aa 7e-42 in ref transcript
  • Cyclin, N-terminal domain. Cyclins regulate cyclin dependent kinases (CDKs). One member is a Uracil-DNA glycosylase that is related to other cyclins. Cyclins contain two domains of similar all-alpha fold, of which this family corresponds with the N-terminal domain.
• Changed! pfam Cyclin_C 126aa 1e-08 in ref transcript
  • Cyclin, C-terminal domain. Cyclins regulate cyclin dependent kinases (CDKs). Human UDG2 is a Uracil-DNA glycosylase that is related to other cyclins. Cyclins contain two domains of similar all-alpha fold, of which this family corresponds with the C-terminal domain.
• Changed! COG COG5024 213aa 5e-23 in ref transcript
  • Cyclin [Cell division and chromosome partitioning].
• Changed! pfam Cyclin_N 121aa 7e-39 in modified transcript
• Changed! pfam Cyclin_C 78aa 3e-07 in modified transcript
• Changed! COG COG5024 234aa 1e-21 in modified transcript

CD40

• CD40.F10 CD40.R9 133 229
• AceView 36.Apr07 CD40
• Alternative 3-prime, size difference: 96
• Inclusion in the protein causing a new stop codon
• Reference transcript: CD40.aApr07

• Changed! cd TNFR 98aa 8e-16 in ref transcript
  • Tumor necrosis factor receptor (TNFR) domain; superfamily of TNF-like receptor domains. When bound to TNF-like cytokines, TNFRs trigger multiple signal transduction pathways, they are involved in inflammation response, apoptosis, autoimmunity and organogenesis. TNFRs domains are elongated with generally three tandem repeats of cysteine-rich domains (CRDs). They fit in the grooves between protomers within the ligand trimer. Some TNFRs, such as NGFR and HveA, bind ligands with no structural similarity to TNF and do not bind ligand trimers.
• Changed! cd TNFR 63aa 3e-04 in ref transcript
• Changed! smart TNFR 39aa 0.004 in ref transcript
  • Tumor necrosis factor receptor / nerve growth factor receptor repeats. Repeats in growth factor receptors that are involved in growth factor binding. TNF/TNFR.

CDC2L1

• CDC2L1.u.f.9 refseq_CDC2L1.R1 197 334
• NCBIGene 36.2 984
• Single exon skipping, size difference: 137
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_001787

• Changed! cd S_TKc 287aa 1e-68 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• Changed! smart S_TKc 276aa 6e-69 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• Changed! PTZ PTZ00024 295aa 2e-55 in ref transcript
  • cyclin-dependent protein kinase; Provisional.

CDC2L2

• CDC2L2.u.f.7 refseq_CDC2L1.R6 140 179
• NCBIGene 36.2 985
• Alternative 5-prime, size difference: 39
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_033531

• cd S_TKc 287aa 1e-68 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• smart S_TKc 276aa 5e-69 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• PTZ PTZ00024 295aa 4e-55 in ref transcript
  • cyclin-dependent protein kinase; Provisional.

CHEK2

• CHEK2.u.f.31 CHEK2.u.r.29 194 256
• AceView 36.Apr07 CHEK2
• Single exon skipping, size difference: 62
• Exclusion in the protein causing a frameshift
• Reference transcript: CHEK2.aApr07

• Changed! cd S_TKc 268aa 7e-68 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• cd FHA 89aa 5e-07 in ref transcript
  • Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins localize to the nucleus, where they participate in establishing or maintaining cell cycle checkpoints, DNA repair, or transcriptional regulation. Members of the FHA family include: Dun1, Rad53, Cds1, Mek1, KAPP(kinase-associated protein phosphatase),and Ki-67 (a human nuclear protein related to cell proliferation).
• Changed! smart S_TKc 257aa 4e-75 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• pfam FHA 79aa 8e-08 in ref transcript
  • FHA domain. The FHA (Forkhead-associated) domain is a phosphopeptide binding motif.
• Changed! PTZ PTZ00263 226aa 5e-43 in ref transcript
  • protein kinase A catalytic subunit; Provisional.
• Changed! cd S_TKc 65aa 7e-09 in modified transcript
• Changed! smart STYKc 64aa 7e-10 in modified transcript
  • Protein kinase; unclassified specificity. Phosphotransferases. The specificity of this class of kinases can not be predicted. Possible dual-specificity Ser/Thr/Tyr kinase.

NLRP1

• DEFCAP.au.11.f NALP1.u.r.25 152 284
• NCBIGene 36.3 22861
• Single exon skipping, size difference: 132
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_033004

• cd LRR_RI 179aa 8e-30 in ref transcript
  • Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1).
• cd AAA 95aa 0.009 in ref transcript
  • The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.
• pfam NACHT 170aa 5e-45 in ref transcript
  • NACHT domain. This NTPase domain is found in apoptosis proteins as well as those involved in MHC transcription activation. This family is closely related to pfam00931.
• pfam CARD 82aa 2e-16 in ref transcript
  • Caspase recruitment domain. Motif contained in proteins involved in apoptotic signaling. Predicted to possess a DEATH (pfam00531) domain-like fold.
• pfam PAAD_DAPIN 58aa 2e-08 in ref transcript
  • PAAD/DAPIN/Pyrin domain. This domain is predicted to contain 6 alpha helices and to have the same fold as the pfam00531 domain. This similarity may mean that this is a protein-protein interaction domain.
• smart LRR_RI 28aa 0.002 in ref transcript
  • Leucine rich repeat, ribonuclease inhibitor type.
• COG RNA1 142aa 0.004 in ref transcript
  • Ran GTPase-activating protein (RanGAP) involved in mRNA processing and transport [Signal transduction mechanisms / RNA processing and modification].

DNMT3B

• DNMT3B.u.f.26 DNMT3B.u.r.28 137 326
• NCBIGene 36.3 1789
• Multiple exon skipping, size difference: 189
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_006892

• cd Dnmt3b_related 87aa 2e-35 in ref transcript
  • The PWWP domain is an essential component of DNA methyltransferase 3 B (Dnmt3b) which is responsible for establishing DNA methylation patterns during embryogenesis and gametogenesis. In tumorigenesis, DNA methylation by Dnmt3b is known to play a role in the inactivation of tumor suppressor genes. In addition, a point mutation in the PWWP domain of Dnmt3b has been identified in patients with ICF syndrome (immunodeficiency, centromeric instability, and facial anomalies), a rare autosomal recessive disorder characterized by hypomethylation of classical satellite DNA. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
• Changed! cd Cyt_C5_DNA_methylase 271aa 4e-13 in ref transcript
  • Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the mammalian genome. These effects include transcriptional repression via inhibition of transcription factor binding or the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability.
• pfam PWWP 73aa 8e-24 in ref transcript
  • PWWP domain. The PWWP domain is named after a conserved Pro-Trp-Trp-Pro motif. The function of the domain is currently unknown.
• pfam DNA_methylase 123aa 8e-08 in ref transcript
  • C-5 cytosine-specific DNA methylase.
• COG Dcm 160aa 5e-13 in ref transcript
  • Site-specific DNA methylase [DNA replication, recombination, and repair].
• Changed! cd Cyt_C5_DNA_methylase 134aa 9e-09 in modified transcript

DBF4B

• DRF1.F1 DRF1.R1 93 158
• AceView 36.Apr07 DBF4B
• Alternative 3-prime, size difference: 65
• Exclusion in the protein causing a frameshift
• Reference transcript: DBF4B.aApr07

• Changed! pfam zf-DBF 49aa 1e-16 in ref transcript
  • DBF zinc finger. This domain is predicted to bind metal ions and is often found associated with pfam00533 and pfam02178.
• Changed! COG DBF4 58aa 3e-04 in ref transcript
  • Protein kinase essential for the initiation of DNA replication [DNA replication, recombination, and repair / Cell division and chromosome partitioning].

DSC3

• DSC3.F1 DSC3.R1 229 272
• NCBIGene 36.3 1825
• Single exon skipping, size difference: 43
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_001941

• cd CA 218aa 9e-36 in ref transcript
  • Cadherin repeat domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion; these domains occur as repeats in the extracellular regions which are thought to mediate cell-cell contact when bound to calcium; plays a role in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-,CNR-,proto-,and FAT-family cadherin, desmocollin, and desmoglein, exists as monomers or dimers (hetero- and homo-); two copies of the repeat are present here.
• cd CA 209aa 8e-31 in ref transcript
• cd CA 210aa 4e-24 in ref transcript
• Changed! cd CA 193aa 1e-19 in ref transcript
• pfam Cadherin_pro 87aa 5e-18 in ref transcript
  • Cadherin prodomain like. Cadherins are a family of proteins that mediate calcium dependent cell-cell adhesion. They are activated through cleavage of a prosequence in the late Golgi. This domain corresponds to the folded region of the prosequence, and is termed the prodomain. The prodomain shows structural resemblance to the cadherin domain, but lacks all the features known to be important for cadherin-cadherin interactions.
• pfam Cadherin 99aa 9e-17 in ref transcript
  • Cadherin domain.
• pfam Cadherin 103aa 2e-11 in ref transcript
• smart CA 77aa 4e-11 in ref transcript
  • Cadherin repeats. Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. Cadherin domains occur as repeats in the extracellular regions which are thought to mediate cell-cell contact when bound to calcium.
• pfam Cadherin 95aa 1e-10 in ref transcript
• Changed! pfam Cadherin_C 63aa 1e-04 in ref transcript
  • Cadherin cytoplasmic region. Cadherins are vital in cell-cell adhesion during tissue differentiation. Cadherins are linked to the cytoskeleton by catenins. Catenins bind to the cytoplasmic tail of the cadherin. Cadherins cluster to form foci of homophilic binding units. A key determinant to the strength of the binding that it is mediated by cadherins is the juxtamembrane region of the cadherin. This region induces clustering and also binds to the protein p120ctn.
• Changed! pfam Cadherin 74aa 0.009 in ref transcript
• Changed! cd CA 192aa 2e-19 in modified transcript

ECT2

• ECT2.F12 ECT2.R11 100 193
• AceView 36.Apr07 ECT2
• Single exon skipping, size difference: 93
• Exclusion in the protein (no frameshift)
• Reference transcript: ECT2.aApr07

• cd PH_etc2 129aa 2e-61 in ref transcript
  • Epithelial cell transforming 2 (ECT2) pleckstrin homology (PH) domain. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinases, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, a well as cytoskeletal associated molecules and in lipid associated enzymes.
• cd RhoGEF 187aa 7e-37 in ref transcript
  • Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.
• cd BRCT 71aa 4e-08 in ref transcript
  • Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks.
• smart RhoGEF 185aa 2e-43 in ref transcript
  • Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases. Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains. Improved coverage.
• smart BRCT 73aa 2e-07 in ref transcript
  • breast cancer carboxy-terminal domain.
• pfam BRCT 72aa 7e-04 in ref transcript
  • BRCA1 C Terminus (BRCT) domain. The BRCT domain is found predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage. It has been suggested that the Retinoblastoma protein contains a divergent BRCT domain, this has not been included in this family. The BRCT domain of XRCC1 forms a homodimer in the crystal structure. This suggests that pairs of BRCT domains associate as homo- or heterodimers.
• COG ROM1 201aa 1e-08 in ref transcript
  • RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms].

F3

• F3.F2 F3.R2 270 430
• AceView 36.Apr07 F3
• Single exon skipping, size difference: 160
• Exclusion in the protein causing a frameshift
• Reference transcript: F3.aApr07

• pfam Tissue_fac 125aa 3e-52 in ref transcript
  • Tissue factor.

FANCA

• FANCA.F13 FANCA.R13 102 231
• AceView 36.Apr07 FANCA
• Single exon skipping, size difference: 129
• Exclusion in the protein (no frameshift)
• Reference transcript: FANCA.aApr07

• pfam Fanconi_A 31aa 5e-10 in ref transcript
  • Fanconi anaemia group A protein.

FANCL

• FANCL.F9 FANCL.R5 153 431
• AceView 36.Apr07 FANCL
• Multiple exon skipping, size difference: 278
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift, Exclusion in the protein (no frameshift), Exclusion in the protein causing a frameshift
• Reference transcript: FANCL.bApr07

• Changed! pfam WD-3 270aa 1e-118 in ref transcript
  • WD-repeat region. This entry is of a region of approximately 100 residues containing three WD repeats and six cysteine residues possibly as three cystine-bridges. These regions are contained within the Fancl protein in humans which is the putative E3 ubiquitin ligase subunit of the FA complex (Fanconi anaemia). Eight subunits of the Fanconi anaemia gene products form a multisubunit nuclear complex which is required for mono-ubiquitination of a downstream FA protein, FANCD2. The WD repeats are required for interaction with other subunits of the FA complex.
• Changed! COG COG5219 62aa 0.003 in ref transcript
  • Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only].

FASTK

• FAST_HUMAN-5 FAST_HUMAN-6 410 730
• AceView 36.Apr07 FASTK
• Multiple exon skipping, size difference: 320
• Exclusion in the protein (no frameshift), Exclusion in the protein causing a frameshift
• Reference transcript: FASTK.aApr07

• Changed! pfam FAST_1 67aa 1e-13 in ref transcript
  • FAST kinase-like protein, subdomain 1. This family represents a conserved region of eukaryotic Fas-activated serine/threonine (FAST) kinases (EC:2.7.1.-) that contains several conserved leucine residues. FAST kinase is rapidly activated during Fas-mediated apoptosis, when it phosphorylates TIA-1, a nuclear RNA-binding protein that has been implicated as an effector of apoptosis. Note that many family members are hypothetical proteins. This region is often found immediately N-terminal to the FAST kinase-like protein, subdomain 2.
• Changed! pfam FAST_2 92aa 8e-13 in ref transcript
  • FAST kinase-like protein, subdomain 2. This family represents a conserved region of eukaryotic Fas-activated serine/threonine (FAST) kinases (EC:2.7.1.-) that contains several conserved leucine residues. FAST kinase is rapidly activated during Fas-mediated apoptosis, when it phosphorylates TIA-1, a nuclear RNA-binding protein that has been implicated as an effector of apoptosis. Note that many family members are hypothetical proteins. This subdomain is often found associated with the FAST kinase-like protein, subdomain 2.
• Changed! pfam RAP 58aa 5e-12 in ref transcript
  • RAP domain. This domain is found in various eukaryotic species, particularly in apicomplexans such as Plasmodium falciparum, where it is found in proteins that are important in various parasite-host cell interactions. It is thought to be an RNA-binding domain.

FGFR1OP

• FGFR1OP.u.f.10 FGFR1OP.u.r.12 108 168
• NCBIGene 36.3 11116
• Single exon skipping, size difference: 60
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_007045

• pfam FOP_dimer 81aa 8e-35 in ref transcript
  • FOP N terminal dimerisation domain. Fibroblast growth factor receptor 1 (FGFR1) oncogene partner (FOP) is a centrosomal protein that is involved in anchoring microtubules to subcellular structures. This domain includes a Lis-homology motif. It forms an alpha helical bundle and is involved in dimerisation.

FGFR2

• FGFR2.F1 FGFR2.R1 205 472
• AceView 36.Apr07 FGFR2
• Single exon skipping, size difference: 267
• Exclusion in the protein (no frameshift)
• Reference transcript: FGFR2.aApr07

• cd PTKc_FGFR2 304aa 0.0 in ref transcript
  • Catalytic Domain of the Protein Tyrosine Kinase, Fibroblast Growth Factor Receptor 2. Protein Tyrosine Kinase (PTK) family; Fibroblast Growth Factor Receptor 2 (FGFR2); catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. FGFR2 is part of the FGFR subfamily, which are receptor tyr kinases (RTKs) containing an extracellular ligand-binding region with three immunoglobulin-like domains, a transmembrane segment, and an intracellular catalytic domain. The binding of FGFRs to their ligands, the FGFs, results in receptor dimerization and activation, and intracellular signaling. The binding of FGFs to FGFRs is promiscuous, in that a receptor may be activated by several ligands and a ligand may bind to more that one type of receptor. There are many splice variants of FGFR2 which show differential expression and binding to FGF ligands. Disruption of either FGFR2 or FGFR2b is lethal in mice, due to defects in the placenta or severe impairment of tissue development including lung, limb, and thyroid, respectively. Disruption of FGFR2c in mice results in defective bone and skull development. Genetic alterations of FGFR2 are associated with many human skeletal disorders including Apert syndrome, Crouzon syndrome, Jackson-Weiss syndrome, and Pfeiffer syndrome.
• cd IGcam 93aa 1e-16 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• cd IGcam 101aa 3e-05 in ref transcript
• Changed! cd IGcam 64aa 8e-05 in ref transcript
• pfam Pkinase_Tyr 277aa 1e-115 in ref transcript
  • Protein tyrosine kinase.
• pfam I-set 75aa 2e-12 in ref transcript
  • Immunoglobulin I-set domain.
• Changed! smart IGc2 57aa 9e-11 in ref transcript
  • Immunoglobulin C-2 Type.
• smart IG_like 96aa 2e-10 in ref transcript
  • Immunoglobulin like. IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
• COG SPS1 252aa 3e-21 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].

FGFR3

• FGFR3.F4 rs.FGFR3.R1 99 435
• NCBIGene 36.3 2261
• Multiple exon skipping, size difference: 336
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_000142

• cd PTKc_FGFR3 334aa 0.0 in ref transcript
  • Catalytic Domain of the Protein Tyrosine Kinase, Fibroblast Growth Factor Receptor 3. Protein Tyrosine Kinase (PTK) family; Fibroblast Growth Factor Receptor 3 (FGFR3); catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. FGFR3 is part of the FGFR subfamily, which are receptor tyr kinases (RTKs) containing an extracellular ligand-binding region with three immunoglobulin-like domains, a transmembrane segment, and an intracellular catalytic domain. The binding of FGFRs to their ligands, the FGFs, results in receptor dimerization and activation, and intracellular signaling. The binding of FGFs to FGFRs is promiscuous, in that a receptor may be activated by several ligands and a ligand may bind to more that one type of receptor. Many FGFR3 splice variants have been reported with the IIIb and IIIc isoforms being the predominant forms. FGFR3 IIIc is the isoform expressed in chondrocytes, the cells affected in dwarfism, while IIIb is expressed in epithelial cells. FGFR3 ligands include FGF1, FGF2, FGF4, FGF8, FGF9, and FGF23. It is a negative regulator of long bone growth. In the cochlear duct and in the lens, FGFR3 is involved in differentiation while it appears to have a role in cell proliferation in epithelial cells. Germline mutations in FGFR3 are associated with skeletal disorders including several forms of dwarfism. Some missense mutations are associated with multiple myeloma and carcinomas of the bladder and cervix. Overexpression of FGFR3 is found in thyroid carcinoma.
• cd IGcam 93aa 4e-16 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• Changed! cd IGcam 94aa 8e-08 in ref transcript
• pfam Pkinase_Tyr 277aa 1e-117 in ref transcript
  • Protein tyrosine kinase.
• pfam I-set 75aa 2e-13 in ref transcript
  • Immunoglobulin I-set domain.
• Changed! smart IG_like 94aa 2e-10 in ref transcript
  • Immunoglobulin like. IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
• smart IGc2 58aa 6e-06 in ref transcript
  • Immunoglobulin C-2 Type.
• COG SPS1 275aa 6e-22 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].
• Changed! smart IG_like 43aa 0.009 in modified transcript

FGFR4

• FGFR4.F23 FGFR4.R11 275 469
• AceView 36.Apr07 FGFR4
• Alternative 3-prime, size difference: 194
• Inclusion in the protein causing a frameshift
• Reference transcript: FGFR4.bApr07

• Changed! cd PTKc_FGFR4 311aa 0.0 in ref transcript
  • Catalytic Domain of the Protein Tyrosine Kinase, Fibroblast Growth Factor Receptor 4. Protein Tyrosine Kinase (PTK) family; Fibroblast Growth Factor Receptor 4 (FGFR4); catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. FGFR4 is part of the FGFR subfamily, which are receptor tyr kinases (RTKs) containing an extracellular ligand-binding region with three immunoglobulin-like domains, a transmembrane segment, and an intracellular catalytic domain. The binding of FGFRs to their ligands, the FGFs, results in receptor dimerization and activation, and intracellular signaling. The binding of FGFs to FGFRs is promiscuous, in that a receptor may be activated by several ligands and a ligand may bind to more that one type of receptor. Unlike other FGFRs, there is only one splice form of FGFR4. It binds FGF1, FGF2, FGF6, FGF19, and FGF23. FGF19 is a selective ligand for FGFR4. Although disruption of FGFR4 in mice causes no obvious phenotype, in vivo inhibition of FGFR4 in cultured skeletal muscle cells resulted in an arrest of muscle progenitor differentiation. FGF6 and FGFR4 are uniquely expressed in myofibers and satellite cells. FGF6/FGFR4 signaling appears to play a key role in the regulation of muscle regeneration. A polymorphism in FGFR4 is found in head and neck squamous cell carcinoma.
• cd IGcam 93aa 6e-17 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• cd IGcam 101aa 2e-07 in ref transcript
• cd IGcam 67aa 0.003 in ref transcript
• Changed! pfam Pkinase_Tyr 277aa 1e-114 in ref transcript
  • Protein tyrosine kinase.
• smart IGc2 67aa 4e-15 in ref transcript
  • Immunoglobulin C-2 Type.
• smart IG_like 96aa 6e-12 in ref transcript
  • Immunoglobulin like. IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
• smart IGc2 58aa 8e-09 in ref transcript
• Changed! COG SPS1 251aa 7e-23 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].

FN1

• FN1.u.f.30 FN1.u.r.34 296 569
• NCBIGene 36.3 2335
• Single exon skipping, size difference: 273
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_212482

• cd FN2 48aa 2e-16 in ref transcript
  • Fibronectin Type II domain: FN2 is one of three types of internal repeats which combine to form larger domains within fibronectin. Fibronectin, a plasma protein that binds cell surfaces and various compounds including collagen, fibrin, heparin, DNA, and actin, usually exists as a dimer in plasma and as an insoluble multimer in extracellular matrices. Dimers of nearly identical subunits are linked by a disulfide bond close to their C-terminus. Fibronectin is composed of 3 types of modules, FN1,FN2 and FN3. The collagen binding domain contains four FN1 and two FN2 repeats.
• cd FN2 48aa 3e-16 in ref transcript
• cd FN3 83aa 4e-10 in ref transcript
  • Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.
• cd FN1 44aa 4e-09 in ref transcript
  • Fibronectin type 1 domain, approximately 40 residue long with two conserved disulfide bridges. FN1 is one of three types of internal repeats which combine to form larger domains within fibronectin. Fibronectin, a plasma protein that binds cell surfaces and various compounds including collagen, fibrin, heparin, DNA, and actin, usually exists as a dimer in plasma and as an insoluble multimer in extracellular matrices. Dimers of nearly identical subunits are linked by a disulfide bond close to their C-terminus. FN1 domains also found in coagulation factor XII, HGF activator, and tissue-type plasminogen activator. In tissue plasminogen activator, FN1 domains may form functional fibrin-binding units with EGF-like domains C-terminal to FN1.
• cd FN3 81aa 8e-09 in ref transcript
• cd FN3 80aa 1e-08 in ref transcript
• cd FN1 40aa 4e-08 in ref transcript
• cd FN1 42aa 5e-08 in ref transcript
• cd FN1 45aa 8e-08 in ref transcript
• cd FN3 88aa 1e-07 in ref transcript
• cd FN3 88aa 2e-07 in ref transcript
• cd FN1 44aa 2e-07 in ref transcript
• cd FN3 87aa 3e-07 in ref transcript
• cd FN1 38aa 4e-07 in ref transcript
• cd FN3 81aa 9e-07 in ref transcript
• cd FN3 82aa 1e-06 in ref transcript
• cd FN3 88aa 1e-06 in ref transcript
• cd FN1 41aa 1e-06 in ref transcript
• Changed! cd FN3 93aa 2e-06 in ref transcript
• cd FN1 45aa 2e-06 in ref transcript
• cd FN1 42aa 2e-06 in ref transcript
• cd FN3 81aa 6e-06 in ref transcript
• cd FN3 90aa 8e-06 in ref transcript
• cd FN3 73aa 9e-06 in ref transcript
• cd FN1 44aa 1e-05 in ref transcript
• cd FN1 43aa 3e-05 in ref transcript
• cd FN1 39aa 0.003 in ref transcript
• cd FN3 73aa 0.006 in ref transcript
• smart FN2 49aa 9e-20 in ref transcript
  • Fibronectin type 2 domain. One of three types of internal repeat within the plasma protein, fibronectin. Also occurs in coagulation factor XII, 2 type IV collagenases, PDC-109, and cation-independent mannose-6-phosphate and secretory phospholipase A2 receptors. In fibronectin, PDC-109, and the collagenases, this domain contributes to collagen-binding function.
• smart FN2 49aa 4e-19 in ref transcript
• pfam fn3 82aa 8e-17 in ref transcript
  • Fibronectin type III domain.
• smart FN1 45aa 6e-13 in ref transcript
  • Fibronectin type 1 domain. One of three types of internal repeat within the plasma protein, fibronectin. Found also in coagulation factor XII, HGF activator and tissue-type plasminogen activator. In t-PA and fibronectin, this domain type contributes to fibrin-binding.
• pfam fn1 39aa 1e-12 in ref transcript
  • Fibronectin type I domain.
• pfam fn3 81aa 3e-12 in ref transcript
• pfam fn3 81aa 3e-12 in ref transcript
• smart FN1 45aa 3e-12 in ref transcript
• smart FN1 42aa 3e-12 in ref transcript
• smart FN1 45aa 5e-12 in ref transcript
• smart FN1 39aa 2e-11 in ref transcript
• pfam fn3 81aa 4e-11 in ref transcript
• Changed! pfam fn3 83aa 5e-11 in ref transcript
• pfam fn3 67aa 8e-11 in ref transcript
• pfam fn1 39aa 8e-11 in ref transcript
• pfam fn3 81aa 1e-10 in ref transcript
• pfam fn3 80aa 1e-10 in ref transcript
• smart FN1 43aa 2e-10 in ref transcript
• pfam fn3 80aa 5e-10 in ref transcript
• smart FN1 44aa 7e-10 in ref transcript
• pfam fn3 81aa 8e-09 in ref transcript
• pfam fn3 85aa 9e-09 in ref transcript
• pfam fn3 70aa 1e-08 in ref transcript
• pfam fn3 65aa 2e-08 in ref transcript
• smart FN1 41aa 3e-08 in ref transcript
• pfam fn3 81aa 3e-07 in ref transcript
• smart FN1 41aa 5e-07 in ref transcript
• pfam fn3 54aa 5e-05 in ref transcript
• pfam fn1 31aa 9e-05 in ref transcript

FN1

• FN1.u.f.40 FN1.u.r.45 126 396
• NCBIGene 36.3 2335
• Single exon skipping, size difference: 270
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_212482

• cd FN2 48aa 2e-16 in ref transcript
  • Fibronectin Type II domain: FN2 is one of three types of internal repeats which combine to form larger domains within fibronectin. Fibronectin, a plasma protein that binds cell surfaces and various compounds including collagen, fibrin, heparin, DNA, and actin, usually exists as a dimer in plasma and as an insoluble multimer in extracellular matrices. Dimers of nearly identical subunits are linked by a disulfide bond close to their C-terminus. Fibronectin is composed of 3 types of modules, FN1,FN2 and FN3. The collagen binding domain contains four FN1 and two FN2 repeats.
• cd FN2 48aa 3e-16 in ref transcript
• cd FN3 83aa 4e-10 in ref transcript
  • Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.
• cd FN1 44aa 4e-09 in ref transcript
  • Fibronectin type 1 domain, approximately 40 residue long with two conserved disulfide bridges. FN1 is one of three types of internal repeats which combine to form larger domains within fibronectin. Fibronectin, a plasma protein that binds cell surfaces and various compounds including collagen, fibrin, heparin, DNA, and actin, usually exists as a dimer in plasma and as an insoluble multimer in extracellular matrices. Dimers of nearly identical subunits are linked by a disulfide bond close to their C-terminus. FN1 domains also found in coagulation factor XII, HGF activator, and tissue-type plasminogen activator. In tissue plasminogen activator, FN1 domains may form functional fibrin-binding units with EGF-like domains C-terminal to FN1.
• cd FN3 81aa 8e-09 in ref transcript
• cd FN3 80aa 1e-08 in ref transcript
• cd FN1 40aa 4e-08 in ref transcript
• cd FN1 42aa 5e-08 in ref transcript
• cd FN1 45aa 8e-08 in ref transcript
• cd FN3 88aa 1e-07 in ref transcript
• cd FN3 88aa 2e-07 in ref transcript
• cd FN1 44aa 2e-07 in ref transcript
• cd FN3 87aa 3e-07 in ref transcript
• cd FN1 38aa 4e-07 in ref transcript
• Changed! cd FN3 81aa 9e-07 in ref transcript
• cd FN3 82aa 1e-06 in ref transcript
• Changed! cd FN3 88aa 1e-06 in ref transcript
• cd FN1 41aa 1e-06 in ref transcript
• cd FN3 93aa 2e-06 in ref transcript
• cd FN1 45aa 2e-06 in ref transcript
• cd FN1 42aa 2e-06 in ref transcript
• cd FN3 81aa 6e-06 in ref transcript
• cd FN3 90aa 8e-06 in ref transcript
• cd FN3 73aa 9e-06 in ref transcript
• cd FN1 44aa 1e-05 in ref transcript
• cd FN1 43aa 3e-05 in ref transcript
• cd FN1 39aa 0.003 in ref transcript
• cd FN3 73aa 0.006 in ref transcript
• smart FN2 49aa 9e-20 in ref transcript
  • Fibronectin type 2 domain. One of three types of internal repeat within the plasma protein, fibronectin. Also occurs in coagulation factor XII, 2 type IV collagenases, PDC-109, and cation-independent mannose-6-phosphate and secretory phospholipase A2 receptors. In fibronectin, PDC-109, and the collagenases, this domain contributes to collagen-binding function.
• smart FN2 49aa 4e-19 in ref transcript
• pfam fn3 82aa 8e-17 in ref transcript
  • Fibronectin type III domain.
• smart FN1 45aa 6e-13 in ref transcript
  • Fibronectin type 1 domain. One of three types of internal repeat within the plasma protein, fibronectin. Found also in coagulation factor XII, HGF activator and tissue-type plasminogen activator. In t-PA and fibronectin, this domain type contributes to fibrin-binding.
• Changed! pfam fn1 39aa 1e-12 in ref transcript
  • Fibronectin type I domain.
• pfam fn3 81aa 3e-12 in ref transcript
• pfam fn3 81aa 3e-12 in ref transcript
• smart FN1 45aa 3e-12 in ref transcript
• smart FN1 42aa 3e-12 in ref transcript
• smart FN1 45aa 5e-12 in ref transcript
• smart FN1 39aa 2e-11 in ref transcript
• pfam fn3 81aa 4e-11 in ref transcript
• pfam fn3 83aa 5e-11 in ref transcript
• pfam fn3 67aa 8e-11 in ref transcript
• pfam fn1 39aa 8e-11 in ref transcript
• pfam fn3 81aa 1e-10 in ref transcript
• pfam fn3 80aa 1e-10 in ref transcript
• smart FN1 43aa 2e-10 in ref transcript
• pfam fn3 80aa 5e-10 in ref transcript
• smart FN1 44aa 7e-10 in ref transcript
• pfam fn3 81aa 8e-09 in ref transcript
• pfam fn3 85aa 9e-09 in ref transcript
• pfam fn3 70aa 1e-08 in ref transcript
• pfam fn3 65aa 2e-08 in ref transcript
• smart FN1 41aa 3e-08 in ref transcript
• Changed! pfam fn3 81aa 3e-07 in ref transcript
• smart FN1 41aa 5e-07 in ref transcript
• pfam fn3 54aa 5e-05 in ref transcript
• pfam fn1 31aa 9e-05 in ref transcript
• Changed! cd FN3 89aa 3e-07 in modified transcript
• Changed! smart FN1 44aa 2e-12 in modified transcript

FN1

• FN1.u.f.55 FN1.u.r.62 129 204
• NCBIGene 36.3 2335
• Alternative 3-prime, size difference: 75
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_212482

• cd FN2 48aa 2e-16 in ref transcript
  • Fibronectin Type II domain: FN2 is one of three types of internal repeats which combine to form larger domains within fibronectin. Fibronectin, a plasma protein that binds cell surfaces and various compounds including collagen, fibrin, heparin, DNA, and actin, usually exists as a dimer in plasma and as an insoluble multimer in extracellular matrices. Dimers of nearly identical subunits are linked by a disulfide bond close to their C-terminus. Fibronectin is composed of 3 types of modules, FN1,FN2 and FN3. The collagen binding domain contains four FN1 and two FN2 repeats.
• cd FN2 48aa 3e-16 in ref transcript
• cd FN3 83aa 4e-10 in ref transcript
  • Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.
• cd FN1 44aa 4e-09 in ref transcript
  • Fibronectin type 1 domain, approximately 40 residue long with two conserved disulfide bridges. FN1 is one of three types of internal repeats which combine to form larger domains within fibronectin. Fibronectin, a plasma protein that binds cell surfaces and various compounds including collagen, fibrin, heparin, DNA, and actin, usually exists as a dimer in plasma and as an insoluble multimer in extracellular matrices. Dimers of nearly identical subunits are linked by a disulfide bond close to their C-terminus. FN1 domains also found in coagulation factor XII, HGF activator, and tissue-type plasminogen activator. In tissue plasminogen activator, FN1 domains may form functional fibrin-binding units with EGF-like domains C-terminal to FN1.
• cd FN3 81aa 8e-09 in ref transcript
• cd FN3 80aa 1e-08 in ref transcript
• cd FN1 40aa 4e-08 in ref transcript
• cd FN1 42aa 5e-08 in ref transcript
• cd FN1 45aa 8e-08 in ref transcript
• cd FN3 88aa 1e-07 in ref transcript
• cd FN3 88aa 2e-07 in ref transcript
• cd FN1 44aa 2e-07 in ref transcript
• cd FN3 87aa 3e-07 in ref transcript
• cd FN1 38aa 4e-07 in ref transcript
• cd FN3 81aa 9e-07 in ref transcript
• cd FN3 82aa 1e-06 in ref transcript
• cd FN3 88aa 1e-06 in ref transcript
• cd FN1 41aa 1e-06 in ref transcript
• cd FN3 93aa 2e-06 in ref transcript
• cd FN1 45aa 2e-06 in ref transcript
• cd FN1 42aa 2e-06 in ref transcript
• cd FN3 81aa 6e-06 in ref transcript
• cd FN3 90aa 8e-06 in ref transcript
• cd FN3 73aa 9e-06 in ref transcript
• cd FN1 44aa 1e-05 in ref transcript
• cd FN1 43aa 3e-05 in ref transcript
• cd FN1 39aa 0.003 in ref transcript
• cd FN3 73aa 0.006 in ref transcript
• smart FN2 49aa 9e-20 in ref transcript
  • Fibronectin type 2 domain. One of three types of internal repeat within the plasma protein, fibronectin. Also occurs in coagulation factor XII, 2 type IV collagenases, PDC-109, and cation-independent mannose-6-phosphate and secretory phospholipase A2 receptors. In fibronectin, PDC-109, and the collagenases, this domain contributes to collagen-binding function.
• smart FN2 49aa 4e-19 in ref transcript
• pfam fn3 82aa 8e-17 in ref transcript
  • Fibronectin type III domain.
• smart FN1 45aa 6e-13 in ref transcript
  • Fibronectin type 1 domain. One of three types of internal repeat within the plasma protein, fibronectin. Found also in coagulation factor XII, HGF activator and tissue-type plasminogen activator. In t-PA and fibronectin, this domain type contributes to fibrin-binding.
• pfam fn1 39aa 1e-12 in ref transcript
  • Fibronectin type I domain.
• pfam fn3 81aa 3e-12 in ref transcript
• pfam fn3 81aa 3e-12 in ref transcript
• smart FN1 45aa 3e-12 in ref transcript
• smart FN1 42aa 3e-12 in ref transcript
• smart FN1 45aa 5e-12 in ref transcript
• smart FN1 39aa 2e-11 in ref transcript
• pfam fn3 81aa 4e-11 in ref transcript
• pfam fn3 83aa 5e-11 in ref transcript
• pfam fn3 67aa 8e-11 in ref transcript
• pfam fn1 39aa 8e-11 in ref transcript
• pfam fn3 81aa 1e-10 in ref transcript
• pfam fn3 80aa 1e-10 in ref transcript
• smart FN1 43aa 2e-10 in ref transcript
• pfam fn3 80aa 5e-10 in ref transcript
• smart FN1 44aa 7e-10 in ref transcript
• pfam fn3 81aa 8e-09 in ref transcript
• pfam fn3 85aa 9e-09 in ref transcript
• pfam fn3 70aa 1e-08 in ref transcript
• pfam fn3 65aa 2e-08 in ref transcript
• smart FN1 41aa 3e-08 in ref transcript
• pfam fn3 81aa 3e-07 in ref transcript
• smart FN1 41aa 5e-07 in ref transcript
• pfam fn3 54aa 5e-05 in ref transcript
• pfam fn1 31aa 9e-05 in ref transcript

FN1

• FN1.u.f.56 FN1.u.r.67 231 319
• NCBIGene 36.3 2335
• Intron retention, size difference: 93
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_212482

• cd FN2 48aa 2e-16 in ref transcript
  • Fibronectin Type II domain: FN2 is one of three types of internal repeats which combine to form larger domains within fibronectin. Fibronectin, a plasma protein that binds cell surfaces and various compounds including collagen, fibrin, heparin, DNA, and actin, usually exists as a dimer in plasma and as an insoluble multimer in extracellular matrices. Dimers of nearly identical subunits are linked by a disulfide bond close to their C-terminus. Fibronectin is composed of 3 types of modules, FN1,FN2 and FN3. The collagen binding domain contains four FN1 and two FN2 repeats.
• cd FN2 48aa 3e-16 in ref transcript
• cd FN3 83aa 4e-10 in ref transcript
  • Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.
• cd FN1 44aa 4e-09 in ref transcript
  • Fibronectin type 1 domain, approximately 40 residue long with two conserved disulfide bridges. FN1 is one of three types of internal repeats which combine to form larger domains within fibronectin. Fibronectin, a plasma protein that binds cell surfaces and various compounds including collagen, fibrin, heparin, DNA, and actin, usually exists as a dimer in plasma and as an insoluble multimer in extracellular matrices. Dimers of nearly identical subunits are linked by a disulfide bond close to their C-terminus. FN1 domains also found in coagulation factor XII, HGF activator, and tissue-type plasminogen activator. In tissue plasminogen activator, FN1 domains may form functional fibrin-binding units with EGF-like domains C-terminal to FN1.
• cd FN3 81aa 8e-09 in ref transcript
• cd FN3 80aa 1e-08 in ref transcript
• cd FN1 40aa 4e-08 in ref transcript
• cd FN1 42aa 5e-08 in ref transcript
• cd FN1 45aa 8e-08 in ref transcript
• cd FN3 88aa 1e-07 in ref transcript
• cd FN3 88aa 2e-07 in ref transcript
• cd FN1 44aa 2e-07 in ref transcript
• cd FN3 87aa 3e-07 in ref transcript
• cd FN1 38aa 4e-07 in ref transcript
• cd FN3 81aa 9e-07 in ref transcript
• cd FN3 82aa 1e-06 in ref transcript
• cd FN3 88aa 1e-06 in ref transcript
• cd FN1 41aa 1e-06 in ref transcript
• cd FN3 93aa 2e-06 in ref transcript
• cd FN1 45aa 2e-06 in ref transcript
• cd FN1 42aa 2e-06 in ref transcript
• cd FN3 81aa 6e-06 in ref transcript
• cd FN3 90aa 8e-06 in ref transcript
• cd FN3 73aa 9e-06 in ref transcript
• cd FN1 44aa 1e-05 in ref transcript
• cd FN1 43aa 3e-05 in ref transcript
• cd FN1 39aa 0.003 in ref transcript
• cd FN3 73aa 0.006 in ref transcript
• smart FN2 49aa 9e-20 in ref transcript
  • Fibronectin type 2 domain. One of three types of internal repeat within the plasma protein, fibronectin. Also occurs in coagulation factor XII, 2 type IV collagenases, PDC-109, and cation-independent mannose-6-phosphate and secretory phospholipase A2 receptors. In fibronectin, PDC-109, and the collagenases, this domain contributes to collagen-binding function.
• smart FN2 49aa 4e-19 in ref transcript
• pfam fn3 82aa 8e-17 in ref transcript
  • Fibronectin type III domain.
• smart FN1 45aa 6e-13 in ref transcript
  • Fibronectin type 1 domain. One of three types of internal repeat within the plasma protein, fibronectin. Found also in coagulation factor XII, HGF activator and tissue-type plasminogen activator. In t-PA and fibronectin, this domain type contributes to fibrin-binding.
• pfam fn1 39aa 1e-12 in ref transcript
  • Fibronectin type I domain.
• pfam fn3 81aa 3e-12 in ref transcript
• pfam fn3 81aa 3e-12 in ref transcript
• smart FN1 45aa 3e-12 in ref transcript
• smart FN1 42aa 3e-12 in ref transcript
• smart FN1 45aa 5e-12 in ref transcript
• smart FN1 39aa 2e-11 in ref transcript
• pfam fn3 81aa 4e-11 in ref transcript
• pfam fn3 83aa 5e-11 in ref transcript
• pfam fn3 67aa 8e-11 in ref transcript
• pfam fn1 39aa 8e-11 in ref transcript
• pfam fn3 81aa 1e-10 in ref transcript
• pfam fn3 80aa 1e-10 in ref transcript
• smart FN1 43aa 2e-10 in ref transcript
• pfam fn3 80aa 5e-10 in ref transcript
• smart FN1 44aa 7e-10 in ref transcript
• pfam fn3 81aa 8e-09 in ref transcript
• pfam fn3 85aa 9e-09 in ref transcript
• pfam fn3 70aa 1e-08 in ref transcript
• pfam fn3 65aa 2e-08 in ref transcript
• smart FN1 41aa 3e-08 in ref transcript
• pfam fn3 81aa 3e-07 in ref transcript
• smart FN1 41aa 5e-07 in ref transcript
• pfam fn3 54aa 5e-05 in ref transcript
• pfam fn1 31aa 9e-05 in ref transcript

ARID4B

• FOX.ARID4BandRBM34.F1 FOX.ARID4BandRBM34.R1 137 395
• NCBIGene 36.3 51742
• Single exon skipping, size difference: 258
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_016374

• pfam ARID 94aa 6e-27 in ref transcript
  • ARID/BRIGHT DNA binding domain. This domain is know as ARID for AT-Rich Interaction Domain, and also known as the BRIGHT domain.
• pfam RBB1NT 93aa 3e-15 in ref transcript
  • RBB1NT (NUC162) domain. This domain is found N terminal to the ARID/BRIGHT domain in DNA-binding proteins of the Retinoblastoma-binding protein 1 family.
• smart TUDOR 56aa 1e-05 in ref transcript
  • Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).

FN1

• FOX.FN1.F1 FOX.FN1.R1 124 397
• NCBIGene 36.3 2335
• Single exon skipping, size difference: 273
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_212482

• cd FN2 48aa 2e-16 in ref transcript
  • Fibronectin Type II domain: FN2 is one of three types of internal repeats which combine to form larger domains within fibronectin. Fibronectin, a plasma protein that binds cell surfaces and various compounds including collagen, fibrin, heparin, DNA, and actin, usually exists as a dimer in plasma and as an insoluble multimer in extracellular matrices. Dimers of nearly identical subunits are linked by a disulfide bond close to their C-terminus. Fibronectin is composed of 3 types of modules, FN1,FN2 and FN3. The collagen binding domain contains four FN1 and two FN2 repeats.
• cd FN2 48aa 3e-16 in ref transcript
• cd FN3 83aa 4e-10 in ref transcript
  • Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.
• cd FN1 44aa 4e-09 in ref transcript
  • Fibronectin type 1 domain, approximately 40 residue long with two conserved disulfide bridges. FN1 is one of three types of internal repeats which combine to form larger domains within fibronectin. Fibronectin, a plasma protein that binds cell surfaces and various compounds including collagen, fibrin, heparin, DNA, and actin, usually exists as a dimer in plasma and as an insoluble multimer in extracellular matrices. Dimers of nearly identical subunits are linked by a disulfide bond close to their C-terminus. FN1 domains also found in coagulation factor XII, HGF activator, and tissue-type plasminogen activator. In tissue plasminogen activator, FN1 domains may form functional fibrin-binding units with EGF-like domains C-terminal to FN1.
• cd FN3 81aa 8e-09 in ref transcript
• cd FN3 80aa 1e-08 in ref transcript
• cd FN1 40aa 4e-08 in ref transcript
• cd FN1 42aa 5e-08 in ref transcript
• cd FN1 45aa 8e-08 in ref transcript
• cd FN3 88aa 1e-07 in ref transcript
• cd FN3 88aa 2e-07 in ref transcript
• cd FN1 44aa 2e-07 in ref transcript
• cd FN3 87aa 3e-07 in ref transcript
• cd FN1 38aa 4e-07 in ref transcript
• cd FN3 81aa 9e-07 in ref transcript
• cd FN3 82aa 1e-06 in ref transcript
• cd FN3 88aa 1e-06 in ref transcript
• cd FN1 41aa 1e-06 in ref transcript
• Changed! cd FN3 93aa 2e-06 in ref transcript
• cd FN1 45aa 2e-06 in ref transcript
• cd FN1 42aa 2e-06 in ref transcript
• cd FN3 81aa 6e-06 in ref transcript
• cd FN3 90aa 8e-06 in ref transcript
• cd FN3 73aa 9e-06 in ref transcript
• cd FN1 44aa 1e-05 in ref transcript
• cd FN1 43aa 3e-05 in ref transcript
• cd FN1 39aa 0.003 in ref transcript
• cd FN3 73aa 0.006 in ref transcript
• smart FN2 49aa 9e-20 in ref transcript
  • Fibronectin type 2 domain. One of three types of internal repeat within the plasma protein, fibronectin. Also occurs in coagulation factor XII, 2 type IV collagenases, PDC-109, and cation-independent mannose-6-phosphate and secretory phospholipase A2 receptors. In fibronectin, PDC-109, and the collagenases, this domain contributes to collagen-binding function.
• smart FN2 49aa 4e-19 in ref transcript
• pfam fn3 82aa 8e-17 in ref transcript
  • Fibronectin type III domain.
• smart FN1 45aa 6e-13 in ref transcript
  • Fibronectin type 1 domain. One of three types of internal repeat within the plasma protein, fibronectin. Found also in coagulation factor XII, HGF activator and tissue-type plasminogen activator. In t-PA and fibronectin, this domain type contributes to fibrin-binding.
• pfam fn1 39aa 1e-12 in ref transcript
  • Fibronectin type I domain.
• pfam fn3 81aa 3e-12 in ref transcript
• pfam fn3 81aa 3e-12 in ref transcript
• smart FN1 45aa 3e-12 in ref transcript
• smart FN1 42aa 3e-12 in ref transcript
• smart FN1 45aa 5e-12 in ref transcript
• smart FN1 39aa 2e-11 in ref transcript
• pfam fn3 81aa 4e-11 in ref transcript
• Changed! pfam fn3 83aa 5e-11 in ref transcript
• pfam fn3 67aa 8e-11 in ref transcript
• pfam fn1 39aa 8e-11 in ref transcript
• pfam fn3 81aa 1e-10 in ref transcript
• pfam fn3 80aa 1e-10 in ref transcript
• smart FN1 43aa 2e-10 in ref transcript
• pfam fn3 80aa 5e-10 in ref transcript
• smart FN1 44aa 7e-10 in ref transcript
• pfam fn3 81aa 8e-09 in ref transcript
• pfam fn3 85aa 9e-09 in ref transcript
• pfam fn3 70aa 1e-08 in ref transcript
• pfam fn3 65aa 2e-08 in ref transcript
• smart FN1 41aa 3e-08 in ref transcript
• pfam fn3 81aa 3e-07 in ref transcript
• smart FN1 41aa 5e-07 in ref transcript
• pfam fn3 54aa 5e-05 in ref transcript
• pfam fn1 31aa 9e-05 in ref transcript

INSR

• FOX.INSR.F1 FOX.INSR.R1 194 230
• NCBIGene 36.3 3643
• Single exon skipping, size difference: 36
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000208

• cd PTKc_InsR 288aa 1e-179 in ref transcript
  • Catalytic Domain of the Protein Tyrosine Kinase, Insulin Receptor. Protein Tyrosine Kinase (PTK) family; Insulin Receptor (InsR); catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. InsR is a receptor tyr kinase (RTK) that is composed of two alphabeta heterodimers. Binding of the insulin ligand to the extracellular alpha subunit activates the intracellular tyr kinase domain of the transmembrane beta subunit. Receptor activation leads to autophosphorylation, stimulating downstream kinase activities, which initiate signaling cascades and biological function. InsR signaling plays an important role in many cellular processes including glucose homeostasis, glycogen synthesis, lipid and protein metabolism, ion and amino acid transport, cell cycle and proliferation, cell differentiation, gene transcription, and nitric oxide synthesis. Insulin resistance, caused by abnormalities in InsR signaling, has been described in diabetes, hypertension, cardiovascular disease, metabolic syndrome, heart failure, and female infertility.
• cd FN3 78aa 3e-07 in ref transcript
  • Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.
• cd FU 48aa 2e-06 in ref transcript
  • Furin-like repeats. Cysteine rich region. Exact function of the domain is not known. Furin is a serine-kinase dependent proprotein processor. Other members of this family include endoproteases and cell surface receptors.
• cd FN3 45aa 7e-04 in ref transcript
• pfam Pkinase_Tyr 268aa 1e-118 in ref transcript
  • Protein tyrosine kinase.
• pfam Furin-like 162aa 5e-57 in ref transcript
  • Furin-like cysteine rich region.
• pfam Recep_L_domain 114aa 1e-25 in ref transcript
  • Receptor L domain. The L domains from these receptors make up the bilobal ligand binding site. Each L domain consists of a single-stranded right hand beta-helix. This Pfam entry is missing the first 50 amino acid residues of the domain.
• pfam Recep_L_domain 113aa 2e-25 in ref transcript
• smart FN3 71aa 5e-05 in ref transcript
  • Fibronectin type 3 domain. One of three types of internal repeat within the plasma protein, fibronectin. The tenth fibronectin type III repeat contains a RGD cell recognition sequence in a flexible loop between 2 strands. Type III modules are present in both extracellular and intracellular proteins.
• COG SPS1 265aa 2e-18 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].

KIF2A

• FOX.KIF2AandIPO11.F1 rs.KIF2A.R1 157 271
• NCBIGene 36.3 3796
• Single exon skipping, size difference: 114
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001098511

• Changed! cd KISc_KIF2_like 330aa 1e-142 in ref transcript
  • Kinesin motor domain, KIF2-like group. KIF2 is a protein expressed in neurons, which has been associated with axonal transport and neuron development; alternative splice forms have been implicated in lysosomal translocation. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In this subgroup the motor domain is found in the middle (M-type) of the protein chain. M-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second (KIF2 may be slower). To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-coil domain close to a second tubulin dimer, about 80 Angstroms along the microtubule. Meanwhile, ATP hydrolysis takes place, and when the second head domain binds to the microtubule, the first domain again replaces ADP with ATP, triggering a conformational change that pulls the first domain forward.
• Changed! smart KISc 337aa 1e-109 in ref transcript
  • Kinesin motor, catalytic domain. ATPase. Microtubule-dependent molecular motors that play important roles in intracellular transport of organelles and in cell division.
• Changed! COG KIP1 327aa 7e-51 in ref transcript
  • Kinesin-like protein [Cytoskeleton].
• Changed! cd KISc_KIF2_like 330aa 1e-142 in modified transcript
• Changed! smart KISc 336aa 1e-109 in modified transcript
• Changed! COG KIP1 344aa 5e-51 in modified transcript

SYNE2

• FOX.SYNE2.F1 FOX.SYNE2.R1 266 335
• NCBIGene 36.3 23224
• Single exon skipping, size difference: 69
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_182914

• cd SPEC 214aa 1e-12 in ref transcript
  • Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here.
• cd CH 103aa 5e-12 in ref transcript
  • Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav).
• cd SPEC 215aa 1e-10 in ref transcript
• cd CH 103aa 6e-10 in ref transcript
• cd SPEC 214aa 4e-09 in ref transcript
• cd SPEC 221aa 8e-08 in ref transcript
• cd SPEC 216aa 1e-07 in ref transcript
• cd SPEC 207aa 2e-05 in ref transcript
• pfam KASH 60aa 7e-14 in ref transcript
  • Nuclear envelope localisation domain. The KASH (for Klarsicht/ANC-1/Syne-1 homology) or KLS domain is a highly hydrophobic nuclear envelope localisation domain of approximately 60 amino acids comprising an 20-amino-acid transmembrane region and a 30-35-residue C-terminal region that lies between the inner and the outer nuclear membranes.
• pfam CH 99aa 2e-13 in ref transcript
  • Calponin homology (CH) domain. The CH domain is found in both cytoskeletal proteins and signal transduction proteins. The CH domain is involved in actin binding in some members of the family. However in calponins there is evidence that the CH domain is not involved in its actin binding activity. Most proteins have two copies of the CH domain, however some proteins such as calponin have only a single copy.
• smart CH 102aa 2e-13 in ref transcript
  • Calponin homology domain. Actin binding domains present in duplicate at the N-termini of spectrin-like proteins (including dystrophin, alpha-actinin). These domains cross-link actin filaments into bundles and networks. A calponin homology domain is predicted in yeasst Cdc24p.
• pfam SMC_N 302aa 1e-06 in ref transcript
  • RecF/RecN/SMC N terminal domain. This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.
• TIGR SMC_prok_B 305aa 4e-05 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• smart SPEC 102aa 9e-05 in ref transcript
  • Spectrin repeats.
• smart SPEC 104aa 3e-04 in ref transcript
• TIGR SMC_prok_A 303aa 3e-04 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent.
• TIGR SMC_prok_A 375aa 4e-04 in ref transcript
• pfam SMC_N 281aa 0.002 in ref transcript
• COG SAC6 255aa 3e-22 in ref transcript
  • Ca2+-binding actin-bundling protein fimbrin/plastin (EF-Hand superfamily) [Cytoskeleton].
• COG Smc 266aa 3e-04 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].

GDNF

• GDNF.u.f.4 refseq_GDNF.R2 190 268
• NCBIGene 36.3 2668
• Alternative 5-prime, size difference: 78
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000514

• pfam TGF_beta 94aa 8e-15 in ref transcript
  • Transforming growth factor beta like domain.

GNB3

• GNB3.F12 GNB3.R2 177 418
• AceView 36.Apr07 GNB3
• Intron retention, size difference: 241
• Inclusion in the protein causing a new stop codon
• Reference transcript: GNB3.aApr07

• Changed! cd WD40 293aa 1e-65 in ref transcript
  • WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.
• Changed! smart WD40 39aa 3e-05 in ref transcript
  • WD40 repeats. Note that these repeats are permuted with respect to the structural repeats (blades) of the beta propeller domain.
• Changed! smart WD40 35aa 2e-04 in ref transcript
• Changed! pfam WD40 39aa 3e-04 in ref transcript
  • WD domain, G-beta repeat.
• Changed! pfam WD40 39aa 0.002 in ref transcript
• Changed! COG COG2319 297aa 1e-33 in ref transcript
  • FOG: WD40 repeat [General function prediction only].

HMGA1

• HMGA1.au.0.f HMGA1.u.r.18 268 334
• AceView 36.Apr07 HMGA1
• Exon skipping and alternative 3-prime or 5-prime, size difference: 71
• Inclusion in the protein causing a frameshift, Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: HMGA1.aApr07

HMMR

• HMMR.F1 HMMR.R1 144 189
• NCBIGene 36.3 3161
• Single exon skipping, size difference: 45
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_012484

• pfam SMC_N 239aa 3e-05 in ref transcript
  • RecF/RecN/SMC N terminal domain. This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.
• Changed! TIGR SMC_prok_A 213aa 9e-05 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent.
• COG Smc 236aa 4e-05 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].
• PRK PRK05771 196aa 0.002 in ref transcript
  • V-type ATP synthase subunit I; Validated.
• Changed! TIGR SMC_prok_A 223aa 3e-04 in modified transcript

HNRPAB

• HNRPAB-F1 HNRPAB-R1 269 416
• NCBIGene 36.3 3182
• Single exon skipping, size difference: 141
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_031266

• cd RRM 70aa 6e-14 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• cd RRM 48aa 4e-10 in ref transcript
• TIGR SF-CC1 137aa 2e-18 in ref transcript
  • A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed.
• pfam CBFNT 71aa 6e-06 in ref transcript
  • CBFNT (NUC161) domain. This N terminal domain is found in proteins of CARG-binding factor A-like proteins.
• COG COG0724 142aa 6e-08 in ref transcript
  • RNA-binding proteins (RRM domain) [General function prediction only].

CADM1

• IGSF4.F6 IGSF4.R1 132 165
• AceView 36.Apr07 CADM1
• Single exon skipping, size difference: 33
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: CADM1.bApr07

• cd IGcam 71aa 1e-07 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• cd IG 72aa 0.004 in ref transcript
  • Immunoglobulin domain family; members are components of immunoglobulins, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• smart IG_like 80aa 3e-10 in ref transcript
  • Immunoglobulin like. IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
• pfam C2-set_2 70aa 3e-08 in ref transcript
  • CD80-like C2-set immunoglobulin domain. These domains belong to the immunoglobulin superfamily.
• smart IG_like 92aa 9e-08 in ref transcript

INSR

• INSR.u.f.15 INSR.u.r.18 130 166
• NCBIGene 36.3 3643
• Single exon skipping, size difference: 36
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000208

• cd PTKc_InsR 288aa 1e-179 in ref transcript
  • Catalytic Domain of the Protein Tyrosine Kinase, Insulin Receptor. Protein Tyrosine Kinase (PTK) family; Insulin Receptor (InsR); catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. InsR is a receptor tyr kinase (RTK) that is composed of two alphabeta heterodimers. Binding of the insulin ligand to the extracellular alpha subunit activates the intracellular tyr kinase domain of the transmembrane beta subunit. Receptor activation leads to autophosphorylation, stimulating downstream kinase activities, which initiate signaling cascades and biological function. InsR signaling plays an important role in many cellular processes including glucose homeostasis, glycogen synthesis, lipid and protein metabolism, ion and amino acid transport, cell cycle and proliferation, cell differentiation, gene transcription, and nitric oxide synthesis. Insulin resistance, caused by abnormalities in InsR signaling, has been described in diabetes, hypertension, cardiovascular disease, metabolic syndrome, heart failure, and female infertility.
• cd FN3 78aa 3e-07 in ref transcript
  • Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.
• cd FU 48aa 2e-06 in ref transcript
  • Furin-like repeats. Cysteine rich region. Exact function of the domain is not known. Furin is a serine-kinase dependent proprotein processor. Other members of this family include endoproteases and cell surface receptors.
• cd FN3 45aa 7e-04 in ref transcript
• pfam Pkinase_Tyr 268aa 1e-118 in ref transcript
  • Protein tyrosine kinase.
• pfam Furin-like 162aa 5e-57 in ref transcript
  • Furin-like cysteine rich region.
• pfam Recep_L_domain 114aa 1e-25 in ref transcript
  • Receptor L domain. The L domains from these receptors make up the bilobal ligand binding site. Each L domain consists of a single-stranded right hand beta-helix. This Pfam entry is missing the first 50 amino acid residues of the domain.
• pfam Recep_L_domain 113aa 2e-25 in ref transcript
• smart FN3 71aa 5e-05 in ref transcript
  • Fibronectin type 3 domain. One of three types of internal repeat within the plasma protein, fibronectin. The tenth fibronectin type III repeat contains a RGD cell recognition sequence in a flexible loop between 2 strands. Type III modules are present in both extracellular and intracellular proteins.
• COG SPS1 265aa 2e-18 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].

KITLG

• KITLG.u.f.9 KITLG.u.r.10 215 299
• NCBIGene 36.3 4254
• Single exon skipping, size difference: 84
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000899

• Changed! pfam SCF 273aa 1e-134 in ref transcript
  • Stem cell factor. Stem cell factor (SCF) is a homodimer involved in hematopoiesis. SCF binds to and activates the SCF receptor (SCFR), a receptor tyrosine kinase. The crystal structure of human SCF has been resolved and a potential receptor-binding site identified.
• Changed! pfam SCF 245aa 1e-121 in modified transcript

LGALS9

• LGALS9.F10 LGALS9.R6 135 231
• NCBIGene 36.3 3965
• Single exon skipping, size difference: 96
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_009587

• cd GLECT 131aa 2e-36 in ref transcript
  • Galectin/galactose-binding lectin. This domain exclusively binds beta-galactosides, such as lactose, and does not require metal ions for activity. GLECT domains occur as homodimers or tandemly repeated domains. They are developmentally regulated and may be involved in differentiation, cell-cell interaction and cellular regulation.
• cd GLECT 128aa 5e-33 in ref transcript
• smart GLECT 131aa 4e-40 in ref transcript
  • Galectin. Galectin - galactose-binding lectin.
• pfam Gal-bind_lectin 128aa 3e-35 in ref transcript
  • Galactoside-binding lectin. This family contains galactoside binding lectins. The family also includes enzymes such as human eosinophil lysophospholipase (EC:3.1.1.5).

LIG3

• LIG3.u.f.1 LIG3.u.r.6 148 378
• AceView 36.Apr07 LIG3
• Alternative 3-prime, size difference: 230
• Exclusion of the protein initiation site
• Reference transcript: LIG3.aApr07

• TIGR dnl1 513aa 0.0 in ref transcript
  • All proteins in this family with known functions are ATP-dependent DNA ligases. Functions include DNA repair, DNA replication, and DNA recombination (or any process requiring ligation of two single-stranded DNA sections). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
• pfam zf-PARP 57aa 4e-16 in ref transcript
  • Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region. Poly(ADP-ribose) polymerase is an important regulatory component of the cellular response to DNA damage. The amino-terminal region of Poly(ADP-ribose) polymerase consists of two PARP-type zinc fingers. This region acts as a DNA nick sensor.
• smart BRCT 68aa 5e-05 in ref transcript
  • breast cancer carboxy-terminal domain.
• PRK PRK01109 556aa 6e-74 in ref transcript
  • ATP-dependent DNA ligase; Provisional.

LIG4

• LIG4.F1 LIG4.R1 267 340
• AceView 36.Apr07 LIG4
• Single exon skipping, size difference: 73
• Exclusion in 5'UTR
• Reference transcript: LIG4.bApr07

• cd BRCT 71aa 7e-06 in ref transcript
  • Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks.
• TIGR dnl1 522aa 1e-171 in ref transcript
  • All proteins in this family with known functions are ATP-dependent DNA ligases. Functions include DNA repair, DNA replication, and DNA recombination (or any process requiring ligation of two single-stranded DNA sections). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
• smart BRCT 77aa 2e-07 in ref transcript
  • breast cancer carboxy-terminal domain.
• pfam BRCT 70aa 0.003 in ref transcript
  • BRCA1 C Terminus (BRCT) domain. The BRCT domain is found predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage. It has been suggested that the Retinoblastoma protein contains a divergent BRCT domain, this has not been included in this family. The BRCT domain of XRCC1 forms a homodimer in the crystal structure. This suggests that pairs of BRCT domains associate as homo- or heterodimers.
• PRK PRK01109 574aa 6e-59 in ref transcript
  • ATP-dependent DNA ligase; Provisional.

LRDD

• LRDD.u.f.7 LRDD.u.r.3 121 181
• NCBIGene 36.3 55367
• Alternative 3-prime, size difference: 60
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_145886

• Changed! pfam Death 79aa 3e-09 in ref transcript
  • Death domain.
• Changed! pfam Peptidase_S68 34aa 2e-08 in ref transcript
  • Peptidase S68. This family of serine peptidases contains PIDD proteins. PIDD forms a complex with RAIDD and procaspase-2 that is known as the 'PIDDosome'. The PIDDosome forms when DNA damage occurs and either activates NF-kappaB, leading to cell survival, or caspase-2, which leads to apoptosis.
• Changed! smart ZU5 63aa 9e-04 in ref transcript
  • Domain present in ZO-1 and Unc5-like netrin receptors. Domain of unknown function.
• Changed! COG COG4886 96aa 3e-07 in ref transcript
  • Leucine-rich repeat (LRR) protein [Function unknown].

MAPT

• MAPT_x56_x127_f MAPT_x56_x127_r 162 360
• NCBIGene 36.3 4137
• Single exon skipping, size difference: 198
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_016835

• pfam Tubulin-binding 31aa 8e-10 in ref transcript
  • Tau and MAP protein, tubulin-binding repeat. This family includes the vertebrate proteins MAP2, MAP4 and Tau, as well as other animal homologs. MAP4 is present in many tissues but is usually absent from neurons; MAP2 and Tau are mainly neuronal. Members of this family have the ability to bind to and stabilise microtubules. As a result, they are involved in neuronal migration, supporting dendrite elongation, and regulating microtubules during mitotic metaphase. Note that Tau is involved in neurofibrillary tangle formation in Alzheimer's disease and some other dementias. This family features a C-terminal microtubule binding repeat that contains a conserved KXGS motif.
• pfam Tubulin-binding 31aa 2e-08 in ref transcript
• pfam Tubulin-binding 32aa 2e-06 in ref transcript
• pfam Tubulin-binding 32aa 3e-06 in ref transcript
• pfam Hid1 123aa 3e-04 in ref transcript
  • High-temperature-induced dauer-formation protein. Hid1 (high-temperature-induced dauer-formation protein 1) represents proteins of approximately 800 residues long and is conserved from fungi to humans. It contains up to seven potential transmembrane domains separated by regions of low complexity. Functionally it might be involved in vesicle secretion or be an inter-cellular signalling protein or be a novel insulin receptor.

MCL1

• MCL1.F1 MCL1.R1 134 382
• NCBIGene 36.3 4170
• Single exon skipping, size difference: 248
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_021960

• Changed! cd Bcl-2_like 144aa 7e-37 in ref transcript
  • Apoptosis regulator proteins of the Bcl-2 family, named after B-cell lymphoma 2. This alignment model spans what have been described as Bcl-2 homology regions BH1, BH2, BH3, and BH4. Many members of this family have an additional C-terminal transmembrane segment. Some homologous proteins, which are not included in this model, may miss either the BH4 (Bax, Bak) or the BH2 (Bcl-X(S)) region, and some appear to only share the BH3 region (Bik, Bim, Bad, Bid, Egl-1). This family is involved in the regulation of the outer mitochondrial membrane's permeability and in promoting or preventing the release of apoptogenic factors, which in turn may trigger apoptosis by activating caspases. Bcl-2 and the closely related Bcl-X(L) are anti-apoptotic key regulators of programmed cell death. They are assumed to function via heterodimeric protein-protein interactions, binding pro-apoptotic proteins such as Bad (BCL2-antagonist of cell death), Bid, and Bim, by specifically interacting with their BH3 regions. Interfering with this heterodimeric interaction via small-molecule inhibitors may prove effective in targeting various cancers. This family also includes the Caenorhabditis elegans Bcl-2 homolog CED-9, which binds to CED-4, the C. Elegans homolog of mammalian Apaf-1. Apaf-1, however, does not seem to be inhibited by Bcl-2 directly.
• Changed! pfam Bcl-2 100aa 5e-32 in ref transcript
  • Apoptosis regulator proteins, Bcl-2 family.
• Changed! cd Bcl-2_like 56aa 2e-04 in modified transcript

NOTCH3

• NOTCH3.F2 NOTCH3.R2 286 442
• AceView 36.Apr07 NOTCH3
• Single exon skipping, size difference: 156
• Exclusion in the protein (no frameshift)
• Reference transcript: NOTCH3.aApr07

• cd ANK 127aa 4e-24 in ref transcript
  • ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats.
• cd ANK 148aa 8e-07 in ref transcript
• cd EGF_CA 38aa 1e-06 in ref transcript
  • Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements.
• Changed! cd EGF_CA 38aa 8e-05 in ref transcript
• cd EGF_CA 37aa 3e-04 in ref transcript
• cd EGF_CA 39aa 4e-04 in ref transcript
• Changed! cd EGF_CA 36aa 6e-04 in ref transcript
• cd EGF_CA 33aa 0.001 in ref transcript
• cd EGF_CA 37aa 0.002 in ref transcript
• cd EGF_CA 38aa 0.002 in ref transcript
• cd EGF_CA 37aa 0.003 in ref transcript
• cd EGF_CA 32aa 0.003 in ref transcript
• cd EGF_CA 37aa 0.005 in ref transcript
• cd EGF_CA 36aa 0.008 in ref transcript
• pfam NODP 55aa 4e-14 in ref transcript
  • NOTCH protein. NOTCH signalling plays a fundamental role during a great number of developmental processes in multicellular animals. NOD and NODP represent a region present in many NOTCH proteins and NOTCH homologs in multiple species such as NOTCH2 and NOTCH3, LIN12, SC1 and TAN1. The role of the NOD and NODP domains remains to be elucidated.
• pfam NOD 55aa 2e-11 in ref transcript
  • NOTCH protein. NOTCH signalling plays a fundamental role during a great number of developmental processes in multicellular animals. NOD and NODP represent a region present in many NOTCH proteins and NOTCH homologs in multiple species such as NOTCH2 and NOTCH3, LIN12, SC1 and TAN1. Role of NOD domain remains to be elucidated.
• smart EGF_CA 38aa 2e-07 in ref transcript
  • Calcium-binding EGF-like domain.
• pfam Notch 33aa 5e-06 in ref transcript
  • LNR domain. The LNR (Lin-12/Notch repeat) domain is found in three tandem copies in Notch related proteins. The structure of the domain has been determined by NMR and was shown to contain three disulphide bonds and coordinate a calcium ion. Three repeats are also found in the PAPP-A peptidase.
• smart NL 38aa 5e-06 in ref transcript
  • Domain found in Notch and Lin-12. The Notch protein is essential for the proper differentiation of the Drosophila ectoderm. This protein contains 3 NL domains.
• pfam Notch 29aa 2e-05 in ref transcript
• Changed! smart EGF_CA 38aa 8e-05 in ref transcript
• smart EGF_CA 39aa 8e-05 in ref transcript
• smart EGF_CA 37aa 1e-04 in ref transcript
• TIGR trp 139aa 1e-04 in ref transcript
  • after chronic exposure to capsaicin. (McCleskey and Gold, 1999).
• Changed! smart EGF_CA 36aa 3e-04 in ref transcript
• smart EGF_CA 37aa 3e-04 in ref transcript
• smart EGF_CA 37aa 0.001 in ref transcript
• smart EGF_CA 37aa 0.001 in ref transcript
• smart EGF_CA 33aa 0.001 in ref transcript
• smart EGF_CA 38aa 0.002 in ref transcript
• smart EGF_CA 36aa 0.003 in ref transcript
• smart EGF_CA 32aa 0.004 in ref transcript
• COG Arp 154aa 5e-17 in ref transcript
  • FOG: Ankyrin repeat [General function prediction only].

NRG1

• NRG1.u.f.21 NRG1.u.r.25 372 396
• NCBIGene 36.3 3084
• Single exon skipping, size difference: 24
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_013956

• cd IGcam 89aa 2e-05 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• pfam Neuregulin 396aa 1e-109 in ref transcript
  • Neuregulin family.
• smart IG_like 87aa 1e-07 in ref transcript
  • Immunoglobulin like. IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
• pfam EGF 32aa 0.006 in ref transcript
  • EGF-like domain. There is no clear separation between noise and signal. pfam00053 is very similar, but has 8 instead of 6 conserved cysteines. Includes some cytokine receptors. The EGF domain misses the N-terminus regions of the Ca2+ binding EGF domains (this is the main reason of discrepancy between Swiss-Prot domain start/end and Pfam). The family is hard to model due to many similar but different sub-types of EGF domains. Pfam certainly misses a number of EGF domains.

NUP98

• NUP98.F1 NUP98.R1 260 482
• NCBIGene 36.3 4928
• Single exon skipping, size difference: 222
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_016320

• pfam Nucleoporin2 156aa 2e-63 in ref transcript
  • Nucleoporin autopeptidase.

OPA1

• OPA1.u.f.9 OPA1.u.r.8 143 254
• NCBIGene 36.3 4976
• Single exon skipping, size difference: 111
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_130837

• pfam Dynamin_N 179aa 4e-38 in ref transcript
  • Dynamin family.

PAXIP1

• PAXIP1.F1 PAXIP1.R1 114 185
• AceView 36.Apr07 PAXIP1
• Alternative 5-prime, size difference: 71
• Inclusion in the protein causing a new stop codon
• Reference transcript: PAXIP1.aApr07

• cd BRCT 68aa 6e-07 in ref transcript
  • Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks.
• cd BRCT 68aa 7e-07 in ref transcript
• cd BRCT 70aa 8e-07 in ref transcript
• cd BRCT 75aa 4e-06 in ref transcript
• pfam BRCT 73aa 4e-11 in ref transcript
  • BRCA1 C Terminus (BRCT) domain. The BRCT domain is found predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage. It has been suggested that the Retinoblastoma protein contains a divergent BRCT domain, this has not been included in this family. The BRCT domain of XRCC1 forms a homodimer in the crystal structure. This suggests that pairs of BRCT domains associate as homo- or heterodimers.
• pfam BRCT 72aa 6e-10 in ref transcript
• pfam BRCT 66aa 8e-07 in ref transcript
• smart BRCT 81aa 3e-06 in ref transcript
  • breast cancer carboxy-terminal domain.

PCSK6

• PCSK6.F2 PCSK6.R2 116 260
• AceView 36.Apr07 PCSK6
• Single exon skipping, size difference: 144
• Exclusion in the protein (no frameshift)
• Reference transcript: PCSK6.aApr07

• cd FU 51aa 6e-07 in ref transcript
  • Furin-like repeats. Cysteine rich region. Exact function of the domain is not known. Furin is a serine-kinase dependent proprotein processor. Other members of this family include endoproteases and cell surface receptors.
• cd FU 43aa 2e-06 in ref transcript
• cd FU 47aa 3e-06 in ref transcript
• cd FU 53aa 1e-05 in ref transcript
• Changed! pfam Peptidase_S8 301aa 2e-94 in ref transcript
  • Subtilase family. Subtilases are a family of serine proteases. They appear to have independently and convergently evolved an Asp/Ser/His catalytic triad, like that found in the trypsin serine proteases (see pfam00089). Structure is an alpha/beta fold containing a 7-stranded parallel beta sheet, order 2314567.
• pfam P_proprotein 91aa 4e-34 in ref transcript
  • Proprotein convertase P-domain. A unique feature of the eukaryotic subtilisin-like proprotein convertases is the presence of an additional highly conserved sequence of approximately 150 residues (P domain) located immediately downstream of the catalytic domain.
• smart FU 48aa 2e-08 in ref transcript
  • Furin-like repeats.
• smart FU 44aa 2e-08 in ref transcript
• smart FU 44aa 1e-06 in ref transcript
• pfam Furin-like 112aa 4e-06 in ref transcript
  • Furin-like cysteine rich region.
• pfam VSP 115aa 5e-04 in ref transcript
  • Giardia variant-specific surface protein.
• Changed! COG AprE 324aa 1e-20 in ref transcript
  • Subtilisin-like serine proteases [Posttranslational modification, protein turnover, chaperones].
• COG COG4935 91aa 1e-15 in ref transcript
  • Regulatory P domain of the subtilisin-like proprotein convertases and other proteases [Posttranslational modification, protein turnover, chaperones].
• COG NapH 83aa 0.009 in ref transcript
  • Polyferredoxin [Energy production and conversion].
• Changed! pfam Peptidase_S8 261aa 2e-76 in modified transcript
• Changed! COG AprE 281aa 2e-13 in modified transcript

PLD1

• PLD1.F1 PLD1.R1 124 238
• AceView 36.Apr07 PLD1
• Single exon skipping, size difference: 114
• Exclusion in the protein (no frameshift)
• Reference transcript: PLD1.aApr07

• cd PLDc 142aa 1e-21 in ref transcript
  • Phospholipase D. Active site motifs; The PLD superfamily includes enzymes involved in signal transduction, lipid biosynthesis, endonucleases and open reading frames in pathogenic viruses and bacteria. PLD hydrolyzes the terminal phosphodiester bond of phospholipids to phosphatidic acid and a hydrophilic constituent. Phosphatidic acid is a compound that is heavily involved in signal transduction. The common features of the family members are that they can bind to a phosphodiester moiety, and that most of these enzymes are active as bi-lobed monomers or dimers.
• cd PLDc 221aa 1e-15 in ref transcript
• cd PH_PLD 62aa 8e-12 in ref transcript
  • Phospholipase D (PLD) pleckstrin homology (PH) domain. PLD hydrolyzes phosphatidylcholine to phosphatidic acid (PtdOH), which can bind target proteins. PLD contains a PH domain, a PX domain and four conserved PLD signature domains. The PLD PH domain is specific for bisphosphorylated inositides. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
• pfam PLDc 28aa 0.001 in ref transcript
  • Phospholipase D Active site motif. Phosphatidylcholine-hydrolysing phospholipase D (PLD) isoforms are activated by ADP-ribosylation factors (ARFs). PLD produces phosphatidic acid from phosphatidylcholine, which may be essential for the formation of certain types of transport vesicles or may be constitutive vesicular transport to signal transduction pathways. PC-hydrolysing PLD is a homologue of cardiolipin synthase, phosphatidylserine synthase, bacterial PLDs, and viral proteins. Each of these appears to possess a domain duplication which is apparent by the presence of two motifs containing well-conserved histidine, lysine, and/or asparagine residues which may contribute to the active site. aspartic acid. An Escherichia coli endonuclease (nuc) and similar proteins appear to be PLD homologues but possess only one of these motifs. The profile contained here represents only the putative active site regions, since an accurate multiple alignment of the repeat units has not been achieved.
• smart PLDc 27aa 0.002 in ref transcript
  • Phospholipase D. Active site motifs. Phosphatidylcholine-hydrolyzing phospholipase D (PLD) isoforms are activated by ADP-ribosylation factors (ARFs). PLD produces phosphatidic acid from phosphatidylcholine, which may be essential for the formation of certain types of transport vesicles or may be constitutive vesicular transport to signal transduction pathways. PC-hydrolysing PLD is a homologue of cardiolipin synthase, phosphatidylserine synthase, bacterial PLDs, and viral proteins. Each of these appears to possess a domain duplication which is apparent by the presence of two motifs containing well-conserved histidine, lysine, aspartic acid, and/or asparagine residues which may contribute to the active site. An E. coli endonuclease (nuc) and similar proteins appear to be PLD homologues but possess only one of these motifs. The profile contained here represents only the putative active site regions, since an accurate multiple alignment of the repeat units has not been achieved.
• COG Cls 261aa 9e-15 in ref transcript
  • Phosphatidylserine/phosphatidylglycerophosphate/cardioli pin synthases and related enzymes [Lipid metabolism].
• COG Cls 171aa 0.001 in ref transcript

POLB

• POLB.F7 POLB.R13 213 271
• AceView 36.Apr07 POLB
• Single exon skipping, size difference: 58
• Exclusion in the protein causing a frameshift
• Reference transcript: POLB.bApr07

• Changed! cd POLXc 332aa 1e-104 in ref transcript
  • DNA polymerase X family; includes vertebrate DNA polymerase beta and terminal deoxynucleotidyltransferase. An N-terminal 8kD domain and a 31kD C-terminal polymerase domain are connected with a protease-sensitive hinge. The activity of the N-terminal domain seems to be variable, in DNA polymerase beta it has metal dependent nuclease activity and metal independent lyase activity.
• Changed! smart POLXc 325aa 1e-103 in ref transcript
  • DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases.
• Changed! COG POL4 299aa 5e-28 in ref transcript
  • DNA polymerase IV (family X) [DNA replication, recombination, and repair].

POLI

• POLI.F8 POLI.R14 197 303
• AceView 36.Apr07 POLI
• Intron retention, size difference: 106
• Inclusion in 5'UTR
• Reference transcript: POLI.dApr07

• cd Pol_iota 33aa 2e-07 in ref transcript
  • Pol iota is member of the DNA polymerase Y-family, and has also been called Rad30 homolog B. Unlike classic DNA polymerases,Y-family polymerases are induced by DNA damage. They can transverse normal replication-blocking DNA lesions. Unlike Pol eta, Pol iota is unable to replicate through a cis-syn T-T dimer. In human Pol iota, the base-pairing mode in the active site at the replicative end mat bee Hoogsteen instead of Watson-Click. Human Pol iota can incorporate the correct nucleotide opposite a purine much more efficiently than opposite a pyrimidine. Pol iota prefers to insert Guanosine instead of Adenosine opposite Thymidine.
• TIGR dmsA_ynfE 133aa 0.002 in ref transcript
  • Members of this family include known and probable dimethyl sulfoxide reductase (DMSO reductase) A chains. In E. coli, dmsA encodes the canonical anaerobic DMSO reductase A chain. The paralog ynfE, as part of ynfFGH expressed from a multicopy plasmid, could complement a dmsABC deletion, suggesting a similar function and some overlap in specificity, although YnfE could not substitute for DmsA in a mixed complex.

POLM

• POLM.u.f.1 POLM.u.r.6 316 586
• AceView 36.Apr07 POLM
• Multiple exon skipping, size difference: 270
• Exclusion in the protein (no frameshift), Exclusion in the protein (no frameshift)
• Reference transcript: POLM.aApr07

• cd POLXc 118aa 1e-17 in ref transcript
  • DNA polymerase X family; includes vertebrate DNA polymerase beta and terminal deoxynucleotidyltransferase. An N-terminal 8kD domain and a 31kD C-terminal polymerase domain are connected with a protease-sensitive hinge. The activity of the N-terminal domain seems to be variable, in DNA polymerase beta it has metal dependent nuclease activity and metal independent lyase activity.
• Changed! cd POLXc 77aa 3e-10 in ref transcript
• smart POLXc 105aa 2e-14 in ref transcript
  • DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases.
• Changed! smart POLXc 49aa 3e-07 in ref transcript
• COG POL4 48aa 1e-05 in ref transcript
  • DNA polymerase IV (family X) [DNA replication, recombination, and repair].

PPP3CB

• PPP3CB.u.f.21 PPP3CB.u.r.22 117 147
• AceView 36.Apr07 PPP3CB
• Single exon skipping, size difference: 30
• Exclusion in the protein (no frameshift)
• Reference transcript: PPP3CB.aApr07

• cd PP2Ac 278aa 1e-100 in ref transcript
  • Protein phosphatase 2A homologues, catalytic domain. Large family of serine/threonine phosphatases, including PP1, PP2A and PP2B (calcineurin) family members.
• smart PP2Ac 272aa 1e-112 in ref transcript
  • Protein phosphatase 2A homologues, catalytic domain. Large family of serine/threonine phosphatases, that includes PP1, PP2A and PP2B (calcineurin) family members.
• PTZ PTZ00239 278aa 6e-60 in ref transcript
  • serine/threonine protein phosphatase 2A; Provisional.

PTK2B

• PTK2B_x66_x147_f PTK2B_x66_x147_r 170 296
• NCBIGene 36.3 2185
• Single exon skipping, size difference: 126
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_173174

• cd PTKc_FAK 270aa 1e-146 in ref transcript
  • Catalytic Domain of the Protein Tyrosine Kinase, Focal Adhesion Kinase. Protein Tyrosine Kinase (PTK) family; Focal Adhesion kinase (FAK); catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. FAK is a cytoplasmic (or nonreceptor) tyr kinase that contains an autophosphorylation site and a FERM domain at the N-terminus, a central tyr kinase domain, proline-rich regions, and a C-terminal FAT (focal adhesion targeting) domain. FAK activity is dependent on integrin-mediated cell adhesion, which facilitates N-terminal autophosphorylation. Full activation is achieved by the phosphorylation of its two adjacent A-loop tyrosines. FAK is important in mediating signaling initiated at sites of cell adhesions and at growth factor receptors. Through diverse molecular interactions, FAK functions as a biosensor or integrator to control cell motility. It is a key regulator of cell survival, proliferation, migration and invasion, and thus plays an important role in the development and progression of cancer. Src binds to autophosphorylated FAK forming the FAK-Src dual kinase complex, which is activated in a wide variety of tumor cells and generates signals promoting growth and metastasis. FAK is being developed as a target for cancer therapy.
• pfam Pkinase_Tyr 233aa 5e-98 in ref transcript
  • Protein tyrosine kinase.
• pfam Focal_AT 139aa 6e-59 in ref transcript
  • Focal adhesion targeting region. Focal adhesion kinase (FAK) is a tyrosine kinase found in focal adhesions, intracellular signaling complexes that are formed following engagement of the extracellular matrix by integrins. The C-terminal 'focal adhesion targeting' (FAT) region is necessary and sufficient for localising FAK to focal adhesions. The crystal structure of FAT shows it forms a four-helix bundle that resembles those found in two other proteins involved in cell adhesion, alpha-catenin and vinculin. The binding of FAT to the focal adhesion protein, paxillin, requires the integrity of the helical bundle, whereas binding to another focal adhesion protein, talin, does not.
• smart B41 227aa 2e-31 in ref transcript
  • Band 4.1 homologues. Also known as ezrin/radixin/moesin (ERM) protein domains. Present in myosins, ezrin, radixin, moesin, protein tyrosine phosphatases. Plasma membrane-binding domain. These proteins play structural and regulatory roles in the assembly and stabilization of specialized plasmamembrane domains. Some PDZ domain containing proteins bind one or more of this family. Now includes JAKs.
• COG SPS1 229aa 2e-16 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].

PTPN13

• PTPN13.F7 PTPN13.R7 133 190
• NCBIGene 36.3 5783
• Single exon skipping, size difference: 57
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_080685

• cd PTPc 228aa 3e-79 in ref transcript
  • Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active.
• cd PDZ_signaling 85aa 7e-16 in ref transcript
  • PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of PDZ domains an N-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in proteases.
• cd PDZ_signaling 80aa 1e-15 in ref transcript
• cd PDZ_signaling 90aa 2e-13 in ref transcript
• cd FERM_C 94aa 2e-13 in ref transcript
  • The FERM_C domain is the third structural domain within the FERM domain. The FERM domain is found in the cytoskeletal-associated proteins such as ezrin, moesin, radixin, 4.1R, and merlin. These proteins provide a link between the membrane and cytoskeleton and are involved in signal transduction pathways. The FERM_C domain is also found in protein tyrosine phosphatases (PTPs) , the tryosine kinases FAKand JAK, in addition to other proteins involved in signaling. This domain is structuraly similar to the PH and PTB domains and consequently is capable of binding to both peptides and phospholipids at different sites.
• cd PDZ_signaling 79aa 2e-08 in ref transcript
• cd PDZ_signaling 88aa 6e-08 in ref transcript
• smart PTPc 253aa 5e-91 in ref transcript
  • Protein tyrosine phosphatase, catalytic domain.
• smart KIND 188aa 2e-42 in ref transcript
  • kinase non-catalytic C-lobe domain. It is an interaction domain identified as being similar to the C-terminal protein kinase catalytic fold (C lobe). Its presence at the N terminus of signalling proteins and the absence of the active-site residues in the catalytic and activation loops suggest that it folds independently and is likely to be non-catalytic. The occurrence of KIND only in metazoa implies that it has evolved from the catalytic protein kinase domain into an interaction domain possibly by keeping the substrate-binding features.
• smart B41 210aa 4e-40 in ref transcript
  • Band 4.1 homologues. Also known as ezrin/radixin/moesin (ERM) protein domains. Present in myosins, ezrin, radixin, moesin, protein tyrosine phosphatases. Plasma membrane-binding domain. These proteins play structural and regulatory roles in the assembly and stabilization of specialized plasmamembrane domains. Some PDZ domain containing proteins bind one or more of this family. Now includes JAKs.
• pfam FERM_C 88aa 2e-17 in ref transcript
  • FERM C-terminal PH-like domain.
• smart PDZ 90aa 1e-16 in ref transcript
  • Domain present in PSD-95, Dlg, and ZO-1/2. Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities.
• smart PDZ 92aa 2e-15 in ref transcript
• smart PDZ 83aa 1e-13 in ref transcript
• smart PDZ 92aa 2e-11 in ref transcript
• smart PDZ 84aa 9e-08 in ref transcript
• COG PTP2 267aa 1e-40 in ref transcript
  • Protein tyrosine phosphatase [Signal transduction mechanisms].
• COG Prc 80aa 9e-05 in ref transcript
  • Periplasmic protease [Cell envelope biogenesis, outer membrane].
• COG Prc 54aa 3e-04 in ref transcript
• COG Prc 76aa 3e-04 in ref transcript
• COG Prc 68aa 0.006 in ref transcript

PTPRB

• PTPRB.F6 PTPRB.R6 131 395
• AceView 36.Apr07 PTPRB
• Single exon skipping, size difference: 264
• Exclusion in the protein (no frameshift)
• Reference transcript: PTPRB.aApr07

• cd PTPc 232aa 6e-89 in ref transcript
  • Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active.
• cd FN3 83aa 2e-05 in ref transcript
  • Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.
• cd FN3 89aa 7e-05 in ref transcript
• cd FN3 87aa 2e-04 in ref transcript
• cd FN3 76aa 3e-04 in ref transcript
• cd RICIN 73aa 0.003 in ref transcript
  • Ricin-type beta-trefoil; Carbohydrate-binding domain formed from presumed gene triplication. The domain is found in a variety of molecules serving diverse functions such as enzymatic activity, inhibitory toxicity and signal transduction. Highly specific ligand binding occurs on exposed surfaces of the compact domain sturcture.
• smart PTPc 259aa 1e-100 in ref transcript
  • Protein tyrosine phosphatase, catalytic domain.
• pfam fn3 84aa 6e-11 in ref transcript
  • Fibronectin type III domain.
• pfam fn3 78aa 5e-09 in ref transcript
• pfam fn3 81aa 1e-08 in ref transcript
• pfam fn3 78aa 3e-08 in ref transcript
• pfam fn3 75aa 3e-08 in ref transcript
• pfam fn3 76aa 3e-07 in ref transcript
• pfam fn3 76aa 9e-07 in ref transcript
• pfam fn3 75aa 1e-06 in ref transcript
• pfam fn3 78aa 4e-06 in ref transcript
• pfam fn3 76aa 1e-05 in ref transcript
• pfam fn3 76aa 2e-05 in ref transcript
• pfam fn3 82aa 3e-05 in ref transcript
• Changed! pfam fn3 63aa 4e-05 in ref transcript
• pfam fn3 68aa 0.003 in ref transcript
• pfam fn3 65aa 0.004 in ref transcript
• pfam Ricin_B_lectin 77aa 0.006 in ref transcript
  • Ricin-type beta-trefoil lectin domain.
• COG PTP2 266aa 5e-48 in ref transcript
  • Protein tyrosine phosphatase [Signal transduction mechanisms].

RAC1

• RAC1.F18 rs.RAC1.R1 328 386
• NCBIGene 36.3 5879
• Single exon skipping, size difference: 58
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_018890

• Changed! cd Rac1_like 192aa 1e-107 in ref transcript
  • Rac1-like subfamily. The Rac1-like subfamily consists of Rac1, Rac2, and Rac3 proteins, plus the splice variant Rac1b that contains a 19-residue insertion near switch II relative to Rac1. While Rac1 is ubiquitously expressed, Rac2 and Rac3 are largely restricted to hematopoietic and neural tissues respectively. Rac1 stimulates the formation of actin lamellipodia and membrane ruffles. It also plays a role in cell-matrix adhesion and cell anoikis. In intestinal epithelial cells, Rac1 is an important regulator of migration and mediates apoptosis. Rac1 is also essential for RhoA-regulated actin stress fiber and focal adhesion complex formation. In leukocytes, Rac1 and Rac2 have distinct roles in regulating cell morphology, migration, and invasion, but are not essential for macrophage migration or chemotaxis. Rac3 has biochemical properties that are closely related to Rac1, such as effector interaction, nucleotide binding, and hydrolysis; Rac2 has a slower nucleotide association and is more efficiently activated by the RacGEF Tiam1. Both Rac1 and Rac3 have been implicated in the regulation of cell migration and invasion in human metastatic breast cancer. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.
• Changed! smart RHO 189aa 1e-98 in ref transcript
  • Rho (Ras homology) subfamily of Ras-like small GTPases. Members of this subfamily of Ras-like small GTPases include Cdc42 and Rac, as well as Rho isoforms.
• Changed! COG COG1100 193aa 1e-27 in ref transcript
  • GTPase SAR1 and related small G proteins [General function prediction only].

CLIP1

• RSN.F10 RSN.R9 155 500
• AceView 36.Apr07 CLIP1
• Exon skipping and alternative 3-prime or 5-prime, size difference: 345
• Exclusion in the protein (no frameshift), Exclusion in the protein (no frameshift)
• Reference transcript: CLIP1.aApr07

• pfam CAP_GLY 66aa 6e-27 in ref transcript
  • CAP-Gly domain. Cytoskeleton-associated proteins (CAPs) are involved in the organisation of microtubules and transportation of vesicles and organelles along the cytoskeletal network. A conserved motif, CAP-Gly, has been identified in a number of CAPs, including CLIP-170 and dynactins. The crystal structure of Caenorhabditis elegans F53F4.3 protein CAP-Gly domain was recently solved. The domain contains three beta-strands. The most conserved sequence, GKNDG, is located in two consecutive sharp turns on the surface, forming the entrance to a groove.
• pfam CAP_GLY 66aa 6e-26 in ref transcript
• Changed! TIGR SMC_prok_A 315aa 1e-13 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent.
• TIGR SMC_prok_B 189aa 2e-07 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• Changed! pfam SMC_N 386aa 5e-05 in ref transcript
  • RecF/RecN/SMC N terminal domain. This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.
• COG NIP100 61aa 2e-11 in ref transcript
  • Dynactin complex subunit involved in mitotic spindle partitioning in anaphase B [Cell division and chromosome partitioning].
• Changed! COG Smc 306aa 4e-11 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].
• COG NIP100 62aa 2e-10 in ref transcript
• Changed! PRK PRK03918 589aa 1e-06 in ref transcript
  • chromosome segregation protein; Provisional.
• Changed! TIGR SMC_prok_B 231aa 5e-07 in modified transcript
• Changed! TIGR SMC_prok_B 360aa 6e-06 in modified transcript
• Changed! COG Smc 191aa 9e-04 in modified transcript
• Changed! PRK PRK03918 512aa 0.001 in modified transcript

CLIP1

• RSN.F35 RSN.R13 248 281
• AceView 36.Apr07 CLIP1
• Single exon skipping, size difference: 33
• Exclusion in the protein (no frameshift)
• Reference transcript: CLIP1.aApr07

• pfam CAP_GLY 66aa 6e-27 in ref transcript
  • CAP-Gly domain. Cytoskeleton-associated proteins (CAPs) are involved in the organisation of microtubules and transportation of vesicles and organelles along the cytoskeletal network. A conserved motif, CAP-Gly, has been identified in a number of CAPs, including CLIP-170 and dynactins. The crystal structure of Caenorhabditis elegans F53F4.3 protein CAP-Gly domain was recently solved. The domain contains three beta-strands. The most conserved sequence, GKNDG, is located in two consecutive sharp turns on the surface, forming the entrance to a groove.
• pfam CAP_GLY 66aa 6e-26 in ref transcript
• TIGR SMC_prok_A 315aa 1e-13 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent.
• Changed! TIGR SMC_prok_B 189aa 2e-07 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• Changed! pfam SMC_N 386aa 5e-05 in ref transcript
  • RecF/RecN/SMC N terminal domain. This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.
• COG NIP100 61aa 2e-11 in ref transcript
  • Dynactin complex subunit involved in mitotic spindle partitioning in anaphase B [Cell division and chromosome partitioning].
• COG Smc 306aa 4e-11 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].
• COG NIP100 62aa 2e-10 in ref transcript
• Changed! PRK PRK03918 589aa 1e-06 in ref transcript
  • chromosome segregation protein; Provisional.
• Changed! TIGR SMC_prok_B 178aa 8e-08 in modified transcript
• Changed! TIGR SMC_prok_B 349aa 2e-07 in modified transcript
• Changed! PRK PRK03918 578aa 5e-07 in modified transcript

RUNX2

• RUNX2.F1 RUNX2.R1 169 235
• NCBIGene 36.3 860
• Single exon skipping, size difference: 66
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001024630

• pfam Runt 134aa 9e-74 in ref transcript
  • Runt domain.
• pfam RunxI 78aa 2e-32 in ref transcript
  • Runx inhibition domain. This domain lies to the C-terminus of Runx-related transcription factors and homologous proteins (AML, CBF-alpha, PEBP2). Its function might be to interact with functional cofactors.

SDCCAG8

• SDCCAG8-F1 SDCCAG8-R1 180 417
• AceView 36.Apr07 SDCCAG8
• Multiple exon skipping, size difference: 237
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: SDCCAG8.aApr07

• Changed! TIGR SMC_prok_B 270aa 2e-06 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• Changed! TIGR SMC_prok_B 306aa 5e-06 in ref transcript
• Changed! COG Smc 382aa 4e-07 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].
• Changed! TIGR SMC_prok_B 283aa 2e-10 in modified transcript
• Changed! COG Smc 300aa 6e-07 in modified transcript

SHC1

• SHC1.F7 SHC1.R7 111 165
• AceView 36.Apr07 SHC1
• Single exon skipping, size difference: 54
• Exclusion in the protein (no frameshift)
• Reference transcript: SHC1.aApr07

• Changed! cd SHC 166aa 3e-73 in ref transcript
  • SHC phosphotyrosine-binding (PTB) domain. SHC is a substrate for receptor tyrosine kinases, which can interact with phosphoproteins at NPXY motifs. SHC contains an PTB domain followed by an SH2 domain. PTB domains have a PH-like fold and are found in various eukaryotic signaling molecules. They were initially identified based upon their ability to recognize phosphorylated tyrosine residues In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. More recent studies have found that some types of PTB domains can bind to peptides which are not tyrosine phosphorylated or lack tyrosine residues altogether.
• cd SH2 92aa 7e-13 in ref transcript
  • Src homology 2 domains; Signal transduction, involved in recognition of phosphorylated tyrosine (pTyr). SH2 domains typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites.
• Changed! pfam PID 156aa 6e-39 in ref transcript
  • Phosphotyrosine interaction domain (PTB/PID).
• pfam SH2 45aa 4e-14 in ref transcript
  • SH2 domain.
• Changed! cd SHC 148aa 2e-59 in modified transcript
• Changed! pfam PID 138aa 2e-26 in modified transcript

SHMT1

• SHMT1.u.f.24 SHMT1.u.r.18 108 225
• NCBIGene 36.3 6470
• Single exon skipping, size difference: 117
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_004169

• Changed! cd SHMT 427aa 0.0 in ref transcript
  • Serine-glycine hydroxymethyltransferase (SHMT). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). SHMT carries out interconversion of serine and glycine; it catalyzes the transfer of hydroxymethyl group of N5, N10-methylene tetrahydrofolate to glycine resulting in the formation of serine and tetrahydrofolate. Both eukaryotic and prokaryotic SHMT enzymes form tight obligate homodimers; the mammalian enzyme forms a homotetramer comprising four pyridoxal phosphate-bound active sites.
• Changed! pfam SHMT 400aa 0.0 in ref transcript
  • Serine hydroxymethyltransferase.
• Changed! PTZ PTZ00094 457aa 0.0 in ref transcript
  • serine hydroxymethyltransferase; Provisional.
• Changed! cd SHMT 388aa 1e-167 in modified transcript
• Changed! pfam SHMT 361aa 1e-178 in modified transcript
• Changed! PTZ PTZ00094 418aa 0.0 in modified transcript

SLIT2

• SLIT2.F36 SLIT2.R4 222 234
• AceView 36.Apr07 SLIT2
• Single exon skipping, size difference: 12
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: SLIT2.aApr07

• cd LamG 154aa 3e-26 in ref transcript
  • Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules.
• cd EGF_CA 37aa 1e-04 in ref transcript
  • Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements.
• cd EGF_CA 37aa 0.002 in ref transcript
• smart LamG 137aa 5e-33 in ref transcript
  • Laminin G domain.
• TIGR PCC 77aa 4e-10 in ref transcript
  • Note: this model is restricted to the amino half because a full-length model is incompatible with the HMM software package.
• TIGR PCC 156aa 1e-09 in ref transcript
• Changed! TIGR PCC 63aa 3e-05 in ref transcript
• smart EGF_CA 37aa 3e-04 in ref transcript
  • Calcium-binding EGF-like domain.
• TIGR PCC 64aa 4e-04 in ref transcript
• smart LRRNT 32aa 8e-04 in ref transcript
  • Leucine rich repeat N-terminal domain.
• smart LRRNT 32aa 0.001 in ref transcript
• smart LRRNT 33aa 0.003 in ref transcript
• pfam EGF 32aa 0.003 in ref transcript
  • EGF-like domain. There is no clear separation between noise and signal. pfam00053 is very similar, but has 8 instead of 6 conserved cysteines. Includes some cytokine receptors. The EGF domain misses the N-terminus regions of the Ca2+ binding EGF domains (this is the main reason of discrepancy between Swiss-Prot domain start/end and Pfam). The family is hard to model due to many similar but different sub-types of EGF domains. Pfam certainly misses a number of EGF domains.
• COG COG4886 164aa 2e-07 in ref transcript
  • Leucine-rich repeat (LRR) protein [Function unknown].
• COG COG4886 156aa 6e-06 in ref transcript
• Changed! COG COG4886 230aa 3e-04 in ref transcript
• COG COG4886 286aa 6e-04 in ref transcript
• Changed! TIGR PCC 79aa 2e-05 in modified transcript
• Changed! COG COG4886 234aa 0.001 in modified transcript

SPP1

• SPP1-3 SPP1-4 181 223
• NCBIGene 36.3 6696
• Single exon skipping, size difference: 42
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001040058

• Changed! pfam Osteopontin 314aa 1e-96 in ref transcript
  • Osteopontin.
• Changed! pfam Osteopontin 300aa 9e-89 in modified transcript

STIM1

• STIM1.F1 STIM1.R1 202 295
• AceView 36.Apr07 STIM1
• Single exon skipping, size difference: 93
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: STIM1.aApr07

• cd SAM 69aa 4e-04 in ref transcript
  • Sterile alpha motif.; Widespread domain in signalling and nuclear proteins. In EPH-related tyrosine kinases, appears to mediate cell-cell initiated signal transduction via the binding of SH2-containing proteins to a conserved tyrosine that is phosphorylated. In many cases mediates homodimerization.
• TIGR SMC_prok_A 132aa 3e-06 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent.
• smart SAM 65aa 3e-05 in ref transcript
  • Sterile alpha motif. Widespread domain in signalling and nuclear proteins. In EPH-related tyrosine kinases, appears to mediate cell-cell initiated signal transduction via the binding of SH2-containing proteins to a conserved tyrosine that is phosphorylated. In many cases mediates homodimerisation.
• COG Smc 255aa 7e-05 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].

SYK

• SYK.F1 SYK.R16 244 313
• AceView 36.Apr07 SYK
• Single exon skipping, size difference: 69
• Exclusion in the protein (no frameshift)
• Reference transcript: SYK.bApr07

• cd PTKc_Syk 257aa 1e-155 in ref transcript
  • Catalytic Domain of the Protein Tyrosine Kinase, Spleen tyrosine kinase. Protein Tyrosine Kinase (PTK) family; Spleen tyrosine kinase (Syk); catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Syk, together with Zap-70, form the Syk subfamily of kinases which are cytoplasmic (or nonreceptor) tyr kinases containing two Src homology 2 (SH2) domains N-terminal to the catalytic tyr kinase domain. Syk was first cloned from the spleen, and its function in hematopoietic cells is well-established. Syk is involved in the signaling downstream of activated receptors (including B-cell and Fc receptors) that contain ITAMs (immunoreceptor tyr activation motifs), leading to processes such as cell proliferation, differentiation, survival, adhesion, migration, and phagocytosis. More recently, Syk expression has been detected in other cell types (including epithelial cells, vascular endothelial cells, neurons, hepatocytes, and melanocytes), suggesting a variety of biological functions in non-immune cells. Syk plays a critical role in maintaining vascular integrity and in wound healing during embryogenesis. It also regulates Vav3, which is important in osteoclast function including bone development. In breast epithelial cells, where Syk acts as a negative regulator for epidermal growth factor receptor (EGFR) signaling, loss of Syk expression is associated with abnormal proliferation during cancer development suggesting a potential role as a tumor suppressor. In mice, Syk has been shown to inhibit malignant transformation of mammary epithelial cells induced with murine mammary tumor virus (MMTV).
• cd SH2 93aa 4e-18 in ref transcript
  • Src homology 2 domains; Signal transduction, involved in recognition of phosphorylated tyrosine (pTyr). SH2 domains typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites.
• cd SH2 93aa 1e-16 in ref transcript
• pfam Pkinase_Tyr 253aa 2e-96 in ref transcript
  • Protein tyrosine kinase.
• pfam SH2 77aa 4e-22 in ref transcript
  • SH2 domain.
• smart SH2 85aa 2e-19 in ref transcript
  • Src homology 2 domains. Src homology 2 domains bind phosphotyrosine-containing polypeptides via 2 surface pockets. Specificity is provided via interaction with residues that are distinct from the phosphotyrosine. Only a single occurrence of a SH2 domain has been found in S. cerevisiae.
• COG SPS1 251aa 4e-18 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].

SYNE2

• SYNE2.u.f.128 SYNE2.u.r.124 119 188
• NCBIGene 36.3 23224
• Single exon skipping, size difference: 69
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_182914

• cd SPEC 214aa 1e-12 in ref transcript
  • Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here.
• cd CH 103aa 5e-12 in ref transcript
  • Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav).
• cd SPEC 215aa 1e-10 in ref transcript
• cd CH 103aa 6e-10 in ref transcript
• cd SPEC 214aa 4e-09 in ref transcript
• cd SPEC 221aa 8e-08 in ref transcript
• cd SPEC 216aa 1e-07 in ref transcript
• cd SPEC 207aa 2e-05 in ref transcript
• pfam KASH 60aa 7e-14 in ref transcript
  • Nuclear envelope localisation domain. The KASH (for Klarsicht/ANC-1/Syne-1 homology) or KLS domain is a highly hydrophobic nuclear envelope localisation domain of approximately 60 amino acids comprising an 20-amino-acid transmembrane region and a 30-35-residue C-terminal region that lies between the inner and the outer nuclear membranes.
• pfam CH 99aa 2e-13 in ref transcript
  • Calponin homology (CH) domain. The CH domain is found in both cytoskeletal proteins and signal transduction proteins. The CH domain is involved in actin binding in some members of the family. However in calponins there is evidence that the CH domain is not involved in its actin binding activity. Most proteins have two copies of the CH domain, however some proteins such as calponin have only a single copy.
• smart CH 102aa 2e-13 in ref transcript
  • Calponin homology domain. Actin binding domains present in duplicate at the N-termini of spectrin-like proteins (including dystrophin, alpha-actinin). These domains cross-link actin filaments into bundles and networks. A calponin homology domain is predicted in yeasst Cdc24p.
• pfam SMC_N 302aa 1e-06 in ref transcript
  • RecF/RecN/SMC N terminal domain. This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.
• TIGR SMC_prok_B 305aa 4e-05 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• smart SPEC 102aa 9e-05 in ref transcript
  • Spectrin repeats.
• smart SPEC 104aa 3e-04 in ref transcript
• TIGR SMC_prok_A 303aa 3e-04 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent.
• TIGR SMC_prok_A 375aa 4e-04 in ref transcript
• pfam SMC_N 281aa 0.002 in ref transcript
• COG SAC6 255aa 3e-22 in ref transcript
  • Ca2+-binding actin-bundling protein fimbrin/plastin (EF-Hand superfamily) [Cytoskeleton].
• COG Smc 266aa 3e-04 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].

TGFBR2

• TGFBR2.F3 rs.TGFBR2.R1 219 294
• NCBIGene 36.3 7048
• Single exon skipping, size difference: 75
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001024847

• cd S_TKc 288aa 5e-35 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• pfam ecTbetaR2 104aa 4e-49 in ref transcript
  • Transforming growth factor beta receptor 2 ectodomain. The Transforming growth factor beta receptor 2 ectodomain is a compact fold consisting of nine beta-strands and a single helix stabilised by a network of six intra strand disulphide bonds. The folding topology includes a central five-stranded antiparallel beta-sheet, eight-residues long at its centre, covered by a second layer consisting of two segments of two-stranded antiparallel beta-sheets (beta1-beta4, beta3-beta9).
• pfam Pkinase 291aa 8e-45 in ref transcript
  • Protein kinase domain.
• COG SPS1 287aa 2e-16 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].

MYO18A

• TIAF1-3 TIAF1-4 279 324
• NCBIGene 36.3 399687
• Single exon skipping, size difference: 45
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_078471

• cd MYSc_type_XVIII 779aa 0.0 in ref transcript
  • Myosin motor domain, type XVIII myosins. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle.
• cd PDZ_signaling 80aa 6e-10 in ref transcript
  • PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of PDZ domains an N-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in proteases.
• smart MYSc 786aa 1e-105 in ref transcript
  • Myosin. Large ATPases. ATPase; molecular motor. Muscle contraction consists of a cyclical interaction between myosin and actin. The core of the myosin structure is similar in fold to that of kinesin.
• pfam Myosin_tail_1 527aa 1e-36 in ref transcript
  • Myosin tail. The myosin molecule is a multi-subunit complex made up of two heavy chains and four light chains it is a fundamental contractile protein found in all eukaryote cell types. This family consists of the coiled-coil myosin heavy chain tail region. The coiled-coil is composed of the tail from two molecules of myosin. These can then assemble into the macromolecular thick filament. The coiled-coil region provides the structural backbone the thick filament.
• Changed! TIGR SMC_prok_B 288aa 2e-11 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• smart PDZ 81aa 5e-08 in ref transcript
  • Domain present in PSD-95, Dlg, and ZO-1/2. Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities.
• COG COG5022 1200aa 1e-103 in ref transcript
  • Myosin heavy chain [Cytoskeleton].
• Changed! COG Smc 738aa 5e-21 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].
• Changed! TIGR SMC_prok_B 331aa 2e-08 in modified transcript
• Changed! COG Smc 691aa 1e-18 in modified transcript

TNFRSF10B

• TNFRSF10B.u.f.10 tnfrsf10b.r.3 303 390
• NCBIGene 36.3 8795
• Intron retention, size difference: 87
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_003842

• cd TNFR 86aa 2e-16 in ref transcript
  • Tumor necrosis factor receptor (TNFR) domain; superfamily of TNF-like receptor domains. When bound to TNF-like cytokines, TNFRs trigger multiple signal transduction pathways, they are involved in inflammation response, apoptosis, autoimmunity and organogenesis. TNFRs domains are elongated with generally three tandem repeats of cysteine-rich domains (CRDs). They fit in the grooves between protomers within the ligand trimer. Some TNFRs, such as NGFR and HveA, bind ligands with no structural similarity to TNF and do not bind ligand trimers.
• smart DEATH 87aa 2e-17 in ref transcript
  • DEATH domain, found in proteins involved in cell death (apoptosis). Alpha-helical domain present in a variety of proteins with apoptotic functions. Some (but not all) of these domains form homotypic and heterotypic dimers.
• smart TNFR 41aa 3e-06 in ref transcript
  • Tumor necrosis factor receptor / nerve growth factor receptor repeats. Repeats in growth factor receptors that are involved in growth factor binding. TNF/TNFR.
• smart TNFR 40aa 2e-04 in ref transcript

TOPBP1

• TOPBP1.u.f.8 TOPBP1.u.r.8 128 143
• AceView 36.Apr07 TOPBP1
• Alternative 3-prime, size difference: 15
• Exclusion in the protein (no frameshift)
• Reference transcript: TOPBP1.aApr07

• cd BRCT 71aa 4e-09 in ref transcript
  • Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks.
• cd BRCT 70aa 6e-08 in ref transcript
• cd BRCT 71aa 2e-06 in ref transcript
• cd BRCT 70aa 2e-06 in ref transcript
• cd BRCT 58aa 7e-05 in ref transcript
• pfam BRCT 73aa 2e-13 in ref transcript
  • BRCA1 C Terminus (BRCT) domain. The BRCT domain is found predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage. It has been suggested that the Retinoblastoma protein contains a divergent BRCT domain, this has not been included in this family. The BRCT domain of XRCC1 forms a homodimer in the crystal structure. This suggests that pairs of BRCT domains associate as homo- or heterodimers.
• pfam BRCT 74aa 5e-11 in ref transcript
• pfam BRCT 72aa 3e-10 in ref transcript
• pfam BRCT 71aa 5e-08 in ref transcript
• pfam BRCT 79aa 1e-07 in ref transcript
• smart BRCT 53aa 3e-06 in ref transcript
  • breast cancer carboxy-terminal domain.

TRAF3

• TRAF3.u.f.1 TRAF3.u.r.3 161 300
• NCBIGene 36.3 7187
• Single exon skipping, size difference: 139
• Exclusion in 5'UTR
• Reference transcript: NM_145725

• cd MATH_TRAF3 186aa 1e-106 in ref transcript
  • Tumor Necrosis Factor Receptor (TNFR)-Associated Factor (TRAF) family, TRAF3 subfamily, TRAF domain; TRAF molecules serve as adapter proteins that link TNFRs and downstream kinase cascades resulting in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses. TRAF3 was first described as a molecule that binds the cytoplasmic tail of CD40. However, it is not required for CD40 signaling. More recently, TRAF3 has been identified as a key regulator of type I interferon (IFN) production and the mammalian innate antiviral immunity. It mediates IFN responses in Toll-like receptor (TLR)-dependent as well as TLR-independent viral recognition pathways. It is also a key element in immunological homeostasis through its regulation of the anti-inflammatory cytokine interleukin-10. TRAF3 contains a RING finger domain, five zinc finger domains, and a TRAF domain. The TRAF domain can be divided into a more divergent N-terminal alpha helical region (TRAF-N), and a highly conserved C-terminal MATH subdomain (TRAF-C) with an eight-stranded beta-sandwich structure. TRAF-N mediates trimerization while TRAF-C interacts with receptors.
• pfam MATH 126aa 4e-18 in ref transcript
  • MATH domain. This motif has been called the Meprin And TRAF-Homology (MATH) domain. This domain is hugely expanded in the nematode Caenorhabditis elegans.
• pfam zf-TRAF 57aa 1e-11 in ref transcript
  • TRAF-type zinc finger.
• pfam Cast 176aa 2e-05 in ref transcript
  • RIM-binding protein of the cytomatrix active zone. This is a family of proteins that form part of the CAZ (cytomatrix at the active zone) complex which is involved in determining the site of synaptic vesicle fusion. The C-terminus is a PDZ-binding motif that binds directly to RIM (a small G protein Rab-3A effector). The family also contains four coiled-coil domains.
• smart RING 36aa 0.002 in ref transcript
  • Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s).
• TIGR rad18 203aa 0.005 in ref transcript
  • This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
• COG Smc 161aa 5e-07 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].
• COG COG5222 59aa 0.005 in ref transcript
  • Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only].

TSSC4

• TSSC4.F10 TSSC4.R7 140 332
• AceView 36.Apr07 TSSC4
• Intron retention, size difference: 192
• Exclusion in the protein (no frameshift)
• Reference transcript: TSSC4.dApr07

TUBA4A

• TUBA1.F5 TUBA1.R5 101 324
• AceView 36.Apr07 TUBA4A
• Single exon skipping, size difference: 223
• Exclusion in the protein causing a frameshift
• Reference transcript: TUBA4A.aApr07

• Changed! cd alpha_tubulin 434aa 0.0 in ref transcript
  • The tubulin superfamily includes five distinct families, the alpha-, beta-, gamma-, delta-, and epsilon-tubulins and a sixth family (zeta-tubulin) which is present only in kinetoplastid protozoa. The alpha- and beta-tubulins are the major components of microtubules, while gamma-tubulin plays a major role in the nucleation of microtubule assembly. The delta- and epsilon-tubulins are widespread but unlike the alpha, beta, and gamma-tubulins they are not ubiquitous among eukaryotes. The alpha/beta-tubulin heterodimer is the structural subunit of microtubules. The alpha- and beta-tubulins share 40% amino-acid sequence identity, exist in several isotype forms, and undergo a variety of posttranslational modifications. The structures of alpha- and beta-tubulin are basically identical: each monomer is formed by a core of two beta-sheets surrounded by alpha-helices. The monomer structure is very compact, but can be divided into three regions based on function: the amino-terminal nucleotide-binding region, an intermediate taxol-binding region and the carboxy-terminal region which probably constitutes the binding surface for motor proteins.
• Changed! pfam Tubulin 243aa 2e-67 in ref transcript
  • Tubulin/FtsZ family, GTPase domain. This family includes the tubulin alpha, beta and gamma chains, as well as the bacterial FtsZ family of proteins. Members of this family are involved in polymer formation. FtsZ is the polymer-forming protein of bacterial cell division. It is part of a ring in the middle of the dividing cell that is required for constriction of cell membrane and cell envelope to yield two daughter cells. FtsZ and tubulin are GTPases. FtsZ can polymerise into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria and archaea. Tubulin is the major component of microtubules.
• Changed! pfam Tubulin_C 136aa 3e-52 in ref transcript
  • Tubulin/FtsZ family, C-terminal domain. This family includes the tubulin alpha, beta and gamma chains, as well as the bacterial FtsZ family of proteins. Members of this family are involved in polymer formation. FtsZ is the polymer-forming protein of bacterial cell division. It is part of a ring in the middle of the dividing cell that is required for constriction of cell membrane and cell envelope to yield two daughter cells. FtsZ and tubulin are GTPases. FtsZ can polymerise into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria and archaea. Tubulin is the major component of microtubules.
• Changed! PTZ PTZ00012 447aa 0.0 in ref transcript
  • alpha-tubulin II; Provisional.

UTRN

• UTRN.u.f.81 UTRN.u.r.78 231 270
• AceView 36.Apr07 UTRN
• Single exon skipping, size difference: 39
• Exclusion in the protein (no frameshift)
• Reference transcript: UTRN.aApr07

• cd ZZ_dystrophin 49aa 2e-23 in ref transcript
  • Zinc finger, ZZ type. Zinc finger present in dystrophin and dystrobrevin. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dystrophin attaches actin filaments to an integral membrane glycoprotein complex in muscle cells. The ZZ domain in dystrophin has been shown to be essential for binding to the membrane protein beta-dystroglycan.
• cd SPEC 219aa 2e-18 in ref transcript
  • Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here.
• cd CH 105aa 2e-14 in ref transcript
  • Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav).
• cd SPEC 203aa 6e-14 in ref transcript
• cd SPEC 241aa 6e-13 in ref transcript
• cd SPEC 211aa 1e-09 in ref transcript
• cd SPEC 208aa 4e-09 in ref transcript
• cd CH 104aa 3e-08 in ref transcript
• cd SPEC 213aa 6e-08 in ref transcript
• cd SPEC 117aa 2e-06 in ref transcript
• cd SPEC 214aa 2e-05 in ref transcript
• cd SPEC 201aa 4e-04 in ref transcript
• cd SPEC 205aa 5e-04 in ref transcript
• cd WW 29aa 6e-04 in ref transcript
  • Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
• pfam efhand_1 121aa 2e-49 in ref transcript
  • EF hand. Members of this family adopt a helix-loop-helix motif, as per other EF hand domains. However, since they do not contain the canonical pattern of calcium binding residues found in many EF hand domains, they do not bind calcium ions. The main function of this domain is the provision of specificity in beta-dystroglycan recognition, though in dystrophin it serves an additional role: stabilisation of the WW domain (pfam00397), enhancing dystroglycan binding.
• pfam efhand_2 92aa 1e-36 in ref transcript
  • EF-hand. Members of this family adopt a helix-loop-helix motif, as per other EF hand domains. However, since they do not contain the canonical pattern of calcium binding residues found in many EF hand domains, they do not bind calcium ions. The main function of this domain is the provision of specificity in beta-dystroglycan recognition, though in dystrophin it serves an additional role: stabilisation of the WW domain (pfam00397), enhancing dystroglycan binding.
• pfam ZZ 46aa 1e-17 in ref transcript
  • Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300. ZZ in dystrophin binds calmodulin. Putative zinc finger; binding not yet shown. Four to six cysteine residues in its sequence are responsible for coordinating zinc ions, to reinforce the structure.
• pfam CH 104aa 5e-17 in ref transcript
  • Calponin homology (CH) domain. The CH domain is found in both cytoskeletal proteins and signal transduction proteins. The CH domain is involved in actin binding in some members of the family. However in calponins there is evidence that the CH domain is not involved in its actin binding activity. Most proteins have two copies of the CH domain, however some proteins such as calponin have only a single copy.
• pfam CH 103aa 2e-10 in ref transcript
• smart SPEC 102aa 9e-10 in ref transcript
  • Spectrin repeats.
• smart SPEC 102aa 2e-08 in ref transcript
• smart SPEC 106aa 7e-07 in ref transcript
• smart SPEC 94aa 2e-06 in ref transcript
• TIGR SMC_prok_B 742aa 2e-05 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• pfam SMC_N 241aa 2e-04 in ref transcript
  • RecF/RecN/SMC N terminal domain. This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.
• pfam SMC_N 302aa 2e-04 in ref transcript
• pfam WW 30aa 4e-04 in ref transcript
  • WW domain. The WW domain is a protein module with two highly conserved tryptophans that binds proline-rich peptide motifs in vitro.
• TIGR SMC_prok_B 783aa 0.001 in ref transcript
• TIGR SMC_prok_B 348aa 0.008 in ref transcript
• COG SAC6 238aa 2e-23 in ref transcript
  • Ca2+-binding actin-bundling protein fimbrin/plastin (EF-Hand superfamily) [Cytoskeleton].
• COG Smc 764aa 8e-08 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].
• COG SbcC 623aa 7e-06 in ref transcript
  • ATPase involved in DNA repair [DNA replication, recombination, and repair].
• COG Smc 335aa 8e-06 in ref transcript
• COG Smc 817aa 5e-05 in ref transcript

BCL2L1

• bcl2l1.f.2 bcl2l1.r.2 193 382
• NCBIGene 36.3 598
• Alternative 5-prime, size difference: 189
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_138578

• Changed! cd Bcl-2_like 114aa 2e-40 in ref transcript
  • Apoptosis regulator proteins of the Bcl-2 family, named after B-cell lymphoma 2. This alignment model spans what have been described as Bcl-2 homology regions BH1, BH2, BH3, and BH4. Many members of this family have an additional C-terminal transmembrane segment. Some homologous proteins, which are not included in this model, may miss either the BH4 (Bax, Bak) or the BH2 (Bcl-X(S)) region, and some appear to only share the BH3 region (Bik, Bim, Bad, Bid, Egl-1). This family is involved in the regulation of the outer mitochondrial membrane's permeability and in promoting or preventing the release of apoptogenic factors, which in turn may trigger apoptosis by activating caspases. Bcl-2 and the closely related Bcl-X(L) are anti-apoptotic key regulators of programmed cell death. They are assumed to function via heterodimeric protein-protein interactions, binding pro-apoptotic proteins such as Bad (BCL2-antagonist of cell death), Bid, and Bim, by specifically interacting with their BH3 regions. Interfering with this heterodimeric interaction via small-molecule inhibitors may prove effective in targeting various cancers. This family also includes the Caenorhabditis elegans Bcl-2 homolog CED-9, which binds to CED-4, the C. Elegans homolog of mammalian Apaf-1. Apaf-1, however, does not seem to be inhibited by Bcl-2 directly.
• Changed! TIGR bcl-2 233aa 1e-89 in ref transcript
  • in artificial membranes at acidic pH, proapoptotic Bcl-2 family proteins (including Bax and Bak) probably induce the mitochondrial permeability transition and cytochrome c release by interacting with permeability transition pores, the most important component for pore fomation of which is VDAC.
• Changed! cd Bcl-2_like 45aa 1e-08 in modified transcript
• Changed! TIGR bcl-2 125aa 1e-35 in modified transcript
• Changed! TIGR bcl-2 45aa 6e-09 in modified transcript

CASP9

• primer-113212 primer-113213 360 670
• AceView 36.Apr07 CASP9
• Exon skipping and alternative 3-prime or 5-prime, size difference: 310
• Inclusion in the protein causing a new stop codon, Inclusion in the protein (no stop codon or frameshift), Inclusion in the protein (no stop codon or frameshift), Inclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: CASP9.dApr07

• Changed! cd CASc 125aa 2e-26 in ref transcript
  • Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs.
• Changed! smart CASc 124aa 3e-26 in ref transcript
  • Caspase, interleukin-1 beta converting enzyme (ICE) homologues. Cysteine aspartases that mediate programmed cell death (apoptosis). Caspases are synthesised as zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologues.
• smart CARD 91aa 1e-15 in ref transcript
  • Caspase recruitment domain. Motif contained in proteins involved in apoptotic signalling. Mediates homodimerisation. Structure consists of six antiparallel helices arranged in a topology homologue to the DEATH and the DED domain.

A2BP1

• refseq_A2BP1.F1 refseq_A2BP1.R1 189 267
• NCBIGene 36.3 54715
• Alternative 3-prime, size difference: 78
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_145891

• cd RRM 72aa 8e-21 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• smart RRM_2 72aa 1e-20 in ref transcript
  • RNA recognition motif.
• TIGR hnRNP-R-Q 159aa 7e-04 in ref transcript
  • Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.
• pfam PAT1 133aa 0.009 in ref transcript
  • Topoisomerase II-associated protein PAT1. Members of this family are necessary for accurate chromosome transmission during cell division.
• COG COG0724 101aa 1e-12 in ref transcript
  • RNA-binding proteins (RRM domain) [General function prediction only].

A2BP1

• refseq_A2BP1.F3 refseq_A2BP1.R3 112 165
• NCBIGene 36.3 54715
• Single exon skipping, size difference: 53
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_145891

• cd RRM 72aa 8e-21 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• smart RRM_2 72aa 1e-20 in ref transcript
  • RNA recognition motif.
• TIGR hnRNP-R-Q 159aa 7e-04 in ref transcript
  • Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.
• Changed! pfam PAT1 133aa 0.009 in ref transcript
  • Topoisomerase II-associated protein PAT1. Members of this family are necessary for accurate chromosome transmission during cell division.
• COG COG0724 101aa 1e-12 in ref transcript
  • RNA-binding proteins (RRM domain) [General function prediction only].

AAA1

• refseq_AAA1.F1 refseq_AAA1.R1 121 271
• NCBIGene 36.2 404744
• Single exon skipping, size difference: 150
• Exclusion of the stop codon
• Reference transcript: NM_207288

AAA1

• refseq_AAA1.F2 refseq_AAA1.R3 204 324
• NCBIGene 36.2 404744
• Single exon skipping, size difference: 120
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_207288

ABCB4

• refseq_ABCB4.F1 refseq_ABCB4.R1 106 127
• NCBIGene 36.3 5244
• Alternative 3-prime, size difference: 21
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_018849

• cd ABC_MTABC3_MDL1_MDL2 238aa 1e-116 in ref transcript
  • MTABC3 (also known as ABCB6) is a mitochondrial ATP-binding cassette protein involved in iron homeostasis and one of four ABC transporters expressed in the mitochondrial inner membrane, the other three being MDL1(ABC7), MDL2, and ATM1. In fact, the yeast MDL1 (multidrug resistance-like protein 1) and MDL2 (multidrug resistance-like protein 2) transporters are also included in this CD. MDL1 is an ATP-dependent permease that acts as a high-copy suppressor of ATM1 and is thought to have a role in resistance to oxidative stress. Interestingly, subfamily B is more closely related to the carboxyl-terminal component of subfamily C than the two halves of ABCC molecules are with one another.
• Changed! cd ABC_MTABC3_MDL1_MDL2 247aa 1e-113 in ref transcript
• TIGR 3a01208 587aa 1e-115 in ref transcript
• Changed! TIGR 3a01208 495aa 2e-95 in ref transcript
• COG MdlB 524aa 1e-111 in ref transcript
  • ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms].
• Changed! PTZ PTZ00265 773aa 3e-98 in ref transcript
  • multidrug resistance protein (mdr1); Provisional.
• Changed! cd ABC_MTABC3_MDL1_MDL2 240aa 1e-115 in modified transcript
• Changed! TIGR 3a01208 488aa 1e-97 in modified transcript
• Changed! COG MdlB 498aa 3e-98 in modified transcript

ABCB4

• refseq_ABCB4.F3 refseq_ABCB4.R3 179 320
• NCBIGene 36.3 5244
• Single exon skipping, size difference: 141
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_018849

• cd ABC_MTABC3_MDL1_MDL2 238aa 1e-116 in ref transcript
  • MTABC3 (also known as ABCB6) is a mitochondrial ATP-binding cassette protein involved in iron homeostasis and one of four ABC transporters expressed in the mitochondrial inner membrane, the other three being MDL1(ABC7), MDL2, and ATM1. In fact, the yeast MDL1 (multidrug resistance-like protein 1) and MDL2 (multidrug resistance-like protein 2) transporters are also included in this CD. MDL1 is an ATP-dependent permease that acts as a high-copy suppressor of ATM1 and is thought to have a role in resistance to oxidative stress. Interestingly, subfamily B is more closely related to the carboxyl-terminal component of subfamily C than the two halves of ABCC molecules are with one another.
• cd ABC_MTABC3_MDL1_MDL2 247aa 1e-113 in ref transcript
• TIGR 3a01208 587aa 1e-115 in ref transcript
• Changed! TIGR 3a01208 495aa 2e-95 in ref transcript
• COG MdlB 524aa 1e-111 in ref transcript
  • ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms].
• Changed! PTZ PTZ00265 773aa 3e-98 in ref transcript
  • multidrug resistance protein (mdr1); Provisional.
• Changed! TIGR 3a01208 448aa 2e-91 in modified transcript
• Changed! PTZ PTZ00265 726aa 2e-86 in modified transcript

ABCB9

• refseq_ABCB9.F1 refseq_ABCB9.R1 184 373
• NCBIGene 36.2 23457
• Single exon skipping, size difference: 189
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_019625

• Changed! cd ABCC_TAP 226aa 1e-110 in ref transcript
  • TAP, the Transporter Associated with Antigen Processing; TAP is essential for peptide delivery from the cytosol into the lumen of the endoplasmic reticulum (ER), where these peptides are loaded on major histocompatibility complex (MHC) I molecules. Loaded MHC I leave the ER and display their antigenic cargo on the cell surface to cytotoxic T cells. Subsequently, virus-infected or malignantly transformed cells can be eliminated. TAP belongs to the large family of ATP-binding cassette (ABC) transporters, which translocate a vast variety of solutes across membranes.
• Changed! TIGR 3a01208 695aa 0.0 in ref transcript
• Changed! COG MdlB 573aa 1e-127 in ref transcript
  • ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms].
• Changed! cd ABCC_TAP 197aa 4e-94 in modified transcript
• Changed! TIGR 3a01208 632aa 1e-180 in modified transcript
• Changed! COG SunT 506aa 1e-94 in modified transcript
  • ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain [Defense mechanisms].

ABCB9

• refseq_ABCB9.F4 refseq_ABCB9.R4 219 348
• NCBIGene 36.3 23457
• Single exon skipping, size difference: 129
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_203444

• cd ABCC_TAP 226aa 1e-110 in ref transcript
  • TAP, the Transporter Associated with Antigen Processing; TAP is essential for peptide delivery from the cytosol into the lumen of the endoplasmic reticulum (ER), where these peptides are loaded on major histocompatibility complex (MHC) I molecules. Loaded MHC I leave the ER and display their antigenic cargo on the cell surface to cytotoxic T cells. Subsequently, virus-infected or malignantly transformed cells can be eliminated. TAP belongs to the large family of ATP-binding cassette (ABC) transporters, which translocate a vast variety of solutes across membranes.
• Changed! TIGR 3a01208 695aa 0.0 in ref transcript
• Changed! COG MdlB 573aa 1e-127 in ref transcript
  • ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms].
• Changed! TIGR MsbA_rel 525aa 1e-110 in modified transcript
  • This protein is related to a Proteobacterial ATP transporter that exports lipid A and to eukaryotic P-glycoproteins.
• Changed! COG MdlB 530aa 1e-110 in modified transcript

ABCC11

• refseq_ABCC11.F1 refseq_ABCC11.R1 241 355
• NCBIGene 36.3 85320
• Single exon skipping, size difference: 114
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_032583

• Changed! cd ABCC_MRP_domain2 221aa 2e-95 in ref transcript
  • Domain 2 of the ABC subfamily C. This family is also known as MRP (mulrtidrug resisitance-associated protein). Some of the MRP members have five additional transmembrane segments in their N-terminus, but the function of these additional membrane-spanning domains is not clear. The MRP was found in the multidrug-resistance lung cancer cell in which p-glycoprotein was not overexpressed. MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions, such as glutathione, glucuronate, and sulfate.
• cd ABCC_MRP_domain1 193aa 7e-80 in ref transcript
  • Domain 1 of the ABC subfamily C. This family is also known as MRP (mulrtidrug resisitance-associated protein). Some of the MRP members have five additional transmembrane segments in their N-terminas, but the function of these additional membrane-spanning domains is not clear. The MRP was found in the multidrug-resisting lung cancer cell in which p-glycoprotein was not overexpressed. MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions, such as glutathione, glucuronate, and sulfate.
• Changed! TIGR MRP_assoc_pro 1298aa 0.0 in ref transcript
  • This model describes multi drug resistance-associated protein (MRP) in eukaryotes. The multidrug resistance-associated protein is an integral membrane protein that causes multidrug resistance when overexpressed in mammalian cells. It belongs to ABC transporter superfamily. The protein topology and function was experimentally demonstrated by epitope tagging and immunofluorescence. Insertion of tags in the critical regions associated with drug efflux, abrogated its function. The C-terminal domain seem to highly conserved.
• Changed! PTZ PTZ00243 893aa 1e-153 in ref transcript
  • ABC transporter; Provisional.
• COG MdlB 583aa 2e-51 in ref transcript
  • ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms].
• Changed! cd ABCC_MRP_domain2 183aa 2e-73 in modified transcript
• Changed! TIGR MRP_assoc_pro 1260aa 0.0 in modified transcript
• Changed! PTZ PTZ00243 855aa 1e-139 in modified transcript

ABCC9

• refseq_ABCC9.F2 refseq_ABCC9.R2 236 344
• NCBIGene 36.3 10060
• Single exon skipping, size difference: 108
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_020297

• cd ABCC_SUR2 240aa 1e-137 in ref transcript
  • The SUR domain 2. The sulfonylurea receptor SUR is an ATP binding cassette (ABC) protein of the ABCC/MRP family. Unlike other ABC proteins, it has no intrinsic transport function, neither active nor passive, but associates with the potassium channel proteins Kir6.1 or Kir6.2 to form the ATP-sensitive potassium (K(ATP)) channel. Within the channel complex, SUR serves as a regulatory subunit that fine-tunes the gating of Kir6.x in response to alterations in cellular metabolism. It constitutes a major pharmaceutical target as it binds numerous drugs, K(ATP) channel openers and blockers, capable of up- or down-regulating channel activity.
• Changed! cd ABCC_SUR1_N 218aa 1e-125 in ref transcript
  • The SUR domain 1. The sulfonylurea receptor SUR is an ATP transporter of the ABCC/MRP family with tandem ATPase binding domains. Unlike other ABC proteins, it has no intrinsic transport function, neither active nor passive, but associates with the potassium channel proteins Kir6.1 or Kir6.2 to form the ATP-sensitive potassium (K(ATP)) channel. Within the channel complex, SUR serves as a regulatory subunit that fine-tunes the gating of Kir6.x in response to alterations in cellular metabolism. It constitutes a major pharmaceutical target as it binds numerous drugs, K(ATP) channel openers and blockers, capable of up- or down-regulating channel activity.
• Changed! TIGR MRP_assoc_pro 1325aa 0.0 in ref transcript
  • This model describes multi drug resistance-associated protein (MRP) in eukaryotes. The multidrug resistance-associated protein is an integral membrane protein that causes multidrug resistance when overexpressed in mammalian cells. It belongs to ABC transporter superfamily. The protein topology and function was experimentally demonstrated by epitope tagging and immunofluorescence. Insertion of tags in the critical regions associated with drug efflux, abrogated its function. The C-terminal domain seem to highly conserved.
• Changed! PTZ PTZ00243 1183aa 1e-170 in ref transcript
  • ABC transporter; Provisional.
• Changed! cd ABCC_SUR1_N 217aa 1e-124 in modified transcript
• Changed! TIGR MRP_assoc_pro 1289aa 0.0 in modified transcript
• Changed! PTZ PTZ00243 1147aa 1e-170 in modified transcript

ABCD4

• refseq_ABCD4.F1 refseq_ABCD4.R1 155 283
• NCBIGene 36.3 5826
• Single exon skipping, size difference: 128
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_005050

• Changed! cd ABCD_peroxisomal_ALDP 212aa 2e-55 in ref transcript
  • Peroxisomal ATP-binding cassette transporter (Pat) is involved in the import of very long-chain fatty acids (VLCFA) into the peroxisome. The peroxisomal membrane forms a permeability barrier for a wide variety of metabolites required for and formed during fatty acid beta-oxidation. To communicate with the cytoplasm and mitochondria, peroxisomes need dedicated proteins to transport such hydrophilic molecules across their membranes. X-linked adrenoleukodystrophy (X-ALD) is caused by mutations in the ALD gene, which encodes ALDP (adrenoleukodystrophy protein ), a peroxisomal integral membrane protein that is a member of the ATP-binding cassette (ABC) transporter protein family. The disease is characterized by a striking and unpredictable variation in phenotypic expression. Phenotypes include the rapidly progressive childhood cerebral form (CCALD), the milder adult form, adrenomyeloneuropathy (AMN), and variants without neurologic involvement (i.e. asymptomatic).
• Changed! TIGR 3a01203 522aa 8e-77 in ref transcript
• Changed! COG COG4178 534aa 1e-75 in ref transcript
  • ABC-type uncharacterized transport system, permease and ATPase components [General function prediction only].

ABCD4

• refseq_ABCD4.F3 refseq_ABCD4.R3 159 299
• NCBIGene 36.2 5826
• Single exon skipping, size difference: 140
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_005050

• Changed! cd ABCD_peroxisomal_ALDP 212aa 2e-55 in ref transcript
  • Peroxisomal ATP-binding cassette transporter (Pat) is involved in the import of very long-chain fatty acids (VLCFA) into the peroxisome. The peroxisomal membrane forms a permeability barrier for a wide variety of metabolites required for and formed during fatty acid beta-oxidation. To communicate with the cytoplasm and mitochondria, peroxisomes need dedicated proteins to transport such hydrophilic molecules across their membranes. X-linked adrenoleukodystrophy (X-ALD) is caused by mutations in the ALD gene, which encodes ALDP (adrenoleukodystrophy protein ), a peroxisomal integral membrane protein that is a member of the ATP-binding cassette (ABC) transporter protein family. The disease is characterized by a striking and unpredictable variation in phenotypic expression. Phenotypes include the rapidly progressive childhood cerebral form (CCALD), the milder adult form, adrenomyeloneuropathy (AMN), and variants without neurologic involvement (i.e. asymptomatic).
• Changed! TIGR 3a01203 522aa 8e-77 in ref transcript
• Changed! COG COG4178 534aa 1e-75 in ref transcript
  • ABC-type uncharacterized transport system, permease and ATPase components [General function prediction only].
• Changed! pfam ABC_membrane_2 67aa 9e-09 in modified transcript
  • ABC transporter transmembrane region 2. This domain covers the transmembrane of a small family of ABC transporters and shares sequence similarity with pfam00664. Mutations in this domain in human PMP70 (70 kDa peroxisomal membrane protein) are believed responsible for Zellweger Syndrome-2; mutations in human ALDP (Adrenoleukodystrophy protein) are responsible for recessive X-linked adrenoleukodystrophy. A Saccharomyces cerevisiae homolog is involved in the import of long-chain fatty acids.

ABCF1

• refseq_ABCF1.F2 refseq_ABCF1.R2 135 249
• NCBIGene 36.3 23
• Single exon skipping, size difference: 114
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001025091

• cd ABCF_EF-3 189aa 3e-32 in ref transcript
  • ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated release of the deacylated tRNA from the E site. The reaction requires ATP hydrolysis. EF-3 contains two ATP nucleotide binding sequence (NBS) motifs. NBSI is sufficient for the intrinsic ATPase activity. NBSII is essential for the ribosome-stimulated functions.
• cd ABCF_EF-3 76aa 4e-27 in ref transcript
• cd ABC_cobalt_CbiO_domain1 217aa 6e-18 in ref transcript
  • Domain I of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota. The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. This ABC transport system of the CbiMNQO family is involved in cobalt transport in association with the cobalamin (vitamin B12) biosynthetic pathways. Most of cobalt (Cbi) transport systems possess a separate CbiN component, the cobalt-binding periplasmic protein, and they are encoded by the conserved gene cluster cbiMNQO. Both the CbiM and CbiQ proteins are integral cytoplasmic membrane proteins, and the CbiO protein has the linker peptide and the Walker A and B motifs commonly found in the ATPase components of the ABC-type transport systems.
• pfam ABC_tran 196aa 4e-29 in ref transcript
  • ABC transporter. ABC transporters for a large family of proteins responsible for translocation of a variety of compounds across biological membranes. ABC transporters are the largest family of proteins in many completely sequenced bacteria. ABC transporters are composed of two copies of this domain and two copies of a transmembrane domain pfam00664. These four domains may belong to a single polypeptide or belong in different polypeptide chains.
• pfam ABC_tran 163aa 9e-25 in ref transcript
• TIGR PhnT 49aa 0.004 in ref transcript
  • This ATP-binding component of an ABC transport system is found in Salmonella and Burkholderia lineages in the vicinity of enzymes for the breakdown of 2-aminoethylphosphonate.
• COG Uup 532aa 1e-107 in ref transcript
  • ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only].

ABCG1

• refseq_ABCG1.F1 refseq_ABCG1.R1 125 161
• NCBIGene 36.3 9619
• Alternative 5-prime, size difference: 36
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_004915

• cd ABCG_EPDR 226aa 4e-74 in ref transcript
  • ABCG transporters are involved in eye pigment (EP) precursor transport, regulation of lipid-trafficking mechanisms, and pleiotropic drug resistance (DR). DR is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes. Compared to other members of the ABC transporter subfamilies, the ABCG transporter family is composed of proteins that have an ATP-binding cassette domain at the N-terminus and a TM (transmembrane) domain at the C-terminus.
• Changed! TIGR 3a01204 619aa 0.0 in ref transcript
• COG CcmA 220aa 7e-46 in ref transcript
  • ABC-type multidrug transport system, ATPase component [Defense mechanisms].
• Changed! TIGR 3a01204 607aa 0.0 in modified transcript

ABCG1

• refseq_ABCG1.F3 refseq_ABCG1.R3 204 245
• NCBIGene 36.3 9619
• Single exon skipping, size difference: 41
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_207627

• Changed! cd ABCG_EPDR 226aa 2e-74 in ref transcript
  • ABCG transporters are involved in eye pigment (EP) precursor transport, regulation of lipid-trafficking mechanisms, and pleiotropic drug resistance (DR). DR is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes. Compared to other members of the ABC transporter subfamilies, the ABCG transporter family is composed of proteins that have an ATP-binding cassette domain at the N-terminus and a TM (transmembrane) domain at the C-terminus.
• Changed! TIGR 3a01204 607aa 0.0 in ref transcript
• Changed! COG CcmA 220aa 3e-46 in ref transcript
  • ABC-type multidrug transport system, ATPase component [Defense mechanisms].

ABHD11

• refseq_ABHD11.F1 refseq_ABHD11.R1 114 135
• NCBIGene 36.2 83451
• Alternative 3-prime, size difference: 21
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_148912

• pfam Abhydrolase_1 216aa 4e-13 in ref transcript
  • alpha/beta hydrolase fold. This catalytic domain is found in a very wide range of enzymes.
• PRK PRK10673 246aa 2e-37 in ref transcript
  • hypothetical protein; Provisional.

ABHD2

• refseq_ABHD2.F1 refseq_ABHD2.R1 100 498
• NCBIGene 36.3 11057
• Multiple exon skipping, size difference: 398
• Exclusion in 5'UTR, Exclusion in 5'UTR, Exclusion in 5'UTR, Exclusion in 5'UTR
• Reference transcript: NM_007011

• pfam Abhydrolase_1 230aa 3e-26 in ref transcript
  • alpha/beta hydrolase fold. This catalytic domain is found in a very wide range of enzymes.
• COG COG0429 336aa 4e-44 in ref transcript
  • Predicted hydrolase of the alpha/beta-hydrolase fold [General function prediction only].

ABI1

• refseq_ABI1.F1 refseq_ABI1.R1 135 216
• NCBIGene 36.3 10006
• Single exon skipping, size difference: 81
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_005470

• cd SH3 52aa 3e-15 in ref transcript
  • Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
• pfam Abi_HHR 79aa 4e-32 in ref transcript
  • Abl-interactor HHR. The region featured in this family is found towards the N-terminus of a number of adaptor proteins that interact with Abl-family tyrosine kinases. More specifically, it is termed the homeo-domain homologous region (HHR), as it is similar to the DNA-binding region of homeo-domain proteins. Other homeo-domain proteins have been implicated in specifying positional information during embryonic development, and in the regulation of the expression of cell-type specific genes. The Abl-interactor proteins are thought to coordinate the cytoplasmic and nuclear functions of the Abl-family kinases, and seem to be involved in cytoskeletal reorganisation, but their precise role remains unclear.
• smart SH3 56aa 2e-17 in ref transcript
  • Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.

ABI1

• refseq_ABI1.F3 refseq_ABI1.R3 165 252
• NCBIGene 36.3 10006
• Single exon skipping, size difference: 87
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_005470

• cd SH3 52aa 3e-15 in ref transcript
  • Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
• pfam Abi_HHR 79aa 4e-32 in ref transcript
  • Abl-interactor HHR. The region featured in this family is found towards the N-terminus of a number of adaptor proteins that interact with Abl-family tyrosine kinases. More specifically, it is termed the homeo-domain homologous region (HHR), as it is similar to the DNA-binding region of homeo-domain proteins. Other homeo-domain proteins have been implicated in specifying positional information during embryonic development, and in the regulation of the expression of cell-type specific genes. The Abl-interactor proteins are thought to coordinate the cytoplasmic and nuclear functions of the Abl-family kinases, and seem to be involved in cytoskeletal reorganisation, but their precise role remains unclear.
• smart SH3 56aa 2e-17 in ref transcript
  • Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.

ABLIM1

• refseq_ABLIM1.F1 refseq_ABLIM1.R1 167 272
• NCBIGene 36.3 3983
• Single exon skipping, size difference: 105
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_002313

• smart VHP 36aa 2e-12 in ref transcript
  • Villin headpiece domain.
• pfam LIM 56aa 4e-10 in ref transcript
  • LIM domain. This family represents two copies of the LIM structural domain.
• pfam LIM 56aa 1e-08 in ref transcript
• pfam LIM 45aa 6e-07 in ref transcript
• smart LIM 33aa 5e-05 in ref transcript
  • Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.

ABLIM1

• refseq_ABLIM1.F3 refseq_ABLIM1.R3 119 203
• NCBIGene 36.3 3983
• Single exon skipping, size difference: 84
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_002313

• smart VHP 36aa 2e-12 in ref transcript
  • Villin headpiece domain.
• pfam LIM 56aa 4e-10 in ref transcript
  • LIM domain. This family represents two copies of the LIM structural domain.
• pfam LIM 56aa 1e-08 in ref transcript
• pfam LIM 45aa 6e-07 in ref transcript
• smart LIM 33aa 5e-05 in ref transcript
  • Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.

ABTB1

• refseq_ABTB1.F1 refseq_ABTB1.R1 167 202
• NCBIGene 36.3 80325
• Alternative 5-prime, size difference: 35
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_172027

• Changed! cd ANK 73aa 6e-08 in ref transcript
  • ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats.
• Changed! pfam BTB 76aa 3e-15 in ref transcript
  • BTB/POZ domain. The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN.
• Changed! smart BTB 96aa 1e-14 in ref transcript
  • Broad-Complex, Tramtrack and Bric a brac. Domain in Broad-Complex, Tramtrack and Bric a brac. Also known as POZ (poxvirus and zinc finger) domain. Known to be a protein-protein interaction motif found at the N-termini of several C2H2-type transcription factors as well as Shaw-type potassium channels. Known structure reveals a tightly intertwined dimer formed via interactions between N-terminal strand and helix structures. However in a subset of BTB/POZ domains, these two secondary structures appear to be missing. Be aware SMART predicts BTB/POZ domains without the beta1- and alpha1-secondary structures.

ABTB1

• refseq_ABTB1.F2 refseq_ABTB1.R2 112 158
• NCBIGene 36.3 80325
• Alternative 3-prime, size difference: 46
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_172027

• Changed! cd ANK 73aa 6e-08 in ref transcript
  • ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats.
• Changed! pfam BTB 76aa 3e-15 in ref transcript
  • BTB/POZ domain. The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN.
• Changed! smart BTB 96aa 1e-14 in ref transcript
  • Broad-Complex, Tramtrack and Bric a brac. Domain in Broad-Complex, Tramtrack and Bric a brac. Also known as POZ (poxvirus and zinc finger) domain. Known to be a protein-protein interaction motif found at the N-termini of several C2H2-type transcription factors as well as Shaw-type potassium channels. Known structure reveals a tightly intertwined dimer formed via interactions between N-terminal strand and helix structures. However in a subset of BTB/POZ domains, these two secondary structures appear to be missing. Be aware SMART predicts BTB/POZ domains without the beta1- and alpha1-secondary structures.

ACADVL

• refseq_ACADVL.F2 refseq_ACADVL.R2 327 393
• NCBIGene 36.3 37
• Single exon skipping, size difference: 66
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000018

• cd VLCAD 410aa 0.0 in ref transcript
  • Very long chain acyl-CoA dehydrogenase (VLCAD). VLCAD acyl-CoA dehydrogenases (ACAD), which is found in the mitochondria of eukaryotes and in some bacteria. It catalyzes the alpha,beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. The reduced form of ACAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial respiratory chain coupled with ATP synthesis. VLCAD, which is a homodimer.
• pfam Acyl-CoA_dh_1 147aa 2e-35 in ref transcript
  • Acyl-CoA dehydrogenase, C-terminal domain. C-terminal domain of Acyl-CoA dehydrogenase is an all-alpha, four helical up-and-down bundle.
• TIGR cyc_hxne_CoA_dh 380aa 1e-26 in ref transcript
  • Cyclohex-1-ene-1carboxyl-CoA is an intermediate in the anaerobic degradation of benzoyl-CoA derived from varioius aromatic compounds, in Rhodopseudomonas palustris but not Thauera aromatica. The aliphatic compound cyclohexanecarboxylate, can be converted to the same intermediate in two steps. The first step is its ligation to coenzyme A. The second is the action of this enzyme, cyclohexanecarboxyl-CoA dehydrogenase.
• COG CaiA 380aa 2e-79 in ref transcript
  • Acyl-CoA dehydrogenases [Lipid metabolism].

ACCN2

• refseq_ACCN2.F1 refseq_ACCN2.R1 140 278
• NCBIGene 36.3 41
• Alternative 5-prime, size difference: 138
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_020039

• Changed! TIGR ENaC 538aa 1e-160 in ref transcript
  • This Hmm is designed from the vertebrate members of the ENaC family.
• Changed! TIGR ENaC 492aa 1e-168 in modified transcript

ACCN3

• refseq_ACCN3.F1 refseq_ACCN3.R1 113 133
• NCBIGene 36.3 9311
• Alternative 3-prime, size difference: 20
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_020321

• Changed! pfam ASC 441aa 1e-120 in ref transcript
  • Amiloride-sensitive sodium channel.
• Changed! TIGR ENaC 395aa 1e-120 in modified transcript
  • This Hmm is designed from the vertebrate members of the ENaC family.
• Changed! TIGR deg-1 87aa 4e-05 in modified transcript
  • This Hmm is designed from the invertebrate members of the ENaC family.

ACCN4

• refseq_ACCN4.F1 refseq_ACCN4.R1 182 239
• NCBIGene 36.3 55515
• Single exon skipping, size difference: 57
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_018674

• Changed! TIGR ENaC 362aa 5e-95 in ref transcript
  • This Hmm is designed from the vertebrate members of the ENaC family.
• TIGR ENaC 103aa 0.002 in ref transcript
• Changed! TIGR ENaC 343aa 2e-92 in modified transcript

A1CF

• refseq_ACF.F1 refseq_ACF.R1 113 137
• NCBIGene 36.3 29974
• Alternative 3-prime, size difference: 24
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_138933

• cd RRM 69aa 1e-16 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• cd RRM 68aa 4e-13 in ref transcript
• cd RRM 79aa 7e-09 in ref transcript
• Changed! TIGR hnRNP-R-Q 566aa 0.0 in ref transcript
  • Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.
• COG COG0724 76aa 4e-09 in ref transcript
  • RNA-binding proteins (RRM domain) [General function prediction only].
• COG COG0724 160aa 8e-08 in ref transcript
• Changed! TIGR hnRNP-R-Q 574aa 0.0 in modified transcript

A1CF

• refseq_ACF.F3 refseq_ACF.R3 193 241
• NCBIGene 36.3 29974
• Single exon skipping, size difference: 48
• Exclusion in 5'UTR
• Reference transcript: NM_138932

• cd RRM 69aa 1e-16 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• cd RRM 68aa 5e-13 in ref transcript
• cd RRM 79aa 9e-09 in ref transcript
• TIGR hnRNP-R-Q 593aa 0.0 in ref transcript
  • Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.
• COG COG0724 76aa 7e-09 in ref transcript
  • RNA-binding proteins (RRM domain) [General function prediction only].
• COG COG0724 160aa 2e-07 in ref transcript

A1CF

• refseq_ACF.F5 refseq_ACF.R5 200 343
• NCBIGene 36.3 29974
• Single exon skipping, size difference: 143
• Exclusion of the protein initiation site
• Reference transcript: NM_138933

• cd RRM 69aa 1e-16 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• cd RRM 68aa 4e-13 in ref transcript
• cd RRM 79aa 7e-09 in ref transcript
• Changed! TIGR hnRNP-R-Q 566aa 0.0 in ref transcript
  • Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.
• COG COG0724 76aa 4e-09 in ref transcript
  • RNA-binding proteins (RRM domain) [General function prediction only].
• COG COG0724 160aa 8e-08 in ref transcript
• Changed! TIGR hnRNP-R-Q 585aa 0.0 in modified transcript

ACLY

• refseq_ACLY.F1 refseq_ACLY.R1 141 171
• NCBIGene 36.3 47
• Single exon skipping, size difference: 30
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001096

• cd CCL_ACL-C 238aa 2e-78 in ref transcript
  • Citryl-CoA lyase (CCL), the C-terminal portion of the single-subunit type ATP-citrate lyase (ACL) and the C-terminal portion of the large subunit of the two-subunit type ACL. CCL cleaves citryl-CoA (CiCoA) to acetyl-CoA (AcCoA) and oxaloacetate (OAA). ACL catalyzes an ATP- and a CoA- dependant cleavage of citrate to form AcCoA and OAA in a multistep reaction, the final step of which is likely to involve the cleavage of CiCoA to generate AcCoA and OAA. In fungi, yeast, plants, and animals ACL is cytosolic and generates AcCoA for lipogenesis. ACL may be required for fruiting body maturation in the filamentous fungus Sordaria macrospore. In several groups of autotrophic prokaryotes and archaea, ACL carries out the citrate-cleavage reaction of the reductive tricarboxylic acid (rTCA) cycle. In the family Aquificaceae this latter reaction in the rTCA cycle is carried out via a two enzyme system the second enzyme of which is CCL; the first enzyme is citryl-CoA synthetase (CCS) which is not included in this group. Chlorobium limicola ACL is an example of a two-subunit type ACL. It is comprised of a large and a small subunit; it has been speculated that the large subunit arose from a fusion of the small subunit of the two subunit CCS with CCL. The small ACL subunit is a homolog of the larger CCS subunit. Mammalian ACL is of the single-subunit type and may have arisen from the two-subunit ACL by another gene fusion. Mammalian ACLs are homotetramers; the ACLs of C. limicola and Arabidopsis are a heterooctomers (alpha4beta4). In cancer cells there is a shift in energy metabolism to aerobic glycolysis, the glycolytic end product pyruvate enters a truncated TCA cycle generating citrate which is cleaved in the cytosol by ACL. Inhibiting ACL limits the in-vitro proliferation and survival of these cancer cells, reduces in vivo tumor growth, and induces differentiation.
• TIGR sucCoAalpha 257aa 3e-31 in ref transcript
  • ATP citrate lyases appear to form an outgroup.
• pfam Citrate_synt 188aa 1e-12 in ref transcript
  • Citrate synthase.
• TIGR sucCoAbeta 349aa 3e-12 in ref transcript
  • This family contains a split seen both in a maximum parsimony tree (which ignores gaps) and in the gap pattern near position 85 of the seed alignment. Eukaryotic and most bacterial sequences are longer and contain a region similar to TXQTXXXG. Sequences from Deinococcus radiodurans, Mycobacterium tuberculosis, Streptomyces coelicolor, and the Archaea are 6 amino acids shorter in that region and contain a motif resembling [KR]G.
• COG SucD 256aa 8e-55 in ref transcript
  • Succinyl-CoA synthetase, alpha subunit [Energy production and conversion].
• COG SucC 410aa 5e-46 in ref transcript
  • Succinyl-CoA synthetase, beta subunit [Energy production and conversion].
• COG GltA 235aa 1e-29 in ref transcript
  • Citrate synthase [Energy production and conversion].

ACOT8

• refseq_ACOT8.F1 refseq_ACOT8.R1 146 341
• NCBIGene 36.3 10005
• Single exon skipping, size difference: 195
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_005469

• Changed! cd Thioesterase_II_repeat1 104aa 2e-33 in ref transcript
  • Thioesterase II (TEII) is thought to regenerate misprimed nonribosomal peptide synthetases (NRPSs) as well as modular polyketide synthases (PKSs) by hydrolyzing acetyl groups bound to the peptidyl carrier protein (PCP) and acyl carrier protein (ACP) domains, respectively. TEII has two tandem asymmetric hot dog folds that are structurally similar to one found in PaaI thioesterase, 4-hydroxybenzoyl-CoA thioesterase (4HBT) and beta-hydroxydecanoyl-ACP dehydratase and thus, the TEII monomer is equivalent to the homodimeric form of the latter three enzymes. Human TEII is expressed in T cells and has been shown to bind the product of the HIV-1 Nef gene.
• cd Thioesterase_II_repeat2 91aa 3e-30 in ref transcript
  • Thioesterase II (TEII) is thought to regenerate misprimed nonribosomal peptide synthetases (NRPSs) as well as modular polyketide synthases (PKSs) by hydrolyzing acetyl groups bound to the peptidyl carrier protein (PCP) and acyl carrier protein (ACP) domains, respectively. TEII has two tandem asymmetric hot dog folds that are structurally similar to one found in PaaI thioesterase, 4-hydroxybenzoyl-CoA thioesterase (4HBT) and beta-hydroxydecanoyl-ACP dehydratase and thus, the TEII monomer is equivalent to the homodimeric form of the latter three enzymes. Human TEII is expressed in T cells and has been shown to bind the product of the HIV-1 Nef gene.
• Changed! TIGR tesB 275aa 1e-105 in ref transcript
  • Subunit: homotetramer.
• Changed! COG TesB 283aa 9e-78 in ref transcript
  • Acyl-CoA thioesterase [Lipid metabolism].
• Changed! cd Thioesterase_II_repeat1 29aa 9e-06 in modified transcript
• Changed! TIGR tesB 182aa 5e-60 in modified transcript
• Changed! TIGR tesB 29aa 2e-08 in modified transcript
• Changed! COG TesB 184aa 1e-46 in modified transcript
• Changed! COG TesB 33aa 1e-04 in modified transcript

ACOT8

• refseq_ACOT8.F3 refseq_ACOT8.R3 234 368
• NCBIGene 36.2 10005
• Single exon skipping, size difference: 134
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_005469

• Changed! cd Thioesterase_II_repeat1 104aa 2e-33 in ref transcript
  • Thioesterase II (TEII) is thought to regenerate misprimed nonribosomal peptide synthetases (NRPSs) as well as modular polyketide synthases (PKSs) by hydrolyzing acetyl groups bound to the peptidyl carrier protein (PCP) and acyl carrier protein (ACP) domains, respectively. TEII has two tandem asymmetric hot dog folds that are structurally similar to one found in PaaI thioesterase, 4-hydroxybenzoyl-CoA thioesterase (4HBT) and beta-hydroxydecanoyl-ACP dehydratase and thus, the TEII monomer is equivalent to the homodimeric form of the latter three enzymes. Human TEII is expressed in T cells and has been shown to bind the product of the HIV-1 Nef gene.
• Changed! cd Thioesterase_II_repeat2 91aa 3e-30 in ref transcript
  • Thioesterase II (TEII) is thought to regenerate misprimed nonribosomal peptide synthetases (NRPSs) as well as modular polyketide synthases (PKSs) by hydrolyzing acetyl groups bound to the peptidyl carrier protein (PCP) and acyl carrier protein (ACP) domains, respectively. TEII has two tandem asymmetric hot dog folds that are structurally similar to one found in PaaI thioesterase, 4-hydroxybenzoyl-CoA thioesterase (4HBT) and beta-hydroxydecanoyl-ACP dehydratase and thus, the TEII monomer is equivalent to the homodimeric form of the latter three enzymes. Human TEII is expressed in T cells and has been shown to bind the product of the HIV-1 Nef gene.
• Changed! TIGR tesB 275aa 1e-105 in ref transcript
  • Subunit: homotetramer.
• Changed! COG TesB 283aa 9e-78 in ref transcript
  • Acyl-CoA thioesterase [Lipid metabolism].

ACOT9

• refseq_ACOT9.F2 refseq_ACOT9.R2 103 130
• NCBIGene 36.3 23597
• Single exon skipping, size difference: 27
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001037171

• cd BFIT_BACH 121aa 1e-26 in ref transcript
  • Brown fat-inducible thioesterase (BFIT). Brain acyl-CoA hydrolase (BACH). These enzymes deacylate long-chain fatty acids by hydrolyzing acyl-CoA thioesters to free fatty acids and CoA-SH. Eukaryotic members of this family are expressed in brain, testis, and brown adipose tissues. The archeal and eukaryotic members of this family have two tandem copies of the conserved hot dog fold, while most bacterial members have only one copy.
• cd BFIT_BACH 126aa 2e-17 in ref transcript
• COG COG1607 134aa 6e-11 in ref transcript
  • Acyl-CoA hydrolase [Lipid metabolism].
• COG COG1607 103aa 5e-05 in ref transcript

ACPT

• refseq_ACPT.F1 refseq_ACPT.R1 134 413
• NCBIGene 36.2 93650
• Exon skipping and alternative 3-prime or 5-prime, size difference: 279
• Exclusion in the protein (no frameshift), Exclusion in the protein (no frameshift), Exclusion in the protein (no frameshift)
• Reference transcript: NM_033068

• Changed! cd HP_HAP_like 285aa 1e-24 in ref transcript
  • Histidine phosphatase domain found in histidine acid phosphatases and phytases; contains a His residue which is phosphorylated during the reaction. Catalytic domain of HAP (histidine acid phosphatases) and phytases (myo-inositol hexakisphosphate phosphohydrolases). The conserved catalytic core of this domain contains a His residue which is phosphorylated in the reaction. Functions in this subgroup include roles in metabolism, signaling, or regulation, for example Escherichia coli glucose-1-phosphatase functions to scavenge glucose from glucose-1-phosphate and the signaling molecules inositol 1,3,4,5,6-pentakisphosphate (InsP5) and inositol hexakisphosphate (InsP6) are in vivo substrates for eukaryotic multiple inositol polyphosphate phosphatase 1 (Minpp1). Phytases scavenge phosphate from extracellular sources and are added to animal feed while prostatic acid phosphatase (PAP) has been used for many years as a serum marker for prostate cancer. Recently PAP has been shown in mouse models to suppress pain by functioning as an ecto-5prime-nucleotidase. In vivo it dephosphorylates extracellular adenosine monophosphate (AMP) generating adenosine,and leading to the activation of A1-adenosine receptors in dorsal spinal cord.
• Changed! pfam Acid_phosphat_A 307aa 1e-62 in ref transcript
  • Histidine acid phosphatase.
• Changed! PRK PRK10172 345aa 3e-06 in ref transcript
  • phosphoanhydride phosphorylase; Provisional.
• Changed! cd HP_HAP_like 192aa 4e-18 in modified transcript
• Changed! pfam Acid_phosphat_A 170aa 6e-19 in modified transcript
• Changed! pfam Acid_phosphat_A 63aa 6e-16 in modified transcript
• Changed! PRK PRK10172 175aa 0.008 in modified transcript

ACPT

• refseq_ACPT.F3 refseq_ACPT.R3 231 364
• NCBIGene 36.2 93650
• Single exon skipping, size difference: 133
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_033068

• Changed! cd HP_HAP_like 285aa 1e-24 in ref transcript
  • Histidine phosphatase domain found in histidine acid phosphatases and phytases; contains a His residue which is phosphorylated during the reaction. Catalytic domain of HAP (histidine acid phosphatases) and phytases (myo-inositol hexakisphosphate phosphohydrolases). The conserved catalytic core of this domain contains a His residue which is phosphorylated in the reaction. Functions in this subgroup include roles in metabolism, signaling, or regulation, for example Escherichia coli glucose-1-phosphatase functions to scavenge glucose from glucose-1-phosphate and the signaling molecules inositol 1,3,4,5,6-pentakisphosphate (InsP5) and inositol hexakisphosphate (InsP6) are in vivo substrates for eukaryotic multiple inositol polyphosphate phosphatase 1 (Minpp1). Phytases scavenge phosphate from extracellular sources and are added to animal feed while prostatic acid phosphatase (PAP) has been used for many years as a serum marker for prostate cancer. Recently PAP has been shown in mouse models to suppress pain by functioning as an ecto-5prime-nucleotidase. In vivo it dephosphorylates extracellular adenosine monophosphate (AMP) generating adenosine,and leading to the activation of A1-adenosine receptors in dorsal spinal cord.
• Changed! pfam Acid_phosphat_A 307aa 1e-62 in ref transcript
  • Histidine acid phosphatase.
• Changed! PRK PRK10172 345aa 3e-06 in ref transcript
  • phosphoanhydride phosphorylase; Provisional.
• Changed! cd HP_HAP_like 119aa 9e-23 in modified transcript
• Changed! pfam Acid_phosphat_A 183aa 2e-39 in modified transcript
• Changed! PRK PRK10172 109aa 0.002 in modified transcript

ACRV1

• refseq_ACRV1.F2 refseq_ACRV1.R2 267 387
• NCBIGene 36.3 56
• Single exon skipping, size difference: 120
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001612

• Changed! cd LU 77aa 4e-05 in ref transcript
  • Ly-6 antigen / uPA receptor -like domain; occurs singly in GPI-linked cell-surface glycoproteins (Ly-6 family,CD59, thymocyte B cell antigen, Sgp-2) or as three-fold repeated domain in urokinase-type plasminogen activator receptor. Topology of these domains is similar to that of snake venom neurotoxins.

ACRV1

• refseq_ACRV1.F3 refseq_ACRV1.R3 116 173
• NCBIGene 36.3 56
• Alternative 5-prime, size difference: 57
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001612

• cd LU 77aa 4e-05 in ref transcript
  • Ly-6 antigen / uPA receptor -like domain; occurs singly in GPI-linked cell-surface glycoproteins (Ly-6 family,CD59, thymocyte B cell antigen, Sgp-2) or as three-fold repeated domain in urokinase-type plasminogen activator receptor. Topology of these domains is similar to that of snake venom neurotoxins.

ACSL3

• refseq_ACSL3.F1 refseq_ACSL3.R1 249 356
• NCBIGene 36.3 2181
• Single exon skipping, size difference: 107
• Exclusion in 5'UTR
• Reference transcript: NM_004457

• pfam AMP-binding 477aa 2e-82 in ref transcript
  • AMP-binding enzyme.
• PTZ PTZ00216 617aa 1e-121 in ref transcript
  • acyl-CoA synthetase; Provisional.

ACSL4

• refseq_ACSL4.F1 refseq_ACSL4.R1 137 449
• NCBIGene 36.3 2182
• Exon skipping and alternative 3-prime or 5-prime, size difference: 312
• Exclusion in 5'UTR, Exclusion of the protein initiation site
• Reference transcript: NM_022977

• pfam AMP-binding 476aa 5e-82 in ref transcript
  • AMP-binding enzyme.
• PTZ PTZ00216 585aa 1e-120 in ref transcript
  • acyl-CoA synthetase; Provisional.
• PRK PRK07868 119aa 0.004 in ref transcript
  • acyl-CoA synthetase; Validated.

ACTL6A

• refseq_ACTL6A.F1 refseq_ACTL6A.R1 124 172
• NCBIGene 36.3 86
• Alternative 5-prime, size difference: 48
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_004301

• Changed! cd ACTIN 415aa 1e-111 in ref transcript
  • Actin; An ubiquitous protein involved in the formation of filaments that are a major component of the cytoskeleton. Interaction with myosin provides the basis of muscular contraction and many aspects of cell motility. Each actin protomer binds one molecule of ATP and either calcium or magnesium ions. Actin exists as a monomer in low salt concentrations, but filaments form rapidly as salt concentration rises, with the consequent hydrolysis of ATP. Polymerization is regulated by so-called capping proteins. The ATPase domain of actin shares similarity with ATPase domains of hexokinase and hsp70 proteins.
• Changed! pfam Actin 421aa 1e-145 in ref transcript
  • Actin.
• Changed! PTZ PTZ00281 420aa 2e-70 in ref transcript
  • actin; Provisional.

ACTR3B

• refseq_ACTR3B.F1 refseq_ACTR3B.R1 218 428
• NCBIGene 36.3 57180
• Multiple exon skipping, size difference: 210
• Exclusion in the protein (no frameshift), Exclusion in the protein (no frameshift)
• Reference transcript: NM_020445

• Changed! cd ACTIN 405aa 1e-120 in ref transcript
  • Actin; An ubiquitous protein involved in the formation of filaments that are a major component of the cytoskeleton. Interaction with myosin provides the basis of muscular contraction and many aspects of cell motility. Each actin protomer binds one molecule of ATP and either calcium or magnesium ions. Actin exists as a monomer in low salt concentrations, but filaments form rapidly as salt concentration rises, with the consequent hydrolysis of ATP. Polymerization is regulated by so-called capping proteins. The ATPase domain of actin shares similarity with ATPase domains of hexokinase and hsp70 proteins.
• Changed! smart ACTIN 407aa 1e-129 in ref transcript
  • Actin. ACTIN subfamily of ACTIN/mreB/sugarkinase/Hsp70 superfamily.
• Changed! PTZ PTZ00280 415aa 0.0 in ref transcript
  • actin; Provisional.
• Changed! cd ACTIN 311aa 7e-91 in modified transcript
• Changed! smart ACTIN 312aa 4e-97 in modified transcript
• Changed! PTZ PTZ00280 314aa 1e-148 in modified transcript
• Changed! PTZ PTZ00280 31aa 1e-09 in modified transcript

ACYP1

• refseq_ACYP1.F1 refseq_ACYP1.R1 189 268
• NCBIGene 36.3 97
• Single exon skipping, size difference: 79
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_001107

• Changed! pfam Acylphosphatase 93aa 3e-24 in ref transcript
  • Acylphosphatase.
• Changed! COG AcyP 92aa 2e-11 in ref transcript
  • Acylphosphatases [Energy production and conversion].
• Changed! pfam Acylphosphatase 23aa 0.001 in modified transcript

ADAM22

• refseq_ADAM22.F2 refseq_ADAM22.R2 156 243
• NCBIGene 36.3 53616
• Single exon skipping, size difference: 87
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_021723

• cd ZnMc_adamalysin_II_like 198aa 4e-48 in ref transcript
  • Zinc-dependent metalloprotease; adamalysin_II_like subfamily. Adamalysin II is a snake venom zinc endopeptidase. This subfamily contains other snake venom metalloproteinases, as well as membrane-anchored metalloproteases belonging to the ADAM family. ADAMs (A Disintegrin And Metalloprotease) are glycoproteins, which play roles in cell signaling, cell fusion, and cell-cell interactions.
• pfam Reprolysin 200aa 1e-63 in ref transcript
  • Reprolysin (M12B) family zinc metalloprotease. The members of this family are enzymes that cleave peptides. These proteases require zinc for catalysis. Members of this family are also known as adamalysins. Most members of this family are snake venom endopeptidases, but there are also some mammalian proteins and fertilin. Fertilin and closely related proteins appear to not have some active site residues and may not be active enzymes.
• smart ACR 141aa 2e-40 in ref transcript
  • ADAM Cysteine-Rich Domain.
• pfam Disintegrin 77aa 4e-25 in ref transcript
  • Disintegrin.
• pfam Pep_M12B_propep 104aa 2e-22 in ref transcript
  • Reprolysin family propeptide. This region is the propeptide for members of peptidase family M12B. The propeptide contains a sequence motif similar to the "cysteine switch" of the matrixins. This motif is found at the C terminus of the alignment but is not well aligned.

ADAM22

• refseq_ADAM22.F3 refseq_ADAM22.R3 182 290
• NCBIGene 36.3 53616
• Single exon skipping, size difference: 108
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_021723

• cd ZnMc_adamalysin_II_like 198aa 4e-48 in ref transcript
  • Zinc-dependent metalloprotease; adamalysin_II_like subfamily. Adamalysin II is a snake venom zinc endopeptidase. This subfamily contains other snake venom metalloproteinases, as well as membrane-anchored metalloproteases belonging to the ADAM family. ADAMs (A Disintegrin And Metalloprotease) are glycoproteins, which play roles in cell signaling, cell fusion, and cell-cell interactions.
• pfam Reprolysin 200aa 1e-63 in ref transcript
  • Reprolysin (M12B) family zinc metalloprotease. The members of this family are enzymes that cleave peptides. These proteases require zinc for catalysis. Members of this family are also known as adamalysins. Most members of this family are snake venom endopeptidases, but there are also some mammalian proteins and fertilin. Fertilin and closely related proteins appear to not have some active site residues and may not be active enzymes.
• smart ACR 141aa 2e-40 in ref transcript
  • ADAM Cysteine-Rich Domain.
• pfam Disintegrin 77aa 4e-25 in ref transcript
  • Disintegrin.
• pfam Pep_M12B_propep 104aa 2e-22 in ref transcript
  • Reprolysin family propeptide. This region is the propeptide for members of peptidase family M12B. The propeptide contains a sequence motif similar to the "cysteine switch" of the matrixins. This motif is found at the C terminus of the alignment but is not well aligned.

ADAM33

• refseq_ADAM33.F1 refseq_ADAM33.R1 105 183
• NCBIGene 36.3 80332
• Single exon skipping, size difference: 78
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_025220

• cd ZnMc_adamalysin_II_like 198aa 7e-63 in ref transcript
  • Zinc-dependent metalloprotease; adamalysin_II_like subfamily. Adamalysin II is a snake venom zinc endopeptidase. This subfamily contains other snake venom metalloproteinases, as well as membrane-anchored metalloproteases belonging to the ADAM family. ADAMs (A Disintegrin And Metalloprotease) are glycoproteins, which play roles in cell signaling, cell fusion, and cell-cell interactions.
• pfam Reprolysin 200aa 8e-68 in ref transcript
  • Reprolysin (M12B) family zinc metalloprotease. The members of this family are enzymes that cleave peptides. These proteases require zinc for catalysis. Members of this family are also known as adamalysins. Most members of this family are snake venom endopeptidases, but there are also some mammalian proteins and fertilin. Fertilin and closely related proteins appear to not have some active site residues and may not be active enzymes.
• Changed! smart ACR 142aa 1e-35 in ref transcript
  • ADAM Cysteine-Rich Domain.
• pfam Disintegrin 76aa 2e-29 in ref transcript
  • Disintegrin.
• pfam Pep_M12B_propep 70aa 3e-21 in ref transcript
  • Reprolysin family propeptide. This region is the propeptide for members of peptidase family M12B. The propeptide contains a sequence motif similar to the "cysteine switch" of the matrixins. This motif is found at the C terminus of the alignment but is not well aligned.
• Changed! smart ACR 141aa 8e-35 in modified transcript

ADAMTS13

• refseq_ADAMTS13.F2 refseq_ADAMTS13.R2 135 303
• NCBIGene 36.3 11093
• Alternative 5-prime, size difference: 168
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_139025

• cd ZnMc_ADAMTS_like 204aa 8e-68 in ref transcript
  • Zinc-dependent metalloprotease, ADAMTS_like subgroup. ADAMs (A Disintegrin And Metalloprotease) are glycoproteins, which play roles in cell signaling, cell fusion, and cell-cell interactions. This particular subfamily represents domain architectures that combine ADAM-like metalloproteinases with thrombospondin type-1 repeats. ADAMTS (a disintegrin and metalloproteinase with thrombospondin motifs) proteinases are inhibited by TIMPs (tissue inhibitors of metalloproteinases), and they play roles in coagulation, angiogenesis, development and progression of arthritis. They hydrolyze the von Willebrand factor precursor and various components of the extracellular matrix.
• pfam Reprolysin 206aa 1e-11 in ref transcript
  • Reprolysin (M12B) family zinc metalloprotease. The members of this family are enzymes that cleave peptides. These proteases require zinc for catalysis. Members of this family are also known as adamalysins. Most members of this family are snake venom endopeptidases, but there are also some mammalian proteins and fertilin. Fertilin and closely related proteins appear to not have some active site residues and may not be active enzymes.
• smart TSP1 53aa 3e-11 in ref transcript
  • Thrombospondin type 1 repeats. Type 1 repeats in thrombospondin-1 bind and activate TGF-beta.

ADAMTS13

• refseq_ADAMTS13.F3 refseq_ADAMTS13.R3 193 432
• NCBIGene 36.2 11093
• Alternative 3-prime, size difference: 239
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_139025

• Changed! cd ZnMc_ADAMTS_like 204aa 8e-68 in ref transcript
  • Zinc-dependent metalloprotease, ADAMTS_like subgroup. ADAMs (A Disintegrin And Metalloprotease) are glycoproteins, which play roles in cell signaling, cell fusion, and cell-cell interactions. This particular subfamily represents domain architectures that combine ADAM-like metalloproteinases with thrombospondin type-1 repeats. ADAMTS (a disintegrin and metalloproteinase with thrombospondin motifs) proteinases are inhibited by TIMPs (tissue inhibitors of metalloproteinases), and they play roles in coagulation, angiogenesis, development and progression of arthritis. They hydrolyze the von Willebrand factor precursor and various components of the extracellular matrix.
• Changed! pfam Reprolysin 206aa 1e-11 in ref transcript
  • Reprolysin (M12B) family zinc metalloprotease. The members of this family are enzymes that cleave peptides. These proteases require zinc for catalysis. Members of this family are also known as adamalysins. Most members of this family are snake venom endopeptidases, but there are also some mammalian proteins and fertilin. Fertilin and closely related proteins appear to not have some active site residues and may not be active enzymes.
• Changed! smart TSP1 53aa 3e-11 in ref transcript
  • Thrombospondin type 1 repeats. Type 1 repeats in thrombospondin-1 bind and activate TGF-beta.
• Changed! cd ZnMc_ADAMTS_like 183aa 4e-59 in modified transcript
• Changed! pfam Reprolysin 171aa 6e-09 in modified transcript

ADAMTS13

• refseq_ADAMTS13.F5 refseq_ADAMTS13.R5 127 207
• NCBIGene 36.2 11093
• Alternative 5-prime, size difference: 80
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_139025

• cd ZnMc_ADAMTS_like 204aa 8e-68 in ref transcript
  • Zinc-dependent metalloprotease, ADAMTS_like subgroup. ADAMs (A Disintegrin And Metalloprotease) are glycoproteins, which play roles in cell signaling, cell fusion, and cell-cell interactions. This particular subfamily represents domain architectures that combine ADAM-like metalloproteinases with thrombospondin type-1 repeats. ADAMTS (a disintegrin and metalloproteinase with thrombospondin motifs) proteinases are inhibited by TIMPs (tissue inhibitors of metalloproteinases), and they play roles in coagulation, angiogenesis, development and progression of arthritis. They hydrolyze the von Willebrand factor precursor and various components of the extracellular matrix.
• pfam Reprolysin 206aa 1e-11 in ref transcript
  • Reprolysin (M12B) family zinc metalloprotease. The members of this family are enzymes that cleave peptides. These proteases require zinc for catalysis. Members of this family are also known as adamalysins. Most members of this family are snake venom endopeptidases, but there are also some mammalian proteins and fertilin. Fertilin and closely related proteins appear to not have some active site residues and may not be active enzymes.
• Changed! smart TSP1 53aa 3e-11 in ref transcript
  • Thrombospondin type 1 repeats. Type 1 repeats in thrombospondin-1 bind and activate TGF-beta.

ADAMTSL1

• refseq_ADAMTSL1.F2 refseq_ADAMTSL1.R2 260 311
• NCBIGene 36.2 92949
• Single exon skipping, size difference: 51
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_139238

• smart TSP1 47aa 5e-05 in ref transcript
  • Thrombospondin type 1 repeats. Type 1 repeats in thrombospondin-1 bind and activate TGF-beta.

ADAR

• refseq_ADAR.F2 refseq_ADAR.R2 138 195
• NCBIGene 36.3 103
• Alternative 3-prime, size difference: 57
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001111

• cd DSRM 67aa 5e-13 in ref transcript
  • Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, RNases H1, and dsRNA dependent adenosine deaminases.
• cd DSRM 67aa 1e-10 in ref transcript
• cd DSRM 50aa 0.002 in ref transcript
• smart ADEAMc 384aa 1e-149 in ref transcript
  • tRNA-specific and double-stranded RNA adenosine deaminase (RNA-specific editase).
• pfam z-alpha 65aa 2e-19 in ref transcript
  • Adenosine deaminase z-alpha domain. This family consists of the N-terminus and thus the z-alpha domain of double-stranded RNA-specific adenosine deaminase (ADAR), an RNA- editing enzyme. The z-alpha domain is a Z-DNA binding domain, and binding of this region to B-DNA has been shown to be disfavoured by steric hindrance.
• pfam z-alpha 67aa 4e-19 in ref transcript
• smart DSRM 66aa 1e-15 in ref transcript
  • Double-stranded RNA binding motif.
• smart DSRM 66aa 4e-11 in ref transcript
• smart DSRM 50aa 2e-06 in ref transcript
• PRK rnc 59aa 2e-05 in ref transcript
  • ribonuclease III; Reviewed.
• COG Rnc 67aa 5e-05 in ref transcript
  • dsRNA-specific ribonuclease [Transcription].

ADAR

• refseq_ADAR.F3 refseq_ADAR.R3 143 221
• NCBIGene 36.3 103
• Alternative 5-prime, size difference: 78
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001111

• cd DSRM 67aa 5e-13 in ref transcript
  • Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, RNases H1, and dsRNA dependent adenosine deaminases.
• cd DSRM 67aa 1e-10 in ref transcript
• cd DSRM 50aa 0.002 in ref transcript
• smart ADEAMc 384aa 1e-149 in ref transcript
  • tRNA-specific and double-stranded RNA adenosine deaminase (RNA-specific editase).
• pfam z-alpha 65aa 2e-19 in ref transcript
  • Adenosine deaminase z-alpha domain. This family consists of the N-terminus and thus the z-alpha domain of double-stranded RNA-specific adenosine deaminase (ADAR), an RNA- editing enzyme. The z-alpha domain is a Z-DNA binding domain, and binding of this region to B-DNA has been shown to be disfavoured by steric hindrance.
• pfam z-alpha 67aa 4e-19 in ref transcript
• smart DSRM 66aa 1e-15 in ref transcript
  • Double-stranded RNA binding motif.
• smart DSRM 66aa 4e-11 in ref transcript
• smart DSRM 50aa 2e-06 in ref transcript
• PRK rnc 59aa 2e-05 in ref transcript
  • ribonuclease III; Reviewed.
• Changed! COG Rnc 67aa 5e-05 in ref transcript
  • dsRNA-specific ribonuclease [Transcription].
• Changed! COG Rnc 76aa 5e-05 in modified transcript

ADARB1

• refseq_ADARB1.F2 refseq_ADARB1.R2 112 232
• NCBIGene 36.3 104
• Single exon skipping, size difference: 120
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_015833

• cd DSRM 48aa 5e-06 in ref transcript
  • Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, RNases H1, and dsRNA dependent adenosine deaminases.
• cd DSRM 46aa 3e-05 in ref transcript
• Changed! smart ADEAMc 417aa 1e-133 in ref transcript
  • tRNA-specific and double-stranded RNA adenosine deaminase (RNA-specific editase).
• smart DSRM 48aa 2e-07 in ref transcript
  • Double-stranded RNA binding motif.
• smart DSRM 45aa 4e-06 in ref transcript
• PRK rnc 48aa 0.008 in ref transcript
  • ribonuclease III; Reviewed.
• Changed! smart ADEAMc 377aa 1e-137 in modified transcript

ADARB1

• refseq_ADARB1.F4 refseq_ADARB1.R4 180 298
• NCBIGene 36.3 104
• Single exon skipping, size difference: 118
• Inclusion in 5'UTR
• Reference transcript: NM_015833

• cd DSRM 48aa 5e-06 in ref transcript
  • Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, RNases H1, and dsRNA dependent adenosine deaminases.
• cd DSRM 46aa 3e-05 in ref transcript
• smart ADEAMc 417aa 1e-133 in ref transcript
  • tRNA-specific and double-stranded RNA adenosine deaminase (RNA-specific editase).
• smart DSRM 48aa 2e-07 in ref transcript
  • Double-stranded RNA binding motif.
• smart DSRM 45aa 4e-06 in ref transcript
• PRK rnc 48aa 0.008 in ref transcript
  • ribonuclease III; Reviewed.

ADCY6

• refseq_ADCY6.F1 refseq_ADCY6.R1 235 394
• NCBIGene 36.3 112
• Single exon skipping, size difference: 159
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_015270

• pfam Guanylate_cyc 183aa 6e-59 in ref transcript
  • Adenylate and Guanylate cyclase catalytic domain.
• pfam Guanylate_cyc 194aa 8e-57 in ref transcript
• pfam DUF1053 110aa 3e-38 in ref transcript
  • Domain of Unknown Function (DUF1053). This domain is found in Adenylate cyclases.
• COG CyaA 160aa 6e-17 in ref transcript
  • Adenylate cyclase, family 3 (some proteins contain HAMP domain) [Signal transduction mechanisms].
• COG CyaA 238aa 1e-12 in ref transcript

ADD1

• refseq_ADD1.F1 refseq_ADD1.R1 210 303
• NCBIGene 36.3 118
• Alternative 5-prime, size difference: 93
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_014189

• cd Aldolase_II 211aa 2e-52 in ref transcript
  • Class II Aldolase and Adducin head (N-terminal) domain. Aldolases are ubiquitous enzymes catalyzing central steps of carbohydrate metabolism. Based on enzymatic mechanisms, this superfamily has been divided into two distinct classes (Class I and II). Class II enzymes are further divided into two sub-classes A and B. This family includes class II A aldolases and adducins which has not been ascribed any enzymatic function. Members of this class are primarily bacterial and eukaryotic in origin and include L-fuculose-1-phosphate, L-rhamnulose-1-phosphate aldolases and L-ribulose-5-phosphate 4-epimerases. They all share the ability to promote carbon-carbon bond cleavage and stabilize enolate intermediates using divalent cations.
• pfam Aldolase_II 183aa 1e-50 in ref transcript
  • Class II Aldolase and Adducin N-terminal domain. This family includes class II aldolases and adducins which have not been ascribed any enzymatic function.
• PRK PRK07044 247aa 8e-82 in ref transcript
  • aldolase_II super-family; Provisional.

ADD1

• refseq_ADD1.F3 refseq_ADD1.R3 161 195
• NCBIGene 36.3 118
• Single exon skipping, size difference: 34
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_014189

• cd Aldolase_II 211aa 2e-52 in ref transcript
  • Class II Aldolase and Adducin head (N-terminal) domain. Aldolases are ubiquitous enzymes catalyzing central steps of carbohydrate metabolism. Based on enzymatic mechanisms, this superfamily has been divided into two distinct classes (Class I and II). Class II enzymes are further divided into two sub-classes A and B. This family includes class II A aldolases and adducins which has not been ascribed any enzymatic function. Members of this class are primarily bacterial and eukaryotic in origin and include L-fuculose-1-phosphate, L-rhamnulose-1-phosphate aldolases and L-ribulose-5-phosphate 4-epimerases. They all share the ability to promote carbon-carbon bond cleavage and stabilize enolate intermediates using divalent cations.
• pfam Aldolase_II 183aa 1e-50 in ref transcript
  • Class II Aldolase and Adducin N-terminal domain. This family includes class II aldolases and adducins which have not been ascribed any enzymatic function.
• PRK PRK07044 247aa 8e-82 in ref transcript
  • aldolase_II super-family; Provisional.

ADD2

• refseq_ADD2.F1 refseq_ADD2.R1 226 312
• NCBIGene 36.3 119
• Single exon skipping, size difference: 86
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_001617

• cd Aldolase_II 211aa 1e-54 in ref transcript
  • Class II Aldolase and Adducin head (N-terminal) domain. Aldolases are ubiquitous enzymes catalyzing central steps of carbohydrate metabolism. Based on enzymatic mechanisms, this superfamily has been divided into two distinct classes (Class I and II). Class II enzymes are further divided into two sub-classes A and B. This family includes class II A aldolases and adducins which has not been ascribed any enzymatic function. Members of this class are primarily bacterial and eukaryotic in origin and include L-fuculose-1-phosphate, L-rhamnulose-1-phosphate aldolases and L-ribulose-5-phosphate 4-epimerases. They all share the ability to promote carbon-carbon bond cleavage and stabilize enolate intermediates using divalent cations.
• pfam Aldolase_II 183aa 9e-45 in ref transcript
  • Class II Aldolase and Adducin N-terminal domain. This family includes class II aldolases and adducins which have not been ascribed any enzymatic function.
• PRK PRK07044 250aa 2e-61 in ref transcript
  • aldolase_II super-family; Provisional.

ADD3

• refseq_ADD3.F2 refseq_ADD3.R2 284 380
• NCBIGene 36.3 120
• Single exon skipping, size difference: 96
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_016824

• cd Aldolase_II 210aa 6e-40 in ref transcript
  • Class II Aldolase and Adducin head (N-terminal) domain. Aldolases are ubiquitous enzymes catalyzing central steps of carbohydrate metabolism. Based on enzymatic mechanisms, this superfamily has been divided into two distinct classes (Class I and II). Class II enzymes are further divided into two sub-classes A and B. This family includes class II A aldolases and adducins which has not been ascribed any enzymatic function. Members of this class are primarily bacterial and eukaryotic in origin and include L-fuculose-1-phosphate, L-rhamnulose-1-phosphate aldolases and L-ribulose-5-phosphate 4-epimerases. They all share the ability to promote carbon-carbon bond cleavage and stabilize enolate intermediates using divalent cations.
• pfam Aldolase_II 183aa 1e-43 in ref transcript
  • Class II Aldolase and Adducin N-terminal domain. This family includes class II aldolases and adducins which have not been ascribed any enzymatic function.
• PRK PRK07044 249aa 5e-60 in ref transcript
  • aldolase_II super-family; Provisional.

ADNP

• refseq_ADNP.F1 refseq_ADNP.R1 116 291
• NCBIGene 36.3 23394
• Single exon skipping, size difference: 175
• Exclusion in 5'UTR
• Reference transcript: NM_015339

• cd homeodomain 46aa 3e-06 in ref transcript
  • Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
• smart HOX 43aa 5e-08 in ref transcript
  • Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes.

AFG3L1

• refseq_AFG3L1.F1 refseq_AFG3L1.R1 327 393
• NCBIGene 36.2 172
• Alternative 3-prime, size difference: 66
• Inclusion in 3'UTR
• Reference transcript: NM_001132

• cd AAA 50aa 7e-08 in ref transcript
  • The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.
• TIGR FtsH_fam 46aa 5e-20 in ref transcript
  • HflB(FtsH) is a pleiotropic protein required for correct cell division in bacteria. It has ATP-dependent zinc metalloprotease activity. It was formerly designated cell division protein FtsH.
• CHL ftsH 46aa 3e-19 in ref transcript
  • cell division protein; Validated.
• PRK PRK08116 102aa 4e-04 in ref transcript
  • hypothetical protein; Validated.

AFG3L1

• refseq_AFG3L1.F3 refseq_AFG3L1.R3 112 212
• NCBIGene 36.2 172
• Single exon skipping, size difference: 100
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_001132

• Changed! cd AAA 50aa 7e-08 in ref transcript
  • The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.
• Changed! TIGR FtsH_fam 46aa 5e-20 in ref transcript
  • HflB(FtsH) is a pleiotropic protein required for correct cell division in bacteria. It has ATP-dependent zinc metalloprotease activity. It was formerly designated cell division protein FtsH.
• Changed! CHL ftsH 46aa 3e-19 in ref transcript
  • cell division protein; Validated.
• Changed! PRK PRK08116 102aa 4e-04 in ref transcript
  • hypothetical protein; Validated.

AFG3L1

• refseq_AFG3L1.F6 refseq_AFG3L1.R6 208 281
• NCBIGene 36.2 172
• Alternative 3-prime, size difference: 73
• Inclusion in 5'UTR
• Reference transcript: NM_001132

• cd AAA 50aa 7e-08 in ref transcript
  • The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.
• TIGR FtsH_fam 46aa 5e-20 in ref transcript
  • HflB(FtsH) is a pleiotropic protein required for correct cell division in bacteria. It has ATP-dependent zinc metalloprotease activity. It was formerly designated cell division protein FtsH.
• CHL ftsH 46aa 3e-19 in ref transcript
  • cell division protein; Validated.
• PRK PRK08116 102aa 4e-04 in ref transcript
  • hypothetical protein; Validated.

AFTPH

• refseq_AFTPH.F1 refseq_AFTPH.R1 147 231
• NCBIGene 36.3 54812
• Single exon skipping, size difference: 84
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_203437

ACAN

• refseq_AGC1.F1 refseq_AGC1.R1 166 349
• NCBIGene 36.3 176
• Single exon skipping, size difference: 183
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_013227

• cd CLECT_CSPGs 124aa 9e-79 in ref transcript
  • CLECT_CSPGs: C-type lectin-like domain (CTLD) of the type found in chondroitin sulfate proteoglycan core proteins (CSPGs) in human and chicken aggrecan, frog brevican, and zebra fish dermacan. CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. In cartilage, aggrecan forms cartilage link protein stabilized aggregates with hyaluronan (HA). These aggregates contribute to the tissue's load bearing properties. Aggregates having other CSPGs substituting for aggrecan may contribute to the structural integrity of many different tissues. Xenopus brevican is expressed in the notochord and the brain during early embryogenesis. Zebra fish dermacan is expressed in dermal bones and may play a role in dermal bone development. CSPGs do contain LINK domain(s) which bind HA. These LINK domains are considered by one classification system to be a variety of CTLD, but are omitted from this hierarchical classification based on insignificant sequence similarity.
• cd Link_domain_CSPGs_modules_1_3 95aa 5e-46 in ref transcript
  • Link_domain_CSPGs_modules_1_3; this extracellular link domain is found in the first and third link modules of the chondroitin sulfate proteoglycan core protein (CSPG) aggrecan. In addition, it is found in the first link module of three other CSPGs: versican, neurocan, and brevican. The link domain is a hyaluronan (HA)-binding domain. CSPGs are characterized by an N-terminal globular domain (G1 domain) containing two contiguous link modules (modules 1 and 2). Both link modules of the G1 domain of aggrecan are involved in interaction with HA. In addition, aggrecan contains a second globular domain (G2) which contains link modules 3 and 4. G2 appears to lack HA-binding activity. In cartilage, aggrecan forms cartilage link protein stabilized aggregates with HA. These aggregates contribute to the tissue's load bearing properties. Aggregates having other CSPGs substituting for aggrecan may contribute to the structural integrity of many different tissues. Members of the vertebrate HPLN (hyaluronan/HA and proteoglycan binding link) protein family are physically linked adjacent to CSPG genes.
• cd Link_domain_CSPGs_modules_2_4 96aa 5e-45 in ref transcript
  • Link_domain_CSPGs_modules_2_4; this link domain is found in the second and fourth link modules of the chondroitin sulfate proteoglycan core protein (CSPG) aggrecan and, in the second link module of three other CSPGs: versican, neurocan, and brevican. The link domain is a hyaluronan (HA)-binding domain. CSPGs are characterized by an N-terminal globular domain (G1 domain) containing two contiguous link modules (modules 1 and 2). Both link modules of the G1 domain of aggrecan are involved in interaction with HA. Aggrecan in addition contains a second globular domain (G2) having link modules 3 and 4 which lack HA-binding activity. In cartilage, aggrecan forms cartilage link protein stabilized aggregates with HA. These aggregates contribute to the tissue's load bearing properties. Aggregates having other CSPGs substituting for aggregan may contribute to the structural integrity of many different tissues. Members of the vertebrate HPLN (hyaluronan/HA and proteoglycan binding link) protein family are physically linked adjacent to CSPG genes.
• cd Link_domain_CSPGs_modules_2_4 96aa 4e-44 in ref transcript
• cd Link_domain_CSPGs_modules_1_3 95aa 4e-40 in ref transcript
• Changed! cd CCP 57aa 6e-08 in ref transcript
  • Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR); The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function.
• cd EGF_CA 31aa 3e-04 in ref transcript
  • Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements.
• pfam Xlink 95aa 2e-40 in ref transcript
  • Extracellular link domain.
• pfam Xlink 95aa 9e-40 in ref transcript
• pfam Xlink 96aa 1e-36 in ref transcript
• smart CLECT 122aa 6e-36 in ref transcript
  • C-type lectin (CTL) or carbohydrate-recognition domain (CRD). Many of these domains function as calcium-dependent carbohydrate binding modules.
• smart LINK 99aa 7e-35 in ref transcript
  • Link (Hyaluronan-binding).
• pfam V-set 120aa 9e-09 in ref transcript
  • Immunoglobulin V-set domain. This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.
• Changed! smart CCP 57aa 3e-08 in ref transcript
  • Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR). The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. A missense mutation in seventh CCP domain causes deficiency of the b subunit of factor XIII.
• pfam EGF 31aa 1e-04 in ref transcript
  • EGF-like domain. There is no clear separation between noise and signal. pfam00053 is very similar, but has 8 instead of 6 conserved cysteines. Includes some cytokine receptors. The EGF domain misses the N-terminus regions of the Ca2+ binding EGF domains (this is the main reason of discrepancy between Swiss-Prot domain start/end and Pfam). The family is hard to model due to many similar but different sub-types of EGF domains. Pfam certainly misses a number of EGF domains.

ACAN

• refseq_AGC1.F3 refseq_AGC1.R3 104 218
• NCBIGene 36.3 176
• Single exon skipping, size difference: 114
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_013227

• cd CLECT_CSPGs 124aa 9e-79 in ref transcript
  • CLECT_CSPGs: C-type lectin-like domain (CTLD) of the type found in chondroitin sulfate proteoglycan core proteins (CSPGs) in human and chicken aggrecan, frog brevican, and zebra fish dermacan. CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. In cartilage, aggrecan forms cartilage link protein stabilized aggregates with hyaluronan (HA). These aggregates contribute to the tissue's load bearing properties. Aggregates having other CSPGs substituting for aggrecan may contribute to the structural integrity of many different tissues. Xenopus brevican is expressed in the notochord and the brain during early embryogenesis. Zebra fish dermacan is expressed in dermal bones and may play a role in dermal bone development. CSPGs do contain LINK domain(s) which bind HA. These LINK domains are considered by one classification system to be a variety of CTLD, but are omitted from this hierarchical classification based on insignificant sequence similarity.
• cd Link_domain_CSPGs_modules_1_3 95aa 5e-46 in ref transcript
  • Link_domain_CSPGs_modules_1_3; this extracellular link domain is found in the first and third link modules of the chondroitin sulfate proteoglycan core protein (CSPG) aggrecan. In addition, it is found in the first link module of three other CSPGs: versican, neurocan, and brevican. The link domain is a hyaluronan (HA)-binding domain. CSPGs are characterized by an N-terminal globular domain (G1 domain) containing two contiguous link modules (modules 1 and 2). Both link modules of the G1 domain of aggrecan are involved in interaction with HA. In addition, aggrecan contains a second globular domain (G2) which contains link modules 3 and 4. G2 appears to lack HA-binding activity. In cartilage, aggrecan forms cartilage link protein stabilized aggregates with HA. These aggregates contribute to the tissue's load bearing properties. Aggregates having other CSPGs substituting for aggrecan may contribute to the structural integrity of many different tissues. Members of the vertebrate HPLN (hyaluronan/HA and proteoglycan binding link) protein family are physically linked adjacent to CSPG genes.
• cd Link_domain_CSPGs_modules_2_4 96aa 5e-45 in ref transcript
  • Link_domain_CSPGs_modules_2_4; this link domain is found in the second and fourth link modules of the chondroitin sulfate proteoglycan core protein (CSPG) aggrecan and, in the second link module of three other CSPGs: versican, neurocan, and brevican. The link domain is a hyaluronan (HA)-binding domain. CSPGs are characterized by an N-terminal globular domain (G1 domain) containing two contiguous link modules (modules 1 and 2). Both link modules of the G1 domain of aggrecan are involved in interaction with HA. Aggrecan in addition contains a second globular domain (G2) having link modules 3 and 4 which lack HA-binding activity. In cartilage, aggrecan forms cartilage link protein stabilized aggregates with HA. These aggregates contribute to the tissue's load bearing properties. Aggregates having other CSPGs substituting for aggregan may contribute to the structural integrity of many different tissues. Members of the vertebrate HPLN (hyaluronan/HA and proteoglycan binding link) protein family are physically linked adjacent to CSPG genes.
• cd Link_domain_CSPGs_modules_2_4 96aa 4e-44 in ref transcript
• cd Link_domain_CSPGs_modules_1_3 95aa 4e-40 in ref transcript
• cd CCP 57aa 6e-08 in ref transcript
  • Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR); The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function.
• Changed! cd EGF_CA 31aa 3e-04 in ref transcript
  • Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements.
• pfam Xlink 95aa 2e-40 in ref transcript
  • Extracellular link domain.
• pfam Xlink 95aa 9e-40 in ref transcript
• pfam Xlink 96aa 1e-36 in ref transcript
• smart CLECT 122aa 6e-36 in ref transcript
  • C-type lectin (CTL) or carbohydrate-recognition domain (CRD). Many of these domains function as calcium-dependent carbohydrate binding modules.
• smart LINK 99aa 7e-35 in ref transcript
  • Link (Hyaluronan-binding).
• pfam V-set 120aa 9e-09 in ref transcript
  • Immunoglobulin V-set domain. This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.
• smart CCP 57aa 3e-08 in ref transcript
  • Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR). The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. A missense mutation in seventh CCP domain causes deficiency of the b subunit of factor XIII.
• Changed! pfam EGF 31aa 1e-04 in ref transcript
  • EGF-like domain. There is no clear separation between noise and signal. pfam00053 is very similar, but has 8 instead of 6 conserved cysteines. Includes some cytokine receptors. The EGF domain misses the N-terminus regions of the Ca2+ binding EGF domains (this is the main reason of discrepancy between Swiss-Prot domain start/end and Pfam). The family is hard to model due to many similar but different sub-types of EGF domains. Pfam certainly misses a number of EGF domains.

AGER

• refseq_AGER.F1 refseq_AGER.R1 120 233
• NCBIGene 36.3 177
• Exon skipping and alternative 3-prime or 5-prime, size difference: 113
• Inclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_001136

• Changed! cd IGcam 66aa 3e-06 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• cd IG 77aa 0.004 in ref transcript
  • Immunoglobulin domain family; members are components of immunoglobulins, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• pfam C2-set_2 96aa 4e-18 in ref transcript
  • CD80-like C2-set immunoglobulin domain. These domains belong to the immunoglobulin superfamily.
• smart IG_like 95aa 1e-07 in ref transcript
  • Immunoglobulin like. IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
• Changed! smart IGc2 58aa 4e-07 in ref transcript
  • Immunoglobulin C-2 Type.
• Changed! cd IGcam 27aa 0.008 in modified transcript
• Changed! smart IG_like 26aa 3e-04 in modified transcript

AGER

• refseq_AGER.F3 refseq_AGER.R3 100 142
• NCBIGene 36.3 177
• Alternative 3-prime, size difference: 42
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001136

• cd IGcam 66aa 3e-06 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• Changed! cd IG 77aa 0.004 in ref transcript
  • Immunoglobulin domain family; members are components of immunoglobulins, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• pfam C2-set_2 96aa 4e-18 in ref transcript
  • CD80-like C2-set immunoglobulin domain. These domains belong to the immunoglobulin superfamily.
• Changed! smart IG_like 95aa 1e-07 in ref transcript
  • Immunoglobulin like. IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
• smart IGc2 58aa 4e-07 in ref transcript
  • Immunoglobulin C-2 Type.
• Changed! cd IG 63aa 6e-04 in modified transcript
• Changed! smart IG_like 81aa 6e-08 in modified transcript

AGL

• refseq_AGL.F1 refseq_AGL.R1 117 260
• NCBIGene 36.3 178
• Single exon skipping, size difference: 143
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_000642

• Changed! TIGR glyc_debranch 1511aa 0.0 in ref transcript
  • glycogen debranching enzyme possesses two different catalytic activities; oligo-1,4-->1,4-glucantransferase (EC 2.4.1.25) and amylo-1,6-glucosidase (EC 3.2.1.33). Site directed mutagenesis studies in S. cerevisiae indicate that the transferase and glucosidase activities are independent and located in different regions of the polypeptide chain. Proteins in this model belong to the larger alpha-amylase family. The model covers eukaryotic proteins with a seed composed of human, nematode and yeast sequences. Yeast seed sequence is well characterized. The model is quite rigorous; either query sequence yields large bit score or it fails to hit the model altogether. There doesn't appear to be any middle ground.
• Changed! COG GDB1 462aa 5e-33 in ref transcript
  • Glycogen debranching enzyme [Carbohydrate transport and metabolism].
• Changed! COG AmyA 175aa 8e-05 in ref transcript
  • Glycosidases [Carbohydrate transport and metabolism].

AGL

• refseq_AGL.F2 refseq_AGL.R2 112 392
• NCBIGene 36.3 178
• Alternative 5-prime, size difference: 280
• Exclusion in 5'UTR
• Reference transcript: NM_000028

• TIGR glyc_debranch 1511aa 0.0 in ref transcript
  • glycogen debranching enzyme possesses two different catalytic activities; oligo-1,4-->1,4-glucantransferase (EC 2.4.1.25) and amylo-1,6-glucosidase (EC 3.2.1.33). Site directed mutagenesis studies in S. cerevisiae indicate that the transferase and glucosidase activities are independent and located in different regions of the polypeptide chain. Proteins in this model belong to the larger alpha-amylase family. The model covers eukaryotic proteins with a seed composed of human, nematode and yeast sequences. Yeast seed sequence is well characterized. The model is quite rigorous; either query sequence yields large bit score or it fails to hit the model altogether. There doesn't appear to be any middle ground.
• COG GDB1 462aa 5e-33 in ref transcript
  • Glycogen debranching enzyme [Carbohydrate transport and metabolism].
• COG AmyA 175aa 8e-05 in ref transcript
  • Glycosidases [Carbohydrate transport and metabolism].

AGPAT4

• refseq_AGPAT4.F1 refseq_AGPAT4.R1 102 239
• NCBIGene 36.2 56895
• Single exon skipping, size difference: 137
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_020133

• Changed! smart PlsC 122aa 1e-17 in ref transcript
  • Phosphate acyltransferases. Function in phospholipid biosynthesis and have either glycerolphosphate, 1-acylglycerolphosphate, or 2-acylglycerolphosphoethanolamine acyltransferase activities. Tafazzin, the product of the gene mutated in patients with Barth syndrome, is a member of this family.
• Changed! COG PlsC 196aa 2e-07 in ref transcript
  • 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism].

AGTRAP

• refseq_AGTRAP.F1 refseq_AGTRAP.R1 115 136
• NCBIGene 36.3 57085
• Alternative 5-prime, size difference: 21
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_020350

• Changed! pfam AGTRAP 159aa 1e-78 in ref transcript
  • Angiotensin II, type I receptor-associated protein (AGTRAP). This family consists of several angiotensin II, type I receptor-associated protein (AGTRAP) sequences. AGTRAP is known to interact specifically with the carboxyl-terminal cytoplasmic region of the angiotensin II type 1 (AT(1)) receptor to regulate different aspects of AT(1) receptor physiology. The function of this family is unclear.
• Changed! pfam AGTRAP 152aa 4e-75 in modified transcript

AGTRAP

• refseq_AGTRAP.F2 refseq_AGTRAP.R2 140 237
• NCBIGene 36.3 57085
• Single exon skipping, size difference: 97
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_020350

• Changed! pfam AGTRAP 159aa 1e-78 in ref transcript
  • Angiotensin II, type I receptor-associated protein (AGTRAP). This family consists of several angiotensin II, type I receptor-associated protein (AGTRAP) sequences. AGTRAP is known to interact specifically with the carboxyl-terminal cytoplasmic region of the angiotensin II type 1 (AT(1)) receptor to regulate different aspects of AT(1) receptor physiology. The function of this family is unclear.
• Changed! pfam AGTRAP 20aa 2e-06 in modified transcript

AIFM3

• refseq_AIFL.F1 refseq_AIFL.R1 110 131
• NCBIGene 36.3 150209
• Single exon skipping, size difference: 21
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_144704

• cd Rieske_AIFL_N 95aa 2e-41 in ref transcript
  • AIFL (apoptosis-inducing factor like) family, N-terminal Rieske domain; members of this family show similarity to human AIFL, containing an N-terminal Rieske domain and a C-terminal pyridine nucleotide-disulfide oxidoreductase domain (Pyr_redox). The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. AIFL shares 35% homology with human AIF (apoptosis-inducing factor), mainly in the Pyr_redox domain. AIFL is predominantly localized to the mitochondria. AIFL induces apoptosis in a caspase-dependent manner.
• pfam Pyr_redox_2 278aa 6e-43 in ref transcript
  • Pyridine nucleotide-disulphide oxidoreductase. This family includes both class I and class II oxidoreductases and also NADH oxidases and peroxidases. This domain is actually a small NADH binding domain within a larger FAD binding domain.
• pfam Rieske 88aa 7e-14 in ref transcript
  • Rieske [2Fe-2S] domain. The rieske domain has a [2Fe-2S] centre. Two conserved cysteines that one Fe ion while the other Fe ion is coordinated by two conserved histidines.
• PRK PRK09754 382aa 1e-33 in ref transcript
  • phenylpropionate dioxygenase ferredoxin reductase subunit; Provisional.
• COG {NirD} 96aa 1e-16 in ref transcript
  • Ferredoxin subunits of nitrite reductase and ring-hydroxylating dioxygenases [Inorganic ion transport and metabolism / General function prediction only].

AIPL1

• refseq_AIPL1.F2 refseq_AIPL1.R2 136 325
• NCBIGene 36.3 23746
• Single exon skipping, size difference: 189
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_014336

• cd TPR 117aa 7e-04 in ref transcript
  • Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here.
• pfam FKBP_C 61aa 0.002 in ref transcript
  • FKBP-type peptidyl-prolyl cis-trans isomerase.

AIPL1

• refseq_AIPL1.F4 refseq_AIPL1.R4 186 366
• NCBIGene 36.3 23746
• Single exon skipping, size difference: 180
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_014336

• cd TPR 117aa 7e-04 in ref transcript
  • Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here.
• Changed! pfam FKBP_C 61aa 0.002 in ref transcript
  • FKBP-type peptidyl-prolyl cis-trans isomerase.

AKAP14

• refseq_AKAP14.F1 refseq_AKAP14.R1 144 324
• NCBIGene 36.3 158798
• Single exon skipping, size difference: 180
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_178813

AKAP7

• refseq_AKAP7.F1 refseq_AKAP7.R1 267 336
• NCBIGene 36.3 9465
• Single exon skipping, size difference: 69
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_138633

• pfam AKAP7_RIRII_bdg 61aa 2e-19 in ref transcript
  • PKA-RI-RII subunit binding domain of A-kinase anchor protein. AKAP7_RIRII_bdg is the C-terminal domain of the cyclic AMP-dependent protein kinase A, PKA, anchor protein AKAP7. This protein anchors PKA, for its role in regulating PKA-mediated gene transcription in both somatic cells and oocytes, by binding to its regulatory subunits, RI and RII, hence being known as a dual-specific AKAP. The 25 crucial amino acids of RII-binding domains in general form structurally conserved amphipathic helices with unrelated sequences; hydrophobic amino acid residues form the backbone of the interaction and hydrogen bond- and salt-bridge-forming amino acid residues increase the affinity of the interaction. The N-terminus, of family AKAP7_NLS, carries the nuclear localisation signal.

AKAP9

• refseq_AKAP9.F1 refseq_AKAP9.R1 197 233
• NCBIGene 36.3 10142
• Single exon skipping, size difference: 36
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_147171

• pfam PACT_coil_coil 83aa 2e-26 in ref transcript
  • Pericentrin-AKAP-450 domain of centrosomal targeting protein. This domain is a coiled-coil region close to the C-terminus of centrosomal proteins that is directly responsible for recruiting AKAP-450 and pericentrin to the centrosome. Hence the suggested name for this region is a PACT domain (pericentrin-AKAP-450 centrosomal targeting). This domain is also present at the C-terminus of coiled-coil proteins from Drosophila and S. pombe, and that from the Drosophila protein is sufficient for targeting to the centrosome in mammalian cells. The function of these proteins is unknown but they seem good candidates for having a centrosomal or spindle pole body location. The final 22 residues of this domain in AKAP-450 appear specifically to be a calmodulin-binding domain indicating that this member at least is likely to contribute to centrosome assembly.
• TIGR SMC_prok_B 404aa 6e-07 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• pfam SMC_N 259aa 6e-05 in ref transcript
  • RecF/RecN/SMC N terminal domain. This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.
• TIGR SMC_prok_A 252aa 0.001 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent.
• TIGR SMC_prok_B 709aa 0.002 in ref transcript
• COG Smc 264aa 3e-04 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].
• COG Smc 317aa 7e-04 in ref transcript
• PRK PRK05771 168aa 0.009 in ref transcript
  • V-type ATP synthase subunit I; Validated.

AKAP9

• refseq_AKAP9.F2 refseq_AKAP9.R2 133 157
• NCBIGene 36.3 10142
• Exon skipping and alternative 3-prime or 5-prime, size difference: 24
• Inclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_147171

• pfam PACT_coil_coil 83aa 2e-26 in ref transcript
  • Pericentrin-AKAP-450 domain of centrosomal targeting protein. This domain is a coiled-coil region close to the C-terminus of centrosomal proteins that is directly responsible for recruiting AKAP-450 and pericentrin to the centrosome. Hence the suggested name for this region is a PACT domain (pericentrin-AKAP-450 centrosomal targeting). This domain is also present at the C-terminus of coiled-coil proteins from Drosophila and S. pombe, and that from the Drosophila protein is sufficient for targeting to the centrosome in mammalian cells. The function of these proteins is unknown but they seem good candidates for having a centrosomal or spindle pole body location. The final 22 residues of this domain in AKAP-450 appear specifically to be a calmodulin-binding domain indicating that this member at least is likely to contribute to centrosome assembly.
• TIGR SMC_prok_B 404aa 6e-07 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• pfam SMC_N 259aa 6e-05 in ref transcript
  • RecF/RecN/SMC N terminal domain. This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.
• TIGR SMC_prok_A 252aa 0.001 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent.
• TIGR SMC_prok_B 709aa 0.002 in ref transcript
• COG Smc 264aa 3e-04 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].
• COG Smc 317aa 7e-04 in ref transcript
• PRK PRK05771 168aa 0.009 in ref transcript
  • V-type ATP synthase subunit I; Validated.

AKR1A1

• refseq_AKR1A1.F2 refseq_AKR1A1.R2 166 294
• NCBIGene 36.3 10327
• Single exon skipping, size difference: 128
• Exclusion in 5'UTR
• Reference transcript: NM_006066

• cd Aldo_ket_red 284aa 2e-72 in ref transcript
  • Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial applications. Members have very distinct functions and include the prokaryotic 2,5-diketo-D-gluconic acid reductases and beta-keto ester reductases, the eukaryotic aldose reductases, aldehyde reductases, hydroxysteroid dehydrogenases, steroid 5beta-reductases, potassium channel beta-subunits and aflatoxin aldehyde reductases, among others.
• pfam Aldo_ket_red 287aa 2e-97 in ref transcript
  • Aldo/keto reductase family. This family includes a number of K+ ion channel beta chain regulatory domains - these are reported to have oxidoreductase activity.
• COG ARA1 298aa 4e-81 in ref transcript
  • Aldo/keto reductases, related to diketogulonate reductase [General function prediction only].

ALAD

• refseq_ALAD.F1 refseq_ALAD.R1 188 354
• NCBIGene 36.3 210
• Alternative 3-prime, size difference: 166
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_001003945

• Changed! cd eu_ALAD_PBGS_cysteine_rich 313aa 1e-151 in ref transcript
  • Porphobilinogen synthase (PBGS), which is also called delta-aminolevulinic acid dehydratase (ALAD), catalyzes the condensation of two 5-aminolevulinic acid (ALA) molecules to form the pyrrole porphobilinogen (PBG), which is the second step in the biosynthesis of tetrapyrroles, such as heme, vitamin B12 and chlorophyll. This reaction involves the formation of a Schiff base link between the substrate and the enzyme. PBGSs are metalloenzymes, some of which have a second, allosteric metal binding site, beside the metal ion binding site in their active site. Although PBGS is a family of homologous enzymes, its metal ion utilization at catalytic site varies between zinc and magnesium and/or potassium. PBGS can be classified into two groups based on differences in their active site metal binding site. The eukaryotic PBGSs represented by this model, which contain a cysteine-rich zinc binding motif (DXCXCX(Y/F)X3G(H/Q)CG), require zinc for their activity, they do not contain an additional allosteric metal binding site and do not bind magnesium.
• Changed! pfam ALAD 289aa 1e-138 in ref transcript
  • Delta-aminolevulinic acid dehydratase.
• Changed! PRK PRK09283 284aa 1e-112 in ref transcript
  • delta-aminolevulinic acid dehydratase; Validated.

ALAS1

• refseq_ALAS1.F2 refseq_ALAS1.R2 186 363
• NCBIGene 36.3 211
• Single exon skipping, size difference: 177
• Exclusion in 5'UTR
• Reference transcript: NM_000688

• cd KBL_like 356aa 1e-137 in ref transcript
  • KBL_like; this family belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD corresponds to serine palmitoyltransferase (SPT), 5-aminolevulinate synthase (ALAS), 8-amino-7-oxononanoate synthase (AONS), and 2-amino-3-ketobutyrate CoA ligase (KBL). SPT is responsible for the condensation of L-serine with palmitoyl-CoA to produce 3-ketodihydrospingosine, the reaction of the first step in sphingolipid biosynthesis. ALAS is involved in heme biosynthesis; it catalyzes the synthesis of 5-aminolevulinic acid from glycine and succinyl-coenzyme A. AONS catalyses the decarboxylative condensation of l-alanine and pimeloyl-CoA in the first committed step of biotin biosynthesis. KBL catalyzes the second reaction step of the metabolic degradation pathway for threonine converting 2-amino-3-ketobutyrate, to glycine and acetyl-CoA. The members of this CD are widely found in all three forms of life.
• TIGR 5aminolev_synth 406aa 1e-178 in ref transcript
  • This model represents 5-aminolevulinic acid synthase, an enzyme for one of two routes to the heme precursor 5-aminolevulinate. The protein is a pyridoxal phosphate-dependent enzyme related to 2-amino-3-ketobutyrate CoA tranferase and 8-amino-7-oxononanoate synthase. This enzyme appears restricted to the alpha Proteobacteria and mitochondrial derivatives.
• PRK PRK09064 405aa 1e-167 in ref transcript
  • 5-aminolevulinate synthase; Validated.

ALAS2

• refseq_ALAS2.F1 refseq_ALAS2.R1 178 374
• NCBIGene 36.3 212
• Single exon skipping, size difference: 196
• Exclusion of the protein initiation site
• Reference transcript: NM_000032

• cd KBL_like 352aa 1e-149 in ref transcript
  • KBL_like; this family belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD corresponds to serine palmitoyltransferase (SPT), 5-aminolevulinate synthase (ALAS), 8-amino-7-oxononanoate synthase (AONS), and 2-amino-3-ketobutyrate CoA ligase (KBL). SPT is responsible for the condensation of L-serine with palmitoyl-CoA to produce 3-ketodihydrospingosine, the reaction of the first step in sphingolipid biosynthesis. ALAS is involved in heme biosynthesis; it catalyzes the synthesis of 5-aminolevulinic acid from glycine and succinyl-coenzyme A. AONS catalyses the decarboxylative condensation of l-alanine and pimeloyl-CoA in the first committed step of biotin biosynthesis. KBL catalyzes the second reaction step of the metabolic degradation pathway for threonine converting 2-amino-3-ketobutyrate, to glycine and acetyl-CoA. The members of this CD are widely found in all three forms of life.
• TIGR 5aminolev_synth 406aa 0.0 in ref transcript
  • This model represents 5-aminolevulinic acid synthase, an enzyme for one of two routes to the heme precursor 5-aminolevulinate. The protein is a pyridoxal phosphate-dependent enzyme related to 2-amino-3-ketobutyrate CoA tranferase and 8-amino-7-oxononanoate synthase. This enzyme appears restricted to the alpha Proteobacteria and mitochondrial derivatives.
• Changed! pfam Preseq_ALAS 101aa 1e-55 in ref transcript
  • 5-aminolevulinate synthase presequence. The N terminal presequence domain found in 5-aminolevulinate synthase exists as an amphipathic helix, with a positively charged surface provided by lysine residues and no stable helix at the N-terminus. The domain is essential for the import process by which ALAS is transported into the mitochondria: translocase of the outer membrane (Tom) and translocase of the inner membrane protein complexes appear responsible for recognition and import through the mitochondrial membrane. The protein Tom20 is anchored to the mitochondrial outer membrane, and its interaction with presequences is thought to be the recognition step which allows subsequent import.
• PRK PRK09064 405aa 0.0 in ref transcript
  • 5-aminolevulinate synthase; Validated.
• Changed! pfam Preseq_ALAS 29aa 7e-10 in modified transcript

ALAS2

• refseq_ALAS2.F1 refseq_ALAS2.R5 160 267
• NCBIGene 36.3 212
• Single exon skipping, size difference: 107
• Inclusion in 5'UTR
• Reference transcript: NM_000032

• cd KBL_like 352aa 1e-149 in ref transcript
  • KBL_like; this family belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD corresponds to serine palmitoyltransferase (SPT), 5-aminolevulinate synthase (ALAS), 8-amino-7-oxononanoate synthase (AONS), and 2-amino-3-ketobutyrate CoA ligase (KBL). SPT is responsible for the condensation of L-serine with palmitoyl-CoA to produce 3-ketodihydrospingosine, the reaction of the first step in sphingolipid biosynthesis. ALAS is involved in heme biosynthesis; it catalyzes the synthesis of 5-aminolevulinic acid from glycine and succinyl-coenzyme A. AONS catalyses the decarboxylative condensation of l-alanine and pimeloyl-CoA in the first committed step of biotin biosynthesis. KBL catalyzes the second reaction step of the metabolic degradation pathway for threonine converting 2-amino-3-ketobutyrate, to glycine and acetyl-CoA. The members of this CD are widely found in all three forms of life.
• TIGR 5aminolev_synth 406aa 0.0 in ref transcript
  • This model represents 5-aminolevulinic acid synthase, an enzyme for one of two routes to the heme precursor 5-aminolevulinate. The protein is a pyridoxal phosphate-dependent enzyme related to 2-amino-3-ketobutyrate CoA tranferase and 8-amino-7-oxononanoate synthase. This enzyme appears restricted to the alpha Proteobacteria and mitochondrial derivatives.
• pfam Preseq_ALAS 101aa 1e-55 in ref transcript
  • 5-aminolevulinate synthase presequence. The N terminal presequence domain found in 5-aminolevulinate synthase exists as an amphipathic helix, with a positively charged surface provided by lysine residues and no stable helix at the N-terminus. The domain is essential for the import process by which ALAS is transported into the mitochondria: translocase of the outer membrane (Tom) and translocase of the inner membrane protein complexes appear responsible for recognition and import through the mitochondrial membrane. The protein Tom20 is anchored to the mitochondrial outer membrane, and its interaction with presequences is thought to be the recognition step which allows subsequent import.
• PRK PRK09064 405aa 0.0 in ref transcript
  • 5-aminolevulinate synthase; Validated.

ALAS2

• refseq_ALAS2.F3 refseq_ALAS2.R3 186 297
• NCBIGene 36.3 212
• Single exon skipping, size difference: 111
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000032

• cd KBL_like 352aa 1e-149 in ref transcript
  • KBL_like; this family belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD corresponds to serine palmitoyltransferase (SPT), 5-aminolevulinate synthase (ALAS), 8-amino-7-oxononanoate synthase (AONS), and 2-amino-3-ketobutyrate CoA ligase (KBL). SPT is responsible for the condensation of L-serine with palmitoyl-CoA to produce 3-ketodihydrospingosine, the reaction of the first step in sphingolipid biosynthesis. ALAS is involved in heme biosynthesis; it catalyzes the synthesis of 5-aminolevulinic acid from glycine and succinyl-coenzyme A. AONS catalyses the decarboxylative condensation of l-alanine and pimeloyl-CoA in the first committed step of biotin biosynthesis. KBL catalyzes the second reaction step of the metabolic degradation pathway for threonine converting 2-amino-3-ketobutyrate, to glycine and acetyl-CoA. The members of this CD are widely found in all three forms of life.
• TIGR 5aminolev_synth 406aa 0.0 in ref transcript
  • This model represents 5-aminolevulinic acid synthase, an enzyme for one of two routes to the heme precursor 5-aminolevulinate. The protein is a pyridoxal phosphate-dependent enzyme related to 2-amino-3-ketobutyrate CoA tranferase and 8-amino-7-oxononanoate synthase. This enzyme appears restricted to the alpha Proteobacteria and mitochondrial derivatives.
• pfam Preseq_ALAS 101aa 1e-55 in ref transcript
  • 5-aminolevulinate synthase presequence. The N terminal presequence domain found in 5-aminolevulinate synthase exists as an amphipathic helix, with a positively charged surface provided by lysine residues and no stable helix at the N-terminus. The domain is essential for the import process by which ALAS is transported into the mitochondria: translocase of the outer membrane (Tom) and translocase of the inner membrane protein complexes appear responsible for recognition and import through the mitochondrial membrane. The protein Tom20 is anchored to the mitochondrial outer membrane, and its interaction with presequences is thought to be the recognition step which allows subsequent import.
• PRK PRK09064 405aa 0.0 in ref transcript
  • 5-aminolevulinate synthase; Validated.

ALDH1A2

• refseq_ALDH1A2.F1 refseq_ALDH1A2.R1 311 425
• NCBIGene 36.3 8854
• Single exon skipping, size difference: 114
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_003888

• Changed! pfam Aldedh 464aa 0.0 in ref transcript
  • Aldehyde dehydrogenase family. This family of dehydrogenases act on aldehyde substrates. Members use NADP as a cofactor. The family includes the following members: The prototypical members are the aldehyde dehydrogenases EC:1.2.1.3. Succinate-semialdehyde dehydrogenase EC:1.2.1.16. Lactaldehyde dehydrogenase EC:1.2.1.22. Benzaldehyde dehydrogenase EC:1.2.1.28. Methylmalonate-semialdehyde dehydrogenase EC:1.2.1.27. Glyceraldehyde-3-phosphate dehydrogenase EC:1.2.1.9. Delta-1-pyrroline-5-carboxylate dehydrogenase EC: 1.5.1.12. Acetaldehyde dehydrogenase EC:1.2.1.10. Glutamate-5-semialdehyde dehydrogenase EC:1.2.1.41. This family also includes omega crystallin, an eye lens protein from squid and octopus that has little aldehyde dehydrogenase activity.
• Changed! COG PutA 477aa 1e-155 in ref transcript
  • NAD-dependent aldehyde dehydrogenases [Energy production and conversion].
• Changed! pfam Aldedh 426aa 1e-174 in modified transcript
• Changed! COG PutA 439aa 1e-136 in modified transcript

ALDH3A2

• refseq_ALDH3A2.F1 refseq_ALDH3A2.R1 231 356
• NCBIGene 36.3 224
• Single exon skipping, size difference: 125
• Exclusion of the stop codon
• Reference transcript: NM_001031806

• pfam Aldedh 416aa 7e-73 in ref transcript
  • Aldehyde dehydrogenase family. This family of dehydrogenases act on aldehyde substrates. Members use NADP as a cofactor. The family includes the following members: The prototypical members are the aldehyde dehydrogenases EC:1.2.1.3. Succinate-semialdehyde dehydrogenase EC:1.2.1.16. Lactaldehyde dehydrogenase EC:1.2.1.22. Benzaldehyde dehydrogenase EC:1.2.1.28. Methylmalonate-semialdehyde dehydrogenase EC:1.2.1.27. Glyceraldehyde-3-phosphate dehydrogenase EC:1.2.1.9. Delta-1-pyrroline-5-carboxylate dehydrogenase EC: 1.5.1.12. Acetaldehyde dehydrogenase EC:1.2.1.10. Glutamate-5-semialdehyde dehydrogenase EC:1.2.1.41. This family also includes omega crystallin, an eye lens protein from squid and octopus that has little aldehyde dehydrogenase activity.
• COG PutA 423aa 8e-82 in ref transcript
  • NAD-dependent aldehyde dehydrogenases [Energy production and conversion].

ALDH3B1

• refseq_ALDH3B1.F1 refseq_ALDH3B1.R1 101 211
• NCBIGene 36.3 221
• Single exon skipping, size difference: 110
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_001030010

• Changed! pfam Aldedh 250aa 1e-49 in ref transcript
  • Aldehyde dehydrogenase family. This family of dehydrogenases act on aldehyde substrates. Members use NADP as a cofactor. The family includes the following members: The prototypical members are the aldehyde dehydrogenases EC:1.2.1.3. Succinate-semialdehyde dehydrogenase EC:1.2.1.16. Lactaldehyde dehydrogenase EC:1.2.1.22. Benzaldehyde dehydrogenase EC:1.2.1.28. Methylmalonate-semialdehyde dehydrogenase EC:1.2.1.27. Glyceraldehyde-3-phosphate dehydrogenase EC:1.2.1.9. Delta-1-pyrroline-5-carboxylate dehydrogenase EC: 1.5.1.12. Acetaldehyde dehydrogenase EC:1.2.1.10. Glutamate-5-semialdehyde dehydrogenase EC:1.2.1.41. This family also includes omega crystallin, an eye lens protein from squid and octopus that has little aldehyde dehydrogenase activity.
• Changed! COG PutA 258aa 1e-50 in ref transcript
  • NAD-dependent aldehyde dehydrogenases [Energy production and conversion].
• Changed! TIGR arg_catab_astD 75aa 0.009 in modified transcript
  • Members of this protein family are succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71), the fourth enzyme in the arginine succinyltransferase (AST) pathway for arginine catabolism.
• Changed! COG PutA 54aa 0.005 in modified transcript

ALDH5A1

• refseq_ALDH5A1.F1 refseq_ALDH5A1.R1 125 164
• NCBIGene 36.3 7915
• Single exon skipping, size difference: 39
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_170740

• Changed! TIGR SSADH 464aa 0.0 in ref transcript
  • SSADH enzyme belongs to the aldehyde dehydrogenase family (pfam00171), sharing a common evolutionary origin and enzymatic mechanism with lactaldehyde dehydrogenase. Like in lactaldehyde dehydrogenase and succinate semialdehyde dehydrogenase, the mammalian catalytic glutamic acid and cysteine residues are conserved in all the enzymes of this family (PS00687, PS00070).
• Changed! PRK gabD 484aa 1e-161 in ref transcript
  • succinate-semialdehyde dehydrogenase I; Provisional.
• Changed! TIGR SSADH 451aa 0.0 in modified transcript
• Changed! PRK gabD 471aa 1e-160 in modified transcript

ALDH8A1

• refseq_ALDH8A1.F1 refseq_ALDH8A1.R1 183 345
• NCBIGene 36.3 64577
• Single exon skipping, size difference: 162
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_022568

• Changed! pfam Aldedh 464aa 1e-172 in ref transcript
  • Aldehyde dehydrogenase family. This family of dehydrogenases act on aldehyde substrates. Members use NADP as a cofactor. The family includes the following members: The prototypical members are the aldehyde dehydrogenases EC:1.2.1.3. Succinate-semialdehyde dehydrogenase EC:1.2.1.16. Lactaldehyde dehydrogenase EC:1.2.1.22. Benzaldehyde dehydrogenase EC:1.2.1.28. Methylmalonate-semialdehyde dehydrogenase EC:1.2.1.27. Glyceraldehyde-3-phosphate dehydrogenase EC:1.2.1.9. Delta-1-pyrroline-5-carboxylate dehydrogenase EC: 1.5.1.12. Acetaldehyde dehydrogenase EC:1.2.1.10. Glutamate-5-semialdehyde dehydrogenase EC:1.2.1.41. This family also includes omega crystallin, an eye lens protein from squid and octopus that has little aldehyde dehydrogenase activity.
• Changed! COG PutA 476aa 1e-143 in ref transcript
  • NAD-dependent aldehyde dehydrogenases [Energy production and conversion].
• Changed! pfam Aldedh 410aa 1e-138 in modified transcript
• Changed! COG PutA 422aa 1e-115 in modified transcript

ALG8

• refseq_ALG8.F1 refseq_ALG8.R1 308 383
• NCBIGene 36.3 79053
• Single exon skipping, size difference: 75
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_024079

• Changed! pfam Alg6_Alg8 494aa 1e-139 in ref transcript
  • ALG6, ALG8 glycosyltransferase family. N-linked (asparagine-linked) glycosylation of proteins is mediated by a highly conserved pathway in eukaryotes, in which a lipid (dolichol phosphate)-linked oligosaccharide is assembled at the endoplasmic reticulum membrane prior to the transfer of the oligosaccharide moiety to the target asparagine residues. This oligosaccharide is composed of Glc(3)Man(9)GlcNAc(2). The addition of the three glucose residues is the final series of steps in the synthesis of the oligosaccharide precursor. Alg6 transfers the first glucose residue, and Alg8 transfers the second one. In the human alg6 gene, a C->T transition, which causes Ala333 to be replaced with Val, has been identified as the cause of a congenital disorder of glycosylation, designated as type Ic OMIM:603147.
• Changed! pfam Alg6_Alg8 437aa 1e-121 in modified transcript

ALKBH1

• refseq_ALKBH1.F2 refseq_ALKBH1.R2 117 280
• NCBIGene 36.2 8846
• Single exon skipping, size difference: 163
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_006020

• Changed! TIGR alkb 171aa 3e-72 in ref transcript
  • Proteins in this family have an as of yet undetermined function in the repair of alkylation damage to DNA. Alignment and family designation based on phylogenomic analysis of Jonathan A. Eisen (PhD Thesis, Stanford University, 1999).
• Changed! COG AlkB 137aa 2e-16 in ref transcript
  • Alkylated DNA repair protein [DNA replication, recombination, and repair].

ALKBH6

• refseq_ALKBH6.F2 refseq_ALKBH6.R2 137 175
• NCBIGene 36.3 84964
• Alternative 3-prime, size difference: 38
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_032878

ALKBH6

• refseq_ALKBH6.F4 refseq_ALKBH6.R4 145 177
• NCBIGene 36.2 84964
• Alternative 3-prime, size difference: 32
• Exclusion in 5'UTR
• Reference transcript: NM_032878

ALOX15B

• refseq_ALOX15B.F1 refseq_ALOX15B.R1 128 263
• NCBIGene 36.3 247
• Exon skipping and alternative 3-prime or 5-prime, size difference: 135
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_001141

• cd PLAT_LOX 120aa 7e-37 in ref transcript
  • PLAT domain of 12/15-lipoxygenase. As a unique subfamily of the mammalian lipoxygenases, they catalyze enzymatic lipid peroxidation in complex biological structures via direct dioxygenation of phospholipids and cholesterol esters of biomembranes and plasma lipoproteins. Both types of enzymes are cytosolic but need this domain to access their sequestered membrane or micelle bound substrates.
• Changed! pfam Lipoxygenase 437aa 1e-106 in ref transcript
  • Lipoxygenase.
• pfam PLAT 114aa 2e-17 in ref transcript
  • PLAT/LH2 domain. This domain is found in a variety of membrane or lipid associated proteins. It is called the PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology) domain. The known structure of pancreatic lipase shows this domain binds to procolipase pfam01114, which mediates membrane association. So it appears possible that this domain mediates membrane attachment via other protein binding partners. The structure of this domain is known for many members of the family and is composed of a beta sandwich.
• Changed! pfam Lipoxygenase 392aa 3e-85 in modified transcript

ALOX15B

• refseq_ALOX15B.F4 refseq_ALOX15B.R4 134 221
• NCBIGene 36.3 247
• Single exon skipping, size difference: 87
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001141

• cd PLAT_LOX 120aa 7e-37 in ref transcript
  • PLAT domain of 12/15-lipoxygenase. As a unique subfamily of the mammalian lipoxygenases, they catalyze enzymatic lipid peroxidation in complex biological structures via direct dioxygenation of phospholipids and cholesterol esters of biomembranes and plasma lipoproteins. Both types of enzymes are cytosolic but need this domain to access their sequestered membrane or micelle bound substrates.
• Changed! pfam Lipoxygenase 437aa 1e-106 in ref transcript
  • Lipoxygenase.
• pfam PLAT 114aa 2e-17 in ref transcript
  • PLAT/LH2 domain. This domain is found in a variety of membrane or lipid associated proteins. It is called the PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology) domain. The known structure of pancreatic lipase shows this domain binds to procolipase pfam01114, which mediates membrane association. So it appears possible that this domain mediates membrane attachment via other protein binding partners. The structure of this domain is known for many members of the family and is composed of a beta sandwich.
• Changed! pfam Lipoxygenase 408aa 2e-91 in modified transcript

PARD3B

• refseq_ALS2CR19.F1 refseq_ALS2CR19.R1 119 326
• NCBIGene 36.3 117583
• Single exon skipping, size difference: 207
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_152526

• cd PDZ_signaling 79aa 9e-12 in ref transcript
  • PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of PDZ domains an N-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in proteases.
• cd PDZ_signaling 88aa 1e-05 in ref transcript
• cd PDZ_signaling 32aa 0.008 in ref transcript
• smart PDZ 81aa 2e-13 in ref transcript
  • Domain present in PSD-95, Dlg, and ZO-1/2. Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities.
• smart PDZ 91aa 8e-07 in ref transcript
• COG Prc 81aa 1e-04 in ref transcript
  • Periplasmic protease [Cell envelope biogenesis, outer membrane].

PARD3B

• refseq_ALS2CR19.F3 refseq_ALS2CR19.R3 100 403
• NCBIGene 36.3 117583
• Single exon skipping, size difference: 303
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_152526

• cd PDZ_signaling 79aa 9e-12 in ref transcript
  • PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of PDZ domains an N-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in proteases.
• cd PDZ_signaling 88aa 1e-05 in ref transcript
• cd PDZ_signaling 32aa 0.008 in ref transcript
• smart PDZ 81aa 2e-13 in ref transcript
  • Domain present in PSD-95, Dlg, and ZO-1/2. Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities.
• smart PDZ 91aa 8e-07 in ref transcript
• COG Prc 81aa 1e-04 in ref transcript
  • Periplasmic protease [Cell envelope biogenesis, outer membrane].

PARD3B

• refseq_ALS2CR19.F4 refseq_ALS2CR19.R4 156 342
• NCBIGene 36.3 117583
• Single exon skipping, size difference: 186
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_152526

• cd PDZ_signaling 79aa 9e-12 in ref transcript
  • PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of PDZ domains an N-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in proteases.
• cd PDZ_signaling 88aa 1e-05 in ref transcript
• Changed! cd PDZ_signaling 32aa 0.008 in ref transcript
• smart PDZ 81aa 2e-13 in ref transcript
  • Domain present in PSD-95, Dlg, and ZO-1/2. Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities.
• smart PDZ 91aa 8e-07 in ref transcript
• COG Prc 81aa 1e-04 in ref transcript
  • Periplasmic protease [Cell envelope biogenesis, outer membrane].
• Changed! cd PDZ_signaling 78aa 2e-10 in modified transcript
• Changed! smart PDZ 88aa 2e-10 in modified transcript
• Changed! TIGR degP_htrA_DO 147aa 1e-05 in modified transcript
  • This family consists of a set proteins various designated DegP, heat shock protein HtrA, and protease DO. The ortholog in Pseudomonas aeruginosa is designated MucD and is found in an operon that controls mucoid phenotype. This family also includes the DegQ (HhoA) paralog in E. coli which can rescue a DegP mutant, but not the smaller DegS paralog, which cannot. Members of this family are located in the periplasm and have separable functions as both protease and chaperone. Members have a trypsin domain and two copies of a PDZ domain. This protein protects bacteria from thermal and other stresses and may be important for the survival of bacterial pathogens.// The chaperone function is dominant at low temperatures, whereas the proteolytic activity is turned on at elevated temperatures.

AMACR

• refseq_AMACR.F1 refseq_AMACR.R1 189 350
• NCBIGene 36.3 23600
• Single exon skipping, size difference: 161
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_014324

• Changed! pfam CoA_transf_3 192aa 1e-68 in ref transcript
  • CoA-transferase family III. CoA-transferases are found in organisms from all lines of descent. Most of these enzymes belong to two well-known enzyme families, but recent work on unusual biochemical pathways of anaerobic bacteria has revealed the existence of a third family of CoA-transferases. The members of this enzyme family differ in sequence and reaction mechanism from CoA-transferases of the other families. Currently known enzymes of the new family are a formyl-CoA: oxalate CoA-transferase, a succinyl-CoA: (R)-benzylsuccinate CoA-transferase, an (E)-cinnamoyl-CoA: (R)-phenyllactate CoA-transferase, and a butyrobetainyl-CoA: (R)-carnitine CoA-transferase. In addition, a large number of proteins of unknown or differently annotated function from Bacteria, Archaea and Eukarya apparently belong to this enzyme family. Properties and reaction mechanisms of the CoA-transferases of family III are described and compared to those of the previously known CoA-transferases.
• Changed! COG CaiB 371aa 2e-85 in ref transcript
  • Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion].
• Changed! pfam CoA_transf_3 79aa 6e-28 in modified transcript
• Changed! TIGR oxalate_frc 161aa 1e-21 in modified transcript
  • This enzyme, formyl-CoA transferase, transfers coenzyme A from formyl-CoA to oxalate. It forms a pathway, together with oxalyl-CoA decarboxylase, for oxalate degradation; decarboxylation by the latter gene regenerates formyl-CoA. The two enzymes typically are encoded by a two-gene operon.
• Changed! COG CaiB 129aa 3e-37 in modified transcript

AMD1

• refseq_AMD1.F2 refseq_AMD1.R2 108 425
• NCBIGene 36.3 262
• Multiple exon skipping, size difference: 317
• Exclusion in the protein (no frameshift), Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_001634

• Changed! pfam SAM_decarbox 328aa 1e-124 in ref transcript
  • Adenosylmethionine decarboxylase. This is a family of S-adenosylmethionine decarboxylase (SAMDC) proenzymes. In the biosynthesis of polyamines SAMDC produces decarboxylated S-adenosylmethionine, which serves as the aminopropyl moiety necessary for spermidine and spermine biosynthesis from putrescine. The Pfam alignment contains both the alpha and beta chains that are cleaved to form the active enzyme.
• Changed! pfam SAM_decarbox 41aa 2e-09 in modified transcript

AMMECR1

• refseq_AMMECR1.F2 refseq_AMMECR1.R2 252 363
• NCBIGene 36.3 9949
• Single exon skipping, size difference: 111
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_015365

• Changed! pfam AMMECR1 172aa 4e-45 in ref transcript
  • AMMECR1. This family consists of several AMMECR1 as well as several uncharacterised proteins. The contiguous gene deletion syndrome AMME is characterised by Alport syndrome, midface hypoplasia, mental retardation and elliptocytosis and is caused by a deletion in Xq22.3, comprising several genes including COL4A5, FACL4 and AMMECR1. This family contains sequences from several eukaryotic species as well as archaebacteria and it has been suggested that the AMMECR1 protein may have a basic cellular function, potentially in either the transcription, replication, repair or translation machinery.
• Changed! COG AMMECR1 153aa 1e-24 in ref transcript
  • Uncharacterized conserved protein [Function unknown].
• Changed! pfam AMMECR1 106aa 6e-28 in modified transcript
• Changed! COG AMMECR1 85aa 7e-15 in modified transcript

AMZ2

• refseq_AMZ2.F1 refseq_AMZ2.R1 175 349
• NCBIGene 36.3 51321
• Single exon skipping, size difference: 174
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_016627

• Changed! pfam Peptidase_M54 154aa 9e-12 in ref transcript
  • Peptidase family M54. This is a family of metallopeptidases. Two human proteins have been reported to degrade synthetic substrates and peptides.
• Changed! COG COG1913 178aa 2e-18 in ref transcript
  • Predicted Zn-dependent proteases [General function prediction only].
• Changed! pfam Peptidase_M54 128aa 6e-12 in modified transcript
• Changed! COG COG1913 143aa 3e-17 in modified transcript

ANAPC11

• refseq_ANAPC11.F2 refseq_ANAPC11.R3 141 204
• NCBIGene 36.3 51529
• Single exon skipping, size difference: 63
• Inclusion in 5'UTR
• Reference transcript: NM_001002244

• COG APC11 37aa 5e-07 in ref transcript
  • Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning].

ANAPC11

• refseq_ANAPC11.F3 refseq_ANAPC11.R4 102 403
• NCBIGene 36.3 51529
• Single exon skipping, size difference: 301
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_001002244

• Changed! COG APC11 37aa 5e-07 in ref transcript
  • Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning].
• Changed! COG APC11 84aa 1e-16 in modified transcript

ANGPTL4

• refseq_ANGPTL4.F2 refseq_ANGPTL4.R2 104 218
• NCBIGene 36.3 51129
• Single exon skipping, size difference: 114
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_139314

• Changed! cd FReD 218aa 1e-68 in ref transcript
  • Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation.
• Changed! smart FBG 217aa 2e-62 in ref transcript
  • Fibrinogen-related domains (FReDs). Domain present at the C-termini of fibrinogen beta and gamma chains, and a variety of fibrinogen-related proteins, including tenascin and Drosophila scabrous.
• Changed! cd FReD 179aa 5e-56 in modified transcript
• Changed! smart FBG 179aa 1e-50 in modified transcript

ANK1

• refseq_ANK1.F1 refseq_ANK1.R1 157 223
• NCBIGene 36.2 286
• Single exon skipping, size difference: 66
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000037

• cd ANK 126aa 1e-31 in ref transcript
  • ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats.
• cd ANK 126aa 2e-31 in ref transcript
• cd ANK 126aa 3e-31 in ref transcript
• cd ANK 124aa 1e-30 in ref transcript
• cd ANK 126aa 1e-30 in ref transcript
• cd ANK 120aa 2e-28 in ref transcript
• cd ANK 126aa 3e-28 in ref transcript
• cd ANK 155aa 2e-27 in ref transcript
• cd ANK 126aa 8e-24 in ref transcript
• pfam ZU5 105aa 2e-42 in ref transcript
  • ZU5 domain. Domain present in ZO-1 and Unc5-like netrin receptors Domain of unknown function.
• smart DEATH 87aa 1e-18 in ref transcript
  • DEATH domain, found in proteins involved in cell death (apoptosis). Alpha-helical domain present in a variety of proteins with apoptotic functions. Some (but not all) of these domains form homotypic and heterotypic dimers.
• TIGR trp 253aa 4e-10 in ref transcript
  • after chronic exposure to capsaicin. (McCleskey and Gold, 1999).
• TIGR trp 143aa 4e-09 in ref transcript
• TIGR trp 163aa 5e-09 in ref transcript
• TIGR trp 237aa 5e-06 in ref transcript
• pfam Ank 31aa 3e-05 in ref transcript
  • Ankyrin repeat. There's no clear separation between noise and signal on the HMM search Ankyrin repeats generally consist of a beta, alpha, alpha, beta order of secondary structures. The repeats associate to form a higher order structure.
• COG Arp 158aa 2e-17 in ref transcript
  • FOG: Ankyrin repeat [General function prediction only].
• COG Arp 178aa 2e-16 in ref transcript
• COG Arp 187aa 4e-14 in ref transcript
• COG Arp 128aa 1e-13 in ref transcript
• COG Arp 160aa 1e-12 in ref transcript

ANK3

• refseq_ANK3.F1 refseq_ANK3.R1 104 413
• NCBIGene 36.3 288
• Single exon skipping, size difference: 309
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_020987

• cd ANK 126aa 2e-33 in ref transcript
  • ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats.
• cd ANK 126aa 5e-33 in ref transcript
• cd ANK 126aa 5e-33 in ref transcript
• cd ANK 126aa 8e-33 in ref transcript
• cd ANK 126aa 4e-32 in ref transcript
• cd ANK 125aa 2e-31 in ref transcript
• cd ANK 122aa 2e-31 in ref transcript
• pfam ZU5 105aa 9e-37 in ref transcript
  • ZU5 domain. Domain present in ZO-1 and Unc5-like netrin receptors Domain of unknown function.
• smart DEATH 87aa 3e-21 in ref transcript
  • DEATH domain, found in proteins involved in cell death (apoptosis). Alpha-helical domain present in a variety of proteins with apoptotic functions. Some (but not all) of these domains form homotypic and heterotypic dimers.
• TIGR trp 213aa 3e-14 in ref transcript
  • after chronic exposure to capsaicin. (McCleskey and Gold, 1999).
• TIGR trp 308aa 1e-07 in ref transcript
• TIGR trp 186aa 2e-07 in ref transcript
• TIGR trp 131aa 6e-06 in ref transcript
• pfam Ank 32aa 3e-05 in ref transcript
  • Ankyrin repeat. There's no clear separation between noise and signal on the HMM search Ankyrin repeats generally consist of a beta, alpha, alpha, beta order of secondary structures. The repeats associate to form a higher order structure.
• pfam Ank 32aa 7e-05 in ref transcript
• COG Arp 191aa 2e-17 in ref transcript
  • FOG: Ankyrin repeat [General function prediction only].
• COG Arp 145aa 1e-14 in ref transcript
• COG Arp 219aa 3e-14 in ref transcript
• COG Arp 127aa 3e-13 in ref transcript
• COG Arp 130aa 2e-12 in ref transcript
• COG Arp 221aa 9e-11 in ref transcript
• PTZ PTZ00322 70aa 6e-04 in ref transcript
  • 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase; Provisional.

ANK3

• refseq_ANK3.F2 refseq_ANK3.R2 108 135
• NCBIGene 36.3 288
• Single exon skipping, size difference: 27
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_020987

• cd ANK 126aa 2e-33 in ref transcript
  • ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats.
• cd ANK 126aa 5e-33 in ref transcript
• cd ANK 126aa 5e-33 in ref transcript
• cd ANK 126aa 8e-33 in ref transcript
• cd ANK 126aa 4e-32 in ref transcript
• cd ANK 125aa 2e-31 in ref transcript
• cd ANK 122aa 2e-31 in ref transcript
• pfam ZU5 105aa 9e-37 in ref transcript
  • ZU5 domain. Domain present in ZO-1 and Unc5-like netrin receptors Domain of unknown function.
• smart DEATH 87aa 3e-21 in ref transcript
  • DEATH domain, found in proteins involved in cell death (apoptosis). Alpha-helical domain present in a variety of proteins with apoptotic functions. Some (but not all) of these domains form homotypic and heterotypic dimers.
• TIGR trp 213aa 3e-14 in ref transcript
  • after chronic exposure to capsaicin. (McCleskey and Gold, 1999).
• TIGR trp 308aa 1e-07 in ref transcript
• TIGR trp 186aa 2e-07 in ref transcript
• TIGR trp 131aa 6e-06 in ref transcript
• pfam Ank 32aa 3e-05 in ref transcript
  • Ankyrin repeat. There's no clear separation between noise and signal on the HMM search Ankyrin repeats generally consist of a beta, alpha, alpha, beta order of secondary structures. The repeats associate to form a higher order structure.
• pfam Ank 32aa 7e-05 in ref transcript
• COG Arp 191aa 2e-17 in ref transcript
  • FOG: Ankyrin repeat [General function prediction only].
• COG Arp 145aa 1e-14 in ref transcript
• COG Arp 219aa 3e-14 in ref transcript
• COG Arp 127aa 3e-13 in ref transcript
• COG Arp 130aa 2e-12 in ref transcript
• COG Arp 221aa 9e-11 in ref transcript
• PTZ PTZ00322 70aa 6e-04 in ref transcript
  • 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase; Provisional.

ANKMY1

• refseq_ANKMY1.F2 refseq_ANKMY1.R2 123 372
• NCBIGene 36.3 51281
• Multiple exon skipping, size difference: 249
• Exclusion in the protein (no frameshift), Exclusion in the protein (no frameshift)
• Reference transcript: NM_016552

• Changed! cd ANK 166aa 6e-13 in ref transcript
  • ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats.
• cd ANK 83aa 1e-08 in ref transcript
• Changed! pfam Ank 34aa 3e-04 in ref transcript
  • Ankyrin repeat. There's no clear separation between noise and signal on the HMM search Ankyrin repeats generally consist of a beta, alpha, alpha, beta order of secondary structures. The repeats associate to form a higher order structure.
• pfam Ank 33aa 0.004 in ref transcript
• Changed! COG Arp 119aa 1e-06 in ref transcript
  • FOG: Ankyrin repeat [General function prediction only].
• Changed! COG Arp 86aa 6e-05 in ref transcript
• COG COG4642 83aa 1e-04 in ref transcript
  • Uncharacterized protein conserved in bacteria [Function unknown].
• Changed! cd ANK 105aa 1e-07 in modified transcript
• Changed! COG Arp 107aa 1e-05 in modified transcript

ANKMY1

• refseq_ANKMY1.F4 refseq_ANKMY1.R4 234 397
• NCBIGene 36.3 51281
• Single exon skipping, size difference: 163
• Inclusion in 5'UTR
• Reference transcript: NM_016552

• cd ANK 166aa 6e-13 in ref transcript
  • ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats.
• cd ANK 83aa 1e-08 in ref transcript
• pfam Ank 34aa 3e-04 in ref transcript
  • Ankyrin repeat. There's no clear separation between noise and signal on the HMM search Ankyrin repeats generally consist of a beta, alpha, alpha, beta order of secondary structures. The repeats associate to form a higher order structure.
• pfam Ank 33aa 0.004 in ref transcript
• COG Arp 119aa 1e-06 in ref transcript
  • FOG: Ankyrin repeat [General function prediction only].
• COG Arp 86aa 6e-05 in ref transcript
• COG COG4642 83aa 1e-04 in ref transcript
  • Uncharacterized protein conserved in bacteria [Function unknown].

ANKRD16

• refseq_ANKRD16.F1 refseq_ANKRD16.R1 136 215
• NCBIGene 36.3 54522
• Single exon skipping, size difference: 79
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_019046

• cd ANK 121aa 5e-22 in ref transcript
  • ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats.
• Changed! cd ANK 156aa 5e-20 in ref transcript
• cd ANK 128aa 3e-19 in ref transcript
• TIGR trp 142aa 4e-05 in ref transcript
  • after chronic exposure to capsaicin. (McCleskey and Gold, 1999).
• Changed! TIGR trp 223aa 3e-04 in ref transcript
• Changed! COG Arp 184aa 7e-12 in ref transcript
  • FOG: Ankyrin repeat [General function prediction only].
• COG Arp 122aa 1e-10 in ref transcript
• Changed! cd ANK 112aa 2e-18 in modified transcript
• Changed! pfam Ank 32aa 0.003 in modified transcript
  • Ankyrin repeat. There's no clear separation between noise and signal on the HMM search Ankyrin repeats generally consist of a beta, alpha, alpha, beta order of secondary structures. The repeats associate to form a higher order structure.
• Changed! TIGR trp 177aa 0.004 in modified transcript
• Changed! COG Arp 145aa 4e-13 in modified transcript

ANKRD5

• refseq_ANKRD5.F2 refseq_ANKRD5.R2 339 403
• NCBIGene 36.3 63926
• Single exon skipping, size difference: 64
• Exclusion in 5'UTR
• Reference transcript: NM_022096

• cd ANK 125aa 1e-25 in ref transcript
  • ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats.
• cd ANK 115aa 4e-15 in ref transcript
• cd ANK 124aa 6e-14 in ref transcript
• cd EFh 59aa 0.005 in ref transcript
  • EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers.
• pfam Ank 30aa 3e-06 in ref transcript
  • Ankyrin repeat. There's no clear separation between noise and signal on the HMM search Ankyrin repeats generally consist of a beta, alpha, alpha, beta order of secondary structures. The repeats associate to form a higher order structure.
• TIGR trp 119aa 7e-06 in ref transcript
  • after chronic exposure to capsaicin. (McCleskey and Gold, 1999).
• pfam Ank 33aa 4e-04 in ref transcript
• pfam Ank 28aa 0.002 in ref transcript
• COG Arp 196aa 2e-13 in ref transcript
  • FOG: Ankyrin repeat [General function prediction only].
• COG Arp 143aa 4e-04 in ref transcript
• COG Arp 91aa 0.003 in ref transcript

ANKS1B

• refseq_ANKS1B.F2 refseq_ANKS1B.R2 169 241
• NCBIGene 36.3 56899
• Single exon skipping, size difference: 72
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_152788

• cd AIDA-1b 132aa 1e-50 in ref transcript
  • AIDA-1b Phosphotyrosine-binding (PTB) domain. AIDA-1b is an amyloid-beta precursor protein interacting protein. It consists of ankyrin repeats, a SAM domain and a C-terminal PTB domain. PTB domains have a PH-like fold and are found in various eukaryotic signaling molecules. They were initially identified based upon their ability to recognize phosphorylated tyrosine residues In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. More recent studies have found that some types of PTB domains can bind to peptides which are not tyrosine phosphorylated or lack tyrosine residues altogether.
• cd ANK 129aa 3e-29 in ref transcript
  • ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats.
• cd ANK 125aa 4e-25 in ref transcript
• cd SAM 62aa 2e-11 in ref transcript
  • Sterile alpha motif.; Widespread domain in signalling and nuclear proteins. In EPH-related tyrosine kinases, appears to mediate cell-cell initiated signal transduction via the binding of SH2-containing proteins to a conserved tyrosine that is phosphorylated. In many cases mediates homodimerization.
• cd SAM 63aa 3e-08 in ref transcript
• pfam PID 131aa 3e-29 in ref transcript
  • Phosphotyrosine interaction domain (PTB/PID).
• smart SAM 66aa 2e-13 in ref transcript
  • Sterile alpha motif. Widespread domain in signalling and nuclear proteins. In EPH-related tyrosine kinases, appears to mediate cell-cell initiated signal transduction via the binding of SH2-containing proteins to a conserved tyrosine that is phosphorylated. In many cases mediates homodimerisation.
• smart SAM 62aa 3e-11 in ref transcript
• TIGR trp 191aa 1e-06 in ref transcript
  • after chronic exposure to capsaicin. (McCleskey and Gold, 1999).
• pfam Ank 32aa 4e-04 in ref transcript
  • Ankyrin repeat. There's no clear separation between noise and signal on the HMM search Ankyrin repeats generally consist of a beta, alpha, alpha, beta order of secondary structures. The repeats associate to form a higher order structure.
• COG Arp 134aa 2e-14 in ref transcript
  • FOG: Ankyrin repeat [General function prediction only].
• COG Arp 184aa 2e-08 in ref transcript

ANXA13

• refseq_ANXA13.F1 refseq_ANXA13.R1 100 223
• NCBIGene 36.3 312
• Single exon skipping, size difference: 123
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001003954

• pfam Annexin 66aa 6e-21 in ref transcript
  • Annexin. This family of annexins also includes giardin that has been shown to function as an annexin.
• pfam Annexin 66aa 2e-20 in ref transcript
• pfam Annexin 67aa 7e-17 in ref transcript
• pfam Annexin 66aa 3e-12 in ref transcript

ANXA6

• refseq_ANXA6.F1 refseq_ANXA6.R1 102 120
• NCBIGene 36.3 309
• Single exon skipping, size difference: 18
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001155

• pfam Annexin 66aa 3e-21 in ref transcript
  • Annexin. This family of annexins also includes giardin that has been shown to function as an annexin.
• pfam Annexin 66aa 8e-20 in ref transcript
• pfam Annexin 66aa 2e-18 in ref transcript
• pfam Annexin 65aa 8e-18 in ref transcript
• pfam Annexin 66aa 3e-17 in ref transcript
• pfam Annexin 67aa 2e-15 in ref transcript
• pfam Annexin 65aa 1e-12 in ref transcript
• Changed! pfam Annexin 67aa 3e-11 in ref transcript
• Changed! pfam Annexin 67aa 6e-11 in modified transcript

ANXA7

• refseq_ANXA7.F2 refseq_ANXA7.R2 288 354
• NCBIGene 36.3 310
• Single exon skipping, size difference: 66
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_004034

• pfam Annexin 66aa 7e-24 in ref transcript
  • Annexin. This family of annexins also includes giardin that has been shown to function as an annexin.
• pfam Annexin 66aa 3e-22 in ref transcript
• pfam Annexin 66aa 5e-21 in ref transcript
• pfam Annexin 67aa 6e-14 in ref transcript

AOC2

• refseq_AOC2.F1 refseq_AOC2.R1 140 221
• NCBIGene 36.3 314
• Alternative 5-prime, size difference: 81
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_009590

• Changed! pfam Cu_amine_oxid 416aa 1e-136 in ref transcript
  • Copper amine oxidase, enzyme domain. Copper amine oxidases are a ubiquitous and novel group of quinoenzymes that catalyse the oxidative deamination of primary amines to the corresponding aldehydes, with concomitant reduction of molecular oxygen to hydrogen peroxide. The enzymes are dimers of identical 70-90 kDa subunits, each of which contains a single copper ion and a covalently bound cofactor formed by the post-translational modification of a tyrosine side chain to 2,4,5-trihydroxyphenylalanine quinone (TPQ). This family corresponds to the catalytic domain of the enzyme.
• pfam Cu_amine_oxidN3 99aa 1e-23 in ref transcript
  • Copper amine oxidase, N3 domain. This domain is the second or third structural domain in copper amine oxidases, it is known as the N3 domain. Its function is uncertain. The catalytic domain can be found in pfam01179. Copper amine oxidases are a ubiquitous and novel group of quinoenzymes that catalyse the oxidative deamination of primary amines to the corresponding aldehydes, with concomitant reduction of molecular oxygen to hydrogen peroxide. The enzymes are dimers of identical 70-90 kDa subunits, each of which contains a single copper ion and a covalently bound cofactor formed by the post-translational modification of a tyrosine side chain to 2,4,5-trihydroxyphenylalanine quinone (TPQ).
• pfam Cu_amine_oxidN2 86aa 9e-20 in ref transcript
  • Copper amine oxidase, N2 domain. This domain is the first or second structural domain in copper amine oxidases, it is known as the N2 domain. Its function is uncertain. The catalytic domain can be found in pfam01179. Copper amine oxidases are a ubiquitous and novel group of quinoenzymes that catalyse the oxidative deamination of primary amines to the corresponding aldehydes, with concomitant reduction of molecular oxygen to hydrogen peroxide. The enzymes are dimers of identical 70-90 kDa subunits, each of which contains a single copper ion and a covalently bound cofactor formed by the post-translational modification of a tyrosine side chain to 2,4,5-trihydroxyphenylalanine quinone (TPQ).
• Changed! COG TynA 416aa 1e-45 in ref transcript
  • Cu2+-containing amine oxidase [Secondary metabolites biosynthesis, transport, and catabolism].
• Changed! pfam Cu_amine_oxid 389aa 1e-126 in modified transcript
• Changed! COG TynA 389aa 1e-41 in modified transcript

AP1B1

• refseq_AP1B1.F1 refseq_AP1B1.R1 119 140
• NCBIGene 36.3 162
• Single exon skipping, size difference: 21
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001127

• cd ARM 113aa 2e-09 in ref transcript
  • Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model.
• pfam Adaptin_N 524aa 1e-163 in ref transcript
  • Adaptin N terminal region. This family consists of the N terminal region of various alpha, beta and gamma subunits of the AP-1, AP-2 and AP-3 adaptor protein complexes. The adaptor protein (AP) complexes are involved in the formation of clathrin-coated pits and vesicles. The N-terminal region of the various adaptor proteins (APs) is constant by comparison to the C-terminal which is variable within members of the AP-2 family; and it has been proposed that this constant region interacts with another uniform component of the coated vesicles.
• pfam B2-adapt-app_C 114aa 2e-34 in ref transcript
  • Beta2-adaptin appendage, C-terminal sub-domain. Members of this family adopt a structure consisting of a 5 stranded beta-sheet, flanked by one alpha helix on the outer side, and by two alpha helices on the inner side. This domain is required for binding to clathrin, and its subsequent polymerisation. Furthermore, a hydrophobic patch present in the domain also binds to a subset of D-phi-F/W motif-containing proteins that are bound by the alpha-adaptin appendage domain (epsin, AP180, eps15).
• smart Alpha_adaptinC2 101aa 2e-16 in ref transcript
  • Adaptin C-terminal domain. Adaptins are components of the adaptor complexes which link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. Gamma-adaptin is a subunit of the golgi adaptor. Alpha adaptin is a heterotetramer that regulates clathrin-bud formation. The carboxyl-terminal appendage of the alpha subunit regulates translocation of endocytic accessory proteins to the bud site. This Ig-fold domain is found in alpha, beta and gamma adaptins and consists of a beta-sandwich containing 7 strands in 2 beta-sheets in a greek-key topology PUBMED:10430869, PUBMED:12176391. The adaptor appendage contains an additional N-terminal strand.
• COG COG5096 548aa 1e-113 in ref transcript
  • Vesicle coat complex, various subunits [Intracellular trafficking and secretion].

AP1GBP1

• refseq_AP1GBP1.F1 refseq_AP1GBP1.R1 159 195
• NCBIGene 36.3 11276
• Single exon skipping, size difference: 36
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_007247

• cd EH 52aa 3e-09 in ref transcript
  • Eps15 homology domain; found in proteins implicated in endocytosis, vesicle transport, and signal transduction. The alignment contains a pair of EF-hand motifs, typically one of them is canonical and binds to Ca2+, while the other may not bind to Ca2+. A hydrophobic binding pocket is formed by residues from both EF-hand motifs. The EH domain binds to proteins containing NPF (class I), [WF]W or SWG (class II), or H[TS]F (class III) sequence motifs.
• smart EH 62aa 6e-08 in ref transcript
  • Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.

AP2A1

• refseq_AP2A1.F1 refseq_AP2A1.R1 132 198
• NCBIGene 36.3 160
• Single exon skipping, size difference: 66
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_014203

• pfam Adaptin_N 563aa 1e-151 in ref transcript
  • Adaptin N terminal region. This family consists of the N terminal region of various alpha, beta and gamma subunits of the AP-1, AP-2 and AP-3 adaptor protein complexes. The adaptor protein (AP) complexes are involved in the formation of clathrin-coated pits and vesicles. The N-terminal region of the various adaptor proteins (APs) is constant by comparison to the C-terminal which is variable within members of the AP-2 family; and it has been proposed that this constant region interacts with another uniform component of the coated vesicles.
• pfam Alpha_adaptin_C 109aa 7e-50 in ref transcript
  • Alpha adaptin AP2, C-terminal domain. Alpha adaptin is a hetero tetramer which regulates clathrin-bud formation. The carboxyl-terminal appendage of the alpha subunit regulates translocation of endocytic accessory proteins to the bud site.
• pfam Alpha_adaptinC2 106aa 2e-13 in ref transcript
  • Adaptin C-terminal domain. Alpha adaptin is a heterotetramer which regulates clathrin-bud formation. The carboxyl-terminal appendage of the alpha subunit regulates translocation of endocytic accessory proteins to the bud site. This ig-fold domain is found in alpha, beta and gamma adaptins.
• COG COG5096 549aa 3e-11 in ref transcript
  • Vesicle coat complex, various subunits [Intracellular trafficking and secretion].

AP2B1

• refseq_AP2B1.F1 refseq_AP2B1.R1 196 238
• NCBIGene 36.3 163
• Single exon skipping, size difference: 42
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001030006

• cd ARM 113aa 1e-09 in ref transcript
  • Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model.
• pfam Adaptin_N 497aa 1e-160 in ref transcript
  • Adaptin N terminal region. This family consists of the N terminal region of various alpha, beta and gamma subunits of the AP-1, AP-2 and AP-3 adaptor protein complexes. The adaptor protein (AP) complexes are involved in the formation of clathrin-coated pits and vesicles. The N-terminal region of the various adaptor proteins (APs) is constant by comparison to the C-terminal which is variable within members of the AP-2 family; and it has been proposed that this constant region interacts with another uniform component of the coated vesicles.
• pfam B2-adapt-app_C 111aa 4e-35 in ref transcript
  • Beta2-adaptin appendage, C-terminal sub-domain. Members of this family adopt a structure consisting of a 5 stranded beta-sheet, flanked by one alpha helix on the outer side, and by two alpha helices on the inner side. This domain is required for binding to clathrin, and its subsequent polymerisation. Furthermore, a hydrophobic patch present in the domain also binds to a subset of D-phi-F/W motif-containing proteins that are bound by the alpha-adaptin appendage domain (epsin, AP180, eps15).
• smart Alpha_adaptinC2 101aa 3e-17 in ref transcript
  • Adaptin C-terminal domain. Adaptins are components of the adaptor complexes which link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. Gamma-adaptin is a subunit of the golgi adaptor. Alpha adaptin is a heterotetramer that regulates clathrin-bud formation. The carboxyl-terminal appendage of the alpha subunit regulates translocation of endocytic accessory proteins to the bud site. This Ig-fold domain is found in alpha, beta and gamma adaptins and consists of a beta-sandwich containing 7 strands in 2 beta-sheets in a greek-key topology PUBMED:10430869, PUBMED:12176391. The adaptor appendage contains an additional N-terminal strand.
• COG COG5096 548aa 1e-112 in ref transcript
  • Vesicle coat complex, various subunits [Intracellular trafficking and secretion].

AP2S1

• refseq_AP2S1.F1 refseq_AP2S1.R1 179 293
• NCBIGene 36.3 1175
• Single exon skipping, size difference: 114
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_004069

• Changed! pfam Clat_adaptor_s 142aa 6e-57 in ref transcript
  • Clathrin adaptor complex small chain.
• Changed! COG APS2 142aa 6e-42 in ref transcript
  • Clathrin adaptor complex, small subunit [Intracellular trafficking and secretion].
• Changed! pfam Clat_adaptor_s 104aa 2e-33 in modified transcript
• Changed! COG APS2 104aa 3e-22 in modified transcript

AP3M1

• refseq_AP3M1.F1 refseq_AP3M1.R1 268 394
• NCBIGene 36.3 26985
• Single exon skipping, size difference: 126
• Exclusion in 5'UTR
• Reference transcript: NM_207012

• pfam Adap_comp_sub 254aa 3e-77 in ref transcript
  • Adaptor complexes medium subunit family. This family also contains members which are coatomer subunits.
• pfam Clat_adaptor_s 144aa 0.002 in ref transcript
  • Clathrin adaptor complex small chain.
• COG APS2 140aa 0.002 in ref transcript
  • Clathrin adaptor complex, small subunit [Intracellular trafficking and secretion].

AP3S1

• refseq_AP3S1.F1 refseq_AP3S1.R1 179 215
• NCBIGene 36.2 1176
• Single exon skipping, size difference: 36
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_001284

• Changed! pfam Clat_adaptor_s 148aa 7e-47 in ref transcript
  • Clathrin adaptor complex small chain.
• Changed! COG APS2 152aa 5e-44 in ref transcript
  • Clathrin adaptor complex, small subunit [Intracellular trafficking and secretion].
• Changed! pfam Clat_adaptor_s 23aa 4e-05 in modified transcript
• Changed! COG APS2 22aa 2e-04 in modified transcript

APOL1

• refseq_APOL1.F1 refseq_APOL1.R1 245 399
• NCBIGene 36.3 8542
• Single exon skipping, size difference: 154
• Exclusion of the protein initiation site
• Reference transcript: NM_145343

• pfam ApoL 299aa 1e-108 in ref transcript
  • Apolipoprotein L. Apo L belongs to the high density lipoprotein family that plays a central role in cholesterol transport. The cholesterol content of membranes is important in cellular processes such as modulating gene transcription and signal transduction both in the adult brain and during neurodevelopment. There are six apo L genes located in close proximity to each other on chromosome 22q12 in humans. 22q12 is a confirmed high-susceptibility locus for schizophrenia and close to the region associated with velocardiofacial syndrome that includes symptoms of schizophrenia.

APOL3

• refseq_APOL3.F1 refseq_APOL3.R1 112 175
• NCBIGene 36.3 80833
• Single exon skipping, size difference: 63
• Exclusion in 5'UTR
• Reference transcript: NM_145641

• pfam ApoL 196aa 3e-50 in ref transcript
  • Apolipoprotein L. Apo L belongs to the high density lipoprotein family that plays a central role in cholesterol transport. The cholesterol content of membranes is important in cellular processes such as modulating gene transcription and signal transduction both in the adult brain and during neurodevelopment. There are six apo L genes located in close proximity to each other on chromosome 22q12 in humans. 22q12 is a confirmed high-susceptibility locus for schizophrenia and close to the region associated with velocardiofacial syndrome that includes symptoms of schizophrenia.

APOL4

• refseq_APOL4.F1 refseq_APOL4.R1 218 407
• NCBIGene 36.3 80832
• Single exon skipping, size difference: 189
• Exclusion in 5'UTR
• Reference transcript: NM_030643

• pfam ApoL 190aa 1e-49 in ref transcript
  • Apolipoprotein L. Apo L belongs to the high density lipoprotein family that plays a central role in cholesterol transport. The cholesterol content of membranes is important in cellular processes such as modulating gene transcription and signal transduction both in the adult brain and during neurodevelopment. There are six apo L genes located in close proximity to each other on chromosome 22q12 in humans. 22q12 is a confirmed high-susceptibility locus for schizophrenia and close to the region associated with velocardiofacial syndrome that includes symptoms of schizophrenia.

APRT

• refseq_APRT.F1 refseq_APRT.R1 263 397
• NCBIGene 36.3 353
• Alternative 3-prime, size difference: 134
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_000485

• Changed! TIGR apt 171aa 1e-70 in ref transcript
  • A phylogenetic analysis suggested omitting the bi-directional best hit homologs from the spirochetes from the seed for this HMM and making only tentative predictions of adenine phosphoribosyltransferase function for this lineage. The trusted cutoff score is made high for this reason. Most proteins scoring between the trusted and noise cutoffs are likely to act as adenine phosphotransferase.
• Changed! PRK PRK02304 175aa 7e-67 in ref transcript
  • adenine phosphoribosyltransferase; Provisional.
• Changed! TIGR apt 125aa 7e-53 in modified transcript
• Changed! PRK PRK02304 128aa 1e-49 in modified transcript

APTX

• refseq_APTX.F1 refseq_APTX.R1 192 307
• NCBIGene 36.3 54840
• Alternative 3-prime, size difference: 115
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_175073

• Changed! cd aprataxin_related 102aa 6e-35 in ref transcript
  • aprataxin related: Aprataxin, a HINT family hydrolase is mutated in ataxia oculomotor apraxia syndrome. All the members of this subgroup have the conserved HxHxHxx (where x is a hydrophobic residue) signature motif. Members of this subgroup are predominantly eukaryotic in origin.
• Changed! cd FHA 94aa 2e-05 in ref transcript
  • Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins localize to the nucleus, where they participate in establishing or maintaining cell cycle checkpoints, DNA repair, or transcriptional regulation. Members of the FHA family include: Dun1, Rad53, Cds1, Mek1, KAPP(kinase-associated protein phosphatase),and Ki-67 (a human nuclear protein related to cell proliferation).
• Changed! TIGR PNK-3'Pase 105aa 1e-14 in ref transcript
  • Note that the EC number for the kinase function is: 2.7.1.78.
• Changed! pfam HIT 91aa 6e-06 in ref transcript
  • HIT domain.
• Changed! COG Hit 83aa 1e-05 in ref transcript
  • Diadenosine tetraphosphate (Ap4A) hydrolase and other HIT family hydrolases [Nucleotide transport and metabolism / Carbohydrate transport and metabolism / General function prediction only].
• Changed! TIGR PNK-3'Pase 58aa 2e-07 in modified transcript

APTX

• refseq_APTX.F3 refseq_APTX.R3 195 231
• NCBIGene 36.3 54840
• Alternative 3-prime, size difference: 36
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_175073

• cd aprataxin_related 102aa 6e-35 in ref transcript
  • aprataxin related: Aprataxin, a HINT family hydrolase is mutated in ataxia oculomotor apraxia syndrome. All the members of this subgroup have the conserved HxHxHxx (where x is a hydrophobic residue) signature motif. Members of this subgroup are predominantly eukaryotic in origin.
• cd FHA 94aa 2e-05 in ref transcript
  • Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins localize to the nucleus, where they participate in establishing or maintaining cell cycle checkpoints, DNA repair, or transcriptional regulation. Members of the FHA family include: Dun1, Rad53, Cds1, Mek1, KAPP(kinase-associated protein phosphatase),and Ki-67 (a human nuclear protein related to cell proliferation).
• TIGR PNK-3'Pase 105aa 1e-14 in ref transcript
  • Note that the EC number for the kinase function is: 2.7.1.78.
• pfam HIT 91aa 6e-06 in ref transcript
  • HIT domain.
• COG Hit 83aa 1e-05 in ref transcript
  • Diadenosine tetraphosphate (Ap4A) hydrolase and other HIT family hydrolases [Nucleotide transport and metabolism / Carbohydrate transport and metabolism / General function prediction only].

APTX

• refseq_APTX.F4 refseq_APTX.R4 114 220
• NCBIGene 36.3 54840
• Single exon skipping, size difference: 106
• Exclusion in 5'UTR
• Reference transcript: NM_175073

• cd aprataxin_related 102aa 6e-35 in ref transcript
  • aprataxin related: Aprataxin, a HINT family hydrolase is mutated in ataxia oculomotor apraxia syndrome. All the members of this subgroup have the conserved HxHxHxx (where x is a hydrophobic residue) signature motif. Members of this subgroup are predominantly eukaryotic in origin.
• cd FHA 94aa 2e-05 in ref transcript
  • Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins localize to the nucleus, where they participate in establishing or maintaining cell cycle checkpoints, DNA repair, or transcriptional regulation. Members of the FHA family include: Dun1, Rad53, Cds1, Mek1, KAPP(kinase-associated protein phosphatase),and Ki-67 (a human nuclear protein related to cell proliferation).
• TIGR PNK-3'Pase 105aa 1e-14 in ref transcript
  • Note that the EC number for the kinase function is: 2.7.1.78.
• pfam HIT 91aa 6e-06 in ref transcript
  • HIT domain.
• COG Hit 83aa 1e-05 in ref transcript
  • Diadenosine tetraphosphate (Ap4A) hydrolase and other HIT family hydrolases [Nucleotide transport and metabolism / Carbohydrate transport and metabolism / General function prediction only].

ARF1

• refseq_ARF1.F1 refseq_ARF1.R1 114 136
• NCBIGene 36.3 375
• Alternative 5-prime, size difference: 22
• Exclusion in 5'UTR
• Reference transcript: NM_001024227

• cd Arf1_5_like 159aa 1e-98 in ref transcript
  • Arf1-Arf5-like subfamily. This subfamily contains Arf1, Arf2, Arf3, Arf4, Arf5, and related proteins. Arfs1-5 are soluble proteins that are crucial for assembling coat proteins during vesicle formation. Each contains an N-terminal myristoylated amphipathic helix that is folded into the protein in the GDP-bound state. GDP/GTP exchange exposes the helix, which anchors to the membrane. Following GTP hydrolysis, the helix dissociates from the membrane and folds back into the protein. A general feature of Arf1-5 signaling may be the cooperation of two Arfs at the same site. Arfs1-5 are generally considered to be interchangeable in function and location, but some specific functions have been assigned. Arf1 localizes to the early/cis-Golgi, where it is activated by GBF1 and recruits the coat protein COPI. It also localizes to the trans-Golgi network (TGN), where it is activated by BIG1/BIG2 and recruits the AP1, AP3, AP4, and GGA proteins. Humans, but not rodents and other lower eukaryotes, lack Arf2. Human Arf3 shares 96% sequence identity with Arf1 and is believed to generally function interchangeably with Arf1. Human Arf4 in the activated (GTP-bound) state has been shown to interact with the cytoplasmic domain of epidermal growth factor receptor (EGFR) and mediate the EGF-dependent activation of phospholipase D2 (PLD2), leading to activation of the activator protein 1 (AP-1) transcription factor. Arf4 has also been shown to recognize the C-terminal sorting signal of rhodopsin and regulate its incorporation into specialized post-Golgi rhodopsin transport carriers (RTCs). There is some evidence that Arf5 functions at the early-Golgi and the trans-Golgi to affect Golgi-associated alpha-adaptin homology Arf-binding proteins (GGAs).
• smart ARF 175aa 1e-98 in ref transcript
  • ARF-like small GTPases; ARF, ADP-ribosylation factor. Ras homologues involved in vesicular transport. Activator of phospholipase D isoforms. Unlike Ras proteins they lack cysteine residues at their C-termini and therefore are unlikely to be prenylated. ARFs are N-terminally myristoylated. Contains ATP/GTP-binding motif (P-loop).
• PTZ PTZ00133 181aa 4e-96 in ref transcript
  • ADP-ribosylation factor; Provisional.

ARF1

• refseq_ARF1.F3 refseq_ARF1.R3 187 272
• NCBIGene 36.3 375
• Alternative 5-prime, size difference: 85
• Exclusion in 5'UTR
• Reference transcript: NM_001024226

• cd Arf1_5_like 159aa 1e-98 in ref transcript
  • Arf1-Arf5-like subfamily. This subfamily contains Arf1, Arf2, Arf3, Arf4, Arf5, and related proteins. Arfs1-5 are soluble proteins that are crucial for assembling coat proteins during vesicle formation. Each contains an N-terminal myristoylated amphipathic helix that is folded into the protein in the GDP-bound state. GDP/GTP exchange exposes the helix, which anchors to the membrane. Following GTP hydrolysis, the helix dissociates from the membrane and folds back into the protein. A general feature of Arf1-5 signaling may be the cooperation of two Arfs at the same site. Arfs1-5 are generally considered to be interchangeable in function and location, but some specific functions have been assigned. Arf1 localizes to the early/cis-Golgi, where it is activated by GBF1 and recruits the coat protein COPI. It also localizes to the trans-Golgi network (TGN), where it is activated by BIG1/BIG2 and recruits the AP1, AP3, AP4, and GGA proteins. Humans, but not rodents and other lower eukaryotes, lack Arf2. Human Arf3 shares 96% sequence identity with Arf1 and is believed to generally function interchangeably with Arf1. Human Arf4 in the activated (GTP-bound) state has been shown to interact with the cytoplasmic domain of epidermal growth factor receptor (EGFR) and mediate the EGF-dependent activation of phospholipase D2 (PLD2), leading to activation of the activator protein 1 (AP-1) transcription factor. Arf4 has also been shown to recognize the C-terminal sorting signal of rhodopsin and regulate its incorporation into specialized post-Golgi rhodopsin transport carriers (RTCs). There is some evidence that Arf5 functions at the early-Golgi and the trans-Golgi to affect Golgi-associated alpha-adaptin homology Arf-binding proteins (GGAs).
• smart ARF 175aa 1e-98 in ref transcript
  • ARF-like small GTPases; ARF, ADP-ribosylation factor. Ras homologues involved in vesicular transport. Activator of phospholipase D isoforms. Unlike Ras proteins they lack cysteine residues at their C-termini and therefore are unlikely to be prenylated. ARFs are N-terminally myristoylated. Contains ATP/GTP-binding motif (P-loop).
• PTZ PTZ00133 181aa 4e-96 in ref transcript
  • ADP-ribosylation factor; Provisional.

ARFGAP1

• refseq_ARFGAP1.F1 refseq_ARFGAP1.R1 136 166
• NCBIGene 36.3 55738
• Single exon skipping, size difference: 30
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_175609

• pfam ArfGap 118aa 3e-48 in ref transcript
  • Putative GTPase activating protein for Arf. Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs.
• COG COG5347 159aa 4e-31 in ref transcript
  • GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion].

ARFIP1

• refseq_ARFIP1.F1 refseq_ARFIP1.R1 145 280
• NCBIGene 36.3 27236
• Alternative 5-prime, size difference: 135
• Exclusion in 5'UTR
• Reference transcript: NM_001025595

• cd Arfaptin 202aa 1e-51 in ref transcript
  • Arfaptin domain; arfaptin is a ubiquitously expressed protein implicated in mediating cross-talk between Rac, a member of the Rho family, and Arf small GTPases; Arfaptin binds to GTP-bound Arf1 and Arf6, but binds Rac.GTP and Rac.GDP with similar affinities. Structures of Arfaptin with Rac bound to either GDP or the slowly hydrolysable analogue GMPPNP show that the switch regions adopt similar conformations in both complexes. Arf1 and Arf6 are thought to bind to the same surface as Rac.
• pfam Arfaptin 196aa 5e-70 in ref transcript
  • Arfaptin-like domain. Arfaptin interacts with ARF1, a small GTPase involved in vesicle budding at the Golgi complex and immature secretory granules. The structure of arfaptin shows that upon binding to a small GTPase, arfaptin forms a an elongated, crescent-shaped dimer of three-helix coiled-coils. The N-terminal region of ICA69 is similar to arfaptin.

ARFIP1

• refseq_ARFIP1.F2 refseq_ARFIP1.R2 290 386
• NCBIGene 36.3 27236
• Single exon skipping, size difference: 96
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001025595

• cd Arfaptin 202aa 1e-51 in ref transcript
  • Arfaptin domain; arfaptin is a ubiquitously expressed protein implicated in mediating cross-talk between Rac, a member of the Rho family, and Arf small GTPases; Arfaptin binds to GTP-bound Arf1 and Arf6, but binds Rac.GTP and Rac.GDP with similar affinities. Structures of Arfaptin with Rac bound to either GDP or the slowly hydrolysable analogue GMPPNP show that the switch regions adopt similar conformations in both complexes. Arf1 and Arf6 are thought to bind to the same surface as Rac.
• pfam Arfaptin 196aa 5e-70 in ref transcript
  • Arfaptin-like domain. Arfaptin interacts with ARF1, a small GTPase involved in vesicle budding at the Golgi complex and immature secretory granules. The structure of arfaptin shows that upon binding to a small GTPase, arfaptin forms a an elongated, crescent-shaped dimer of three-helix coiled-coils. The N-terminal region of ICA69 is similar to arfaptin.

ARHGAP17

• refseq_ARHGAP17.F1 refseq_ARHGAP17.R1 162 396
• NCBIGene 36.3 55114
• Single exon skipping, size difference: 234
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001006634

• cd RhoGAP_nadrin 201aa 1e-85 in ref transcript
  • RhoGAP_nadrin: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of Nadrin-like proteins. Nadrin, also named Rich-1, has been shown to be involved in the regulation of Ca2+-dependent exocytosis in neurons and recently has been implicated in tight junction maintenance in mammalian epithelium. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
• pfam BAR 238aa 1e-51 in ref transcript
  • BAR domain. BAR domains are dimerisation, lipid binding and curvature sensing modules found in many different protein families. A BAR domain with an additional N-terminal amphipathic helix (an N-BAR) can drive membrane curvature. These N-BAR domains are found in amphiphysin, endophilin, BRAP and Nadrin. BAR domains are also frequently found alongside domains that determine lipid specificity, like pfam00169 and pfam00787 domains in beta centaurins and sorting nexins respectively.
• smart RhoGAP 176aa 6e-41 in ref transcript
  • GTPase-activator protein for Rho-like GTPases. GTPase activator proteins towards Rho/Rac/Cdc42-like small GTPases. etter domain limits and outliers.

ARHGAP6

• refseq_ARHGAP6.F1 refseq_ARHGAP6.R1 103 199
• NCBIGene 36.3 395
• Single exon skipping, size difference: 96
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_013427

• cd RhoGAP_ARHGAP6 207aa 1e-93 in ref transcript
  • RhoGAP_ARHGAP6: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of ArhGAP6-like proteins. ArhGAP6 shows GAP activity towards RhoA, but not towards Cdc42 and Rac1. ArhGAP6 is often deleted in microphthalmia with linear skin defects syndrome (MLS); MLS is a severe X-linked developmental disorder. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
• pfam RhoGAP 160aa 4e-45 in ref transcript
  • RhoGAP domain. GTPase activator proteins towards Rho/Rac/Cdc42-like small GTPases.

ARHGAP6

• refseq_ARHGAP6.F4 refseq_ARHGAP6.R4 186 276
• NCBIGene 36.3 395
• Single exon skipping, size difference: 90
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_013427

• cd RhoGAP_ARHGAP6 207aa 1e-93 in ref transcript
  • RhoGAP_ARHGAP6: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of ArhGAP6-like proteins. ArhGAP6 shows GAP activity towards RhoA, but not towards Cdc42 and Rac1. ArhGAP6 is often deleted in microphthalmia with linear skin defects syndrome (MLS); MLS is a severe X-linked developmental disorder. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
• pfam RhoGAP 160aa 4e-45 in ref transcript
  • RhoGAP domain. GTPase activator proteins towards Rho/Rac/Cdc42-like small GTPases.

ARHGAP8

• refseq_ARHGAP8.F2 refseq_ARHGAP8.R2 141 234
• NCBIGene 36.3 23779
• Single exon skipping, size difference: 93
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001017526

• cd RhoGAP-p50rhoGAP 191aa 4e-73 in ref transcript
  • RhoGAP-p50rhoGAP: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of p50RhoGAP-like proteins; p50RhoGAP, also known as RhoGAP-1, contains a C-terminal RhoGAP domain and an N-terminal Sec14 domain which binds phosphatidylinositol 3,4,5-trisphosphate (PtdIns(3,4,5)P3). It is ubiquitously expressed and preferentially active on Cdc42. This subgroup also contains closely related ARHGAP8. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
• Changed! cd SEC14 177aa 2e-18 in ref transcript
  • Sec14p-like lipid-binding domain. Found in secretory proteins, such as S. cerevisiae phosphatidylinositol transfer protein (Sec14p), and in lipid regulated proteins such as RhoGAPs, RhoGEFs and neurofibromin (NF1). SEC14 domain of Dbl is known to associate with G protein beta/gamma subunits.
• pfam RhoGAP 149aa 3e-41 in ref transcript
  • RhoGAP domain. GTPase activator proteins towards Rho/Rac/Cdc42-like small GTPases.
• Changed! smart SEC14 181aa 1e-17 in ref transcript
  • Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p). Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) and in RhoGAPs, RhoGEFs and the RasGAP, neurofibromin (NF1). Lipid-binding domain. The SEC14 domain of Dbl is known to associate with G protein beta/gamma subunits.
• Changed! cd SEC14 146aa 3e-22 in modified transcript
• Changed! smart SEC14 150aa 2e-22 in modified transcript

ARHGEF1

• refseq_ARHGEF1.F2 refseq_ARHGEF1.R2 265 364
• NCBIGene 36.3 9138
• Single exon skipping, size difference: 99
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_199002

• cd RhoGEF 187aa 3e-37 in ref transcript
  • Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.
• Changed! pfam RGS-like 191aa 3e-59 in ref transcript
  • Regulator of G protein signalling-like domain. Members of this family adopt a structure consisting of twelve helices that fold into a compact domain that contains the overall structural scaffold observed in other RGS proteins and three additional helical elements that pack closely to it. Helices 1-9 comprise the RGS (pfam00615) fold, in which helices 4-7 form a classic antiparallel bundle adjacent to the other helices. Like other RGS structures, helices 7 and 8 span the length of the folded domain and form essentially one continuous helix with a kink in the middle. Helices 10-12 form an apparently stable C-terminal extension of the structural domain, and although other RGS proteins lack this structure, these elements are intimately associated with the rest of the structural framework by hydrophobic interactions. Members of the family bind to active G-alpha proteins, promoting GTP hydrolysis by the alpha subunit of heterotrimeric G proteins, thereby inactivating the G protein and rapidly switching off G protein-coupled receptor signalling pathways.
• smart RhoGEF 185aa 2e-42 in ref transcript
  • Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases. Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains. Improved coverage.
• COG ROM1 256aa 3e-13 in ref transcript
  • RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms].
• Changed! pfam RGS-like 158aa 1e-32 in modified transcript

ARHGEF10L

• refseq_ARHGEF10L.F1 refseq_ARHGEF10L.R1 192 309
• NCBIGene 36.3 55160
• Single exon skipping, size difference: 117
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_018125

• cd RhoGEF 167aa 4e-31 in ref transcript
  • Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.
• smart RhoGEF 164aa 2e-33 in ref transcript
  • Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases. Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains. Improved coverage.
• COG ROM1 175aa 2e-05 in ref transcript
  • RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms].

ARHGEF11

• refseq_ARHGEF11.F2 refseq_ARHGEF11.R2 316 436
• NCBIGene 36.3 9826
• Single exon skipping, size difference: 120
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_198236

• cd RhoGEF 187aa 3e-39 in ref transcript
  • Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.
• cd PDZ_signaling 75aa 2e-13 in ref transcript
  • PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of PDZ domains an N-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in proteases.
• pfam RGS-like 180aa 3e-69 in ref transcript
  • Regulator of G protein signalling-like domain. Members of this family adopt a structure consisting of twelve helices that fold into a compact domain that contains the overall structural scaffold observed in other RGS proteins and three additional helical elements that pack closely to it. Helices 1-9 comprise the RGS (pfam00615) fold, in which helices 4-7 form a classic antiparallel bundle adjacent to the other helices. Like other RGS structures, helices 7 and 8 span the length of the folded domain and form essentially one continuous helix with a kink in the middle. Helices 10-12 form an apparently stable C-terminal extension of the structural domain, and although other RGS proteins lack this structure, these elements are intimately associated with the rest of the structural framework by hydrophobic interactions. Members of the family bind to active G-alpha proteins, promoting GTP hydrolysis by the alpha subunit of heterotrimeric G proteins, thereby inactivating the G protein and rapidly switching off G protein-coupled receptor signalling pathways.
• smart RhoGEF 185aa 7e-45 in ref transcript
  • Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases. Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains. Improved coverage.
• smart PDZ 77aa 1e-15 in ref transcript
  • Domain present in PSD-95, Dlg, and ZO-1/2. Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities.
• COG ROM1 260aa 5e-15 in ref transcript
  • RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms].
• COG DegQ 79aa 6e-05 in ref transcript
  • Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones].

ARID1B

• refseq_ARID1B.F1 refseq_ARID1B.R1 191 230
• NCBIGene 36.3 57492
• Single exon skipping, size difference: 39
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_017519

• pfam ARID 104aa 1e-30 in ref transcript
  • ARID/BRIGHT DNA binding domain. This domain is know as ARID for AT-Rich Interaction Domain, and also known as the BRIGHT domain.
• pfam PAT1 152aa 2e-05 in ref transcript
  • Topoisomerase II-associated protein PAT1. Members of this family are necessary for accurate chromosome transmission during cell division.

ARID1B

• refseq_ARID1B.F3 refseq_ARID1B.R3 157 316
• NCBIGene 36.3 57492
• Single exon skipping, size difference: 159
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_017519

• pfam ARID 104aa 1e-30 in ref transcript
  • ARID/BRIGHT DNA binding domain. This domain is know as ARID for AT-Rich Interaction Domain, and also known as the BRIGHT domain.
• pfam PAT1 152aa 2e-05 in ref transcript
  • Topoisomerase II-associated protein PAT1. Members of this family are necessary for accurate chromosome transmission during cell division.

ARID5A

• refseq_ARID5A.F1 refseq_ARID5A.R1 107 246
• NCBIGene 36.2 10865
• Single exon skipping, size difference: 139
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_212481

• Changed! smart BRIGHT 88aa 5e-25 in ref transcript
  • BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure.

ARL5A

• refseq_ARL5A.F1 refseq_ARL5A.R1 181 437
• NCBIGene 36.3 26225
• Alternative 5-prime and 3-prime, size difference: 256
• Exclusion of the protein initiation site, Exclusion in the protein causing a frameshift
• Reference transcript: NM_012097

• Changed! cd Arl5_Arl8 173aa 1e-94 in ref transcript
  • Arl5/Arl8 subfamily. Arl5 (Arf-like 5) and Arl8, like Arl4 and Arl7, are localized to the nucleus and nucleolus. Arl5 is developmentally regulated during embryogenesis in mice. Human Arl5 interacts with the heterochromatin protein 1-alpha (HP1alpha), a nonhistone chromosomal protein that is associated with heterochromatin and telomeres, and prevents telomere fusion. Arl5 may also play a role in embryonic nuclear dynamics and/or signaling cascades. Arl8 was identified from a fetal cartilage cDNA library. It is found in brain, heart, lung, cartilage, and kidney. No function has been assigned for Arl8 to date.
• Changed! pfam Arf 158aa 2e-61 in ref transcript
  • ADP-ribosylation factor family. Pfam combines a number of different Prosite families together.
• Changed! PTZ PTZ00133 179aa 5e-55 in ref transcript
  • ADP-ribosylation factor; Provisional.
• Changed! cd Arl5_Arl8 138aa 6e-76 in modified transcript
• Changed! pfam Arf 135aa 3e-50 in modified transcript
• Changed! PTZ PTZ00133 142aa 4e-43 in modified transcript

ARL6

• refseq_ARL6.F2 refseq_ARL6.R2 179 219
• NCBIGene 36.3 84100
• Mutually exclusive exon skipping, size difference: 40
• Inclusion in 5'UTR, Exclusion in 5'UTR
• Reference transcript: NM_177976

• cd Arl6 162aa 1e-88 in ref transcript
  • Arl6 subfamily. Arl6 (Arf-like 6) forms a subfamily of the Arf family of small GTPases. Arl6 expression is limited to the brain and kidney in adult mice, but it is expressed in the neural plate and somites during embryogenesis, suggesting a possible role for Arl6 in early development. Arl6 is also believed to have a role in cilia or flagella function. Several proteins have been identified that bind Arl6, including Arl6 interacting protein (Arl6ip), and SEC61beta, a subunit of the heterotrimeric conducting channel SEC61p. Based on Arl6 binding to these effectors, Arl6 is also proposed to play a role in protein transport, membrane trafficking, or cell signaling during hematopoietic maturation. At least three specific homozygous Arl6 mutations in humans have been found to cause Bardet-Biedl syndrome, a disorder characterized by obesity, retinopathy, polydactyly, renal and cardiac malformations, learning disabilities, and hypogenitalism. Older literature suggests that Arl6 is a part of the Arl4/Arl7 subfamily, but analyses based on more recent sequence data place Arl6 in its own subfamily.
• pfam Arf 167aa 3e-49 in ref transcript
  • ADP-ribosylation factor family. Pfam combines a number of different Prosite families together.
• PTZ PTZ00133 182aa 2e-37 in ref transcript
  • ADP-ribosylation factor; Provisional.

ARMC8

• refseq_ARMC8.F1 refseq_ARMC8.R1 281 335
• NCBIGene 36.3 25852
• Alternative 3-prime, size difference: 54
• Inclusion in 5'UTR
• Reference transcript: NM_015396

• cd ARM 116aa 7e-07 in ref transcript
  • Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model.
• cd ARM 111aa 2e-06 in ref transcript
• cd ARM 112aa 0.007 in ref transcript
• COG COG5369 234aa 1e-18 in ref transcript
  • Uncharacterized conserved protein [Function unknown].
• COG SRP1 185aa 2e-05 in ref transcript
  • Karyopherin (importin) alpha [Intracellular trafficking and secretion].

ARMCX2

• refseq_ARMCX2.F1 refseq_ARMCX2.R1 137 232
• NCBIGene 36.3 9823
• Exon skipping and alternative 3-prime or 5-prime, size difference: 95
• Exclusion in 5'UTR, Exclusion in 5'UTR
• Reference transcript: NM_177949

• cd ARM 118aa 1e-06 in ref transcript
  • Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model.
• pfam DUF634 244aa 1e-107 in ref transcript
  • Protein of unknown function (DUF634). Mammalian protein of unknown function.

ARMCX2

• refseq_ARMCX2.F4 refseq_ARMCX2.R4 158 202
• NCBIGene 36.3 9823
• Alternative 3-prime, size difference: 44
• Inclusion in 5'UTR
• Reference transcript: NM_177949

• cd ARM 118aa 1e-06 in ref transcript
  • Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model.
• pfam DUF634 244aa 1e-107 in ref transcript
  • Protein of unknown function (DUF634). Mammalian protein of unknown function.

ARMCX3

• refseq_ARMCX3.F1 refseq_ARMCX3.R1 102 130
• NCBIGene 36.3 51566
• Alternative 3-prime, size difference: 28
• Inclusion in 5'UTR
• Reference transcript: NM_177947

• cd ARM 86aa 3e-04 in ref transcript
  • Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model.
• pfam DUF634 253aa 1e-106 in ref transcript
  • Protein of unknown function (DUF634). Mammalian protein of unknown function.

ARMCX6

• refseq_ARMCX6.F2 refseq_ARMCX6.R2 291 373
• NCBIGene 36.3 54470
• Single exon skipping, size difference: 82
• Exclusion in 5'UTR
• Reference transcript: NM_019007

• pfam DUF634 191aa 6e-32 in ref transcript
  • Protein of unknown function (DUF634). Mammalian protein of unknown function.

ARNT

• refseq_ARNT.F1 refseq_ARNT.R1 149 194
• NCBIGene 36.3 405
• Single exon skipping, size difference: 45
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001668

• cd PAS 97aa 1e-11 in ref transcript
  • PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.
• Changed! cd HLH 57aa 2e-09 in ref transcript
  • Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins.
• cd PAS 63aa 1e-05 in ref transcript
• pfam PAS_3 89aa 5e-14 in ref transcript
  • PAS fold. The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs. The PAS fold appears in archaea, eubacteria and eukarya.
• Changed! pfam HLH 54aa 3e-11 in ref transcript
  • Helix-loop-helix DNA-binding domain.
• pfam PAS 107aa 4e-08 in ref transcript
  • PAS fold. The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs. The PAS fold appears in archaea, eubacteria and eukarya.
• Changed! cd HLH 53aa 1e-09 in modified transcript
• Changed! pfam HLH 54aa 3e-11 in modified transcript

ARNTL

• refseq_ARNTL.F1 refseq_ARNTL.R1 162 217
• NCBIGene 36.3 406
• Single exon skipping, size difference: 55
• Exclusion in 5'UTR
• Reference transcript: NM_001178

• cd PAS 96aa 9e-12 in ref transcript
  • PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.
• cd HLH 56aa 5e-11 in ref transcript
  • Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins.
• cd PAS 95aa 4e-08 in ref transcript
• pfam HLH 54aa 4e-13 in ref transcript
  • Helix-loop-helix DNA-binding domain.
• smart PAS 60aa 1e-09 in ref transcript
  • PAS domain. PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels ([1]; Ponting & Aravind, in press).
• smart PAS 54aa 1e-07 in ref transcript

ARNTL

• refseq_ARNTL.F4 refseq_ARNTL.R4 254 325
• NCBIGene 36.3 406
• Single exon skipping, size difference: 71
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_001178

• Changed! cd PAS 96aa 9e-12 in ref transcript
  • PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.
• Changed! cd HLH 56aa 5e-11 in ref transcript
  • Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins.
• Changed! cd PAS 95aa 4e-08 in ref transcript
• Changed! pfam HLH 54aa 4e-13 in ref transcript
  • Helix-loop-helix DNA-binding domain.
• Changed! smart PAS 60aa 1e-09 in ref transcript
  • PAS domain. PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels ([1]; Ponting & Aravind, in press).
• Changed! smart PAS 54aa 1e-07 in ref transcript

ARRB1

• refseq_ARRB1.F1 refseq_ARRB1.R1 123 147
• NCBIGene 36.3 408
• Single exon skipping, size difference: 24
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_004041

• pfam Arrestin_N 157aa 5e-30 in ref transcript
  • Arrestin (or S-antigen), N-terminal domain. Ig-like beta-sandwich fold. Scop reports duplication with C-terminal domain.
• Changed! pfam Arrestin_C 160aa 4e-14 in ref transcript
  • Arrestin (or S-antigen), C-terminal domain. Ig-like beta-sandwich fold. Scop reports duplication with N-terminal domain.
• Changed! pfam Arrestin_C 152aa 4e-14 in modified transcript

ARRB2

• refseq_ARRB2.F1 refseq_ARRB2.R1 127 172
• NCBIGene 36.3 409
• Single exon skipping, size difference: 45
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_004313

• Changed! pfam Arrestin_N 157aa 1e-24 in ref transcript
  • Arrestin (or S-antigen), N-terminal domain. Ig-like beta-sandwich fold. Scop reports duplication with C-terminal domain.
• pfam Arrestin_C 156aa 2e-18 in ref transcript
  • Arrestin (or S-antigen), C-terminal domain. Ig-like beta-sandwich fold. Scop reports duplication with N-terminal domain.
• Changed! pfam Arrestin_N 142aa 4e-23 in modified transcript

ARS2

• refseq_ARS2.F1 refseq_ARS2.R1 135 209
• NCBIGene 36.3 51593
• Single exon skipping, size difference: 74
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_015908

• Changed! pfam ARS2 222aa 8e-79 in ref transcript
  • Arsenite-resistance protein 2. Arsenite is a carcinogenic compound which can act as a co-mutagen by inhibiting DNA repair. Arsenite-resistance protein 2 is thought to play a role in arsenite resistance.

ASB3

• refseq_ASB3.F1 refseq_ASB3.R1 167 376
• NCBIGene 36.3 51130
• Single exon skipping, size difference: 209
• Exclusion of the protein initiation site
• Reference transcript: NM_016115

• cd ANK 122aa 3e-22 in ref transcript
  • ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats.
• Changed! cd ANK 130aa 9e-22 in ref transcript
• cd SOCS_ASB3 51aa 6e-20 in ref transcript
  • SOCS (suppressors of cytokine signaling) box of ASB3-like proteins. ASB family members have a C-terminal SOCS box and an N-terminal ankyrin-related sequence. ABS3 has been shown to be negative regulator of TNF-R2-mediated cellular responses to TNF-alpha by direct targeting of tumor necrosis factor receptor II (TNF-R2) for ubiquitination and proteasome-mediated degradation. The general function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions.
• cd ANK 101aa 3e-07 in ref transcript
• pfam SOCS_box 39aa 2e-06 in ref transcript
  • SOCS box. The SOCS box acts as a bridge between specific substrate- binding domains and more generic proteins that comprise a large family of E3 ubiquitin protein ligases.
• pfam Ank 32aa 3e-05 in ref transcript
  • Ankyrin repeat. There's no clear separation between noise and signal on the HMM search Ankyrin repeats generally consist of a beta, alpha, alpha, beta order of secondary structures. The repeats associate to form a higher order structure.
• TIGR trp 154aa 1e-04 in ref transcript
  • after chronic exposure to capsaicin. (McCleskey and Gold, 1999).
• Changed! COG Arp 183aa 4e-12 in ref transcript
  • FOG: Ankyrin repeat [General function prediction only].
• Changed! PTZ PTZ00322 82aa 0.004 in ref transcript
  • 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase; Provisional.
• Changed! cd ANK 122aa 3e-24 in modified transcript
• Changed! COG Arp 124aa 2e-13 in modified transcript
• Changed! COG Arp 153aa 1e-07 in modified transcript

ASB6

• refseq_ASB6.F1 refseq_ASB6.R1 169 278
• NCBIGene 36.3 140459
• Single exon skipping, size difference: 109
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_017873

• Changed! cd SOCS_ASB6 44aa 2e-18 in ref transcript
  • SOCS (suppressors of cytokine signaling) box of ASB6-like proteins. ASB family members have a C-terminal SOCS box and an N-terminal ankyrin-related sequence. ASB6 interacts with the adaptor protein APS and recruits elongin B/C to the insulin receptor signaling complex. The general function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions.
• Changed! cd ANK 127aa 1e-14 in ref transcript
  • ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats.
• Changed! cd ANK 124aa 3e-04 in ref transcript
• Changed! pfam SOCS_box 37aa 8e-06 in ref transcript
  • SOCS box. The SOCS box acts as a bridge between specific substrate- binding domains and more generic proteins that comprise a large family of E3 ubiquitin protein ligases.
• pfam Ank 31aa 2e-05 in ref transcript
  • Ankyrin repeat. There's no clear separation between noise and signal on the HMM search Ankyrin repeats generally consist of a beta, alpha, alpha, beta order of secondary structures. The repeats associate to form a higher order structure.
• Changed! TIGR trp 167aa 2e-04 in ref transcript
  • after chronic exposure to capsaicin. (McCleskey and Gold, 1999).
• Changed! PTZ PTZ00322 83aa 1e-04 in ref transcript
  • 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase; Provisional.
• Changed! PTZ PTZ00322 57aa 0.001 in ref transcript
• Changed! PTZ PTZ00322 131aa 0.002 in ref transcript
• Changed! cd ANK 104aa 4e-10 in modified transcript
• Changed! TIGR trp 119aa 0.004 in modified transcript
• Changed! COG Arp 127aa 0.001 in modified transcript
  • FOG: Ankyrin repeat [General function prediction only].

ASB9

• refseq_ASB9.F1 refseq_ASB9.R1 219 280
• NCBIGene 36.3 140462
• Alternative 5-prime, size difference: 61
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_001031739

• cd ANK 125aa 6e-22 in ref transcript
  • ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats.
• Changed! cd SOCS_ASB_9_11 42aa 9e-15 in ref transcript
  • SOCS (suppressors of cytokine signaling) box of ASB9 and 11 proteins. ASB family members have a C-terminal SOCS box and an N-terminal ankyrin-related sequence. The general function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions.
• Changed! pfam SOCS_box 36aa 2e-06 in ref transcript
  • SOCS box. The SOCS box acts as a bridge between specific substrate- binding domains and more generic proteins that comprise a large family of E3 ubiquitin protein ligases.
• TIGR trp 134aa 2e-05 in ref transcript
  • after chronic exposure to capsaicin. (McCleskey and Gold, 1999).
• pfam Ank 29aa 6e-04 in ref transcript
  • Ankyrin repeat. There's no clear separation between noise and signal on the HMM search Ankyrin repeats generally consist of a beta, alpha, alpha, beta order of secondary structures. The repeats associate to form a higher order structure.
• COG Arp 173aa 2e-12 in ref transcript
  • FOG: Ankyrin repeat [General function prediction only].
• Changed! COG Arp 156aa 1e-05 in ref transcript
• Changed! PTZ PTZ00322 108aa 0.002 in modified transcript
  • 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase; Provisional.

ASGR2

• refseq_ASGR2.F1 refseq_ASGR2.R1 101 189
• NCBIGene 36.3 433
• Alternative 3-prime, size difference: 88
• Inclusion in 5'UTR
• Reference transcript: NM_001181

• cd CLECT_DC-SIGN_like 126aa 1e-40 in ref transcript
  • CLECT_DC-SIGN_like: C-type lectin-like domain (CTLD) of the type found in human dendritic cell (DC)-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN) and the related receptor, DC-SIGN receptor (DC-SIGNR). This group also contains proteins similar to hepatic asialoglycoprotein receptor (ASGP-R) and langerin in human. These proteins are type II membrane proteins with a CTLD ectodomain. CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. DC-SIGN is thought to mediate the initial contact between dendritic cells and resting T cells, and may also mediate the rolling of DCs on epithelium. DC-SIGN and DC-SIGNR bind to oligosaccharides present on human tissues, as well as, on pathogens including parasites, bacteria, and viruses. DC-SIGN and DC-SIGNR bind to HIV enhancing viral infection of T cells. DC-SIGN and DC-SIGNR are homotetrameric, and contain four CTLDs stabilized by a coiled coil of alpha helices. The hepatic ASGP-R is an endocytic recycling receptor which binds and internalizes desialylated glycoproteins having a terminal galactose or N-acetylgalactosamine residues on their N-linked carbohydrate chains, via the clathrin-coated pit mediated endocytic pathway, and delivers them to lysosomes for degradation. It has been proposed that glycoproteins bearing terminal Sia (sialic acid) alpha2, 6GalNAc and Sia alpha2, 6Gal are endogenous ligands for ASGP-R and that ASGP-R participates in regulating the relative concentration of serum glycoproteins bearing alpha 2,6-linked Sia. The human ASGP-R is a hetero-oligomer composed of two subunits, both of which are found within this group. Langerin is expressed in a subset of dendritic leukocytes, the Langerhans cells (LC). Langerin induces the formation of Birbeck Granules (BGs) and associates with these BGs following internalization. Langerin binds, in a calcium-dependent manner, to glyco-conjugates containing mannose and related sugars mediating their uptake and degradation. Langerin molecules oligomerize as trimers with three CTLDs held together by a coiled-coil of alpha helices.
• pfam Lectin_N 143aa 5e-55 in ref transcript
  • Hepatic lectin, N-terminal domain.
• pfam Lectin_C 109aa 4e-32 in ref transcript
  • Lectin C-type domain. This family includes both long and short form C-type.

ASL

• refseq_ASL.F1 refseq_ASL.R1 130 190
• NCBIGene 36.3 435
• Single exon skipping, size difference: 60
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000048

• Changed! cd Argininosuccinate_lyase 430aa 1e-173 in ref transcript
  • Argininosuccinate lyase (argininosuccinase, ASAL). This group contains proteins similar to ASAL, a member of the Lyase class I family. Members of this family for the most part catalyze similar beta-elimination reactions in which a C-N or C-O bond is cleaved with the release of fumarate as one of the products. These proteins are active as tetramers. The four active sites of the homotetrameric enzyme are each formed by residues from three different subunits. ASAL is a cytosolic enzyme which catalyzes the reversible breakdown of argininosuccinate to arginine and fumarate during arginine biosynthesis. In ureotleic species ASAL also catalyzes a reaction involved in the production of urea. Included in this group are the major soluble avian eye lens proteins from duck, delta 1 and delta 2 crystallin. Of these two isoforms only delta 2 has retained ASAL activity. These crystallins may have evolved by, gene recruitment of ASAL followed by gene duplication. In humans, mutations in ASAL result in the autosomal recessive disorder argininosuccinic aciduria.
• Changed! TIGR argH 445aa 1e-163 in ref transcript
  • This model describes argininosuccinate lyase, but may include examples of avian delta crystallins, in which argininosuccinate lyase activity may or may not be present and the biological role is to provide the optically clear cellular protein of the eye lens.
• Changed! PRK PRK00855 452aa 0.0 in ref transcript
  • argininosuccinate lyase; Provisional.
• Changed! cd Argininosuccinate_lyase 410aa 1e-159 in modified transcript
• Changed! TIGR argH 425aa 1e-149 in modified transcript
• Changed! PRK PRK00855 432aa 1e-167 in modified transcript

ASL

• refseq_ASL.F3 refseq_ASL.R3 119 197
• NCBIGene 36.3 435
• Single exon skipping, size difference: 78
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000048

• Changed! cd Argininosuccinate_lyase 430aa 1e-173 in ref transcript
  • Argininosuccinate lyase (argininosuccinase, ASAL). This group contains proteins similar to ASAL, a member of the Lyase class I family. Members of this family for the most part catalyze similar beta-elimination reactions in which a C-N or C-O bond is cleaved with the release of fumarate as one of the products. These proteins are active as tetramers. The four active sites of the homotetrameric enzyme are each formed by residues from three different subunits. ASAL is a cytosolic enzyme which catalyzes the reversible breakdown of argininosuccinate to arginine and fumarate during arginine biosynthesis. In ureotleic species ASAL also catalyzes a reaction involved in the production of urea. Included in this group are the major soluble avian eye lens proteins from duck, delta 1 and delta 2 crystallin. Of these two isoforms only delta 2 has retained ASAL activity. These crystallins may have evolved by, gene recruitment of ASAL followed by gene duplication. In humans, mutations in ASAL result in the autosomal recessive disorder argininosuccinic aciduria.
• Changed! TIGR argH 445aa 1e-163 in ref transcript
  • This model describes argininosuccinate lyase, but may include examples of avian delta crystallins, in which argininosuccinate lyase activity may or may not be present and the biological role is to provide the optically clear cellular protein of the eye lens.
• Changed! PRK PRK00855 452aa 0.0 in ref transcript
  • argininosuccinate lyase; Provisional.
• Changed! cd Argininosuccinate_lyase 404aa 1e-159 in modified transcript
• Changed! TIGR argH 419aa 1e-149 in modified transcript
• Changed! PRK PRK00855 426aa 1e-167 in modified transcript

ASNS

• refseq_ASNS.F2 refseq_ASNS.R2 115 393
• NCBIGene 36.3 440
• Single exon skipping, size difference: 278
• Exclusion in 5'UTR
• Reference transcript: NM_183356

• cd AsnB 190aa 2e-43 in ref transcript
  • Glutamine amidotransferases class-II (GATase) asparagine synthase_B type. Asparagine synthetase B catalyses the ATP-dependent conversion of aspartate to asparagine. This enzyme is a homodimer, with each monomer composed of a glutaminase domain and a synthetase domain. The N-terminal glutaminase domain hydrolyzes glutamine to glutamic acid and ammonia.
• cd Asn_Synthase_B_C 238aa 2e-34 in ref transcript
  • The C-terminal domain of Asparagine Synthase B. This domain is always found associated n-terminal amidotransferase domain. Family members that contain this domain catalyse the conversion of aspartate to asparagine. Asparagine synthetase B catalyzes the assembly of asparagine from aspartate, Mg(2+)ATP, and glutamine. The three-dimensional architecture of the N-terminal domain of asparagine synthetase B is similar to that observed for glutamine phosphoribosylpyrophosphate amidotransferase while the molecular motif of the C-domain is reminiscent to that observed for GMP synthetase.
• TIGR asn_synth_AEB 467aa 1e-134 in ref transcript
  • This model describes the glutamine-hydrolysing asparagine synthase. A poorly conserved C-terminal extension was removed from the model. Bacterial members of the family tend to have a long, poorly conserved insert lacking from archaeal and eukaryotic sequences. Multiple isozymes have been demonstrated, such as in Bacillus subtilis. Long-branch members of the phylogenetic tree (which typically were also second or third candidate members from their genomes) were removed from the seed alignment and score below trusted cutoff.
• TIGR eps_aminotran_1 141aa 1e-12 in ref transcript
  • The predicted protein-sorting transpeptidase that we call exosortase (see TIGR02602) has distinct subclasses that associated with different types of exopolysaccharide production loci. This model represents a distinct clade among a set of amidotransferases largely annotated (not necessarily accurately) as glutatime-hydrolyzing asparagine synthases. Members of this clade are essentially restricted to the characteristic exopolysaccharide (EPS) regions that contain the exosortase 1 genome (xrtA), in genomes that also have numbers of PEP-CTERM domain (TIGR02595) proteins.
• PRK asnB 555aa 1e-136 in ref transcript
  • asparagine synthetase B; Provisional.

ASPH

• refseq_ASPH.F1 refseq_ASPH.R1 178 223
• NCBIGene 36.3 444
• Single exon skipping, size difference: 45
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_020164

• Changed! pfam Asp-B-Hydro_N 71aa 1e-15 in ref transcript
  • Aspartyl beta-hydroxylase N-terminal region. This family includes the N-terminal regions of the junctin, junctate and aspartyl beta-hydroxylase proteins. Junctate is an integral ER/SR membrane calcium binding protein, which comes from an alternatively spliced form of the same gene that generates aspartyl beta-hydroxylase and junctin. Aspartyl beta-hydroxylase catalyses the post-translational hydroxylation of aspartic acid or asparagine residues contained within epidermal growth factor (EGF) domains of proteins.
• pfam Asp-B-Hydro_N 77aa 1e-10 in ref transcript
• Changed! pfam Asp-B-Hydro_N 56aa 2e-18 in modified transcript

ASTN2

• refseq_ASTN2.F1 refseq_ASTN2.R1 217 370
• NCBIGene 36.3 23245
• Single exon skipping, size difference: 153
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_198187

• smart MACPF 184aa 1e-36 in ref transcript
  • membrane-attack complex / perforin.

ATF3

• refseq_ATF3.F2 refseq_ATF3.R2 208 359
• NCBIGene 36.2 467
• Exon skipping and alternative 3-prime or 5-prime, size difference: 151
• Inclusion in the protein causing a new stop codon, Exclusion in the protein causing a frameshift
• Reference transcript: NM_001030287

• Changed! smart BRLZ 45aa 7e-05 in ref transcript
  • basic region leucin zipper.

ATG16L1

• refseq_ATG16L1.F1 refseq_ATG16L1.R1 254 311
• NCBIGene 36.3 55054
• Single exon skipping, size difference: 57
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_030803

• cd WD40 291aa 4e-48 in ref transcript
  • WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.
• pfam ATG16 195aa 2e-56 in ref transcript
  • Autophagy protein 16 (ATG16). Autophagy is a ubiquitous intracellular degradation system for eukaryotic cells. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. ATG16 (also known as Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate in the yeast autophagy pathway.
• smart WD40 36aa 7e-06 in ref transcript
  • WD40 repeats. Note that these repeats are permuted with respect to the structural repeats (blades) of the beta propeller domain.
• smart WD40 38aa 1e-05 in ref transcript
• TIGR propeller_TolB 52aa 2e-05 in ref transcript
  • The Tol-PAL system is required for bacterial outer membrane integrity. E. coli TolB is involved in the tonB-independent uptake of group A colicins (colicins A, E1, E2, E3 and K), and is necessary for the colicins to reach their respective targets after initial binding to the bacteria. It is also involved in uptake of filamentous DNA. Study of its structure suggest that the TolB protein might be involved in the recycling of peptidoglycan or in its covalent linking with lipoproteins. The Tol-Pal system is also implicated in pathogenesis of E. coli, Haemophilus ducreyi, Salmonella enterica and Vibrio cholerae, but the mechanism(s) is unclear.
• pfam SGL 128aa 0.009 in ref transcript
  • SMP-30/Gluconolaconase/LRE-like region. This family describes a region that is found in proteins expressed by a variety of eukaryotic and prokaryotic species. These proteins include various enzymes, such as senescence marker protein 30 (SMP-30), gluconolactonase and luciferin-regenerating enzyme (LRE). SMP-30 is known to hydrolyse diisopropyl phosphorofluoridate in the liver, and has been noted as having sequence similarity, in the region described in this family, with PON1 and LRE.
• COG COG2319 260aa 6e-25 in ref transcript
  • FOG: WD40 repeat [General function prediction only].
• Changed! COG Smc 153aa 4e-06 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].
• Changed! COG Smc 145aa 5e-06 in modified transcript

ATG4A

• refseq_ATG4A.F1 refseq_ATG4A.R1 184 370
• NCBIGene 36.3 115201
• Exon skipping and alternative 3-prime or 5-prime, size difference: 186
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_052936

• Changed! pfam Peptidase_C54 300aa 1e-123 in ref transcript
  • Peptidase family C54.
• Changed! pfam Peptidase_C54 238aa 7e-93 in modified transcript

ATG4C

• refseq_ATG4C.F1 refseq_ATG4C.R1 143 191
• NCBIGene 36.3 84938
• Alternative 5-prime, size difference: 48
• Exclusion in 5'UTR
• Reference transcript: NM_032852

• pfam Peptidase_C54 330aa 1e-108 in ref transcript
  • Peptidase family C54.

ATP11C

• refseq_ATP11C.F2 refseq_ATP11C.R2 127 232
• NCBIGene 36.3 286410
• Single exon skipping, size difference: 105
• Exclusion of the stop codon
• Reference transcript: NM_173694

• TIGR ATPase-Plipid 1028aa 0.0 in ref transcript
  • This model describes the P-type ATPase responsible for transporting phospholipids from one leaflet of bilayer membranes to the other. These ATPases are found only in eukaryotes.
• COG MgtA 659aa 5e-70 in ref transcript
  • Cation transport ATPase [Inorganic ion transport and metabolism].
• COG MgtA 205aa 8e-24 in ref transcript

ATP2A1

• refseq_ATP2A1.F1 refseq_ATP2A1.R1 103 145
• NCBIGene 36.3 487
• Single exon skipping, size difference: 42
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_173201

• TIGR ATPase-IIA1_Ca 937aa 0.0 in ref transcript
  • The calcium P-type ATPases have been characterized as Type IIA based on a phylogenetic analysis which distinguishes this group from the Type IIB PMCA calcium pump modelled by TIGR01517. A separate analysis divides Type IIA into sub-types, SERCA and PMR1 the latter of which is modelled by TIGR01522.
• pfam Cation_ATPase_N 75aa 1e-23 in ref transcript
  • Cation transporter/ATPase, N-terminus. Members of this families are involved in Na+/K+, H+/K+, Ca++ and Mg++ transport.
• COG MgtA 991aa 0.0 in ref transcript
  • Cation transport ATPase [Inorganic ion transport and metabolism].

ATP2B3

• refseq_ATP2B3.F1 refseq_ATP2B3.R1 218 372
• NCBIGene 36.3 492
• Single exon skipping, size difference: 154
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_001001344

• TIGR ATPase-IIB_Ca 704aa 0.0 in ref transcript
  • The calcium P-type ATPases have been characterized as Type IIB based on a phylogenetic analysis which distinguishes this group from the Type IIA SERCA calcium pump. A separate analysis divides Type IIA into sub-types (SERCA and PMR1) which are modelled by two corresponding HMMs (TIGR01116 and TIGR01522). This model is well separated from those.
• TIGR ATPase-IIB_Ca 266aa 2e-80 in ref transcript
• TIGR ATPase-IB_hvy 313aa 2e-13 in ref transcript
  • This model encompasses two equivalog models for the copper and cadmium-type heavy metal transporting P-type ATPases (TIGR01511 and TIGR01512) as well as those species which score ambiguously between both models. For more comments and references, see the files on TIGR01511 and 01512.
• COG MgtA 993aa 1e-154 in ref transcript
  • Cation transport ATPase [Inorganic ion transport and metabolism].

ATP2B4

• refseq_ATP2B4.F1 refseq_ATP2B4.R1 198 376
• NCBIGene 36.3 493
• Single exon skipping, size difference: 178
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_001684

• cd HAD_like 159aa 0.007 in ref transcript
  • Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others, all of which use a nucleophilic aspartate in their phosphoryl transfer reaction. All members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. Members of this superfamily are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases.
• TIGR ATPase-IIB_Ca 1037aa 0.0 in ref transcript
  • The calcium P-type ATPases have been characterized as Type IIB based on a phylogenetic analysis which distinguishes this group from the Type IIA SERCA calcium pump. A separate analysis divides Type IIA into sub-types (SERCA and PMR1) which are modelled by two corresponding HMMs (TIGR01116 and TIGR01522). This model is well separated from those.
• COG MgtA 681aa 1e-132 in ref transcript
  • Cation transport ATPase [Inorganic ion transport and metabolism].
• COG MgtA 236aa 3e-28 in ref transcript

ATP5C1

• refseq_ATP5C1.F1 refseq_ATP5C1.R1 132 169
• NCBIGene 36.3 509
• Single exon skipping, size difference: 37
• Exclusion of the stop codon
• Reference transcript: NM_001001973

• TIGR ATPsyn_F1gamma 272aa 6e-95 in ref transcript
  • This model describes the ATP synthase gamma subunit in bacteria and its equivalents in organelles, namely, mitochondria and chloroplast. F1/F0-ATP synthase is a multisubunit, membrane associated enzyme found in bacteria and organelles of higher eukaryotes, namely, mitochondria and chloroplast. This enzyme is principally involed in the synthesis of ATP from ADP and inorganic phosphate by coupling the energy derived from the proton electrochemical gradient across the biological membrane. A brief description of this multisubunit enzyme complex: F1 and F0 represent two major clusters of subunits. The gamma subunit is the part of F1 cluster. Surrounding the gamma subunit in a cylinder-like structure are three alpha and three subunits in an alternating fashion. This is the central catalytic unit whose different conformations permit the binding of ADP and inorganic phosphate and release of ATP.
• PRK PRK05621 273aa 7e-66 in ref transcript
  • F0F1 ATP synthase subunit gamma; Validated.

ATP5G1

• refseq_ATP5G1.F1 refseq_ATP5G1.R1 115 185
• NCBIGene 36.3 516
• Alternative 5-prime, size difference: 70
• Exclusion in 5'UTR
• Reference transcript: NM_005175

• pfam ATP-synt_C 46aa 1e-10 in ref transcript
  • ATP synthase subunit C.
• PRK PRK07558 46aa 7e-09 in ref transcript
  • F0F1 ATP synthase subunit C; Validated.

ATP5G2

• refseq_ATP5G2.F1 refseq_ATP5G2.R1 213 336
• NCBIGene 36.3 517
• Alternative 5-prime, size difference: 123
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_005176

• pfam ATP-synt_C 46aa 3e-11 in ref transcript
  • ATP synthase subunit C.
• PRK PRK07558 46aa 3e-09 in ref transcript
  • F0F1 ATP synthase subunit C; Validated.

ATP5H

• refseq_ATP5H.F1 refseq_ATP5H.R1 104 176
• NCBIGene 36.3 10476
• Single exon skipping, size difference: 72
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_006356

• Changed! pfam Mt_ATP-synt_D 160aa 1e-60 in ref transcript
  • ATP synthase D chain, mitochondrial (ATP5H). This family consists of several ATP synthase D chain, mitochondrial (ATP5H) proteins. Subunit d has no extensive hydrophobic sequences, and is not apparently related to any subunit described in the simpler ATP synthases in bacteria and chloroplasts.
• Changed! pfam Mt_ATP-synt_D 136aa 5e-47 in modified transcript

ATP5J

• refseq_ATP5J.F2 refseq_ATP5J.R2 251 301
• NCBIGene 36.3 522
• Alternative 5-prime, size difference: 50
• Exclusion of the protein initiation site
• Reference transcript: NM_001003701

• pfam ATP-synt_F6 92aa 6e-33 in ref transcript
  • Mitochondrial ATP synthase coupling factor 6. Coupling factor 6 (F6) is a component of mitochondrial ATP synthase which is required for the interactions of the catalytic and proton-translocating segments.

ATP5J2

• refseq_ATP5J2.F2 refseq_ATP5J2.R2 100 118
• NCBIGene 36.3 9551
• Alternative 5-prime, size difference: 18
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_004889

• pfam WRW 76aa 3e-10 in ref transcript
  • Mitochondrial F1F0-ATP synthase, subunit f. This is a family of small proteins of approximately 110 amino acids, which are highly conserved from nematodes to humans. Some members of the family have been annotated in Swiss-Prot as being the f subunit of mitochondrial F1F0-ATP synthase but this could not be confirmed. The sequence has a well-conserved WRW motif. The exact function of the protein is not known.

ATP5J2

• refseq_ATP5J2.F3 refseq_ATP5J2.R3 266 383
• NCBIGene 36.3 9551
• Single exon skipping, size difference: 117
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_004889

• Changed! pfam WRW 76aa 3e-10 in ref transcript
  • Mitochondrial F1F0-ATP synthase, subunit f. This is a family of small proteins of approximately 110 amino acids, which are highly conserved from nematodes to humans. Some members of the family have been annotated in Swiss-Prot as being the f subunit of mitochondrial F1F0-ATP synthase but this could not be confirmed. The sequence has a well-conserved WRW motif. The exact function of the protein is not known.
• Changed! pfam WRW 37aa 0.001 in modified transcript

ATP5S

• refseq_ATP5S.F1 refseq_ATP5S.R1 179 351
• NCBIGene 36.3 27109
• Single exon skipping, size difference: 172
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_001003803

ATP6V0A4

• refseq_ATP6V0A4.F1 refseq_ATP6V0A4.R1 292 395
• NCBIGene 36.3 50617
• Single exon skipping, size difference: 103
• Exclusion in 5'UTR
• Reference transcript: NM_020632

• pfam V_ATPase_I 806aa 0.0 in ref transcript
  • V-type ATPase 116kDa subunit family. This family consists of the 116kDa V-type ATPase (vacuolar (H+)-ATPases) subunits, as well as V-type ATP synthase subunit i. The V-type ATPases family are proton pumps that acidify intracellular compartments in eukaryotic cells for example yeast central vacuoles, clathrin-coated and synaptic vesicles. They have important roles in membrane trafficking processes. The 116kDa subunit (subunit a) in the V-type ATPase is part of the V0 functional domain responsible for proton transport. The a subunit is a transmembrane glycoprotein with multiple putative transmembrane helices it has a hydrophilic amino terminal and a hydrophobic carboxy terminal. It has roles in proton transport and assembly of the V-type ATPase complex. This subunit is encoded by two homologous gene in yeast VPH1 and STV1.
• COG NtpI 595aa 5e-45 in ref transcript
  • Archaeal/vacuolar-type H+-ATPase subunit I [Energy production and conversion].
• COG NtpI 115aa 5e-22 in ref transcript

ATP6V0B

• refseq_ATP6V0B.F2 refseq_ATP6V0B.R2 164 213
• NCBIGene 36.3 533
• Single exon skipping, size difference: 49
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_004047

• Changed! TIGR V_ATP_synt_C 108aa 7e-06 in ref transcript
  • The principal role V-ATPases are the acidification of intracellular compartments of eukaryotic cells.
• Changed! pfam ATP-synt_C 62aa 0.002 in ref transcript
  • ATP synthase subunit C.
• Changed! COG AtpE 64aa 4e-04 in ref transcript
  • F0F1-type ATP synthase, subunit c/Archaeal/vacuolar-type H+-ATPase, subunit K [Energy production and conversion].

ATP6V1E1

• refseq_ATP6V1E1.F1 refseq_ATP6V1E1.R1 149 215
• NCBIGene 36.3 529
• Single exon skipping, size difference: 66
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001696

• Changed! pfam vATP-synt_E 199aa 4e-33 in ref transcript
  • ATP synthase (E/31 kDa) subunit. This family includes the vacuolar ATP synthase E subunit, as well as the archaebacterial ATP synthase E subunit.
• COG NtpE 146aa 4e-05 in ref transcript
  • Archaeal/vacuolar-type H+-ATPase subunit E [Energy production and conversion].
• Changed! pfam vATP-synt_E 188aa 5e-34 in modified transcript

ATP6V1E1

• refseq_ATP6V1E1.F3 refseq_ATP6V1E1.R3 246 336
• NCBIGene 36.3 529
• Single exon skipping, size difference: 90
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001696

• Changed! pfam vATP-synt_E 199aa 4e-33 in ref transcript
  • ATP synthase (E/31 kDa) subunit. This family includes the vacuolar ATP synthase E subunit, as well as the archaebacterial ATP synthase E subunit.
• Changed! COG NtpE 146aa 4e-05 in ref transcript
  • Archaeal/vacuolar-type H+-ATPase subunit E [Energy production and conversion].
• Changed! pfam vATP-synt_E 169aa 2e-28 in modified transcript
• Changed! COG NtpE 116aa 7e-05 in modified transcript

ATP6V1G2

• refseq_ATP6V1G2.F2 refseq_ATP6V1G2.R2 122 276
• NCBIGene 36.3 534
• Alternative 5-prime, size difference: 154
• Exclusion of the protein initiation site
• Reference transcript: NM_130463

• Changed! pfam V-ATPase_G 105aa 1e-13 in ref transcript
  • Vacuolar (H+)-ATPase G subunit. This family represents the eukaryotic vacuolar (H+)-ATPase (V-ATPase) G subunit. V-ATPases generate an acidic environment in several intracellular compartments. Correspondingly, they are found as membrane-attached proteins in several organelles. They are also found in the plasma membranes of some specialised cells. V-ATPases consist of peripheral (V1) and membrane integral (V0) heteromultimeric complexes. The G subunit is part of the V1 subunit, but is also thought to be strongly attached to the V0 complex. It may be involved in the coupling of ATP degradation to H+ translocation.
• Changed! pfam V-ATPase_G 66aa 3e-11 in modified transcript

ATP6V1G3

• refseq_ATP6V1G3.F1 refseq_ATP6V1G3.R1 119 165
• NCBIGene 36.3 127124
• Single exon skipping, size difference: 46
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_133262

• Changed! pfam V-ATPase_G 105aa 3e-18 in ref transcript
  • Vacuolar (H+)-ATPase G subunit. This family represents the eukaryotic vacuolar (H+)-ATPase (V-ATPase) G subunit. V-ATPases generate an acidic environment in several intracellular compartments. Correspondingly, they are found as membrane-attached proteins in several organelles. They are also found in the plasma membranes of some specialised cells. V-ATPases consist of peripheral (V1) and membrane integral (V0) heteromultimeric complexes. The G subunit is part of the V1 subunit, but is also thought to be strongly attached to the V0 complex. It may be involved in the coupling of ATP degradation to H+ translocation.
• Changed! pfam V-ATPase_G 25aa 2e-04 in modified transcript

ATP6V1H

• refseq_ATP6V1H.F2 refseq_ATP6V1H.R2 181 235
• NCBIGene 36.3 51606
• Single exon skipping, size difference: 54
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_015941

• Changed! cd VATPase_H 449aa 1e-176 in ref transcript
  • VATPase_H, regulatory vacuolar ATP synthase subunit H (Vma13p); activation component of the peripheral V1 complex of V-ATPase, a heteromultimeric enzyme which uses ATP to actively transport protons into organelles and extracellular compartments. The topology is that of a superhelical spiral, in part the geometry is similar to superhelices composed of armadillo repeat motifs, as found in importins for example.
• Changed! pfam V-ATPase_H 415aa 1e-178 in ref transcript
  • V-ATPase subunit H.
• COG VMA13 261aa 6e-49 in ref transcript
  • Vacuolar H+-ATPase V1 sector, subunit H [Energy production and conversion].
• Changed! cd VATPase_H 431aa 1e-177 in modified transcript
• Changed! pfam V-ATPase_H 397aa 1e-178 in modified transcript

ATP7B

• refseq_ATP7B.F1 refseq_ATP7B.R1 164 299
• NCBIGene 36.3 540
• Single exon skipping, size difference: 135
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000053

• cd HMA 63aa 1e-14 in ref transcript
  • Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain contains two cysteine residues that are important in binding and transfer of metal ions, such as copper, cadmium, cobalt and zinc. In the case of copper, stoichiometry of binding is one Cu+ ion per binding domain. Repeats of the HMA domain in copper chaperone has been associated with Menkes/Wilson disease due to binding of multiple copper ions.
• cd HMA 64aa 1e-12 in ref transcript
• cd HMA 63aa 5e-12 in ref transcript
• cd HMA 59aa 8e-12 in ref transcript
• cd HMA 64aa 1e-11 in ref transcript
• cd HMA 64aa 2e-11 in ref transcript
• cd HAD_like 106aa 0.009 in ref transcript
  • Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others, all of which use a nucleophilic aspartate in their phosphoryl transfer reaction. All members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. Members of this superfamily are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases.
• Changed! TIGR ATPase-IB1_Cu 646aa 0.0 in ref transcript
  • A member from Halobacterium is annotated as "molybdenum-binding protein" although no evidence can be found for this classification.
• pfam HMA 64aa 2e-15 in ref transcript
  • Heavy-metal-associated domain.
• pfam HMA 65aa 5e-14 in ref transcript
• pfam HMA 64aa 9e-14 in ref transcript
• pfam HMA 65aa 3e-13 in ref transcript
• pfam HMA 59aa 6e-13 in ref transcript
• pfam HMA 64aa 7e-13 in ref transcript
• Changed! COG ZntA 791aa 0.0 in ref transcript
  • Cation transport ATPase [Inorganic ion transport and metabolism].
• PRK copA 199aa 3e-09 in ref transcript
  • copper exporting ATPase; Provisional.
• COG CopZ 65aa 1e-08 in ref transcript
  • Copper chaperone [Inorganic ion transport and metabolism].
• PRK copA 172aa 2e-07 in ref transcript
• PRK copA 145aa 9e-07 in ref transcript
• PRK copA 170aa 6e-06 in ref transcript
• Changed! TIGR ATPase-IB1_Cu 601aa 0.0 in modified transcript
• Changed! COG ZntA 746aa 0.0 in modified transcript

ATRX

• refseq_ATRX.F1 refseq_ATRX.R1 112 235
• NCBIGene 36.2 546
• Single exon skipping, size difference: 123
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_000489

• Changed! cd HELICc 147aa 4e-16 in ref transcript
  • Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process.
• Changed! cd DEXDc 163aa 4e-11 in ref transcript
  • DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
• Changed! pfam SNF2_N 317aa 9e-84 in ref transcript
  • SNF2 family N-terminal domain. This domain is found in proteins involved in a variety of processes including transcription regulation (e.g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as well as a variety of other proteins with little functional information (e.g., lodestar, ETL1).
• Changed! pfam Helicase_C 77aa 4e-16 in ref transcript
  • Helicase conserved C-terminal domain. The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.
• Changed! COG HepA 321aa 1e-27 in ref transcript
  • Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair].
• Changed! COG HepA 194aa 6e-22 in ref transcript

ATXN3

• refseq_ATXN3.F1 refseq_ATXN3.R1 240 326
• NCBIGene 36.2 4287
• Single exon skipping, size difference: 86
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_004993

• Changed! pfam Josephin 161aa 2e-69 in ref transcript
  • Josephin.
• Changed! pfam Josephin 71aa 2e-25 in modified transcript

AURKA

• refseq_AURKA.F2 refseq_AURKA.R2 133 341
• NCBIGene 36.3 6790
• Multiple exon skipping, size difference: 208
• Exclusion in 5'UTR, Exclusion in 5'UTR
• Reference transcript: NM_198433

• cd S_TKc 252aa 1e-80 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• smart S_TKc 240aa 2e-80 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• PTZ PTZ00263 244aa 4e-53 in ref transcript
  • protein kinase A catalytic subunit; Provisional.

AURKA

• refseq_AURKA.F3 refseq_AURKA.R3 97 111
• NCBIGene 36.3 6790
• Alternative 5-prime, size difference: 14
• Exclusion in 5'UTR
• Reference transcript: NM_198434

• cd S_TKc 252aa 1e-80 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• smart S_TKc 240aa 2e-80 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• PTZ PTZ00263 244aa 4e-53 in ref transcript
  • protein kinase A catalytic subunit; Provisional.

AURKC

• refseq_AURKC.F1 refseq_AURKC.R1 208 400
• NCBIGene 36.3 6795
• Alternative 5-prime, size difference: 192
• Exclusion of the protein initiation site
• Reference transcript: NM_001015878

• cd S_TKc 252aa 7e-75 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• smart S_TKc 240aa 9e-75 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• PTZ PTZ00263 262aa 2e-50 in ref transcript
  • protein kinase A catalytic subunit; Provisional.

AXL

• refseq_AXL.F1 refseq_AXL.R1 129 156
• NCBIGene 36.3 558
• Single exon skipping, size difference: 27
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_021913

• cd PTKc_Axl 272aa 1e-167 in ref transcript
  • Catalytic Domain of the Protein Tyrosine Kinase, Axl. Protein Tyrosine Kinase (PTK) family; Axl; catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Axl is a member of the Axl subfamily, which is composed of receptor tyr kinases (RTKs) containing an extracellular ligand-binding region with two immunoglobulin-like domains followed by two fibronectin type III repeats, a transmembrane segment, and an intracellular catalytic domain. Binding to their ligands, Gas6 and protein S, leads to receptor dimerization, autophosphorylation, activation, and intracellular signaling. Axl is widely expressed in a variety of organs and cells including epithelial, mesenchymal, hematopoietic, as well as non-transformed cells. Axl signaling is important in many cellular functions such as survival, anti-apoptosis, proliferation, migration, and adhesion. Axl was originally isolated from patients with chronic myelogenous leukemia and a chronic myeloproliferative disorder. Axl is overexpressed in many human cancers including colon, squamous cell, thyroid, breast, and lung carcinomas.
• cd FN3 104aa 2e-06 in ref transcript
  • Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.
• cd IG 77aa 2e-05 in ref transcript
  • Immunoglobulin domain family; members are components of immunoglobulins, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• cd IGcam 84aa 0.006 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• cd FN3 88aa 0.009 in ref transcript
• smart TyrKc 266aa 1e-105 in ref transcript
  • Tyrosine kinase, catalytic domain. Phosphotransferases. Tyrosine-specific kinase subfamily.
• pfam fn3 85aa 2e-06 in ref transcript
  • Fibronectin type III domain.
• smart IG_like 83aa 2e-05 in ref transcript
  • Immunoglobulin like. IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
• pfam fn3 97aa 1e-04 in ref transcript
• pfam I-set 85aa 0.008 in ref transcript
  • Immunoglobulin I-set domain.
• COG SPS1 280aa 7e-23 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].

AZI1

• refseq_AZI1.F2 refseq_AZI1.R2 278 386
• NCBIGene 36.3 22994
• Single exon skipping, size difference: 108
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_014984

• TIGR SMC_prok_B 223aa 5e-09 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• COG Smc 243aa 5e-08 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].

AZIN1

• refseq_AZIN1.F2 refseq_AZIN1.R2 136 282
• NCBIGene 36.3 51582
• Single exon skipping, size difference: 146
• Exclusion in 5'UTR
• Reference transcript: NM_015878

• pfam Orn_Arg_deC_N 236aa 3e-62 in ref transcript
  • Pyridoxal-dependent decarboxylase, pyridoxal binding domain. These pyridoxal-dependent decarboxylases acting on ornithine, lysine, arginine and related substrates This domain has a TIM barrel fold.
• pfam Orn_DAP_Arg_deC 125aa 2e-25 in ref transcript
  • Pyridoxal-dependent decarboxylase, C-terminal sheet domain. These pyridoxal-dependent decarboxylases act on ornithine, lysine, arginine and related substrates.
• COG LysA 367aa 2e-51 in ref transcript
  • Diaminopimelate decarboxylase [Amino acid transport and metabolism].

B3GALNT1

• refseq_B3GALNT1.F1 refseq_B3GALNT1.R1 247 340
• NCBIGene 36.3 8706
• Single exon skipping, size difference: 93
• Exclusion in 5'UTR
• Reference transcript: NM_001038628

• pfam Galactosyl_T 194aa 4e-55 in ref transcript
  • Galactosyltransferase. This family includes the galactosyltransferases UDP-galactose:2-acetamido-2-deoxy-D-glucose3beta- galactosyltrans ferase and UDP-Gal:beta-GlcNAc beta 1,3-galactosyltranferase. Specific galactosyltransferases transfer galactose to GlcNAc terminal chains in the synthesis of the lacto-series oligosaccharides types 1 and 2.

B3GALNT1

• refseq_B3GALNT1.F3 refseq_B3GALNT1.R3 217 336
• NCBIGene 36.3 8706
• Single exon skipping, size difference: 119
• Exclusion in 5'UTR
• Reference transcript: NM_001038628

• pfam Galactosyl_T 194aa 4e-55 in ref transcript
  • Galactosyltransferase. This family includes the galactosyltransferases UDP-galactose:2-acetamido-2-deoxy-D-glucose3beta- galactosyltrans ferase and UDP-Gal:beta-GlcNAc beta 1,3-galactosyltranferase. Specific galactosyltransferases transfer galactose to GlcNAc terminal chains in the synthesis of the lacto-series oligosaccharides types 1 and 2.

B3GALNT1

• refseq_B3GALNT1.F5 refseq_B3GALNT1.R5 100 211
• NCBIGene 36.3 8706
• Single exon skipping, size difference: 111
• Exclusion in 5'UTR
• Reference transcript: NM_001038628

• pfam Galactosyl_T 194aa 4e-55 in ref transcript
  • Galactosyltransferase. This family includes the galactosyltransferases UDP-galactose:2-acetamido-2-deoxy-D-glucose3beta- galactosyltrans ferase and UDP-Gal:beta-GlcNAc beta 1,3-galactosyltranferase. Specific galactosyltransferases transfer galactose to GlcNAc terminal chains in the synthesis of the lacto-series oligosaccharides types 1 and 2.

B3GALT5

• refseq_B3GALT5.F2 refseq_B3GALT5.R2 274 383
• NCBIGene 36.3 10317
• Single exon skipping, size difference: 109
• Exclusion in 5'UTR
• Reference transcript: NM_033171

• pfam Galactosyl_T 191aa 3e-44 in ref transcript
  • Galactosyltransferase. This family includes the galactosyltransferases UDP-galactose:2-acetamido-2-deoxy-D-glucose3beta- galactosyltrans ferase and UDP-Gal:beta-GlcNAc beta 1,3-galactosyltranferase. Specific galactosyltransferases transfer galactose to GlcNAc terminal chains in the synthesis of the lacto-series oligosaccharides types 1 and 2.

B4GALT4

• refseq_B4GALT4.F1 refseq_B4GALT4.R1 228 311
• NCBIGene 36.3 8702
• Single exon skipping, size difference: 83
• Exclusion in 5'UTR
• Reference transcript: NM_212543

• cd b4GalT 218aa 1e-102 in ref transcript
  • Beta-4-Galactosyltransferase is involved in the formation of the poly-N-acetyllactosamine core structures present in glycoproteins and glycosphingolipids. Beta-4-Galactosyltransferase transfers galactose from uridine diphosphogalactose to the terminal beta-N-acetylglucosamine residues, hereby forming the poly-N-acetyllactosamine core structures present in glycoproteins and glycosphingolipids. At least seven homologous beta-4-galactosyltransferase isoforms have been identified that use different types of glycoproteins and glycolipids as substrates. Of the seven identified members of the beta-1,4-galactosyltransferase subfamily (beta1,4-Gal-T1 to -T7), b1,4-Gal-T1 is most characterized (biochemically). It is a Golgi-resident type II membrane enzyme with a cytoplasmic domain, membrane spanning region, and a stem region and catalytic domain facing the lumen.
• pfam Galactosyl_T_2 268aa 1e-127 in ref transcript
  • Galactosyltransferase. This is a family of galactosyltransferases from a wide range of Metazoa with three related galactosyltransferases activitys; all three of which are possessed by one sequence in some cases. EC:2.4.1.90, N-acetyllactosamine synthase; EC:2.4.1.38, Beta-N-acetylglucosaminyl-glycopeptide beta-1,4- galactosyltransferase; and EC:2.4.1.22 Lactose synthase. Note that N-acetyllactosamine synthase is a component of Lactose synthase along with alpha-lactalbumin, in the absence of alpha-lactalbumin EC:2.4.1.90 is the catalysed reaction.

BAALC

• refseq_BAALC.F1 refseq_BAALC.R1 215 382
• NCBIGene 36.3 79870
• Single exon skipping, size difference: 167
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_024812

• pfam BAALC_N 31aa 1e-11 in ref transcript
  • BAALC N-terminus. This family represents the N-terminal region of the mammalian BAALC proteins. BAALC (brain and acute leukaemia, cytoplasmic), that is highly conserved among mammals but evidently absent from lower organisms. Two isoforms are specifically expressed in neuroectoderm-derived tissues, but not in tumours or cancer cell lines of non-neural tissue origin. It has been shown that blasts from a subset of patients with acute leukaemia greatly overexpress eight different BAALC transcripts, resulting in five protein isoforms. Among patients with acute myeloid leukaemia, those overexpressing BAALC show distinctly poor prognosis, pointing to a key role of the BAALC products in leukaemia. It has been suggested that BAALC is a gene implicated in both neuroectodermal and hematopoietic cell functions.

BACE1

• refseq_BACE1.F1 refseq_BACE1.R1 113 245
• NCBIGene 36.3 23621
• Alternative 5-prime, size difference: 132
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_012104

• Changed! cd beta_secretase_like 366aa 0.0 in ref transcript
  • Beta-secretase, aspartic-acid protease important in the pathogenesis of Alzheimer's disease. Beta-secretase also called BACE (beta-site of APP cleaving enzyme) or memapsin-2. Beta-secretase is an aspartic-acid protease important in the pathogenesis of Alzheimer's disease, and in the formation of myelin sheaths in peripheral nerve cells. It cleaves amyloid precursor protein (APP) to reveal the N-terminus of the beta-amyloid peptides. The beta-amyloid peptides are the major components of the amyloid plaques formed in the brain of patients with Alzheimer's disease (AD). Since BACE mediates one of the cleavages responsible for generation of AD, it is regarded as a potential target for pharmacological intervention in AD. Beta-secretase is a member of pepsin family of aspartic proteases. Same as other aspartic proteases, beta-secretase is a bilobal enzyme, each lobe contributing a catalytic Asp residue, with an extended active site cleft localized between the two lobes of the molecule. The N- and C-terminal domains, although structurally related by a 2-fold axis, have only limited sequence homology except the vicinity of the active site. This suggests that the enzymes evolved by an ancient duplication event. The enzymes specifically cleave bonds in peptides which have at least six residues in length with hydrophobic residues in both the P1 and P1' positions. The active site is located at the groove formed by the two lobes, with an extended loop projecting over the cleft to form an 11-residue flap, which encloses substrates and inhibitors in the active site. Specificity is determined by nearest-neighbor hydrophobic residues surrounding the catalytic aspartates, and by three residues in the flap. The enzymes are mostly secreted from cells as inactive proenzymes that activate autocatalytically at acidic pH. This family of aspartate proteases is classified by MEROPS as the peptidase family A1 (pepsin A, clan AA).
• Changed! pfam Asp 342aa 5e-36 in ref transcript
  • Eukaryotic aspartyl protease. Aspartyl (acid) proteases include pepsins, cathepsins, and renins. Two-domain structure, probably arising from ancestral duplication. This family does not include the retroviral nor retrotransposon proteases (pfam00077), which are much smaller and appear to be homologous to a single domain of the eukaryotic asp proteases.
• Changed! PTZ PTZ00165 371aa 1e-15 in ref transcript
  • aspartyl protease; Provisional.
• Changed! cd beta_secretase_like 322aa 1e-178 in modified transcript
• Changed! pfam Asp 298aa 2e-26 in modified transcript
• Changed! PTZ PTZ00165 327aa 2e-10 in modified transcript

BACE1

• refseq_BACE1.F4 refseq_BACE1.R4 284 359
• NCBIGene 36.3 23621
• Alternative 3-prime, size difference: 75
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_012104

• Changed! cd beta_secretase_like 366aa 0.0 in ref transcript
  • Beta-secretase, aspartic-acid protease important in the pathogenesis of Alzheimer's disease. Beta-secretase also called BACE (beta-site of APP cleaving enzyme) or memapsin-2. Beta-secretase is an aspartic-acid protease important in the pathogenesis of Alzheimer's disease, and in the formation of myelin sheaths in peripheral nerve cells. It cleaves amyloid precursor protein (APP) to reveal the N-terminus of the beta-amyloid peptides. The beta-amyloid peptides are the major components of the amyloid plaques formed in the brain of patients with Alzheimer's disease (AD). Since BACE mediates one of the cleavages responsible for generation of AD, it is regarded as a potential target for pharmacological intervention in AD. Beta-secretase is a member of pepsin family of aspartic proteases. Same as other aspartic proteases, beta-secretase is a bilobal enzyme, each lobe contributing a catalytic Asp residue, with an extended active site cleft localized between the two lobes of the molecule. The N- and C-terminal domains, although structurally related by a 2-fold axis, have only limited sequence homology except the vicinity of the active site. This suggests that the enzymes evolved by an ancient duplication event. The enzymes specifically cleave bonds in peptides which have at least six residues in length with hydrophobic residues in both the P1 and P1' positions. The active site is located at the groove formed by the two lobes, with an extended loop projecting over the cleft to form an 11-residue flap, which encloses substrates and inhibitors in the active site. Specificity is determined by nearest-neighbor hydrophobic residues surrounding the catalytic aspartates, and by three residues in the flap. The enzymes are mostly secreted from cells as inactive proenzymes that activate autocatalytically at acidic pH. This family of aspartate proteases is classified by MEROPS as the peptidase family A1 (pepsin A, clan AA).
• Changed! pfam Asp 342aa 5e-36 in ref transcript
  • Eukaryotic aspartyl protease. Aspartyl (acid) proteases include pepsins, cathepsins, and renins. Two-domain structure, probably arising from ancestral duplication. This family does not include the retroviral nor retrotransposon proteases (pfam00077), which are much smaller and appear to be homologous to a single domain of the eukaryotic asp proteases.
• Changed! PTZ PTZ00165 371aa 1e-15 in ref transcript
  • aspartyl protease; Provisional.
• Changed! cd beta_secretase_like 341aa 0.0 in modified transcript
• Changed! pfam Asp 317aa 2e-31 in modified transcript
• Changed! PTZ PTZ00013 319aa 5e-12 in modified transcript
  • plasmepsin 4 (PM4); Provisional.

BAIAP2

• refseq_BAIAP2.F1 refseq_BAIAP2.R1 102 148
• NCBIGene 36.3 10458
• Single exon skipping, size difference: 46
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_017451

• cd SH3 57aa 8e-07 in ref transcript
  • Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
• pfam IMD 220aa 5e-90 in ref transcript
  • IRSp53/MIM homology domain. The N-terminal predicted helical stretch of the insulin receptor tyrosine kinase substrate p53 (IRSp53) is an evolutionary conserved F-actin bundling domain involved in filopodium formation. The domain has been named IMD after the IRSp53 and missing in metastasis (MIM) proteins in which it occurs. Filopodium-inducing IMD activity is regulated by Cdc42 and Rac1 and is SH3-independent.
• smart SH3 61aa 8e-07 in ref transcript
  • Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.
• Changed! COG SbcC 220aa 0.008 in ref transcript
  • ATPase involved in DNA repair [DNA replication, recombination, and repair].

BAT1

• refseq_BAT1.F1 refseq_BAT1.R1 233 363
• NCBIGene 36.3 7919
• Alternative 3-prime, size difference: 130
• Inclusion in 5'UTR
• Reference transcript: NM_080598

• cd DEADc 204aa 9e-65 in ref transcript
  • DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP- binding region.
• cd HELICc 127aa 1e-25 in ref transcript
  • Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process.
• pfam DEAD 168aa 3e-42 in ref transcript
  • DEAD/DEAH box helicase. Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.
• pfam Helicase_C 78aa 1e-18 in ref transcript
  • Helicase conserved C-terminal domain. The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.
• COG SrmB 383aa 8e-98 in ref transcript
  • Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis].

BAT3

• refseq_BAT3.F1 refseq_BAT3.R1 116 140
• NCBIGene 36.3 7917
• Alternative 5-prime, size difference: 24
• Exclusion in 5'UTR
• Reference transcript: NM_004639

• cd Scythe_N 71aa 5e-24 in ref transcript
  • Scythe protein (also known as Bat3) is an apoptotic regulator that is highly conserved in eukaryotes and contains a ubiquitin-like domain near its N-terminus. Scythe binds reaper, a potent apoptotic inducer, and Scythe/Reaper are thought to signal apoptosis, in part through regulating the folding and activity of apoptotic signaling molecules.
• smart UBQ 62aa 3e-14 in ref transcript
  • Ubiquitin homologues. Ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression.
• PTZ PTZ00044 69aa 3e-05 in ref transcript
  • ubiquitin; Provisional.

BAT3

• refseq_BAT3.F3 refseq_BAT3.R3 102 120
• NCBIGene 36.3 7917
• Alternative 5-prime and 3-prime, size difference: 18
• Inclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_004639

• cd Scythe_N 71aa 5e-24 in ref transcript
  • Scythe protein (also known as Bat3) is an apoptotic regulator that is highly conserved in eukaryotes and contains a ubiquitin-like domain near its N-terminus. Scythe binds reaper, a potent apoptotic inducer, and Scythe/Reaper are thought to signal apoptosis, in part through regulating the folding and activity of apoptotic signaling molecules.
• smart UBQ 62aa 3e-14 in ref transcript
  • Ubiquitin homologues. Ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression.
• PTZ PTZ00044 69aa 3e-05 in ref transcript
  • ubiquitin; Provisional.

BAX

• refseq_BAX.F1 refseq_BAX.R1 134 173
• NCBIGene 36.3 581
• Alternative 3-prime, size difference: 39
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_138761

• Changed! cd Bcl-2_like 140aa 7e-33 in ref transcript
  • Apoptosis regulator proteins of the Bcl-2 family, named after B-cell lymphoma 2. This alignment model spans what have been described as Bcl-2 homology regions BH1, BH2, BH3, and BH4. Many members of this family have an additional C-terminal transmembrane segment. Some homologous proteins, which are not included in this model, may miss either the BH4 (Bax, Bak) or the BH2 (Bcl-X(S)) region, and some appear to only share the BH3 region (Bik, Bim, Bad, Bid, Egl-1). This family is involved in the regulation of the outer mitochondrial membrane's permeability and in promoting or preventing the release of apoptogenic factors, which in turn may trigger apoptosis by activating caspases. Bcl-2 and the closely related Bcl-X(L) are anti-apoptotic key regulators of programmed cell death. They are assumed to function via heterodimeric protein-protein interactions, binding pro-apoptotic proteins such as Bad (BCL2-antagonist of cell death), Bid, and Bim, by specifically interacting with their BH3 regions. Interfering with this heterodimeric interaction via small-molecule inhibitors may prove effective in targeting various cancers. This family also includes the Caenorhabditis elegans Bcl-2 homolog CED-9, which binds to CED-4, the C. Elegans homolog of mammalian Apaf-1. Apaf-1, however, does not seem to be inhibited by Bcl-2 directly.
• Changed! TIGR bcl-2 188aa 2e-63 in ref transcript
  • in artificial membranes at acidic pH, proapoptotic Bcl-2 family proteins (including Bax and Bak) probably induce the mitochondrial permeability transition and cytochrome c release by interacting with permeability transition pores, the most important component for pore fomation of which is VDAC.
• Changed! cd Bcl-2_like 134aa 7e-31 in modified transcript
• Changed! TIGR bcl-2 175aa 2e-55 in modified transcript

BAX

• refseq_BAX.F3 refseq_BAX.R3 128 226
• NCBIGene 36.3 581
• Single exon skipping, size difference: 98
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_004324

• Changed! cd Bcl-2_like 139aa 5e-31 in ref transcript
  • Apoptosis regulator proteins of the Bcl-2 family, named after B-cell lymphoma 2. This alignment model spans what have been described as Bcl-2 homology regions BH1, BH2, BH3, and BH4. Many members of this family have an additional C-terminal transmembrane segment. Some homologous proteins, which are not included in this model, may miss either the BH4 (Bax, Bak) or the BH2 (Bcl-X(S)) region, and some appear to only share the BH3 region (Bik, Bim, Bad, Bid, Egl-1). This family is involved in the regulation of the outer mitochondrial membrane's permeability and in promoting or preventing the release of apoptogenic factors, which in turn may trigger apoptosis by activating caspases. Bcl-2 and the closely related Bcl-X(L) are anti-apoptotic key regulators of programmed cell death. They are assumed to function via heterodimeric protein-protein interactions, binding pro-apoptotic proteins such as Bad (BCL2-antagonist of cell death), Bid, and Bim, by specifically interacting with their BH3 regions. Interfering with this heterodimeric interaction via small-molecule inhibitors may prove effective in targeting various cancers. This family also includes the Caenorhabditis elegans Bcl-2 homolog CED-9, which binds to CED-4, the C. Elegans homolog of mammalian Apaf-1. Apaf-1, however, does not seem to be inhibited by Bcl-2 directly.
• Changed! TIGR bcl-2 158aa 2e-51 in ref transcript
  • in artificial membranes at acidic pH, proapoptotic Bcl-2 family proteins (including Bax and Bak) probably induce the mitochondrial permeability transition and cytochrome c release by interacting with permeability transition pores, the most important component for pore fomation of which is VDAC.
• Changed! cd Bcl-2_like 100aa 6e-18 in modified transcript
• Changed! TIGR bcl-2 120aa 3e-35 in modified transcript

BAX

• refseq_BAX.F4 bax.r.7 105 252
• NCBIGene 36.3 581
• Single exon skipping, size difference: 147
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_004324

• Changed! cd Bcl-2_like 139aa 5e-31 in ref transcript
  • Apoptosis regulator proteins of the Bcl-2 family, named after B-cell lymphoma 2. This alignment model spans what have been described as Bcl-2 homology regions BH1, BH2, BH3, and BH4. Many members of this family have an additional C-terminal transmembrane segment. Some homologous proteins, which are not included in this model, may miss either the BH4 (Bax, Bak) or the BH2 (Bcl-X(S)) region, and some appear to only share the BH3 region (Bik, Bim, Bad, Bid, Egl-1). This family is involved in the regulation of the outer mitochondrial membrane's permeability and in promoting or preventing the release of apoptogenic factors, which in turn may trigger apoptosis by activating caspases. Bcl-2 and the closely related Bcl-X(L) are anti-apoptotic key regulators of programmed cell death. They are assumed to function via heterodimeric protein-protein interactions, binding pro-apoptotic proteins such as Bad (BCL2-antagonist of cell death), Bid, and Bim, by specifically interacting with their BH3 regions. Interfering with this heterodimeric interaction via small-molecule inhibitors may prove effective in targeting various cancers. This family also includes the Caenorhabditis elegans Bcl-2 homolog CED-9, which binds to CED-4, the C. Elegans homolog of mammalian Apaf-1. Apaf-1, however, does not seem to be inhibited by Bcl-2 directly.
• Changed! TIGR bcl-2 158aa 2e-51 in ref transcript
  • in artificial membranes at acidic pH, proapoptotic Bcl-2 family proteins (including Bax and Bak) probably induce the mitochondrial permeability transition and cytochrome c release by interacting with permeability transition pores, the most important component for pore fomation of which is VDAC.
• Changed! cd Bcl-2_like 81aa 2e-24 in modified transcript
• Changed! TIGR bcl-2 109aa 1e-30 in modified transcript

BAZ1A

• refseq_BAZ1A.F1 refseq_BAZ1A.R1 207 303
• NCBIGene 36.3 11177
• Single exon skipping, size difference: 96
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_013448

• cd Bromo_Acf1_like 113aa 4e-51 in ref transcript
  • Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was identified as a novel human bromodomain gene by cDNA library screening. The Drosophila homologue, Acf1, is part of the CHRAC (chromatin accessibility complex) and regulates ISWI-induced nucleosome remodeling. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
• cd BAH_plant_2 24aa 0.001 in ref transcript
  • BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
• pfam WAC_Acf1_DNA_bd 101aa 2e-39 in ref transcript
  • ATP-utilising chromatin assembly and remodelling N-terminal. ACF (for ATP-utilising chromatin assembly and remodelling factor) is a chromatin-remodelling complex that catalyses the ATP-dependent assembly of periodic nucleosome arrays. The WAC (WSTF/Acf1/cbp146) domain is an approximately 110-residue module present at the N-termini of Acf1-related proteins in a variety of organisms. The DNA-binding region of Acf1 includes the WAC domain, which is necessary for the efficient binding of ACF complex to DNA.
• smart BROMO 92aa 8e-26 in ref transcript
  • bromo domain.
• pfam DDT 63aa 3e-16 in ref transcript
  • DDT domain. This domain is approximately 60 residues in length, and is predicted to be a DNA binding domain. The DDT domain is named after (DNA binding homeobox and Different Transcription factors). It is exclusively associated with nuclear domains, and is thought to be arranged into three alpha helices.
• pfam PHD 46aa 2e-13 in ref transcript
  • PHD-finger. PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
• Changed! COG COG5076 181aa 3e-14 in ref transcript
  • Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription].
• Changed! COG COG5076 143aa 2e-14 in modified transcript

BCAP29

• refseq_BCAP29.F1 refseq_BCAP29.R1 208 287
• NCBIGene 36.3 55973
• Single exon skipping, size difference: 79
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_001008405

• pfam Bap31 220aa 4e-45 in ref transcript
  • B-cell receptor-associated protein 31-like. Bap31 is a polytopic integral protein of the endoplasmic reticulum membrane and a substrate of caspase-8. Bap31 is cleaved within its cytosolic domain, generating pro-apoptotic p20 Bap31.
• Changed! COG COG4372 160aa 0.001 in ref transcript
  • Uncharacterized protein conserved in bacteria with the myosin-like domain [Function unknown].

BCL11A

• refseq_BCL11A.F1 refseq_BCL11A.R1 101 119
• NCBIGene 36.2 53335
• Alternative 3-prime, size difference: 18
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_138553

BCL11B

• refseq_BCL11B.F2 refseq_BCL11B.R2 129 342
• NCBIGene 36.3 64919
• Single exon skipping, size difference: 213
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_138576

BCL2L14

• refseq_BCL2L14.F2 refseq_BCL2L14.R2 199 352
• NCBIGene 36.3 79370
• Alternative 3-prime, size difference: 153
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_138723

• Changed! cd Bcl-2_like 135aa 2e-04 in ref transcript
  • Apoptosis regulator proteins of the Bcl-2 family, named after B-cell lymphoma 2. This alignment model spans what have been described as Bcl-2 homology regions BH1, BH2, BH3, and BH4. Many members of this family have an additional C-terminal transmembrane segment. Some homologous proteins, which are not included in this model, may miss either the BH4 (Bax, Bak) or the BH2 (Bcl-X(S)) region, and some appear to only share the BH3 region (Bik, Bim, Bad, Bid, Egl-1). This family is involved in the regulation of the outer mitochondrial membrane's permeability and in promoting or preventing the release of apoptogenic factors, which in turn may trigger apoptosis by activating caspases. Bcl-2 and the closely related Bcl-X(L) are anti-apoptotic key regulators of programmed cell death. They are assumed to function via heterodimeric protein-protein interactions, binding pro-apoptotic proteins such as Bad (BCL2-antagonist of cell death), Bid, and Bim, by specifically interacting with their BH3 regions. Interfering with this heterodimeric interaction via small-molecule inhibitors may prove effective in targeting various cancers. This family also includes the Caenorhabditis elegans Bcl-2 homolog CED-9, which binds to CED-4, the C. Elegans homolog of mammalian Apaf-1. Apaf-1, however, does not seem to be inhibited by Bcl-2 directly.
• Changed! TIGR bcl-2 29aa 0.008 in ref transcript
  • in artificial membranes at acidic pH, proapoptotic Bcl-2 family proteins (including Bax and Bak) probably induce the mitochondrial permeability transition and cytochrome c release by interacting with permeability transition pores, the most important component for pore fomation of which is VDAC.

BCL7A

• refseq_BCL7A.F2 refseq_BCL7A.R2 334 397
• NCBIGene 36.3 605
• Alternative 5-prime, size difference: 63
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_020993

• pfam BCL_N 49aa 5e-17 in ref transcript
  • BCL7, N-terminal conserver region. Members of the BCL family have significant sequence similarity at their N-terminus, represented in this family. The function of BCL7 proteins is unknown. They may be involved in early development. In addition, BCL7B is commonly hemizygously deleted in patients with Williams syndrome.

BCR

• refseq_BCR.F1 refseq_BCR.R1 138 270
• NCBIGene 36.3 613
• Single exon skipping, size difference: 132
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_004327

• cd RhoGAP_Bcr 201aa 1e-85 in ref transcript
  • RhoGAP_Bcr: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of Bcr (breakpoint cluster region protein)-like proteins. Bcr is a multidomain protein with a variety of enzymatic functions. It contains a RhoGAP and a Rho GEF domain, a Ser/Thr kinase domain, an N-terminal oligomerization domain, and a C-terminal PDZ binding domain, in addition to PH and C2 domains. Bcr is a negative regulator of: i) RacGTPase, via the Rho GAP domain, ii) the Ras-Raf-MEK-ERK pathway, via phosphorylation of the Ras binding protein AF-6, and iii) the Wnt signaling pathway through binding beta-catenin. Bcr can form a complex with beta-catenin and Tcf1. The Wnt signaling pathway is involved in cell proliferation, differentiation, and cell renewal. Bcr was discovered as a fusion partner of Abl. The Bcr-Abl fusion is characteristic for a large majority of chronic myelogenous leukemias (CML). Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
• cd RhoGEF 191aa 3e-29 in ref transcript
  • Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.
• cd PH_BCR-related 61aa 6e-26 in ref transcript
  • BCR (breakpoint cluster region)-related pleckstrin homology (PH) domain. The BCR-related protein has a RhoGEF(DH) domain followed by a PH domain, a C2 domain and a RhoGAP domain. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinases, tyrosine kinases, regulators of G-proteins, endocytotic GTPAses, adaptors, a well as cytoskeletal associated molecules and in lipid associated enzymes.
• cd PH_BCR-related 38aa 7e-12 in ref transcript
• Changed! cd C2 94aa 5e-06 in ref transcript
  • Protein kinase C conserved region 2 (CalB); Ca2+-binding motif present in phospholipases, protein kinases C, and synaptotagmins (among others). Some do not appear to contain Ca2+-binding sites. Particular C2s appear to bind phospholipids, inositol polyphosphates,and intracellular proteins. Synaptotagmin and PLC C2s are permuted in sequence with respect to N- and C-terminal beta strands.
• pfam RhoGEF 189aa 5e-53 in ref transcript
  • RhoGEF domain. Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases Also called Dbl-homologous (DH) domain. It appears that pfam00169 domains invariably occur C-terminal to RhoGEF/DH domains.
• smart RhoGAP 164aa 3e-42 in ref transcript
  • GTPase-activator protein for Rho-like GTPases. GTPase activator proteins towards Rho/Rac/Cdc42-like small GTPases. etter domain limits and outliers.
• pfam Bcr-Abl_Oligo 71aa 3e-33 in ref transcript
  • Bcr-Abl oncoprotein oligomerisation domain. The Bcr-Abl oncoprotein oligomerisation domain consists of a short N-terminal helix (alpha-1), a flexible loop and a long C-terminal helix (alpha-2). Together these form an N-shaped structure, with the loop allowing the two helices to assume a parallel orientation. The monomeric domains associate into a dimer through the formation of an antiparallel coiled coil between the alpha-2 helices and domain swapping of two alpha-1 helices, where one alpha-1 helix swings back and packs against the alpha-2 helix from the second monomer. Two dimers then associate into a tetramer. The oligomerisation domain is essential for the oncogenicity of the Bcr-Abl protein.
• Changed! smart C2 105aa 2e-09 in ref transcript
  • Protein kinase C conserved region 2 (CalB). Ca2+-binding motif present in phospholipases, protein kinases C, and synaptotamins (among others). Some do not appear to contain Ca2+-binding sites. Particular C2s appear to bind phospholipids, inositol polyphosphates, and intracellular proteins. Unusual occurrence in perforin. Synaptotagmin and PLC C2s are permuted in sequence with respect to N- and C-terminal beta strands. SMART detects C2 domains using one or both of two profiles.
• Changed! smart C2 49aa 3e-04 in modified transcript

BDH1

• refseq_BDH1.F1 refseq_BDH1.R1 100 252
• NCBIGene 36.3 622
• Single exon skipping, size difference: 152
• Exclusion in 5'UTR
• Reference transcript: NM_203314

• TIGR 3oxo_ACP_reduc 215aa 3e-18 in ref transcript
  • This model represents 3-oxoacyl-[ACP] reductase, also called 3-ketoacyl-acyl carrier protein reductase, an enzyme of fatty acid biosynthesis.
• PRK PRK06182 263aa 7e-37 in ref transcript
  • short chain dehydrogenase; Validated.

BICD1

• refseq_BICD1.F2 refseq_BICD1.R2 101 405
• NCBIGene 36.3 636
• Exon skipping and alternative 3-prime or 5-prime, size difference: 304
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_001714

• pfam BicD 726aa 0.0 in ref transcript
  • Microtubule-associated protein Bicaudal-D. BicD proteins consist of three coiled-coiled domains and are involved in dynein-mediated minus end-directed transport from the Golgi apparatus to the endoplasmic reticulum (ER). For full functioning they bind with GSK-3beta pfam05350 to maintain the anchoring of microtubules to the centromere. It appears that amino-acid residues 437-617 of BicD and the kinase activity of GSK-3 are necessary for the formation of a complex between BicD and GSK-3beta in intact cells.
• COG Smc 393aa 9e-09 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].

BIN1

• refseq_BIN1.F1 refseq_BIN1.R1 128 260
• NCBIGene 36.3 274
• Multiple exon skipping, size difference: 132
• Exclusion in the protein (no frameshift), Exclusion in the protein (no frameshift)
• Reference transcript: NM_139343

• cd SH3 68aa 5e-08 in ref transcript
  • Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
• smart BAR 253aa 2e-51 in ref transcript
  • BAR domain.
• smart SH3 70aa 1e-09 in ref transcript
  • Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.
• Changed! PRK PRK07764 241aa 0.002 in ref transcript
  • DNA polymerase III subunits gamma and tau; Validated.
• Changed! PRK PRK07764 191aa 2e-04 in modified transcript

BIN1

• refseq_BIN1.F3 refseq_BIN1.R3 255 384
• NCBIGene 36.3 274
• Single exon skipping, size difference: 129
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_139346

• cd SH3 68aa 4e-08 in ref transcript
  • Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
• smart BAR 222aa 2e-45 in ref transcript
  • BAR domain.
• smart SH3 70aa 1e-09 in ref transcript
  • Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.

BIN1

• refseq_BIN1.F4 refseq_BIN1.R4 167 296
• NCBIGene 36.3 274
• Single exon skipping, size difference: 129
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_139343

• cd SH3 68aa 5e-08 in ref transcript
  • Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
• smart BAR 253aa 2e-51 in ref transcript
  • BAR domain.
• smart SH3 70aa 1e-09 in ref transcript
  • Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.
• Changed! PRK PRK07764 241aa 0.002 in ref transcript
  • DNA polymerase III subunits gamma and tau; Validated.
• Changed! PRK PRK07764 175aa 1e-05 in modified transcript

BIN1

• refseq_BIN1.F6 refseq_BIN1.R6 306 399
• NCBIGene 36.3 274
• Single exon skipping, size difference: 93
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_139343

• cd SH3 68aa 5e-08 in ref transcript
  • Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
• Changed! smart BAR 253aa 2e-51 in ref transcript
  • BAR domain.
• smart SH3 70aa 1e-09 in ref transcript
  • Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.
• PRK PRK07764 241aa 0.002 in ref transcript
  • DNA polymerase III subunits gamma and tau; Validated.
• Changed! smart BAR 222aa 1e-47 in modified transcript

BIN1

• refseq_BIN1.F7 refseq_BIN1.R7 126 171
• NCBIGene 36.3 274
• Single exon skipping, size difference: 45
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_139343

• cd SH3 68aa 5e-08 in ref transcript
  • Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
• smart BAR 253aa 2e-51 in ref transcript
  • BAR domain.
• smart SH3 70aa 1e-09 in ref transcript
  • Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.
• Changed! PRK PRK07764 241aa 0.002 in ref transcript
  • DNA polymerase III subunits gamma and tau; Validated.
• Changed! PRK PRK07764 212aa 0.010 in modified transcript

XAF1

• refseq_BIRC4BP.F2 refseq_BIRC4BP.R2 217 274
• NCBIGene 36.3 54739
• Single exon skipping, size difference: 57
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_017523

BMF

• refseq_BMF.F1 refseq_BMF.R1 324 387
• NCBIGene 36.3 90427
• Alternative 5-prime, size difference: 63
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001003940

BMP1

• refseq_BMP1.F1 refseq_BMP1.R1 103 469
• NCBIGene 36.3 649
• Single exon skipping, size difference: 366
• Exclusion of the stop codon
• Reference transcript: NM_006128

• cd ZnMc_BMP1_TLD 195aa 1e-111 in ref transcript
  • Zinc-dependent metalloprotease; BMP1/TLD-like subfamily. BMP1 (Bone morphogenetic protein 1) and TLD (tolloid)-like metalloproteases play vital roles in extracellular matrix formation, by cleaving precursor proteins such as enzymes, structural proteins, and proteins involved in the mineralization of the extracellular matrix. The drosophila protein tolloid and its Xenopus homologue xolloid cleave and inactivate Sog and chordin, respectively, which are inhibitors of Dpp (the Drosophila decapentaplegic gene product) and its homologue BMP4, involved in dorso-ventral patterning.
• cd CUB 112aa 1e-31 in ref transcript
  • CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.
• cd CUB 110aa 2e-31 in ref transcript
• cd CUB 112aa 8e-30 in ref transcript
• cd EGF_CA 42aa 2e-05 in ref transcript
  • Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements.
• pfam Astacin 194aa 4e-89 in ref transcript
  • Astacin (Peptidase family M12A). The members of this family are enzymes that cleave peptides. These proteases require zinc for catalysis. Members of this family contain two conserved disulphide bridges, these are joined 1-4 and 2-3. Members of this family have an amino terminal propeptide which is cleaved to give the active protease domain. All other linked domains are found to the carboxyl terminus of this domain. This family includes: Astacin, a digestive enzyme from Crayfish. Meprin, a multiple domain membrane component that is constructed from a homologous alpha and beta chain. Proteins involved in morphogenesis, and Tolloid from drosophila.
• pfam CUB 110aa 6e-46 in ref transcript
  • CUB domain.
• pfam CUB 110aa 4e-41 in ref transcript
• pfam CUB 110aa 2e-39 in ref transcript
• smart EGF_CA 42aa 2e-06 in ref transcript
  • Calcium-binding EGF-like domain.

BNIP1

• refseq_BNIP1.F1 refseq_BNIP1.R1 130 232
• NCBIGene 36.3 662
• Single exon skipping, size difference: 102
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_013979

• pfam Sec20 92aa 6e-21 in ref transcript
  • Sec20. Sec20 is a membrane glycoprotein associated with secretory pathway.

BNIP1

• refseq_BNIP1.F3 refseq_BNIP1.R3 119 248
• NCBIGene 36.3 662
• Single exon skipping, size difference: 129
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_013979

• pfam Sec20 92aa 6e-21 in ref transcript
  • Sec20. Sec20 is a membrane glycoprotein associated with secretory pathway.

BNIPL

• refseq_BNIPL.F1 refseq_BNIPL.R1 125 279
• NCBIGene 36.2 149428
• Single exon skipping, size difference: 154
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_138278

• Changed! cd SEC14 147aa 2e-17 in ref transcript
  • Sec14p-like lipid-binding domain. Found in secretory proteins, such as S. cerevisiae phosphatidylinositol transfer protein (Sec14p), and in lipid regulated proteins such as RhoGAPs, RhoGEFs and neurofibromin (NF1). SEC14 domain of Dbl is known to associate with G protein beta/gamma subunits.
• Changed! smart SEC14 148aa 2e-14 in ref transcript
  • Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p). Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) and in RhoGAPs, RhoGEFs and the RasGAP, neurofibromin (NF1). Lipid-binding domain. The SEC14 domain of Dbl is known to associate with G protein beta/gamma subunits.
• Changed! cd SEC14 89aa 0.004 in modified transcript

BOLA3

• refseq_BOLA3.F1 refseq_BOLA3.R1 248 337
• NCBIGene 36.3 388962
• Single exon skipping, size difference: 89
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_212552

• Changed! pfam BolA 68aa 8e-08 in ref transcript
  • BolA-like protein. This family consist of the morphoprotein BolA from Escherichia coli and its various homologues. In Escherichia coli over expression of this protein causes round morphology and may be involved in switching the cell between elongation and septation systems during cell division. The expression of BolA is growth rate regulated and is induced during the transition into the the stationary phase. BolA is also induced by stress during early stages of growth and may have a general role in stress response. It has also been suggested that BolA can induce the transcription of penicillin binding proteins 6 and 5.
• Changed! COG BolA 73aa 5e-05 in ref transcript
  • Stress-induced morphogen (activity unknown) [Signal transduction mechanisms].

BPGM

• refseq_BPGM.F1 refseq_BPGM.R1 131 452
• NCBIGene 36.3 669
• Single exon skipping, size difference: 321
• Exclusion in 5'UTR
• Reference transcript: NM_199186

• cd HP_PGM_like 108aa 7e-24 in ref transcript
  • Histidine phosphatase domain found in phosphoglycerate mutases and related proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction. Subgroup of the catalytic domain of a functionally diverse set of proteins, most of which are phosphatases. The conserved catalytic core of this domain contains a His residue which is phosphorylated in the reaction. This subgroup contains cofactor-dependent and cofactor-independent phosphoglycerate mutases (dPGM, and BPGM respectively), fructose-2,6-bisphosphatase (F26BP)ase, Sts-1, SixA, and related proteins. Functions include roles in metabolism, signaling, or regulation, for example, F26BPase affects glycolysis and gluconeogenesis through controlling the concentration of F26BP; BPGM controls the concentration of 2,3-BPG (the main allosteric effector of hemoglobin in human blood cells); human Sts-1 is a T-cell regulator; Escherichia coli Six A participates in the ArcB-dependent His-to-Asp phosphorelay signaling system. Deficiency and mutation in many of the human members result in disease, for example erythrocyte BPGM deficiency is a disease associated with a decrease in the concentration of 2,3-BPG.
• cd HP 67aa 2e-13 in ref transcript
  • Histidine phosphatase domain found in a functionally diverse set of proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction. Catalytic domain of a functionally diverse set of proteins, most of which are phosphatases. The conserved catalytic core of this domain contains a His residue which is phosphorylated in the reaction. This set of proteins includes cofactor-dependent and cofactor-independent phosphoglycerate mutases (dPGM, and BPGM respectively), fructose-2,6-bisphosphatase (F26BP)ase, Sts-1, SixA, histidine acid phosphatases, phytases, and related proteins. Functions include roles in metabolism, signaling, or regulation, for example F26BPase affects glycolysis and gluconeogenesis through controlling the concentration of F26BP; BPGM controls the concentration of 2,3-BPG (the main allosteric effector of hemoglobin in human blood cells); human Sts-1 is a T-cell regulator; Escherichia coli Six A participates in the ArcB-dependent His-to-Asp phosphorelay signaling system; phytases scavenge phosphate from extracellular sources. Deficiency and mutation in many of the human members result in disease, for example erythrocyte BPGM deficiency is a disease associated with a decrease in the concentration of 2,3-BPG. Clinical applications include the use of prostatic acid phosphatase (PAP) as a serum marker for prostate cancer. Agricultural applications include the addition of phytases to animal feed.
• TIGR pgm_1 249aa 2e-94 in ref transcript
  • Most members of this family are phosphoglycerate mutase (EC 5.4.2.1). This enzyme interconverts 2-phosphoglycerate and 3-phosphoglycerate. The enzyme is transiently phosphorylated on an active site histidine by 2,3-diphosphoglyerate, which is both substrate and product. Some members of this family have are phosphoglycerate mutase as a minor activity and act primarily as a bisphoglycerate mutase, interconverting 2,3-diphosphoglycerate and 1,3-diphosphoglycerate (EC 5.4.2.4). This model is designated as a subfamily for this reason. The second and third paralogs in S. cerevisiae are somewhat divergent and apparently inactive (see PUBMED:9544241) but are also part of this subfamily phylogenetically.
• PTZ PTZ00123 240aa 2e-86 in ref transcript
  • phosphoglycerate mutase I; Provisional.

BRCC3

• refseq_BRCC3.F1 refseq_BRCC3.R1 104 179
• NCBIGene 36.3 79184
• Single exon skipping, size difference: 75
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_024332

• smart JAB_MPN 166aa 3e-23 in ref transcript
  • JAB/MPN domain. Domain in Jun kinase activation domain binding protein and proteasomal subunits. Domain at Mpr1p and Pad1p N-termini. Domain of unknown function.
• COG COG1310 31aa 0.001 in ref transcript
  • Predicted metal-dependent protease of the PAD1/JAB1 superfamily [General function prediction only].

BRD8

• refseq_BRD8.F2 refseq_BRD8.R2 191 236
• NCBIGene 36.3 10902
• Single exon skipping, size difference: 45
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_006696

• cd Bromo_brd8_like 104aa 3e-53 in ref transcript
  • Bromodomain, brd8_like subgroup. In mammals, brd8 (bromodomain containing 8) interacts with the thyroid hormone receptor in a ligand-dependent fashion and enhances thyroid hormone-dependent activation from thyroid response elements. Brd8 is thought to be a nuclear receptor coactivator. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
• smart BROMO 103aa 1e-30 in ref transcript
  • bromo domain.
• COG COG5076 105aa 6e-13 in ref transcript
  • Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription].

BRD8

• refseq_BRD8.F4 refseq_BRD8.R4 153 372
• NCBIGene 36.3 10902
• Single exon skipping, size difference: 219
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_139199

• cd Bromo_brd8_like 104aa 8e-53 in ref transcript
  • Bromodomain, brd8_like subgroup. In mammals, brd8 (bromodomain containing 8) interacts with the thyroid hormone receptor in a ligand-dependent fashion and enhances thyroid hormone-dependent activation from thyroid response elements. Brd8 is thought to be a nuclear receptor coactivator. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
• cd Bromo_brd8_like 104aa 3e-45 in ref transcript
• smart BROMO 103aa 5e-30 in ref transcript
  • bromo domain.
• smart BROMO 98aa 1e-26 in ref transcript
• COG COG5076 201aa 8e-14 in ref transcript
  • Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription].
• COG COG5076 105aa 8e-13 in ref transcript

BRD8

• refseq_BRD8.F5 refseq_BRD8.R5 172 289
• NCBIGene 36.3 10902
• Alternative 3-prime, size difference: 117
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_139199

• cd Bromo_brd8_like 104aa 8e-53 in ref transcript
  • Bromodomain, brd8_like subgroup. In mammals, brd8 (bromodomain containing 8) interacts with the thyroid hormone receptor in a ligand-dependent fashion and enhances thyroid hormone-dependent activation from thyroid response elements. Brd8 is thought to be a nuclear receptor coactivator. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
• cd Bromo_brd8_like 104aa 3e-45 in ref transcript
• smart BROMO 103aa 5e-30 in ref transcript
  • bromo domain.
• smart BROMO 98aa 1e-26 in ref transcript
• COG COG5076 201aa 8e-14 in ref transcript
  • Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription].
• Changed! COG COG5076 105aa 8e-13 in ref transcript
• Changed! COG COG5076 81aa 1e-12 in modified transcript

BRD9

• refseq_BRD9.F1 refseq_BRD9.R1 108 168
• NCBIGene 36.3 65980
• Alternative 3-prime, size difference: 60
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_023924

• cd Bromo_brd7_like 98aa 2e-45 in ref transcript
  • Bromodomain, brd7_like subgroup. The BRD7 gene encodes a nuclear protein that has been shown to inhibit cell growth and the progression of the cell cycle by regulating cell-cycle genes at the transcriptional level. BRD7 has been identified as a gene involved in nasopharyngeal carcinoma. The protein interacts with acetylated histone H3 via its bromodomain. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
• Changed! smart BROMO 104aa 2e-22 in ref transcript
  • bromo domain.
• Changed! COG COG5076 125aa 2e-11 in ref transcript
  • Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription].
• PRK PRK08099 62aa 0.002 in ref transcript
  • nicotinamide-nucleotide adenylyltransferase; Provisional.
• Changed! smart BROMO 103aa 1e-22 in modified transcript
• Changed! COG COG5076 99aa 2e-11 in modified transcript

BRE

• refseq_BRE.F1 refseq_BRE.R1 112 178
• NCBIGene 36.3 9577
• Single exon skipping, size difference: 66
• Inclusion in 5'UTR
• Reference transcript: NM_004899

• pfam BRE 333aa 0.0 in ref transcript
  • Brain and reproductive organ-expressed protein (BRE). This family consists of several eukaryotic brain and reproductive organ-expressed (BRE) proteins. BRE is a putative stress-modulating gene, found able to down-regulate TNF-alpha-induced-NF-kappaB activation upon over expression. A total of six isoforms are produced by alternative splicing predominantly at either end of the gene.Compared to normal cells, immortalised human cell lines uniformly express higher levels of BRE. Peripheral blood monocytes respond to LPS by down-regulating the expression of all the BRE isoforms.It is thought that the function of BRE and its isoforms is to regulate peroxisomal activities.

BRMS1

• refseq_BRMS1.F1 refseq_BRMS1.R1 255 337
• NCBIGene 36.3 25855
• Alternative 3-prime, size difference: 82
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_001024957

• pfam Sds3 170aa 1e-33 in ref transcript
  • Sds3-like. Repression of gene transcription is mediated by histone deacetylases containing repressor-co-repressor complexes, which are recruited to promoters of target genes via interactions with sequence-specific transcription factors. The co-repressor complex contains a core of at least seven proteins. This family represents the conserved region found in Sds3, Dep1 and BRMS1-homologue p40 proteins.

BRPF1

• refseq_BRPF1.F2 refseq_BRPF1.R2 102 120
• NCBIGene 36.3 7862
• Alternative 5-prime, size difference: 18
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001003694

• Changed! cd Bromo_brd1_like 104aa 2e-50 in ref transcript
  • Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein assumed to be a transcriptional regulator. BRD1 has been implicated with brain development and susceptibility to schizophrenia and bipolar affective disorder. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
• cd BR140_related 116aa 2e-50 in ref transcript
  • The PWWP domain is found in the BR140 family, which includes peregrin and BR140-like proteins 1 and 2. BR140 is the only family to contain the PWWP domain at the C terminus, with PHD and bromo domains in the N-terminal region. In myeloid leukemias, BR140 is disrupted by chromosomal translocations, similar to translocations of WHSC1 in lymphoid multiple myeloma. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding proteins, that function as transcription factors regulating a variety of developmental processes.
• Changed! smart BROMO 113aa 9e-25 in ref transcript
  • bromo domain.
• pfam EPL1 151aa 2e-15 in ref transcript
  • Enhancer of polycomb-like. This is a family of EPL1 (Enhancer of polycomb-like) proteins. The EPL1 protein is a member of a histone acetyltransferase complex which is involved in transcriptional activation of selected genes.
• smart PWWP 84aa 5e-15 in ref transcript
  • domain with conserved PWWP motif. conservation of Pro-Trp-Trp-Pro residues.
• smart PHD 46aa 3e-07 in ref transcript
  • PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RI NG finger and the FYV E finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BR OMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RI NG fingers misidentified as PHD fingers.
• COG COG5141 435aa 5e-72 in ref transcript
  • PHD zinc finger-containing protein [General function prediction only].
• Changed! COG COG5076 129aa 2e-09 in ref transcript
  • Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription].
• COG SFP1 51aa 0.008 in ref transcript
  • Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning].
• Changed! cd Bromo_brd1_like 98aa 2e-52 in modified transcript
• Changed! smart BROMO 107aa 1e-26 in modified transcript
• Changed! COG COG5076 123aa 4e-11 in modified transcript

BSG

• refseq_BSG.F1 refseq_BSG.R1 100 448
• NCBIGene 36.3 682
• Single exon skipping, size difference: 348
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001728

• Changed! cd IGcam 89aa 3e-07 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• cd IGcam 98aa 5e-04 in ref transcript
• smart IG_like 92aa 7e-09 in ref transcript
  • Immunoglobulin like. IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
• Changed! smart IG_like 85aa 3e-07 in ref transcript

BSG

• refseq_BSG.F3 refseq_BSG.R3 238 395
• NCBIGene 36.3 682
• Single exon skipping, size difference: 157
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_198591

• Changed! cd IGcam 98aa 2e-04 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• Changed! smart IG_like 92aa 1e-09 in ref transcript
  • Immunoglobulin like. IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.

BTBD1

• refseq_BTBD1.F2 refseq_BTBD1.R2 250 338
• NCBIGene 36.3 53339
• Single exon skipping, size difference: 88
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_025238

• Changed! pfam PHR 150aa 1e-49 in ref transcript
  • PHR domain. This domain is called PHR as it was original found in the proteins PAM, highwire and RPM. This domain can be duplicated in the highwire, PFAM and PRM sequence. The C-terminal region of the protein BTBD1 includes the PHR domain and is known to interact with Topoisomerase I, an enzyme which relaxes DNA supercoils.
• pfam BTB 114aa 1e-22 in ref transcript
  • BTB/POZ domain. The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN.
• smart BACK 100aa 9e-12 in ref transcript
  • BTB And C-terminal Kelch. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues.

BTF3

• refseq_BTF3.F2 refseq_BTF3.R2 113 354
• NCBIGene 36.3 689
• Alternative 5-prime, size difference: 241
• Exclusion of the protein initiation site
• Reference transcript: NM_001037637

• pfam NAC 60aa 1e-18 in ref transcript
  • NAC domain.

BTN2A1

• refseq_BTN2A1.F1 refseq_BTN2A1.R1 168 397
• NCBIGene 36.3 11120
• Alternative 3-prime, size difference: 229
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_007049

• Changed! smart SPRY 119aa 5e-29 in ref transcript
  • Domain in SPla and the RYanodine Receptor. Domain of unknown function. Distant homologues are domains in butyrophilin/marenostrin/pyrin homologues.
• Changed! smart PRY 55aa 4e-19 in ref transcript
  • associated with SPRY domains.
• pfam V-set 97aa 2e-10 in ref transcript
  • Immunoglobulin V-set domain. This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.
• pfam C2-set_2 83aa 0.003 in ref transcript
  • CD80-like C2-set immunoglobulin domain. These domains belong to the immunoglobulin superfamily.

BTN3A3

• refseq_BTN3A3.F1 refseq_BTN3A3.R1 226 316
• NCBIGene 36.3 10384
• Single exon skipping, size difference: 90
• Exclusion of the protein initiation site
• Reference transcript: NM_006994

• smart SPRY 123aa 9e-35 in ref transcript
  • Domain in SPla and the RYanodine Receptor. Domain of unknown function. Distant homologues are domains in butyrophilin/marenostrin/pyrin homologues.
• smart PRY 52aa 2e-17 in ref transcript
  • associated with SPRY domains.
• Changed! pfam V-set 105aa 1e-09 in ref transcript
  • Immunoglobulin V-set domain. This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.
• Changed! pfam V-set 91aa 5e-07 in modified transcript

BTNL3

• refseq_BTNL3.F1 refseq_BTNL3.R1 119 227
• NCBIGene 36.2 10917
• Alternative 5-prime, size difference: 108
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_197975

• smart SPRY 124aa 5e-25 in ref transcript
  • Domain in SPla and the RYanodine Receptor. Domain of unknown function. Distant homologues are domains in butyrophilin/marenostrin/pyrin homologues.
• smart PRY 50aa 2e-11 in ref transcript
  • associated with SPRY domains.
• pfam V-set 97aa 2e-06 in ref transcript
  • Immunoglobulin V-set domain. This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.

BTNL3

• refseq_BTNL3.F3 refseq_BTNL3.R3 108 318
• NCBIGene 36.2 10917
• Alternative 5-prime and 3-prime, size difference: 210
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_197975

• smart SPRY 124aa 5e-25 in ref transcript
  • Domain in SPla and the RYanodine Receptor. Domain of unknown function. Distant homologues are domains in butyrophilin/marenostrin/pyrin homologues.
• smart PRY 50aa 2e-11 in ref transcript
  • associated with SPRY domains.
• pfam V-set 97aa 2e-06 in ref transcript
  • Immunoglobulin V-set domain. This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.

BTRC

• refseq_BTRC.F1 refseq_BTRC.R1 284 392
• NCBIGene 36.3 8945
• Single exon skipping, size difference: 108
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_033637

• cd WD40 279aa 2e-60 in ref transcript
  • WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.
• smart WD40 38aa 7e-06 in ref transcript
  • WD40 repeats. Note that these repeats are permuted with respect to the structural repeats (blades) of the beta propeller domain.
• smart WD40 37aa 2e-05 in ref transcript
• smart FBOX 39aa 1e-04 in ref transcript
  • A Receptor for Ubiquitination Targets.
• pfam WD40 36aa 2e-04 in ref transcript
  • WD domain, G-beta repeat.
• smart WD40 38aa 3e-04 in ref transcript
• COG COG2319 311aa 8e-30 in ref transcript
  • FOG: WD40 repeat [General function prediction only].
• Changed! smart WD40 38aa 0.009 in modified transcript
• Changed! smart WD40 35aa 0.010 in modified transcript

C10orf128

• refseq_C10orf128.F1 refseq_C10orf128.R1 106 184
• NCBIGene 36.2 170371
• Alternative 3-prime, size difference: 78
• Exclusion in the protein (no frameshift)
• Reference transcript: XM_926220

C10orf128

• refseq_C10orf128.F1 refseq_C10orf128.R3 206 285
• NCBIGene 36.2 170371
• Single exon skipping, size difference: 79
• Exclusion in the protein causing a frameshift
• Reference transcript: XM_931097

C10orf61

• refseq_C10orf61.F2 refseq_C10orf61.R2 116 197
• NCBIGene 36.2 26123
• Single exon skipping, size difference: 81
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001013840

• Changed! pfam DUF1619 301aa 8e-86 in ref transcript
  • Protein of unknown function (DUF1619). This is a family of sequences derived from hypothetical eukaryotic proteins. The region in question is approximately 330 residues long and has a cysteine rich amino-terminus.
• Changed! pfam DUF1619 274aa 2e-73 in modified transcript

C13orf23

• refseq_C13orf23.F2 refseq_C13orf23.R2 216 282
• NCBIGene 36.3 80209
• Single exon skipping, size difference: 66
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_025138

C14orf102

• refseq_C14orf102.F2 refseq_C14orf102.R2 100 443
• NCBIGene 36.3 55051
• Multiple exon skipping, size difference: 343
• Exclusion in the protein causing a frameshift, Exclusion in the protein (no frameshift)
• Reference transcript: NM_017970

• Changed! pfam DUF1740 238aa 8e-74 in ref transcript
  • Protein of unknown function (DUF1740). This is a family of eukaryotic proteins of unknown function.

INF2

• refseq_C14orf173.F1 refseq_C14orf173.R1 295 352
• NCBIGene 36.3 64423
• Single exon skipping, size difference: 57
• Exclusion of the stop codon
• Reference transcript: NM_022489

• pfam FH2 372aa 2e-66 in ref transcript
  • Formin Homology 2 Domain.
• pfam Drf_FH3 67aa 2e-09 in ref transcript
  • Diaphanous FH3 Domain. This region is found in the Formin-like and and diaphanous proteins.
• pfam Drf_GBD 60aa 6e-08 in ref transcript
  • Diaphanous GTPase-binding Domain. This domain is bound to by GTP-attached Rho proteins, leading to activation of the Drf protein.

ABHD12B

• refseq_C14orf29.F1 refseq_C14orf29.R1 144 247
• NCBIGene 36.3 145447
• Single exon skipping, size difference: 103
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_181814

• Changed! TIGR hydr2_PEP 125aa 1e-09 in ref transcript
  • This group of proteins are members of the alpha/beta hydrolase superfamily. These proteins are generally found in genomes containing the exosortase/PEP-CTERM protein expoert system, specifically the type 1 variant of this system described by the Genome Property GenProp0652. When found in this context they are invariably present in the vicinity of a second, relatively unrelated enzyme (ortholog 1, TIGR03100) of the same superfamily.
• Changed! pfam Peptidase_S9 173aa 2e-04 in ref transcript
  • Prolyl oligopeptidase family.
• Changed! COG COG1073 222aa 2e-15 in ref transcript
  • Hydrolases of the alpha/beta superfamily [General function prediction only].

C15orf21

• refseq_C15orf21.F1 refseq_C15orf21.R1 200 305
• NCBIGene 36.3 283651
• Exon skipping and alternative 3-prime or 5-prime, size difference: 105
• Exclusion of the protein initiation site, Exclusion in the protein causing a frameshift
• Reference transcript: NM_001005266

C15orf21

• refseq_C15orf21.F4 refseq_C15orf21.R4 148 268
• NCBIGene 36.3 283651
• Single exon skipping, size difference: 120
• Exclusion in 5'UTR
• Reference transcript: NM_001005266

C15orf21

• refseq_C15orf21.F4 refseq_C15orf21.R5 104 349
• NCBIGene 36.3 283651
• Multiple exon skipping, size difference: 245
• Exclusion in 5'UTR, Exclusion in 5'UTR
• Reference transcript: NM_001005266

C15orf21

• refseq_C15orf21.F6 refseq_C15orf21.R7 194 271
• NCBIGene 36.3 283651
• Single exon skipping, size difference: 77
• Inclusion in 5'UTR
• Reference transcript: NM_001005267

C17orf58

• refseq_C17orf58.F1 refseq_C17orf58.R1 227 370
• NCBIGene 36.3 284018
• Alternative 5-prime, size difference: 143
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_181655

• Changed! cd NTR_PCOLCE 52aa 3e-07 in ref transcript
  • NTR domain, PCOLCE subfamily; Procollagen C-endopeptidase enhancers (PCOLCEs) are extracellular matrix proteins that enhance the activity of procollagen C-proteases, by binding to the procollagen I C-peptide. They contain a C-terminal NTR domain, which have been suggested to possess inhibitory functions towards specific serine proteases but not towards metzincins, which are inhibited by the related TIMPs.

C18orf1

• refseq_C18orf1.F1 refseq_C18orf1.R1 256 310
• NCBIGene 36.3 753
• Single exon skipping, size difference: 54
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_181481

• cd LDLa 32aa 2e-05 in ref transcript
  • Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure.
• pfam Ldl_recept_a 32aa 1e-05 in ref transcript
  • Low-density lipoprotein receptor domain class A.

C18orf24

• refseq_C18orf24.F1 refseq_C18orf24.R1 143 188
• NCBIGene 36.3 220134
• Alternative 5-prime, size difference: 45
• Exclusion in 5'UTR
• Reference transcript: NM_001039535

• pfam DUF1395 235aa 9e-68 in ref transcript
  • Protein of unknown function (DUF1395). This family consists of several hypothetical eukaryotic proteins of around 250 residues in length. The function of this family is unknown.

C19orf12

• refseq_C19orf12.F2 refseq_C19orf12.R2 175 345
• NCBIGene 36.2 83636
• Single exon skipping, size difference: 170
• Exclusion of the protein initiation site
• Reference transcript: NM_001031726

C19orf2

• refseq_C19orf2.F1 refseq_C19orf2.R1 107 142
• NCBIGene 36.3 8725
• Single exon skipping, size difference: 35
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_003796

• Changed! cd Prefoldin_alpha 103aa 2e-08 in ref transcript
  • Prefoldin alpha subunit; Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils.
• Changed! pfam Prefoldin 110aa 1e-09 in ref transcript
  • Prefoldin subunit. This family comprises of several prefoldin subunits. The biogenesis of the cytoskeletal proteins actin and tubulin involves interaction of nascent chains of each of the two proteins with the oligomeric protein prefoldin (PFD) and their subsequent transfer to the cytosolic chaperonin CCT (chaperonin containing TCP-1). Electron microscopy shows that eukaryotic PFD, which has a similar structure to its archaeal counterpart, interacts with unfolded actin along the tips of its projecting arms. In its PFD-bound state, actin seems to acquire a conformation similar to that adopted when it is bound to CCT.
• Changed! PRK PRK03947 93aa 0.001 in ref transcript
  • prefoldin subunit alpha; Reviewed.

C19orf36

• refseq_C19orf36.F1 refseq_C19orf36.R1 178 232
• NCBIGene 36.3 113177
• Single exon skipping, size difference: 54
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001039846

C19orf48

• refseq_C19orf48.F1 refseq_C19orf48.R1 162 323
• NCBIGene 36.3 84798
• Single exon skipping, size difference: 161
• Exclusion in 5'UTR
• Reference transcript: NM_199249

C19orf6

• refseq_C19orf6.F1 refseq_C19orf6.R1 308 408
• NCBIGene 36.3 91304
• Single exon skipping, size difference: 100
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_001033026

• pfam Membralin 370aa 1e-161 in ref transcript
  • Tumour-associated protein. Membralin is evolutionarily highly conserved; though it seems to represent a unique protein family. The protein appears to contain several transmembrane regions. In humans it is expressed in certain cancers, particularly ovarian cancers.

C1GALT1C1

• refseq_C1GALT1C1.F1 refseq_C1GALT1C1.R1 185 357
• NCBIGene 36.3 29071
• Single exon skipping, size difference: 172
• Exclusion in 5'UTR
• Reference transcript: NM_152692

CAPRIN2

• refseq_C1QDC1.F1 refseq_C1QDC1.R1 161 244
• NCBIGene 36.3 65981
• Single exon skipping, size difference: 83
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_001002259

• Changed! pfam C1q 126aa 8e-34 in ref transcript
  • C1q domain. C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
• Changed! pfam Herpes_BLLF1 204aa 0.009 in ref transcript
  • Herpes virus major outer envelope glycoprotein (BLLF1). This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo.

CAPRIN2

• refseq_C1QDC1.F3 refseq_C1QDC1.R3 205 352
• NCBIGene 36.3 65981
• Single exon skipping, size difference: 147
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001002259

• pfam C1q 126aa 8e-34 in ref transcript
  • C1q domain. C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
• Changed! pfam Herpes_BLLF1 204aa 0.009 in ref transcript
  • Herpes virus major outer envelope glycoprotein (BLLF1). This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo.

C1QTNF1

• refseq_C1QTNF1.F1 refseq_C1QTNF1.R1 231 400
• NCBIGene 36.3 114897
• Single exon skipping, size difference: 169
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_030968

• Changed! pfam C1q 129aa 1e-36 in ref transcript
  • C1q domain. C1q is a subunit of the C1 enzyme complex that activates the serum complement system.
• Changed! pfam Collagen 42aa 1e-05 in ref transcript
  • Collagen triple helix repeat (20 copies). Members of this family belong to the collagen superfamily. Collagens are generally extracellular structural proteins involved in formation of connective tissue structure. The alignment contains 20 copies of the G-X-Y repeat that forms a triple helix. The first position of the repeat is glycine, the second and third positions can be any residue but are frequently proline and hydroxyproline. Collagens are post translationally modified by proline hydroxylase to form the hydroxyproline residues. Defective hydroxylation is the cause of scurvy. Some members of the collagen superfamily are not involved in connective tissue structure but share the same triple helical structure.

C1QTNF3

• refseq_C1QTNF3.F2 refseq_C1QTNF3.R2 131 350
• NCBIGene 36.3 114899
• Alternative 5-prime, size difference: 219
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_181435

• pfam C1q 124aa 2e-35 in ref transcript
  • C1q domain. C1q is a subunit of the C1 enzyme complex that activates the serum complement system.

C1S

• refseq_C1S.F1 refseq_C1S.R1 112 199
• NCBIGene 36.3 716
• Alternative 3-prime, size difference: 87
• Inclusion in 5'UTR
• Reference transcript: NM_001734

• cd Tryp_SPc 241aa 2e-53 in ref transcript
  • Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
• cd CUB 112aa 1e-20 in ref transcript
  • CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.
• cd CUB 113aa 9e-18 in ref transcript
• cd CCP 62aa 1e-04 in ref transcript
  • Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR); The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function.
• cd EGF_CA 35aa 0.005 in ref transcript
  • Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements.
• smart Tryp_SPc 239aa 3e-57 in ref transcript
  • Trypsin-like serine protease. Many of these are synthesised as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. A few, however, are active as single chain molecules, and others are inactive due to substitutions of the catalytic triad residues.
• pfam CUB 113aa 1e-24 in ref transcript
  • CUB domain.
• smart CUB 107aa 7e-22 in ref transcript
  • Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. This domain is found mostly among developmentally-regulated proteins. Spermadhesins contain only this domain.
• pfam Sushi 61aa 6e-06 in ref transcript
  • Sushi domain (SCR repeat).
• smart EGF_CA 41aa 5e-04 in ref transcript
  • Calcium-binding EGF-like domain.
• pfam Sushi 63aa 0.008 in ref transcript
• COG COG5640 251aa 1e-16 in ref transcript
  • Secreted trypsin-like serine protease [Posttranslational modification, protein turnover, chaperones].

C1orf102

• refseq_C1orf102.F1 refseq_C1orf102.R1 166 196
• NCBIGene 36.3 127700
• Single exon skipping, size difference: 30
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_145047

• Changed! pfam Oscp1 184aa 7e-63 in ref transcript
  • Organic solute transport protein 1. Oscp1 is a family of proteins conserved from plants to humans. It is called organic solute transport protein or oxido-red- nitro domain-containing protein 1, however no reference could be find to confirm the function of the protein.
• Changed! pfam Oscp1 174aa 4e-65 in modified transcript

C1orf125

• refseq_C1orf125.F1 refseq_C1orf125.R1 260 482
• NCBIGene 36.3 126859
• Multiple exon skipping, size difference: 222
• Exclusion in the protein (no frameshift), Exclusion in the protein (no frameshift)
• Reference transcript: NM_144696

• pfam Ax_dynein_light 109aa 1e-04 in ref transcript
  • Axonemal dynein light chain. Axonemal dynein light chain proteins play a dynamic role in flagellar and cilia motility. Eukaryotic cilia and flagella are complex organelles consisting of a core structure, the axoneme, which is composed of nine microtubule doublets forming a cylinder that surrounds a pair of central singlet microtubules. This ultra-structural arrangement seems to be one of the most stable micro-tubular assemblies known and is responsible for the flagellar and ciliary movement of a large number of organisms ranging from protozoan to mammals. This light chain interacts directly with the N-terminal half of the heavy chains.

C1orf178

• refseq_C1orf178.F1 refseq_C1orf178.R1 180 302
• NCBIGene 36.2 440603
• Single exon skipping, size difference: 122
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_001010922

C1orf178

• refseq_C1orf178.F3 refseq_C1orf178.R3 102 327
• NCBIGene 36.2 440603
• Single exon skipping, size difference: 225
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001010922

C1orf2

• refseq_C1orf2.F1 refseq_C1orf2.R1 112 400
• NCBIGene 36.3 10712
• Multiple exon skipping, size difference: 288
• Exclusion in the protein (no frameshift), Exclusion in the protein (no frameshift), Exclusion in the protein (no frameshift)
• Reference transcript: NM_006589

C1orf34

• refseq_C1orf34.F1 refseq_C1orf34.R1 130 235
• NCBIGene 36.2 22996
• Alternative 3-prime, size difference: 105
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: XM_930328

• Changed! pfam Deme6 441aa 1e-157 in ref transcript
  • Breast cancer protein. This is a family of proteins conserved from fungi to humans, which, in humans is expressed in primary breast carcinomas but not in normal breast tissue. There appears to be a putative eukaryotic RNP-1 motif and a candidate anchoring transmembrane domain. Deme6 is coordinately regulated with oestrogen receptor, but is not necessarily oestradiol-responsive. Members of this family also carry a TPR_2 domain pfam07719 at their C-terminus.
• Changed! pfam Deme6 476aa 1e-155 in modified transcript

C1orf43

• refseq_C1orf43.F2 refseq_C1orf43.R2 253 307
• NCBIGene 36.3 25912
• Single exon skipping, size difference: 54
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001098616

• Changed! pfam NICE-3 189aa 1e-85 in ref transcript
  • NICE-3 protein. This family consists of several eukaryotic NICE-3 and related proteins. The gene coding for NICE-3 is part of the epidermal differentiation complex (EDC) which comprises a large number of genes that are of crucial importance for the maturation of the human epidermis. The function of NICE-3 is unknown.
• Changed! pfam NICE-3 171aa 4e-72 in modified transcript

C1orf9

• refseq_C1orf9.F2 refseq_C1orf9.R2 310 421
• NCBIGene 36.3 51430
• Single exon skipping, size difference: 111
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_016227

• pfam Sad1_UNC 123aa 6e-40 in ref transcript
  • Sad1 / UNC-like C-terminal. The Caenorhabditis elegans UNC-84 protein is a nuclear envelope protein that is involved in nuclear anchoring and migration during development. The S. pombe Sad1 protein localises at the spindle pole body. UNC-84 and and Sad1 share a common C-terminal region, that is often termed the SUN (Sad1 and UNC) domain. In mammals, the SUN domain is present in two proteins, Sun1 and Sun2. The SUN domain of Sun2 has been demonstrated to be in the periplasm.
• pfam SMC_N 159aa 0.008 in ref transcript
  • RecF/RecN/SMC N terminal domain. This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.

C1orf9

• refseq_C1orf9.F3 refseq_C1orf9.R3 108 129
• NCBIGene 36.3 51430
• Single exon skipping, size difference: 21
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_016227

• Changed! pfam Sad1_UNC 123aa 6e-40 in ref transcript
  • Sad1 / UNC-like C-terminal. The Caenorhabditis elegans UNC-84 protein is a nuclear envelope protein that is involved in nuclear anchoring and migration during development. The S. pombe Sad1 protein localises at the spindle pole body. UNC-84 and and Sad1 share a common C-terminal region, that is often termed the SUN (Sad1 and UNC) domain. In mammals, the SUN domain is present in two proteins, Sun1 and Sun2. The SUN domain of Sun2 has been demonstrated to be in the periplasm.
• pfam SMC_N 159aa 0.008 in ref transcript
  • RecF/RecN/SMC N terminal domain. This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.
• Changed! pfam Sad1_UNC 130aa 9e-40 in modified transcript

C20orf121

• refseq_C20orf121.F1 refseq_C20orf121.R1 103 127
• NCBIGene 36.3 79183
• Single exon skipping, size difference: 24
• Exclusion in 5'UTR
• Reference transcript: NM_024331

• cd SEC14 157aa 2e-31 in ref transcript
  • Sec14p-like lipid-binding domain. Found in secretory proteins, such as S. cerevisiae phosphatidylinositol transfer protein (Sec14p), and in lipid regulated proteins such as RhoGAPs, RhoGEFs and neurofibromin (NF1). SEC14 domain of Dbl is known to associate with G protein beta/gamma subunits.
• pfam CRAL_TRIO 116aa 2e-25 in ref transcript
  • CRAL/TRIO domain. The original profile has been extended to include the carboxyl domain from the known structure of Sec14.
• pfam CRAL_TRIO_N 67aa 2e-07 in ref transcript
  • CRAL/TRIO, N-terminus. This all-alpha domain is found to the N-terminus of pfam00650.

C20orf132

• refseq_C20orf132.F1 refseq_C20orf132.R1 210 315
• NCBIGene 36.3 140699
• Single exon skipping, size difference: 105
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_152503

MACROD2

• refseq_C20orf133.F2 refseq_C20orf133.R2 218 287
• NCBIGene 36.3 140733
• Single exon skipping, size difference: 69
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_080676

• cd Macro_Appr_pase_like 167aa 3e-69 in ref transcript
  • Macro domain, Appr-1"-pase_like family. The macro domain is a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes. This family is composed of uncharacterized proteins that show similarity to Appr-1"-pase, containing conserved putative active site residues. Appr-1"-pase is a phosphatase specific for ADP-ribose-1"-monophosphate.
• pfam Macro 114aa 5e-42 in ref transcript
  • Macro domain. This domain is an ADP-ribose binding module. It is found in a number of otherwise unrelated proteins. It is found at the C-terminus of the macro-H2A histone protein. This domain is found in the non-structural proteins of several types of ssRNA viruses such as NSP3 from alphaviruses. This domain is also found on its own in a family of proteins from bacteria, archaebacteria, and eukaryotes.
• Changed! pfam UPF0560 113aa 4e-04 in ref transcript
  • Uncharacterised protein family UPF0560. This family of proteins has no known function.
• PRK PRK00431 164aa 1e-55 in ref transcript
  • hypothetical protein; Provisional.
• Changed! pfam UPF0560 125aa 2e-04 in modified transcript
• Changed! COG MDN1 169aa 0.007 in modified transcript
  • AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only].

BANF2

• refseq_C20orf179.F2 refseq_C20orf179.R2 202 365
• NCBIGene 36.3 140836
• Single exon skipping, size difference: 163
• Exclusion in 5'UTR
• Reference transcript: NM_178477

• pfam BAF 89aa 2e-31 in ref transcript
  • Barrier to autointegration factor. The BAF protein has a SAM-domain-like bundle of orthogonally packed alpha-hairpins - one classic and one pseudo helix-hairpin-helix motif. The protein is involved in the prevention of retroviral DNA integration.

C20orf24

• refseq_C20orf24.F1 refseq_C20orf24.R1 105 235
• NCBIGene 36.3 55969
• Single exon skipping, size difference: 130
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_199483

• Changed! pfam Rab5ip 64aa 2e-23 in ref transcript
  • Rab5-interacting protein (Rab5ip). This family consists of several Rab5-interacting protein (RIP5 or Rab5ip ) sequences. The ras-related GTPase rab5 is rate-limiting for homotypic early endosome fusion. Rab5ip represents a novel rab5 interacting protein that may function on endocytic vesicles as a receptor for rab5-GDP and participate in the activation of rab5.
• Changed! pfam Rab5ip 114aa 2e-49 in modified transcript

C20orf30

• refseq_C20orf30.F2 refseq_C20orf30.R2 127 220
• NCBIGene 36.3 29058
• Exon skipping and alternative 3-prime or 5-prime, size difference: 93
• Inclusion in 5'UTR, Exclusion in 5'UTR
• Reference transcript: NM_001009924

• pfam DUF872 96aa 4e-15 in ref transcript
  • Eukaryotic protein of unknown function (DUF872). This family consists of several uncharacterised eukaryotic proteins. The function of this family is unknown.

UQCC

• refseq_C20orf44.F1 refseq_C20orf44.R1 111 192
• NCBIGene 36.3 55245
• Exon skipping and alternative 3-prime or 5-prime, size difference: 81
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_018244

• Changed! pfam Ubiq_cyt_C_chap 149aa 3e-64 in ref transcript
  • Ubiquinol-cytochrome C chaperone.
• Changed! COG COG5452 170aa 2e-11 in ref transcript
  • Uncharacterized conserved protein [Function unknown].
• Changed! pfam Ubiq_cyt_C_chap 148aa 2e-64 in modified transcript
• Changed! COG COG5452 138aa 3e-09 in modified transcript

C20orf7

• refseq_C20orf7.F1 refseq_C20orf7.R1 133 217
• NCBIGene 36.3 79133
• Single exon skipping, size difference: 104
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_024120

• Changed! cd AdoMet_MTases 92aa 7e-09 in ref transcript
  • S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.).
• Changed! TIGR BioC 237aa 1e-27 in ref transcript
  • This enzyme, which is found in biotin biosynthetic gene clusters in proteobacteria, firmicutes, green-sulfur bacteria, fusobacterium and bacteroides, is believed to carry out an enzymatic step prior to the formation of pimeloyl-CoA (although attribution of this annotation is not traceable). The enzyme appears related to methyltransferases by homology.
• Changed! COG UbiE 105aa 3e-12 in ref transcript
  • Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism].
• Changed! PRK PRK10258 217aa 8e-08 in ref transcript
  • biotin biosynthesis protein BioC; Provisional.

C20orf7

• refseq_C20orf7.F2 refseq_C20orf7.R2 285 369
• NCBIGene 36.3 79133
• Single exon skipping, size difference: 104
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_024120

• Changed! cd AdoMet_MTases 92aa 7e-09 in ref transcript
  • S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.).
• Changed! TIGR BioC 237aa 1e-27 in ref transcript
  • This enzyme, which is found in biotin biosynthetic gene clusters in proteobacteria, firmicutes, green-sulfur bacteria, fusobacterium and bacteroides, is believed to carry out an enzymatic step prior to the formation of pimeloyl-CoA (although attribution of this annotation is not traceable). The enzyme appears related to methyltransferases by homology.
• Changed! COG UbiE 105aa 3e-12 in ref transcript
  • Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism].
• Changed! PRK PRK10258 217aa 8e-08 in ref transcript
  • biotin biosynthesis protein BioC; Provisional.

C20orf7

• refseq_C20orf7.F3 refseq_C20orf7.R3 214 298
• NCBIGene 36.3 79133
• Single exon skipping, size difference: 104
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_024120

• Changed! cd AdoMet_MTases 92aa 7e-09 in ref transcript
  • S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.).
• Changed! TIGR BioC 237aa 1e-27 in ref transcript
  • This enzyme, which is found in biotin biosynthetic gene clusters in proteobacteria, firmicutes, green-sulfur bacteria, fusobacterium and bacteroides, is believed to carry out an enzymatic step prior to the formation of pimeloyl-CoA (although attribution of this annotation is not traceable). The enzyme appears related to methyltransferases by homology.
• Changed! COG UbiE 105aa 3e-12 in ref transcript
  • Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism].
• Changed! PRK PRK10258 217aa 8e-08 in ref transcript
  • biotin biosynthesis protein BioC; Provisional.

C21orf57

• refseq_C21orf57.F1 refseq_C21orf57.R1 105 427
• NCBIGene 36.3 54059
• Alternative 5-prime, size difference: 322
• Exclusion in 5'UTR
• Reference transcript: NM_058181

• TIGR TIGR00043 115aa 8e-36 in ref transcript
  • This uncharacterized protein family is represented by a single member sequence only in nearly every bacterium.
• PRK PRK00016 117aa 5e-24 in ref transcript
  • putative metalloprotease; Provisional.

C21orf58

• refseq_C21orf58.F1 refseq_C21orf58.R1 203 372
• NCBIGene 36.2 54058
• Alternative 3-prime, size difference: 169
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_058180

C21orf58

• refseq_C21orf58.F3 refseq_C21orf58.R3 176 256
• NCBIGene 36.2 54058
• Alternative 3-prime, size difference: 80
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_058180

C21orf66

• refseq_C21orf66.F1 refseq_C21orf66.R1 96 113
• NCBIGene 36.2 94104
• Alternative 5-prime, size difference: 17
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_016631

• Changed! pfam GCFC 501aa 1e-172 in ref transcript
  • GC-rich sequence DNA-binding factor-like protein. Sequences found in this family are similar to a region of a human GC-rich sequence DNA-binding factor homolog. This is thought to be a protein involved in transcriptional regulation due to partial homologies to a transcription repressor and histone-interacting protein.
• Changed! pfam GCFC 106aa 4e-38 in modified transcript

C2orf28

• refseq_C2orf28.F1 refseq_C2orf28.R1 201 341
• NCBIGene 36.3 51374
• Alternative 5-prime, size difference: 140
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_080592

C3orf17

• refseq_C3orf17.F1 refseq_C3orf17.R1 131 286
• NCBIGene 36.3 25871
• Single exon skipping, size difference: 155
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_015412

C3orf43

• refseq_C3orf43.F1 refseq_C3orf43.R1 176 232
• NCBIGene 36.2 255798
• Alternative 5-prime, size difference: 56
• Inclusion in the protein causing a frameshift
• Reference transcript: XM_931549

C4orf13

• refseq_C4orf13.F1 refseq_C4orf13.R1 232 450
• NCBIGene 36.2 84068
• Multiple exon skipping, size difference: 218
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_001029998

• Changed! COG COG0385 336aa 1e-21 in ref transcript
  • Predicted Na+-dependent transporter [General function prediction only].
• Changed! COG COG0385 185aa 2e-09 in modified transcript

C4orf18

• refseq_C4orf18.F1 refseq_C4orf18.R1 124 148
• NCBIGene 36.3 51313
• Exon skipping and alternative 3-prime or 5-prime, size difference: 24
• Inclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_001031700

C6orf1

• refseq_C6orf1.F1 refseq_C6orf1.R1 179 239
• NCBIGene 36.3 221491
• Alternative 5-prime, size difference: 60
• Exclusion in 5'UTR
• Reference transcript: NM_001008703

• TIGR FadB 33aa 0.002 in ref transcript
  • Members represent alpha subunit of multifunctional enzyme complex of the fatty acid degradation cycle. Activities include: enoyl-CoA hydratase (EC 4.2.1.17), dodecenoyl-CoA delta-isomerase activity (EC 5.3.3.8), 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35), 3-hydroxybutyryl-CoA epimerase (EC 5.1.2.3). A representative is E. coli FadB. This model excludes the FadJ family.

C6orf1

• refseq_C6orf1.F2 refseq_C6orf1.R2 134 386
• NCBIGene 36.3 221491
• Alternative 5-prime, size difference: 252
• Exclusion in 5'UTR
• Reference transcript: NM_178508

• TIGR FadB 33aa 0.002 in ref transcript
  • Members represent alpha subunit of multifunctional enzyme complex of the fatty acid degradation cycle. Activities include: enoyl-CoA hydratase (EC 4.2.1.17), dodecenoyl-CoA delta-isomerase activity (EC 5.3.3.8), 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35), 3-hydroxybutyryl-CoA epimerase (EC 5.1.2.3). A representative is E. coli FadB. This model excludes the FadJ family.

C6orf106

• refseq_C6orf106.F2 refseq_C6orf106.R2 171 369
• NCBIGene 36.3 64771
• Single exon skipping, size difference: 198
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_024294

C6orf134

• refseq_C6orf134.F1 refseq_C6orf134.R1 121 403
• NCBIGene 36.3 79969
• Alternative 5-prime, size difference: 282
• Exclusion of the protein initiation site
• Reference transcript: NM_001031722

• pfam DUF738 121aa 1e-54 in ref transcript
  • Protein of unknown function (DUF738). This family consists of several uncharacterised eukaryotic proteins of unknown function.

C6orf25

• refseq_C6orf25.F1 refseq_C6orf25.R1 278 369
• NCBIGene 36.3 80739
• Single exon skipping, size difference: 91
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_138272

• Changed! pfam V-set 105aa 0.008 in modified transcript
  • Immunoglobulin V-set domain. This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.

C6orf48

• refseq_C6orf48.F1 refseq_C6orf48.R1 175 269
• NCBIGene 36.3 50854
• Single exon skipping, size difference: 94
• Exclusion in 5'UTR
• Reference transcript: NM_001040437

C9orf105

• refseq_C9orf105.F1 refseq_C9orf105.R1 240 342
• NCBIGene 36.2 401505
• Alternative 5-prime, size difference: 102
• Exclusion in the protein (no frameshift)
• Reference transcript: XM_933960

C9orf131

• refseq_C9orf131.F1 refseq_C9orf131.R1 194 299
• NCBIGene 36.3 138724
• Alternative 5-prime, size difference: 105
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_203299

C9orf23

• refseq_C9orf23.F1 refseq_C9orf23.R1 156 360
• NCBIGene 36.3 138716
• Alternative 5-prime, size difference: 204
• Exclusion in 5'UTR
• Reference transcript: NM_148179

• pfam Alba 65aa 5e-14 in ref transcript
  • Alba. Alba is a novel chromosomal protein that coats archaeal DNA without compacting it.

C9orf24

• refseq_C9orf24.F1 refseq_C9orf24.R1 152 306
• NCBIGene 36.3 84688
• Alternative 5-prime, size difference: 154
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_032596

C9orf58

• refseq_C9orf58.F1 refseq_C9orf58.R1 97 119
• NCBIGene 36.2 83543
• Alternative 3-prime, size difference: 22
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_031426

• Changed! cd EFh 61aa 1e-04 in ref transcript
  • EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers.
• Changed! PTZ PTZ00184 69aa 2e-04 in ref transcript
  • calmodulin; Provisional.

CA12

• refseq_CA12.F2 refseq_CA12.R2 143 176
• NCBIGene 36.3 771
• Single exon skipping, size difference: 33
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001218

• cd alpha_CA_XII_XIV 251aa 1e-120 in ref transcript
  • Carbonic anhydrase alpha, isozymes XII and XIV. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionary distinct groups - alpha, beta and gamma carbonic anhydrases - which show no significant sequence identity or structural similarity. Most alpha CAs are monomeric enzymes. The zinc ion is complexed by three histidine residues. This sub-family comprises the membrane proteins CA XII and XIV.
• pfam Carb_anhydrase 258aa 3e-66 in ref transcript
  • Eukaryotic-type carbonic anhydrase.
• COG Cah 264aa 6e-29 in ref transcript
  • Carbonic anhydrase [Inorganic ion transport and metabolism].

CABP1

• refseq_CABP1.F1 refseq_CABP1.R1 126 306
• NCBIGene 36.3 9478
• Single exon skipping, size difference: 180
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_031205

• cd EFh 64aa 8e-13 in ref transcript
  • EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers.
• cd EFh 54aa 5e-04 in ref transcript
• smart EFh 29aa 7e-05 in ref transcript
  • EF-hand, calcium binding motif. EF-hands are calcium-binding motifs that occur at least in pairs. Links between disease states and genes encoding EF-hands, particularly the S100 subclass, are emerging. Each motif consists of a 12 residue loop flanked on either side by a 12 residue alpha-helix. EF-hands undergo a conformational change unpon binding calcium ions.
• smart EFh 28aa 6e-04 in ref transcript
• PTZ PTZ00184 132aa 4e-24 in ref transcript
  • calmodulin; Provisional.
• Changed! smart EH 58aa 0.007 in modified transcript
  • Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.

CABP2

• refseq_CABP2.F1 refseq_CABP2.R1 109 280
• NCBIGene 36.3 51475
• Single exon skipping, size difference: 171
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_016366

• cd EFh 64aa 5e-14 in ref transcript
  • EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers.
• cd EFh 59aa 6e-06 in ref transcript
• pfam efhand 29aa 1e-04 in ref transcript
  • EF hand. The EF-hands can be divided into two classes: signaling proteins and buffering/transport proteins. The first group is the largest and includes the most well-known members of the family such as calmodulin, troponin C and S100B. These proteins typically undergo a calcium-dependent conformational change which opens a target binding site. The latter group is represented by calbindin D9k and do not undergo calcium dependent conformational changes.
• smart EFh 28aa 5e-04 in ref transcript
  • EF-hand, calcium binding motif. EF-hands are calcium-binding motifs that occur at least in pairs. Links between disease states and genes encoding EF-hands, particularly the S100 subclass, are emerging. Each motif consists of a 12 residue loop flanked on either side by a 12 residue alpha-helix. EF-hands undergo a conformational change unpon binding calcium ions.
• Changed! pfam efhand 29aa 0.006 in ref transcript
• PTZ PTZ00184 145aa 1e-27 in ref transcript
  • calmodulin; Provisional.

CABYR

• refseq_CABYR.F2 refseq_CABYR.R2 306 360
• NCBIGene 36.3 26256
• Single exon skipping, size difference: 54
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_012189

• smart RIIa 38aa 3e-08 in ref transcript
  • RIIalpha, Regulatory subunit portion of type II PKA R-subunit. RIIalpha, Regulatory subunit portion of type II PKA R-subunit. Contains dimerisation interface and binding site for A-kinase-anchoring proteins (AKAPs).

CACNA1G

• refseq_CACNA1G.F2 refseq_CACNA1G.R2 106 175
• NCBIGene 36.3 8913
• Single exon skipping, size difference: 69
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_018896

• pfam Ion_trans 187aa 4e-37 in ref transcript
  • Ion transport protein. This family contains Sodium, Potassium, Calcium ion channels. This family is 6 transmembrane helices in which the last two helices flank a loop which determines ion selectivity. In some sub-families (e.g. Na channels) the domain is repeated four times, whereas in others (e.g. K channels) the protein forms as a tetramer in the membrane. A bacterial structure of the protein is known for the last two helices but is not the Pfam family due to it lacking the first four helices.
• pfam Ion_trans 206aa 6e-35 in ref transcript
• pfam Ion_trans 223aa 2e-26 in ref transcript
• pfam Ion_trans 112aa 2e-16 in ref transcript
• pfam Ion_trans 79aa 4e-11 in ref transcript

CACNA1G

• refseq_CACNA1G.F3 refseq_CACNA1G.R3 194 338
• NCBIGene 36.3 8913
• Single exon skipping, size difference: 144
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_018896

• pfam Ion_trans 187aa 4e-37 in ref transcript
  • Ion transport protein. This family contains Sodium, Potassium, Calcium ion channels. This family is 6 transmembrane helices in which the last two helices flank a loop which determines ion selectivity. In some sub-families (e.g. Na channels) the domain is repeated four times, whereas in others (e.g. K channels) the protein forms as a tetramer in the membrane. A bacterial structure of the protein is known for the last two helices but is not the Pfam family due to it lacking the first four helices.
• pfam Ion_trans 206aa 6e-35 in ref transcript
• pfam Ion_trans 223aa 2e-26 in ref transcript
• pfam Ion_trans 112aa 2e-16 in ref transcript
• pfam Ion_trans 79aa 4e-11 in ref transcript

CACNA1G

• refseq_CACNA1G.F4 refseq_CACNA1G.R4 187 322
• NCBIGene 36.3 8913
• Single exon skipping, size difference: 135
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_018896

• pfam Ion_trans 187aa 4e-37 in ref transcript
  • Ion transport protein. This family contains Sodium, Potassium, Calcium ion channels. This family is 6 transmembrane helices in which the last two helices flank a loop which determines ion selectivity. In some sub-families (e.g. Na channels) the domain is repeated four times, whereas in others (e.g. K channels) the protein forms as a tetramer in the membrane. A bacterial structure of the protein is known for the last two helices but is not the Pfam family due to it lacking the first four helices.
• pfam Ion_trans 206aa 6e-35 in ref transcript
• pfam Ion_trans 223aa 2e-26 in ref transcript
• pfam Ion_trans 112aa 2e-16 in ref transcript
• pfam Ion_trans 79aa 4e-11 in ref transcript
• Changed! pfam Atrophin-1 286aa 0.001 in modified transcript
  • Atrophin-1 family. Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteristic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.

CACNA1H

• refseq_CACNA1H.F1 refseq_CACNA1H.R1 100 118
• NCBIGene 36.3 8912
• Single exon skipping, size difference: 18
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_021098

• pfam Ion_trans 223aa 4e-33 in ref transcript
  • Ion transport protein. This family contains Sodium, Potassium, Calcium ion channels. This family is 6 transmembrane helices in which the last two helices flank a loop which determines ion selectivity. In some sub-families (e.g. Na channels) the domain is repeated four times, whereas in others (e.g. K channels) the protein forms as a tetramer in the membrane. A bacterial structure of the protein is known for the last two helices but is not the Pfam family due to it lacking the first four helices.
• pfam Ion_trans 169aa 9e-32 in ref transcript
• pfam Ion_trans 188aa 2e-29 in ref transcript
• pfam Ion_trans 126aa 3e-15 in ref transcript
• pfam Ion_trans 79aa 3e-11 in ref transcript

CACNA1I

• refseq_CACNA1I.F1 refseq_CACNA1I.R1 294 399
• NCBIGene 36.3 8911
• Single exon skipping, size difference: 105
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_021096

• pfam Ion_trans 223aa 4e-35 in ref transcript
  • Ion transport protein. This family contains Sodium, Potassium, Calcium ion channels. This family is 6 transmembrane helices in which the last two helices flank a loop which determines ion selectivity. In some sub-families (e.g. Na channels) the domain is repeated four times, whereas in others (e.g. K channels) the protein forms as a tetramer in the membrane. A bacterial structure of the protein is known for the last two helices but is not the Pfam family due to it lacking the first four helices.
• pfam Ion_trans 209aa 3e-31 in ref transcript
• pfam Ion_trans 188aa 4e-18 in ref transcript
• pfam Ion_trans 89aa 7e-16 in ref transcript
• pfam Ion_trans 79aa 2e-08 in ref transcript

CACNA2D4

• refseq_CACNA2D4.F1 refseq_CACNA2D4.R1 104 149
• NCBIGene 36.2 93589
• Single exon skipping, size difference: 45
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_172364

• cd vWA_VGCC_like 184aa 9e-66 in ref transcript
  • VWA Voltage gated Calcium channel like: Voltage-gated calcium channels are a complex of five proteins: alpha 1, beta 1, gamma, alpha 2 and delta. The alpha 2 and delta subunits result from proteolytic processing of a single gene product and carries at its N-terminus the VWA and cache domains, The alpha 2 delta gene family has orthologues in D. melanogaster and C. elegans but none have been detected in aither A. thaliana or yeast. The exact biochemical function of the VWA domain is not known but the alpha 2 delta complex has been shown to regulate various functional properties of the channel complex.
• pfam VWA_N 117aa 1e-46 in ref transcript
  • VWA N-terminal. This domain is found at the N-terminus of proteins containing von Willebrand factor type A (VWA, pfam00092) and Cache (pfam02743) domains. It has been found in vertebrates, Drosophila and Caenorhabditis elegans but has not yet been identified in other eukaryotes. It is probably involved in the function of some voltage-dependent calcium channel subunits.
• pfam Cache_1 93aa 6e-15 in ref transcript
  • Cache domain.
• smart VWA 180aa 4e-14 in ref transcript
  • von Willebrand factor (vWF) type A domain. VWA domains in extracellular eukaryotic proteins mediate adhesion via metal ion-dependent adhesion sites (MIDAS). Intracellular VWA domains and homologues in prokaryotes have recently been identified. The proposed VWA domains in integrin beta subunits have recently been substantiated using sequence-based methods.
• COG COG2425 346aa 5e-04 in ref transcript
  • Uncharacterized protein containing a von Willebrand factor type A (vWA) domain [General function prediction only].

CACNA2D4

• refseq_CACNA2D4.F3 refseq_CACNA2D4.R3 108 179
• NCBIGene 36.2 93589
• Single exon skipping, size difference: 71
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_172364

• cd vWA_VGCC_like 184aa 9e-66 in ref transcript
  • VWA Voltage gated Calcium channel like: Voltage-gated calcium channels are a complex of five proteins: alpha 1, beta 1, gamma, alpha 2 and delta. The alpha 2 and delta subunits result from proteolytic processing of a single gene product and carries at its N-terminus the VWA and cache domains, The alpha 2 delta gene family has orthologues in D. melanogaster and C. elegans but none have been detected in aither A. thaliana or yeast. The exact biochemical function of the VWA domain is not known but the alpha 2 delta complex has been shown to regulate various functional properties of the channel complex.
• pfam VWA_N 117aa 1e-46 in ref transcript
  • VWA N-terminal. This domain is found at the N-terminus of proteins containing von Willebrand factor type A (VWA, pfam00092) and Cache (pfam02743) domains. It has been found in vertebrates, Drosophila and Caenorhabditis elegans but has not yet been identified in other eukaryotes. It is probably involved in the function of some voltage-dependent calcium channel subunits.
• pfam Cache_1 93aa 6e-15 in ref transcript
  • Cache domain.
• smart VWA 180aa 4e-14 in ref transcript
  • von Willebrand factor (vWF) type A domain. VWA domains in extracellular eukaryotic proteins mediate adhesion via metal ion-dependent adhesion sites (MIDAS). Intracellular VWA domains and homologues in prokaryotes have recently been identified. The proposed VWA domains in integrin beta subunits have recently been substantiated using sequence-based methods.
• Changed! COG COG2425 346aa 5e-04 in ref transcript
  • Uncharacterized protein containing a von Willebrand factor type A (vWA) domain [General function prediction only].
• Changed! COG COG2425 325aa 0.003 in modified transcript

CACNB1

• refseq_CACNB1.F1 refseq_CACNB1.R1 135 270
• NCBIGene 36.3 782
• Mutually exclusive exon skipping, size difference: 135
• Inclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_000723

• cd SH3 57aa 6e-04 in ref transcript
  • Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
• pfam Ca_channel_B 187aa 1e-108 in ref transcript
  • Dihydropyridine sensitive L-type calcium channel (Beta subunit).
• smart SH3 61aa 1e-04 in ref transcript
  • Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.

CACNG6

• refseq_CACNG6.F1 refseq_CACNG6.R1 133 271
• NCBIGene 36.3 59285
• Single exon skipping, size difference: 138
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_145814

CADPS

• refseq_CADPS.F1 refseq_CADPS.R1 118 139
• NCBIGene 36.3 8618
• Single exon skipping, size difference: 21
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_003716

• cd PH_CADPS 110aa 2e-57 in ref transcript
  • CADPS (Ca2+-dependent activator protein) Pleckstrin homology (PH) domain. CADPS is a calcium-dependent activator involved in secretion. It contains a central PH domain that binds to phosphoinositide 4,5 bisphosphate containing liposomes. However, membrane association may also be mediated by binding to phosphatidlyserine via general electrostatic interactions. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
• Changed! pfam DUF1041 106aa 4e-13 in ref transcript
  • Domain of Unknown Function (DUF1041). This family consists of several eukaryotic domains of unknown function. Members of this family are often found in tandem repeats and co-occur with pfam00168, pfam00130 and pfam00169 domains.
• smart PH 102aa 6e-09 in ref transcript
  • Pleckstrin homology domain. Domain commonly found in eukaryotic signalling proteins. The domain family possesses multiple functions including the abilities to bind inositol phosphates, and various proteins. PH domains have been found to possess inserted domains (such as in PLC gamma, syntrophins) and to be inserted within other domains. Mutations in Brutons tyrosine kinase (Btk) within its PH domain cause X-linked agammaglobulinaemia (XLA) in patients. Point mutations cluster into the positively charged end of the molecule around the predicted binding site for phosphatidylinositol lipids.
• Changed! pfam DUF1041 99aa 6e-15 in modified transcript

CADPS

• refseq_CADPS.F4 refseq_CADPS.R4 109 160
• NCBIGene 36.3 8618
• Alternative 5-prime, size difference: 51
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_003716

• cd PH_CADPS 110aa 2e-57 in ref transcript
  • CADPS (Ca2+-dependent activator protein) Pleckstrin homology (PH) domain. CADPS is a calcium-dependent activator involved in secretion. It contains a central PH domain that binds to phosphoinositide 4,5 bisphosphate containing liposomes. However, membrane association may also be mediated by binding to phosphatidlyserine via general electrostatic interactions. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
• pfam DUF1041 106aa 4e-13 in ref transcript
  • Domain of Unknown Function (DUF1041). This family consists of several eukaryotic domains of unknown function. Members of this family are often found in tandem repeats and co-occur with pfam00168, pfam00130 and pfam00169 domains.
• smart PH 102aa 6e-09 in ref transcript
  • Pleckstrin homology domain. Domain commonly found in eukaryotic signalling proteins. The domain family possesses multiple functions including the abilities to bind inositol phosphates, and various proteins. PH domains have been found to possess inserted domains (such as in PLC gamma, syntrophins) and to be inserted within other domains. Mutations in Brutons tyrosine kinase (Btk) within its PH domain cause X-linked agammaglobulinaemia (XLA) in patients. Point mutations cluster into the positively charged end of the molecule around the predicted binding site for phosphatidylinositol lipids.

CADPS

• refseq_CADPS.F6 refseq_CADPS.R6 170 317
• NCBIGene 36.3 8618
• Single exon skipping, size difference: 147
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_003716

• cd PH_CADPS 110aa 2e-57 in ref transcript
  • CADPS (Ca2+-dependent activator protein) Pleckstrin homology (PH) domain. CADPS is a calcium-dependent activator involved in secretion. It contains a central PH domain that binds to phosphoinositide 4,5 bisphosphate containing liposomes. However, membrane association may also be mediated by binding to phosphatidlyserine via general electrostatic interactions. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
• pfam DUF1041 106aa 4e-13 in ref transcript
  • Domain of Unknown Function (DUF1041). This family consists of several eukaryotic domains of unknown function. Members of this family are often found in tandem repeats and co-occur with pfam00168, pfam00130 and pfam00169 domains.
• smart PH 102aa 6e-09 in ref transcript
  • Pleckstrin homology domain. Domain commonly found in eukaryotic signalling proteins. The domain family possesses multiple functions including the abilities to bind inositol phosphates, and various proteins. PH domains have been found to possess inserted domains (such as in PLC gamma, syntrophins) and to be inserted within other domains. Mutations in Brutons tyrosine kinase (Btk) within its PH domain cause X-linked agammaglobulinaemia (XLA) in patients. Point mutations cluster into the positively charged end of the molecule around the predicted binding site for phosphatidylinositol lipids.

CADPS2

• refseq_CADPS2.F1 refseq_CADPS2.R1 382 487
• NCBIGene 36.3 93664
• Single exon skipping, size difference: 120
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_017954

• cd PH_CADPS 110aa 2e-52 in ref transcript
  • CADPS (Ca2+-dependent activator protein) Pleckstrin homology (PH) domain. CADPS is a calcium-dependent activator involved in secretion. It contains a central PH domain that binds to phosphoinositide 4,5 bisphosphate containing liposomes. However, membrane association may also be mediated by binding to phosphatidlyserine via general electrostatic interactions. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
• pfam DUF1041 95aa 1e-13 in ref transcript
  • Domain of Unknown Function (DUF1041). This family consists of several eukaryotic domains of unknown function. Members of this family are often found in tandem repeats and co-occur with pfam00168, pfam00130 and pfam00169 domains.
• smart PH 102aa 2e-09 in ref transcript
  • Pleckstrin homology domain. Domain commonly found in eukaryotic signalling proteins. The domain family possesses multiple functions including the abilities to bind inositol phosphates, and various proteins. PH domains have been found to possess inserted domains (such as in PLC gamma, syntrophins) and to be inserted within other domains. Mutations in Brutons tyrosine kinase (Btk) within its PH domain cause X-linked agammaglobulinaemia (XLA) in patients. Point mutations cluster into the positively charged end of the molecule around the predicted binding site for phosphatidylinositol lipids.

CADPS2

• refseq_CADPS2.F1 refseq_CADPS2.R2 116 236
• NCBIGene 36.3 93664
• Single exon skipping, size difference: 120
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_017954

• cd PH_CADPS 110aa 2e-52 in ref transcript
  • CADPS (Ca2+-dependent activator protein) Pleckstrin homology (PH) domain. CADPS is a calcium-dependent activator involved in secretion. It contains a central PH domain that binds to phosphoinositide 4,5 bisphosphate containing liposomes. However, membrane association may also be mediated by binding to phosphatidlyserine via general electrostatic interactions. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
• pfam DUF1041 95aa 1e-13 in ref transcript
  • Domain of Unknown Function (DUF1041). This family consists of several eukaryotic domains of unknown function. Members of this family are often found in tandem repeats and co-occur with pfam00168, pfam00130 and pfam00169 domains.
• smart PH 102aa 2e-09 in ref transcript
  • Pleckstrin homology domain. Domain commonly found in eukaryotic signalling proteins. The domain family possesses multiple functions including the abilities to bind inositol phosphates, and various proteins. PH domains have been found to possess inserted domains (such as in PLC gamma, syntrophins) and to be inserted within other domains. Mutations in Brutons tyrosine kinase (Btk) within its PH domain cause X-linked agammaglobulinaemia (XLA) in patients. Point mutations cluster into the positively charged end of the molecule around the predicted binding site for phosphatidylinositol lipids.

CAGE1

• refseq_CAGE1.F1 refseq_CAGE1.R1 119 224
• NCBIGene 36.2 285782
• Single exon skipping, size difference: 105
• Exclusion in 3'UTR
• Reference transcript: NM_175745

• pfam SMC_N 256aa 7e-06 in ref transcript
  • RecF/RecN/SMC N terminal domain. This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.
• COG Smc 189aa 2e-05 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].

CAGE1

• refseq_CAGE1.F3 refseq_CAGE1.R3 112 248
• NCBIGene 36.2 285782
• Exon skipping and alternative 3-prime or 5-prime, size difference: 136
• Exclusion in the protein (no frameshift), Exclusion of the stop codon
• Reference transcript: NM_175745

• pfam SMC_N 256aa 7e-06 in ref transcript
  • RecF/RecN/SMC N terminal domain. This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.
• COG Smc 189aa 2e-05 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].

CALB2

• refseq_CALB2.F2 refseq_CALB2.R2 114 154
• NCBIGene 36.3 794
• Single exon skipping, size difference: 40
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_001740

• Changed! cd EFh 70aa 4e-07 in ref transcript
  • EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers.
• cd EFh 73aa 2e-05 in ref transcript
• Changed! cd EFh 67aa 4e-05 in ref transcript
• Changed! PTZ PTZ00184 169aa 4e-07 in ref transcript
  • calmodulin; Provisional.
• Changed! cd EFh 69aa 3e-07 in modified transcript
• Changed! PTZ PTZ00184 167aa 8e-07 in modified transcript

CALML4

• refseq_CALML4.F1 refseq_CALML4.R1 104 434
• NCBIGene 36.2 91860
• Multiple exon skipping, size difference: 330
• Exclusion of the protein initiation site, Exclusion in the protein (no frameshift)
• Reference transcript: NM_001031733

• Changed! cd EFh 63aa 1e-05 in ref transcript
  • EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers.
• Changed! PTZ PTZ00184 107aa 2e-21 in ref transcript
  • calmodulin; Provisional.

CAMK2B

• refseq_CAMK2B.F2 refseq_CAMK2B.R2 117 189
• NCBIGene 36.3 816
• Single exon skipping, size difference: 72
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001220

• cd S_TKc 260aa 2e-82 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• smart S_TKc 249aa 1e-85 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• pfam CaMKII_AD 128aa 1e-58 in ref transcript
  • Calcium/calmodulin dependent protein kinase II Association. This domain is found at the C-terminus of the Calcium/calmodulin dependent protein kinases II (CaMKII). These proteins also have a Ser/Thr protein kinase domain (pfam00069) at their N-terminus. The function of the CaMKII association domain is the assembly of the single proteins into large (8 to 14 subunits) multimers.
• PTZ PTZ00263 249aa 6e-40 in ref transcript
  • protein kinase A catalytic subunit; Provisional.

CAMK2B

• refseq_CAMK2B.F4 refseq_CAMK2B.R4 100 472
• NCBIGene 36.3 816
• Multiple exon skipping, size difference: 372
• Exclusion in the protein (no frameshift), Exclusion in the protein (no frameshift), Exclusion in the protein (no frameshift)
• Reference transcript: NM_001220

• cd S_TKc 260aa 2e-82 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• smart S_TKc 249aa 1e-85 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• pfam CaMKII_AD 128aa 1e-58 in ref transcript
  • Calcium/calmodulin dependent protein kinase II Association. This domain is found at the C-terminus of the Calcium/calmodulin dependent protein kinases II (CaMKII). These proteins also have a Ser/Thr protein kinase domain (pfam00069) at their N-terminus. The function of the CaMKII association domain is the assembly of the single proteins into large (8 to 14 subunits) multimers.
• Changed! PTZ PTZ00263 249aa 6e-40 in ref transcript
  • protein kinase A catalytic subunit; Provisional.
• Changed! COG SPS1 265aa 4e-40 in modified transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].

CAMK2B

• refseq_CAMK2B.F5 refseq_CAMK2B.R5 171 249
• NCBIGene 36.3 816
• Alternative 3-prime, size difference: 78
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001220

• cd S_TKc 260aa 2e-82 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• smart S_TKc 249aa 1e-85 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• Changed! pfam CaMKII_AD 128aa 1e-58 in ref transcript
  • Calcium/calmodulin dependent protein kinase II Association. This domain is found at the C-terminus of the Calcium/calmodulin dependent protein kinases II (CaMKII). These proteins also have a Ser/Thr protein kinase domain (pfam00069) at their N-terminus. The function of the CaMKII association domain is the assembly of the single proteins into large (8 to 14 subunits) multimers.
• PTZ PTZ00263 249aa 6e-40 in ref transcript
  • protein kinase A catalytic subunit; Provisional.
• Changed! pfam CaMKII_AD 102aa 8e-40 in modified transcript

CAMK2G

• refseq_CAMK2G.F2 refseq_CAMK2G.R2 187 257
• NCBIGene 36.2 818
• Alternative 5-prime, size difference: 42
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_172171

• cd S_TKc 260aa 5e-84 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• smart S_TKc 249aa 2e-86 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• pfam CaMKII_AD 128aa 5e-59 in ref transcript
  • Calcium/calmodulin dependent protein kinase II Association. This domain is found at the C-terminus of the Calcium/calmodulin dependent protein kinases II (CaMKII). These proteins also have a Ser/Thr protein kinase domain (pfam00069) at their N-terminus. The function of the CaMKII association domain is the assembly of the single proteins into large (8 to 14 subunits) multimers.
• PTZ PTZ00263 249aa 3e-43 in ref transcript
  • protein kinase A catalytic subunit; Provisional.

CAMK2G

• refseq_CAMK2G.F3 refseq_CAMK2G.R3 215 329
• NCBIGene 36.3 818
• Single exon skipping, size difference: 114
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_172171

• cd S_TKc 260aa 5e-84 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• smart S_TKc 249aa 2e-86 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• pfam CaMKII_AD 128aa 5e-59 in ref transcript
  • Calcium/calmodulin dependent protein kinase II Association. This domain is found at the C-terminus of the Calcium/calmodulin dependent protein kinases II (CaMKII). These proteins also have a Ser/Thr protein kinase domain (pfam00069) at their N-terminus. The function of the CaMKII association domain is the assembly of the single proteins into large (8 to 14 subunits) multimers.
• PTZ PTZ00263 249aa 3e-43 in ref transcript
  • protein kinase A catalytic subunit; Provisional.

CAMK2G

• refseq_CAMK2G.F4 refseq_CAMK2G.R4 126 189
• NCBIGene 36.3 818
• Single exon skipping, size difference: 63
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_172171

• cd S_TKc 260aa 5e-84 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• smart S_TKc 249aa 2e-86 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• pfam CaMKII_AD 128aa 5e-59 in ref transcript
  • Calcium/calmodulin dependent protein kinase II Association. This domain is found at the C-terminus of the Calcium/calmodulin dependent protein kinases II (CaMKII). These proteins also have a Ser/Thr protein kinase domain (pfam00069) at their N-terminus. The function of the CaMKII association domain is the assembly of the single proteins into large (8 to 14 subunits) multimers.
• PTZ PTZ00263 249aa 3e-43 in ref transcript
  • protein kinase A catalytic subunit; Provisional.

CAMK2G

• refseq_CAMK2G.F6 refseq_CAMK2G.R1 106 134
• NCBIGene 36.2 818
• Alternative 3-prime, size difference: 28
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_172171

• cd S_TKc 260aa 5e-84 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• smart S_TKc 249aa 2e-86 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• Changed! pfam CaMKII_AD 128aa 5e-59 in ref transcript
  • Calcium/calmodulin dependent protein kinase II Association. This domain is found at the C-terminus of the Calcium/calmodulin dependent protein kinases II (CaMKII). These proteins also have a Ser/Thr protein kinase domain (pfam00069) at their N-terminus. The function of the CaMKII association domain is the assembly of the single proteins into large (8 to 14 subunits) multimers.
• PTZ PTZ00263 249aa 3e-43 in ref transcript
  • protein kinase A catalytic subunit; Provisional.

CAMKK1

• refseq_CAMKK1.F1 refseq_CAMKK1.R1 133 247
• NCBIGene 36.3 84254
• Single exon skipping, size difference: 114
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_172206

• Changed! cd S_TKc 283aa 9e-69 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• Changed! smart S_TKc 272aa 6e-73 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• Changed! COG SPS1 359aa 2e-36 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].
• Changed! cd S_TKc 321aa 3e-62 in modified transcript
• Changed! smart S_TKc 310aa 1e-65 in modified transcript
• Changed! COG SPS1 397aa 4e-31 in modified transcript

CAMKK2

• refseq_CAMKK2.F2 refseq_CAMKK2.R2 199 242
• NCBIGene 36.3 10645
• Single exon skipping, size difference: 43
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_006549

• cd S_TKc 283aa 5e-68 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• smart S_TKc 272aa 4e-70 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• PTZ PTZ00263 295aa 6e-38 in ref transcript
  • protein kinase A catalytic subunit; Provisional.

CAMKK2

• refseq_CAMKK2.F3 refseq_CAMKK2.R3 134 263
• NCBIGene 36.3 10645
• Single exon skipping, size difference: 129
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_006549

• Changed! cd S_TKc 283aa 5e-68 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• Changed! smart S_TKc 272aa 4e-70 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• Changed! PTZ PTZ00263 295aa 6e-38 in ref transcript
  • protein kinase A catalytic subunit; Provisional.
• Changed! cd S_TKc 278aa 4e-65 in modified transcript
• Changed! smart S_TKc 267aa 3e-67 in modified transcript
• Changed! PTZ PTZ00263 275aa 3e-37 in modified transcript

CANX

• refseq_CANX.F1 refseq_CANX.R1 132 185
• NCBIGene 36.3 821
• Alternative 5-prime, size difference: 53
• Exclusion in 5'UTR
• Reference transcript: NM_001746

• pfam Calreticulin 372aa 1e-143 in ref transcript
  • Calreticulin family.

CAPN9

• refseq_CAPN9.F1 refseq_CAPN9.R1 167 245
• NCBIGene 36.3 10753
• Single exon skipping, size difference: 78
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_006615

• Changed! cd CysPc 305aa 1e-105 in ref transcript
  • Calpains, domains IIa, IIb; calcium-dependent cytoplasmic cysteine proteinases, papain-like. Functions in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction.
• cd Calpain_III 150aa 5e-61 in ref transcript
  • Calpain, subdomain III. Calpains are calcium-activated cytoplasmic cysteine proteinases, participate in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction. Catalytic domain and the two calmodulin-like domains are separated by C2-like domain III. Domain III plays an important role in calcium-induced activation of calpain involving electrostatic interactions with subdomain II. Proposed to mediate calpain's interaction with phospholipids and translocation to cytoplasmic/nuclear membranes. CD includes subdomain III of typical and atypical calpains.
• cd EFh 56aa 0.002 in ref transcript
  • EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers.
• Changed! smart CysPc 316aa 1e-148 in ref transcript
  • Calpain-like thiol protease family. Calpain-like thiol protease family (peptidase family C2). Calcium activated neutral protease (large subunit).
• pfam Calpain_III 147aa 1e-69 in ref transcript
  • Calpain large subunit, domain III. The function of the domain III and I are currently unknown. Domain II is a cysteine protease and domain IV is a calcium binding domain. Calpains are believed to participate in intracellular signaling pathways mediated by calcium ions.
• Changed! cd CysPc 279aa 1e-94 in modified transcript
• Changed! smart CysPc 290aa 1e-132 in modified transcript

CAPS

• refseq_CAPS.F1 refseq_CAPS.R1 159 240
• NCBIGene 36.3 828
• Alternative 5-prime, size difference: 81
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_004058

• cd EFh 62aa 2e-08 in ref transcript
  • EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers.
• cd EFh 58aa 6e-04 in ref transcript
• Changed! COG FRQ1 146aa 6e-07 in ref transcript
  • Ca2+-binding protein (EF-Hand superfamily) [Signal transduction mechanisms / Cytoskeleton / Cell division and chromosome partitioning / General function prediction only].
• Changed! PTZ PTZ00184 129aa 4e-07 in modified transcript
  • calmodulin; Provisional.

CARS

• refseq_CARS.F1 refseq_CARS.R1 115 162
• NCBIGene 36.3 833
• Alternative 3-prime, size difference: 47
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_001014437

• Changed! cd CysRS_core 102aa 1e-47 in ref transcript
  • This is the catalytic core domain of cysteinyl tRNA synthetase (CysRS). This class I enzyme is a monomer, which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding.
• Changed! cd CysRS_core 102aa 5e-37 in ref transcript
• Changed! cd CysRS_core 34aa 4e-05 in ref transcript
• Changed! pfam tRNA-synt_1e 246aa 9e-88 in ref transcript
  • tRNA synthetases class I (C) catalytic domain. This family includes only cysteinyl tRNA synthetases.
• Changed! TIGR cysS 86aa 7e-35 in ref transcript
  • This model finds the cysteinyl-tRNA synthetase from most but not from all species. The enzyme from one archaeal species, Archaeoglobus fulgidus, is found but the equivalent enzymes from some other Archaea, including Methanococcus jannaschii, are not found, although biochemical evidence suggests that tRNA(Cys) in these species are charged directly with Cys rather than through a misacylation and correction pathway as for tRNA(Gln).
• Changed! TIGR leuS_arch 169aa 2e-07 in ref transcript
  • The leucyl-tRNA synthetases belong to two families so broadly different that they are represented by separate models. This model includes both archaeal and cytosolic eukaryotic leucyl-tRNA synthetases; the eubacterial and mitochondrial forms differ so substantially that some other tRNA ligases score higher by this model than does any eubacterial LeuS.
• Changed! COG CysS 424aa 2e-96 in ref transcript
  • Cysteinyl-tRNA synthetase [Translation, ribosomal structure and biogenesis].
• Changed! PRK cysS 81aa 2e-36 in ref transcript
  • cysteinyl-tRNA synthetase; Validated.
• Changed! cd GST_C_EFB1gamma 48aa 0.004 in modified transcript
  • GST_C family, Gamma subunit of Elongation Factor 1B (EFB1gamma) subfamily; EF1Bgamma is part of the eukaryotic translation elongation factor-1 (EF1) complex which plays a central role in the elongation cycle during protein biosynthesis. EF1 consists of two functionally distinct units, EF1A and EF1B. EF1A catalyzes the GTP-dependent binding of aminoacyl-tRNA to the ribosomal A site concomitant with the hydrolysis of GTP. The resulting inactive EF1A:GDP complex is recycled to the active GTP form by the guanine-nucleotide exchange factor EF1B, a complex composed of at least two subunits, alpha and gamma. Metazoan EFB1 contain a third subunit, beta. The EF1B gamma subunit contains a GST fold consisting of an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain. The GST-like domain of EF1Bgamma is believed to mediate the dimerization of the EF1 complex, which in yeast is a dimer of the heterotrimer EF1A:EF1Balpha:EF1Bgamma. In addition to its role in protein biosynthesis, EF1Bgamma may also display other functions. The recombinant rice protein has been shown to possess GSH conjugating activity. The yeast EF1Bgamma binds membranes in a calcium dependent manner and is also part of a complex that binds to the msrA (methionine sulfoxide reductase) promoter suggesting a function in the regulation of its gene expression. Also included in this subfamily is the GST_C-like domain at the N-terminus of human valyl-tRNA synthetase and its homologs from zebrafish and Xenopus. Although not included in the alignment, the GST_C-like domain containing a deletion present in some aminoacyl-tRNA synthetases is recognized by this model. This domain will be represented in the future by a deletion model of GST_C.

CARS

• refseq_CARS.F3 refseq_CARS.R3 149 398
• NCBIGene 36.3 833
• Single exon skipping, size difference: 249
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001014437

• cd CysRS_core 102aa 1e-47 in ref transcript
  • This is the catalytic core domain of cysteinyl tRNA synthetase (CysRS). This class I enzyme is a monomer, which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding.
• cd CysRS_core 102aa 5e-37 in ref transcript
• cd CysRS_core 34aa 4e-05 in ref transcript
• pfam tRNA-synt_1e 246aa 9e-88 in ref transcript
  • tRNA synthetases class I (C) catalytic domain. This family includes only cysteinyl tRNA synthetases.
• TIGR cysS 86aa 7e-35 in ref transcript
  • This model finds the cysteinyl-tRNA synthetase from most but not from all species. The enzyme from one archaeal species, Archaeoglobus fulgidus, is found but the equivalent enzymes from some other Archaea, including Methanococcus jannaschii, are not found, although biochemical evidence suggests that tRNA(Cys) in these species are charged directly with Cys rather than through a misacylation and correction pathway as for tRNA(Gln).
• TIGR leuS_arch 169aa 2e-07 in ref transcript
  • The leucyl-tRNA synthetases belong to two families so broadly different that they are represented by separate models. This model includes both archaeal and cytosolic eukaryotic leucyl-tRNA synthetases; the eubacterial and mitochondrial forms differ so substantially that some other tRNA ligases score higher by this model than does any eubacterial LeuS.
• COG CysS 424aa 2e-96 in ref transcript
  • Cysteinyl-tRNA synthetase [Translation, ribosomal structure and biogenesis].
• PRK cysS 81aa 2e-36 in ref transcript
  • cysteinyl-tRNA synthetase; Validated.

CASC5

• refseq_CASC5.F1 refseq_CASC5.R1 416 494
• NCBIGene 36.3 57082
• Single exon skipping, size difference: 78
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_170589

CASP1

• refseq_CASP1.F2 refseq_CASP1.R2 306 369
• NCBIGene 36.3 834
• Single exon skipping, size difference: 63
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_033292

• cd CASc 250aa 1e-72 in ref transcript
  • Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs.
• smart CASc 250aa 5e-94 in ref transcript
  • Caspase, interleukin-1 beta converting enzyme (ICE) homologues. Cysteine aspartases that mediate programmed cell death (apoptosis). Caspases are synthesised as zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologues.
• pfam CARD 88aa 5e-20 in ref transcript
  • Caspase recruitment domain. Motif contained in proteins involved in apoptotic signaling. Predicted to possess a DEATH (pfam00531) domain-like fold.

CASP4

• refseq_CASP4.F1 refseq_CASP4.R1 141 199
• NCBIGene 36.2 837
• Alternative 3-prime, size difference: 58
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_001225

• Changed! cd CASc 250aa 3e-69 in ref transcript
  • Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs.
• Changed! smart CASc 250aa 2e-93 in ref transcript
  • Caspase, interleukin-1 beta converting enzyme (ICE) homologues. Cysteine aspartases that mediate programmed cell death (apoptosis). Caspases are synthesised as zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologues.
• Changed! smart CARD 89aa 2e-10 in ref transcript
  • Caspase recruitment domain. Motif contained in proteins involved in apoptotic signalling. Mediates homodimerisation. Structure consists of six antiparallel helices arranged in a topology homologue to the DEATH and the DED domain.
• Changed! smart CARD 89aa 3e-11 in modified transcript

CASP6

• refseq_CASP6.F2 refseq_CASP6.R2 102 369
• NCBIGene 36.3 839
• Multiple exon skipping, size difference: 267
• Exclusion in the protein causing a frameshift, Exclusion in the protein (no frameshift), Exclusion in the protein causing a frameshift
• Reference transcript: NM_001226

• Changed! cd CASc 253aa 2e-82 in ref transcript
  • Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs.
• Changed! smart CASc 254aa 7e-91 in ref transcript
  • Caspase, interleukin-1 beta converting enzyme (ICE) homologues. Cysteine aspartases that mediate programmed cell death (apoptosis). Caspases are synthesised as zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologues.
• Changed! cd CASc 187aa 6e-60 in modified transcript
• Changed! smart CASc 184aa 1e-64 in modified transcript

CASP7

• refseq_CASP7.F1 refseq_CASP7.R1 192 226
• NCBIGene 36.3 840
• Exon skipping and alternative 3-prime or 5-prime, size difference: 34
• Inclusion in the protein causing a frameshift, Exclusion in the protein (no frameshift)
• Reference transcript: NM_033338

• Changed! cd CASc 242aa 4e-84 in ref transcript
  • Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs.
• Changed! smart CASc 243aa 2e-90 in ref transcript
  • Caspase, interleukin-1 beta converting enzyme (ICE) homologues. Cysteine aspartases that mediate programmed cell death (apoptosis). Caspases are synthesised as zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologues.
• Changed! cd CASc 105aa 2e-26 in modified transcript
• Changed! smart CASc 90aa 5e-28 in modified transcript

CASP8

• refseq_CASP8.F1 refseq_CASP8.R1 277 373
• NCBIGene 36.3 841
• Single exon skipping, size difference: 96
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_001080125

• cd CASc 253aa 3e-85 in ref transcript
  • Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs.
• cd DED 75aa 3e-17 in ref transcript
  • Death effector domain. DED is part of a superfamily of death domains which also includes death-domain (DD) and caspase recruitment domain (CARD). Protein-protein interactions involving these domains occur through homotypic interactions, such as DED-DED. Caspases are the primary executioners of apoptosis via proteolytic cascades, and upstream caspases such as caspase-8 and caspase-9 are activated by signaling complexes such as the death inducing signaling complex (DISC) and the apoptosome. Binding of caspases to specific adaptor molecules via DED or CARD domains leads to autoactivation of caspases.
• Changed! cd DED 78aa 7e-13 in ref transcript
• smart CASc 252aa 4e-90 in ref transcript
  • Caspase, interleukin-1 beta converting enzyme (ICE) homologues. Cysteine aspartases that mediate programmed cell death (apoptosis). Caspases are synthesised as zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologues.
• pfam DED 84aa 5e-23 in ref transcript
  • Death effector domain.
• Changed! pfam DED 82aa 2e-17 in ref transcript
• Changed! cd DED 75aa 7e-12 in modified transcript
• Changed! pfam DED 81aa 7e-17 in modified transcript

CAST

• refseq_CAST.F2 refseq_CAST.R2 103 282
• NCBIGene 36.2 831
• Exon skipping and alternative 3-prime or 5-prime, size difference: 179
• Inclusion in the protein causing a frameshift, Inclusion in the protein causing a new stop codon
• Reference transcript: NM_001750

• Changed! pfam Calpain_inhib 127aa 3e-19 in ref transcript
  • Calpain inhibitor. This region is found multiple times in calpain inhibitor proteins.
• Changed! pfam Calpain_inhib 118aa 2e-16 in ref transcript
• Changed! pfam Calpain_inhib 99aa 1e-13 in ref transcript
• pfam Calpain_inhib 126aa 2e-11 in ref transcript
• Changed! pfam Calpain_inhib 86aa 2e-12 in modified transcript

CAV2

• refseq_CAV2.F1 refseq_CAV2.R1 207 395
• NCBIGene 36.3 858
• Single exon skipping, size difference: 188
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_001233

• Changed! pfam Caveolin 149aa 4e-55 in ref transcript
  • Caveolin. All three known Caveolin forms have the FEDVIAEP caveolin 'signature motif' within their hydrophilic N-terminal domain. Caveolin 2 (Cav-2) is co-localised and co-expressed with Cav-1/VIP21, forms heterodimers with it and needs Cav-1 for proper membrane localisation. Cav-3 has greater protein sequence similarity to Cav-1 than to Cav-2. Cellular processes caveolins are involved in include vesicular transport, cholesterol homeostasis, signal transduction, and tumour suppression.
• Changed! pfam Caveolin 41aa 2e-04 in modified transcript

CBFB

• refseq_CBFB.F1 refseq_CBFB.R1 141 172
• NCBIGene 36.3 865
• Alternative 5-prime, size difference: 31
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_022845

• Changed! pfam CBF_beta 178aa 4e-73 in ref transcript
  • Core binding factor beta subunit. Core binding factor (CBF) is a heterodimeric transcription factor essential for genetic regulation of hematopoiesis and osteogenesis. The beta subunit enhances DNA-binding ability of the alpha subunit in vitro, and has been show to have a structure related to the OB fold.
• Changed! pfam CBF_beta 170aa 2e-70 in modified transcript

CCDC108

• refseq_CCDC108.F1 refseq_CCDC108.R1 132 287
• NCBIGene 36.3 255101
• Single exon skipping, size difference: 155
• Exclusion of the protein initiation site
• Reference transcript: NM_194302

CCDC55

• refseq_CCDC55.F1 refseq_CCDC55.R1 220 316
• NCBIGene 36.2 84081
• Single exon skipping, size difference: 96
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_032141

• Changed! pfam DUF2040 126aa 7e-07 in ref transcript
  • Coiled-coil domain-containing protein 55 (DUF2040). This entry is a conserved domain of approximately 130 residues of proteins conserved from fungi to humans. The proteins do contain a coiled-coil domain, but the function is unknown.
• Changed! TIGR U2AF_lg 110aa 0.009 in ref transcript
  • Members of this subfamily are found in plants, metazoa and fungi.

CCDC62

• refseq_CCDC62.F1 refseq_CCDC62.R1 260 354
• NCBIGene 36.3 84660
• Single exon skipping, size difference: 94
• Exclusion of the stop codon
• Reference transcript: NM_201435

• pfam SMC_N 256aa 5e-07 in ref transcript
  • RecF/RecN/SMC N terminal domain. This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.
• COG Smc 261aa 6e-06 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].

CCDC7

• refseq_CCDC7.F2 refseq_CCDC7.R2 164 398
• NCBIGene 36.3 221016
• Alternative 5-prime, size difference: 234
• Exclusion in 5'UTR
• Reference transcript: NM_145023

CCL14

• refseq_CCL14.F1 refseq_CCL14.R1 100 148
• NCBIGene 36.3 6358
• Single exon skipping, size difference: 48
• Exclusion in 3'UTR
• Reference transcript: NM_032962

• cd Chemokine_CC 57aa 4e-17 in ref transcript
  • Chemokine_CC: 1 of 4 subgroup designations based on the arrangement of the two N-terminal cysteine residues; includes a number of secreted growth factors and interferons involved in mitogenic, chemotactic, and inflammatory activity; some members (e.g. 2HCC) contain an additional disulfide bond which is thought to compensate for the highly conserved Trp missing in these; chemotatic for monocytes, macrophages, eosinophils, basophils, and T cells, but not neutrophils; exist as monomers and dimers, but are believed to be functional as monomers; found only in vertebrates and a few viruses; a subgroup of CC, identified by an N-terminal DCCL motif (Exodus-1, Exodus-2, and Exodus-3), has been shown to inhibit specific types of human cancer cell growth in a mouse model. See CDs: Chemokine (cd00169) for the general alignment of chemokines, or Chemokine_CXC (cd00273), Chemokine_C (cd00271), and Chemokine_CX3C (cd00274) for the additional chemokine subgroups, and Chemokine_CC_DCCL for the DCCL subgroup of this CD.
• smart SCY 57aa 3e-19 in ref transcript
  • Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). Family of cytokines involved in cell-specific chemotaxis, mediation of cell growth, and the inflammatory response.

CCL23

• refseq_CCL23.F2 refseq_CCL23.R2 270 321
• NCBIGene 36.3 6368
• Alternative 3-prime, size difference: 51
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_005064

• cd Chemokine_CC 57aa 9e-15 in ref transcript
  • Chemokine_CC: 1 of 4 subgroup designations based on the arrangement of the two N-terminal cysteine residues; includes a number of secreted growth factors and interferons involved in mitogenic, chemotactic, and inflammatory activity; some members (e.g. 2HCC) contain an additional disulfide bond which is thought to compensate for the highly conserved Trp missing in these; chemotatic for monocytes, macrophages, eosinophils, basophils, and T cells, but not neutrophils; exist as monomers and dimers, but are believed to be functional as monomers; found only in vertebrates and a few viruses; a subgroup of CC, identified by an N-terminal DCCL motif (Exodus-1, Exodus-2, and Exodus-3), has been shown to inhibit specific types of human cancer cell growth in a mouse model. See CDs: Chemokine (cd00169) for the general alignment of chemokines, or Chemokine_CXC (cd00273), Chemokine_C (cd00271), and Chemokine_CX3C (cd00274) for the additional chemokine subgroups, and Chemokine_CC_DCCL for the DCCL subgroup of this CD.
• smart SCY 59aa 3e-18 in ref transcript
  • Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). Family of cytokines involved in cell-specific chemotaxis, mediation of cell growth, and the inflammatory response.

CCNL2

• refseq_CCNL2.F1 refseq_CCNL2.R1 126 342
• NCBIGene 36.3 81669
• Multiple exon skipping, size difference: 216
• Inclusion in the protein causing a new stop codon, Inclusion in the protein causing a frameshift
• Reference transcript: NM_030937

• cd CYCLIN 90aa 5e-09 in ref transcript
  • Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain.
• cd CYCLIN 74aa 2e-07 in ref transcript
• smart CYCLIN 83aa 3e-12 in ref transcript
  • domain present in cyclins, TFIIB and Retinoblastoma. A helical domain present in cyclins and TFIIB (twice) and Retinoblastoma (once). A protein recognition domain functioning in cell-cycle and transcription control.
• smart CYCLIN 65aa 8e-07 in ref transcript
• TIGR ccl1 224aa 2e-04 in ref transcript
  • University).
• COG CCL1 205aa 2e-27 in ref transcript
  • Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH/TFIIK, cyclin H subunit [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair].

CCR3

• refseq_CCR3.F1 refseq_CCR3.R1 204 283
• NCBIGene 36.3 1232
• Single exon skipping, size difference: 79
• Exclusion in 5'UTR
• Reference transcript: NM_001837

• pfam 7tm_1 245aa 4e-42 in ref transcript
  • 7 transmembrane receptor (rhodopsin family). This family contains, amongst other G-protein-coupled receptors (GCPRs), members of the opsin family, which have been considered to be typical members of the rhodopsin superfamily. They share several motifs, mainly the seven transmembrane helices, GCPRs of the rhodopsin superfamily. All opsins bind a chromophore, such as 11-cis-retinal. The function of most opsins other than the photoisomerases is split into two steps: light absorption and G-protein activation. Photoisomerases, on the other hand, are not coupled to G-proteins - they are thought to generate and supply the chromophore that is used by visual opsins.

CCR9

• refseq_CCR9.F2 refseq_CCR9.R2 246 295
• NCBIGene 36.3 10803
• Single exon skipping, size difference: 49
• Exclusion of the protein initiation site
• Reference transcript: NM_031200

• pfam 7tm_1 247aa 3e-35 in ref transcript
  • 7 transmembrane receptor (rhodopsin family). This family contains, amongst other G-protein-coupled receptors (GCPRs), members of the opsin family, which have been considered to be typical members of the rhodopsin superfamily. They share several motifs, mainly the seven transmembrane helices, GCPRs of the rhodopsin superfamily. All opsins bind a chromophore, such as 11-cis-retinal. The function of most opsins other than the photoisomerases is split into two steps: light absorption and G-protein activation. Photoisomerases, on the other hand, are not coupled to G-proteins - they are thought to generate and supply the chromophore that is used by visual opsins.

CCRK

• refseq_CCRK.F1 refseq_CCRK.R1 176 239
• NCBIGene 36.3 23552
• Single exon skipping, size difference: 63
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001039803

• Changed! cd S_TKc 286aa 2e-64 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• Changed! smart S_TKc 275aa 6e-63 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• Changed! PTZ PTZ00024 292aa 4e-49 in ref transcript
  • cyclin-dependent protein kinase; Provisional.
• Changed! cd S_TKc 265aa 2e-52 in modified transcript
• Changed! smart S_TKc 254aa 3e-50 in modified transcript
• Changed! PTZ PTZ00024 271aa 6e-37 in modified transcript

CCRK

• refseq_CCRK.F4 refseq_CCRK.R4 209 248
• NCBIGene 36.3 23552
• Alternative 3-prime, size difference: 39
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_001039803

• Changed! cd S_TKc 286aa 2e-64 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• Changed! smart S_TKc 275aa 6e-63 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• Changed! PTZ PTZ00024 292aa 4e-49 in ref transcript
  • cyclin-dependent protein kinase; Provisional.
• Changed! cd S_TKc 299aa 7e-62 in modified transcript
• Changed! smart S_TKc 288aa 3e-60 in modified transcript
• Changed! PTZ PTZ00024 305aa 1e-47 in modified transcript

CCT3

• refseq_CCT3.F1 refseq_CCT3.R1 129 243
• NCBIGene 36.3 7203
• Multiple exon skipping, size difference: 114
• Exclusion in the protein (no frameshift), Exclusion in the protein (no frameshift)
• Reference transcript: NM_005998

• Changed! cd TCP1_gamma 520aa 0.0 in ref transcript
  • TCP-1 (CTT or eukaryotic type II) chaperonin family, gamma subunit. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings. In contrast to bacterial group I chaperonins (GroEL), each ring of the eukaryotic cytosolic chaperonin (CTT) consists of eight different, but homologous subunits. Their common function is to sequester nonnative proteins inside their central cavity and promote folding by using energy derived from ATP hydrolysis. The best studied in vivo substrates of CTT are actin and tubulin.
• Changed! TIGR chap_CCT_gamma 524aa 0.0 in ref transcript
  • Members of this family, all eukaryotic, are part of the group II chaperonin complex called CCT (chaperonin containing TCP-1) or TRiC. The archaeal equivalent group II chaperonin is often called the thermosome. Both are somewhat related to the group I chaperonin of bacterial, GroEL/GroES. This family consists exclusively of the CCT gamma chain (part of a paralogous family) from animals, plants, fungi, and other eukaryotes.
• Changed! COG GroL 521aa 1e-117 in ref transcript
  • Chaperonin GroEL (HSP60 family) [Posttranslational modification, protein turnover, chaperones].
• Changed! cd TCP1_gamma 482aa 0.0 in modified transcript
• Changed! TIGR chap_CCT_gamma 486aa 0.0 in modified transcript
• Changed! COG GroL 464aa 5e-99 in modified transcript

CCT6A

• refseq_CCT6A.F1 refseq_CCT6A.R1 171 306
• NCBIGene 36.3 908
• Single exon skipping, size difference: 135
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001762

• Changed! cd TCP1_zeta 520aa 0.0 in ref transcript
  • TCP-1 (CTT or eukaryotic type II) chaperonin family, zeta subunit. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings. In contrast to bacterial group I chaperonins (GroEL), each ring of the eukaryotic cytosolic chaperonin (CTT) consists of eight different, but homologous subunits. Their common function is to sequester nonnative proteins inside their central cavity and promote folding by using energy derived from ATP hydrolysis. The best studied in vivo substrates of CTT are actin and tubulin.
• Changed! TIGR chap_CCT_zeta 528aa 0.0 in ref transcript
  • Members of this family, all eukaryotic, are part of the group II chaperonin complex called CCT (chaperonin containing TCP-1) or TRiC. The archaeal equivalent group II chaperonin is often called the thermosome. Both are somewhat related to the group I chaperonin of bacterial, GroEL/GroES. This family consists exclusively of the CCT zeta chain (part of a paralogous family) from animals, plants, fungi, and other eukaryotes.
• Changed! COG GroL 503aa 5e-93 in ref transcript
  • Chaperonin GroEL (HSP60 family) [Posttranslational modification, protein turnover, chaperones].
• Changed! cd TCP1_zeta 475aa 0.0 in modified transcript
• Changed! TIGR chap_CCT_zeta 483aa 0.0 in modified transcript
• Changed! COG GroL 458aa 8e-73 in modified transcript

CD151

• refseq_CD151.F1 refseq_CD151.R1 101 163
• NCBIGene 36.3 977
• Single exon skipping, size difference: 62
• Exclusion in 5'UTR
• Reference transcript: NM_004357

• cd CD151_like_LEL 109aa 3e-40 in ref transcript
  • Tetraspanin, extracellular domain or large extracellular loop (LEL), CD151_Like family. Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. Tetraspanins are involved in diverse processes and their various functions may relate to their ability to act as molecular facilitators. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web". CD151strongly associates with integrins, especially alpha3beta1, alpha6beta1, alpha7beta1, and alpha6beta4; it may play roles in cell-cell adhesion, cell migration, platelet aggregation, and angiogenesis. For example, CD151 is is involved in regulation of migration of neutrophils, endothelial cells, and various tumor cell lines; it associates specifically with laminin-binding integrins and strengthens alpha6beta1 integrin-mediated adhesion to laminin-1; CD151 also specifically attenuates adhesion-dependent activation of Ras and correspdonding downstream effects, and is involved in epithelial cell-cell adhesion as a modulator of PKC- and Cdc42-dependent actin cytoskeletal reorganization.
• pfam Tetraspannin 234aa 2e-31 in ref transcript
  • Tetraspanin family.

CD163

• refseq_CD163.F2 refseq_CD163.R2 309 392
• NCBIGene 36.3 9332
• Alternative 3-prime, size difference: 83
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_004244

• smart SR 101aa 4e-39 in ref transcript
  • Scavenger receptor Cys-rich. The sea ucrhin egg peptide speract contains 4 repeats of SR domains that contain 6 conserved cysteines. May bind bacterial antigens in the protein MARCO.
• smart SR 101aa 1e-35 in ref transcript
• smart SR 102aa 6e-35 in ref transcript
• smart SR 101aa 1e-34 in ref transcript
• smart SR 101aa 5e-31 in ref transcript
• smart SR 100aa 5e-30 in ref transcript
• smart SR 101aa 1e-28 in ref transcript
• smart SR 101aa 4e-27 in ref transcript
• smart SR 102aa 1e-17 in ref transcript

CD200

• refseq_CD200.F2 refseq_CD200.R2 280 355
• NCBIGene 36.3 4345
• Single exon skipping, size difference: 75
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001004196

• smart IGv 77aa 2e-07 in ref transcript
  • Immunoglobulin V-Type.
• pfam ig 64aa 0.003 in ref transcript
  • Immunoglobulin domain. Members of the immunoglobulin superfamily are found in hundreds of proteins of different functions. Examples include antibodies, the giant muscle kinase titin and receptor tyrosine kinases. Immunoglobulin-like domains may be involved in protein-protein and protein-ligand interactions. The Pfam alignments do not include the first and last strand of the immunoglobulin-like domain.

CD200R1

• refseq_CD200R1.F2 refseq_CD200R1.R2 318 387
• NCBIGene 36.3 131450
• Single exon skipping, size difference: 69
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_138806

• pfam C2-set_2 70aa 0.002 in ref transcript
  • CD80-like C2-set immunoglobulin domain. These domains belong to the immunoglobulin superfamily.

CD34

• refseq_CD34.F1 refseq_CD34.R1 151 346
• NCBIGene 36.3 947
• Alternative 3-prime, size difference: 195
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_001025109

• Changed! pfam CD34_antigen 196aa 3e-55 in ref transcript
  • CD34/Podocalyxin family. This family consists of several mammalian CD34 antigen proteins. The CD34 antigen is a human leukocyte membrane protein expressed specifically by lymphohematopoietic progenitor cells. CD34 is a phosphoprotein. Activation of protein kinase C (PKC) has been found to enhance CD34 phosphorylation. This family contains several eukaryotic podocalyxin proteins. Podocalyxin is a major membrane protein of the glomerular epithelium and is thought to be involved in maintenance of the architecture of the foot processes and filtration slits characteristic of this unique epithelium by virtue of its high negative charge. Podocalyxin functions as an anti-adhesin that maintains an open filtration pathway between neighbouring foot processes in the glomerular epithelium by charge repulsion.
• Changed! pfam CD34_antigen 139aa 3e-38 in modified transcript

CD37

• refseq_CD37.F1 refseq_CD37.R1 172 206
• NCBIGene 36.3 951
• Alternative 5-prime, size difference: 34
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_001774

• Changed! cd CD37_CD82_like_LEL 136aa 9e-38 in ref transcript
  • Tetraspanin, extracellular domain or large extracellular loop (LEL), CD37_CD82_Like family. Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. Tetraspanins are involved in diverse processes and their various functions may relate to their ability to act as molecular facilitators. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web". CD37 is a leukocyte-specific protein, and its restricted expression pattern suggests a role in the immune system. A regulatory role in T-cell proliferation has been suggested. CD82 is a metastasis suppressor implicated in biological processes ranging from fusion, adhesion, and migration to apoptosis and alterations of cell morphology.
• Changed! pfam Tetraspannin 262aa 5e-25 in ref transcript
  • Tetraspanin family.

CD46

• refseq_CD46.F1 refseq_CD46.R1 197 239
• NCBIGene 36.3 4179
• Single exon skipping, size difference: 42
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_172359

• cd CCP 60aa 4e-08 in ref transcript
  • Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR); The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function.
• cd CCP 63aa 1e-06 in ref transcript
• cd CCP 50aa 4e-05 in ref transcript
• pfam Sushi 62aa 5e-09 in ref transcript
  • Sushi domain (SCR repeat).
• pfam Sushi 59aa 2e-08 in ref transcript
• smart CCP 50aa 6e-06 in ref transcript
  • Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR). The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. A missense mutation in seventh CCP domain causes deficiency of the b subunit of factor XIII.
• smart CCP 54aa 5e-04 in ref transcript

CD46

• refseq_CD46.F3 refseq_CD46.R3 120 213
• NCBIGene 36.3 4179
• Single exon skipping, size difference: 93
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_172359

• cd CCP 60aa 4e-08 in ref transcript
  • Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR); The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function.
• cd CCP 63aa 1e-06 in ref transcript
• cd CCP 50aa 4e-05 in ref transcript
• pfam Sushi 62aa 5e-09 in ref transcript
  • Sushi domain (SCR repeat).
• pfam Sushi 59aa 2e-08 in ref transcript
• smart CCP 50aa 6e-06 in ref transcript
  • Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR). The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. A missense mutation in seventh CCP domain causes deficiency of the b subunit of factor XIII.
• smart CCP 54aa 5e-04 in ref transcript

CD46

• refseq_CD46.F4 refseq_CD46.R4 228 273
• NCBIGene 36.3 4179
• Single exon skipping, size difference: 45
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_172359

• cd CCP 60aa 4e-08 in ref transcript
  • Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR); The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function.
• cd CCP 63aa 1e-06 in ref transcript
• Changed! cd CCP 50aa 4e-05 in ref transcript
• pfam Sushi 62aa 5e-09 in ref transcript
  • Sushi domain (SCR repeat).
• pfam Sushi 59aa 2e-08 in ref transcript
• Changed! smart CCP 50aa 6e-06 in ref transcript
  • Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR). The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. A missense mutation in seventh CCP domain causes deficiency of the b subunit of factor XIII.
• smart CCP 54aa 5e-04 in ref transcript
• Changed! cd CCP 56aa 6e-08 in modified transcript
• Changed! smart CCP 56aa 5e-09 in modified transcript

CD68

• refseq_CD68.F1 refseq_CD68.R1 234 315
• NCBIGene 36.3 968
• Alternative 3-prime, size difference: 81
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001251

• pfam Lamp 201aa 2e-34 in ref transcript
  • Lysosome-associated membrane glycoprotein (Lamp).

CD74

• refseq_CD74.F1 refseq_CD74.R1 118 310
• NCBIGene 36.3 972
• Single exon skipping, size difference: 192
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001025159

• Changed! cd TY 60aa 5e-14 in ref transcript
  • Thyroglobulin type I repeats.; The N-terminal region of human thyroglobulin contains 11 type-1 repeats TY repeats are proposed to be inhibitors of cysteine proteases.
• pfam MHC2-interact 113aa 2e-35 in ref transcript
  • CLIP, MHC2 interacting. Members of this family are found in class II invariant chain-associated peptide (CLIP), and are required for association with class II major histocompatibility complex (MHC) in the MHC class II processing pathway.
• pfam MHCassoc_trimer 72aa 1e-31 in ref transcript
  • Class II MHC-associated invariant chain trimerisation domain. The class II associated invariant chain peptide is required for folding and localisation of MHC class II heterodimers. This domain is involved in trimerisation of the ectoderm and interferes with DM/class II binding. The trimeric protein forms a cylindrical shape which is thought to be important for interactions between the invariant chain and class II molecules.
• Changed! pfam Thyroglobulin_1 59aa 1e-16 in ref transcript
  • Thyroglobulin type-1 repeat. Thyroglobulin type 1 repeats are thought to be involved in the control of proteolytic degradation. The domain usually contains six conserved cysteines. These form three disulphide bridges. Cysteines 1 pairs with 2, 3 with 4 and 5 with 6.

CD79A

• refseq_CD79A.F1 refseq_CD79A.R1 202 316
• NCBIGene 36.3 973
• Alternative 5-prime, size difference: 114
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001783

• Changed! cd IGcam 91aa 2e-04 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• Changed! smart IG_like 88aa 2e-11 in ref transcript
  • Immunoglobulin like. IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
• Changed! pfam ITAM 21aa 0.010 in modified transcript
  • Immunoreceptor tyrosine-based activation motif.

CD79B

• refseq_CD79B.F1 refseq_CD79B.R1 101 413
• NCBIGene 36.3 974
• Single exon skipping, size difference: 312
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001039933

• Changed! cd IGv 87aa 0.006 in ref transcript
  • Immunoglobulin domain variable region (v) subfamily; members of the IGv subfamily are components of immunoglobulins and T-cell receptors. In immunoglobulins, each chain is composed of one variable domain (IGv) and one or more constant domains (IGc); these names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. Within the variable domain, there are regions of even more variability called the hypervariable or complementarity-determining regions (CDRs) which are responsible for antigen binding. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• Changed! pfam V-set 101aa 5e-11 in ref transcript
  • Immunoglobulin V-set domain. This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.

CD8A

• refseq_CD8A.F2 refseq_CD8A.R2 155 266
• NCBIGene 36.3 925
• Single exon skipping, size difference: 111
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001768

• cd IGv 94aa 3e-05 in ref transcript
  • Immunoglobulin domain variable region (v) subfamily; members of the IGv subfamily are components of immunoglobulins and T-cell receptors. In immunoglobulins, each chain is composed of one variable domain (IGv) and one or more constant domains (IGc); these names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. Within the variable domain, there are regions of even more variability called the hypervariable or complementarity-determining regions (CDRs) which are responsible for antigen binding. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• pfam V-set 107aa 4e-11 in ref transcript
  • Immunoglobulin V-set domain. This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.

CD8B

• refseq_CD8B.F2 refseq_CD8B.R2 192 250
• NCBIGene 36.3 926
• Alternative 3-prime, size difference: 58
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_172099

• cd IGv 105aa 1e-09 in ref transcript
  • Immunoglobulin domain variable region (v) subfamily; members of the IGv subfamily are components of immunoglobulins and T-cell receptors. In immunoglobulins, each chain is composed of one variable domain (IGv) and one or more constant domains (IGc); these names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. Within the variable domain, there are regions of even more variability called the hypervariable or complementarity-determining regions (CDRs) which are responsible for antigen binding. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• pfam V-set 116aa 3e-19 in ref transcript
  • Immunoglobulin V-set domain. This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.

CD8B

• refseq_CD8B.F2 refseq_CD8B.R5 180 234
• NCBIGene 36.3 926
• Single exon skipping, size difference: 54
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_172213

• cd IGv 105aa 4e-09 in ref transcript
  • Immunoglobulin domain variable region (v) subfamily; members of the IGv subfamily are components of immunoglobulins and T-cell receptors. In immunoglobulins, each chain is composed of one variable domain (IGv) and one or more constant domains (IGc); these names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. Within the variable domain, there are regions of even more variability called the hypervariable or complementarity-determining regions (CDRs) which are responsible for antigen binding. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• pfam V-set 116aa 6e-19 in ref transcript
  • Immunoglobulin V-set domain. This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.

CD8B

• refseq_CD8B.F3 refseq_CD8B.R3 123 213
• NCBIGene 36.3 926
• Single exon skipping, size difference: 90
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_172099

• cd IGv 105aa 1e-09 in ref transcript
  • Immunoglobulin domain variable region (v) subfamily; members of the IGv subfamily are components of immunoglobulins and T-cell receptors. In immunoglobulins, each chain is composed of one variable domain (IGv) and one or more constant domains (IGc); these names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. Within the variable domain, there are regions of even more variability called the hypervariable or complementarity-determining regions (CDRs) which are responsible for antigen binding. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• pfam V-set 116aa 3e-19 in ref transcript
  • Immunoglobulin V-set domain. This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.

CD96

• refseq_CD96.F1 refseq_CD96.R1 191 239
• NCBIGene 36.3 10225
• Single exon skipping, size difference: 48
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_198196

• COG COG5099 153aa 0.008 in ref transcript
  • RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal structure and biogenesis].

CD97

• refseq_CD97.F1 refseq_CD97.R1 204 351
• NCBIGene 36.3 976
• Single exon skipping, size difference: 147
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_078481

• Changed! cd EGF_CA 37aa 3e-05 in ref transcript
  • Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements.
• cd EGF_CA 33aa 4e-05 in ref transcript
• Changed! cd EGF_CA 34aa 6e-05 in ref transcript
• cd EGF_CA 35aa 0.001 in ref transcript
• pfam 7tm_2 250aa 1e-78 in ref transcript
  • 7 transmembrane receptor (Secretin family). This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling.
• Changed! pfam EGF_CA 48aa 4e-10 in ref transcript
  • Calcium binding EGF domain.
• smart GPS 51aa 7e-10 in ref transcript
  • G-protein-coupled receptor proteolytic site domain. Present in latrophilin/CL-1, sea urchin REJ and polycystin.
• Changed! pfam EGF_CA 35aa 2e-09 in ref transcript
• smart EGF_CA 33aa 3e-06 in ref transcript
  • Calcium-binding EGF-like domain.
• pfam EGF_CA 51aa 9e-06 in ref transcript
• COG PutP 125aa 0.004 in ref transcript
  • Na+/proline symporter [Amino acid transport and metabolism / General function prediction only].
• Changed! cd EGF_CA 37aa 1e-05 in modified transcript
• Changed! pfam EGF_CA 35aa 6e-10 in modified transcript
• Changed! smart EGF_CA 44aa 1e-06 in modified transcript

CD99L2

• refseq_CD99L2.F1 refseq_CD99L2.R1 209 356
• NCBIGene 36.3 83692
• Multiple exon skipping, size difference: 147
• Exclusion in the protein (no frameshift), Exclusion in the protein (no frameshift)
• Reference transcript: NM_031462

CDC14B

• refseq_CDC14B.F2 refseq_CDC14B.R2 231 348
• NCBIGene 36.3 8555
• Single exon skipping, size difference: 117
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_033331

• cd DSPc 108aa 1e-09 in ref transcript
  • Dual specificity phosphatases (DSP); Ser/Thr and Tyr protein phosphatases. Structurally similar to tyrosine-specific phosphatases but with a shallower active site cleft and a distinctive active site signature motif, HCxxGxxR. Characterized as VHR- or Cdc25-like.
• smart DSPc 116aa 7e-12 in ref transcript
  • Dual specificity phosphatase, catalytic domain.
• PTZ PTZ00242 139aa 2e-20 in ref transcript
  • protein tyrosine phosphatase; Provisional.

CDC25A

• refseq_CDC25A.F1 refseq_CDC25A.R1 145 265
• NCBIGene 36.3 993
• Single exon skipping, size difference: 120
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001789

• cd Cdc25 119aa 5e-50 in ref transcript
  • Cdc25 phosphatases are members of the Rhodanese Homology Domain superfamily. They activate the cell division kinases throughout the cell cycle progression. Cdc25 phosphatases dephosphorylate phosphotyrosine and phosphothreonine residues, in order to activate their Cdk/cyclin substrates. Cdc25A phosphatase functions to regulate S phase entry and Cdc25B is required for G2/M phase transition of the cell cycle. The Cdc25 domain binds oxyanions at the catalytic site and has the signature motif (H/YCxxxxxR).
• Changed! pfam M-inducer_phosp 244aa 4e-65 in ref transcript
  • M-phase inducer phosphatase. This family represents a region within eukaryotic M-phase inducer phosphatases (EC:3.1.3.48), which also contain the pfam00581 domain. These proteins are involved in the control of mitosis.
• pfam Rhodanese 108aa 4e-24 in ref transcript
  • Rhodanese-like domain. Rhodanese has an internal duplication. This Pfam represents a single copy of this duplicated domain. The domain is found as a single copy in other proteins, including phosphatases and ubiquitin C-terminal hydrolases.
• COG MIH1 233aa 1e-31 in ref transcript
  • Mitotic inducer, protein phosphatase [Cell division and chromosome partitioning].
• Changed! pfam M-inducer_phosp 204aa 2e-54 in modified transcript

CDC25B

• refseq_CDC25B.F2 refseq_CDC25B.R2 129 171
• NCBIGene 36.3 994
• Alternative 3-prime, size difference: 42
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_021873

• cd Cdc25 120aa 9e-49 in ref transcript
  • Cdc25 phosphatases are members of the Rhodanese Homology Domain superfamily. They activate the cell division kinases throughout the cell cycle progression. Cdc25 phosphatases dephosphorylate phosphotyrosine and phosphothreonine residues, in order to activate their Cdk/cyclin substrates. Cdc25A phosphatase functions to regulate S phase entry and Cdc25B is required for G2/M phase transition of the cell cycle. The Cdc25 domain binds oxyanions at the catalytic site and has the signature motif (H/YCxxxxxR).
• pfam M-inducer_phosp 272aa 1e-76 in ref transcript
  • M-phase inducer phosphatase. This family represents a region within eukaryotic M-phase inducer phosphatases (EC:3.1.3.48), which also contain the pfam00581 domain. These proteins are involved in the control of mitosis.
• pfam Rhodanese 109aa 9e-25 in ref transcript
  • Rhodanese-like domain. Rhodanese has an internal duplication. This Pfam represents a single copy of this duplicated domain. The domain is found as a single copy in other proteins, including phosphatases and ubiquitin C-terminal hydrolases.
• COG MIH1 158aa 7e-34 in ref transcript
  • Mitotic inducer, protein phosphatase [Cell division and chromosome partitioning].

CDC25B

• refseq_CDC25B.F3 refseq_CDC25B.R3 101 224
• NCBIGene 36.3 994
• Single exon skipping, size difference: 123
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_021873

• cd Cdc25 120aa 9e-49 in ref transcript
  • Cdc25 phosphatases are members of the Rhodanese Homology Domain superfamily. They activate the cell division kinases throughout the cell cycle progression. Cdc25 phosphatases dephosphorylate phosphotyrosine and phosphothreonine residues, in order to activate their Cdk/cyclin substrates. Cdc25A phosphatase functions to regulate S phase entry and Cdc25B is required for G2/M phase transition of the cell cycle. The Cdc25 domain binds oxyanions at the catalytic site and has the signature motif (H/YCxxxxxR).
• Changed! pfam M-inducer_phosp 272aa 1e-76 in ref transcript
  • M-phase inducer phosphatase. This family represents a region within eukaryotic M-phase inducer phosphatases (EC:3.1.3.48), which also contain the pfam00581 domain. These proteins are involved in the control of mitosis.
• pfam Rhodanese 109aa 9e-25 in ref transcript
  • Rhodanese-like domain. Rhodanese has an internal duplication. This Pfam represents a single copy of this duplicated domain. The domain is found as a single copy in other proteins, including phosphatases and ubiquitin C-terminal hydrolases.
• COG MIH1 158aa 7e-34 in ref transcript
  • Mitotic inducer, protein phosphatase [Cell division and chromosome partitioning].
• Changed! pfam M-inducer_phosp 231aa 9e-65 in modified transcript

CDC25C

• refseq_CDC25C.F1 refseq_CDC25C.R1 133 228
• NCBIGene 36.3 995
• Single exon skipping, size difference: 95
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_001790

• Changed! cd Cdc25 120aa 4e-45 in ref transcript
  • Cdc25 phosphatases are members of the Rhodanese Homology Domain superfamily. They activate the cell division kinases throughout the cell cycle progression. Cdc25 phosphatases dephosphorylate phosphotyrosine and phosphothreonine residues, in order to activate their Cdk/cyclin substrates. Cdc25A phosphatase functions to regulate S phase entry and Cdc25B is required for G2/M phase transition of the cell cycle. The Cdc25 domain binds oxyanions at the catalytic site and has the signature motif (H/YCxxxxxR).
• Changed! pfam M-inducer_phosp 180aa 1e-43 in ref transcript
  • M-phase inducer phosphatase. This family represents a region within eukaryotic M-phase inducer phosphatases (EC:3.1.3.48), which also contain the pfam00581 domain. These proteins are involved in the control of mitosis.
• Changed! pfam Rhodanese 107aa 6e-22 in ref transcript
  • Rhodanese-like domain. Rhodanese has an internal duplication. This Pfam represents a single copy of this duplicated domain. The domain is found as a single copy in other proteins, including phosphatases and ubiquitin C-terminal hydrolases.
• Changed! COG MIH1 241aa 1e-35 in ref transcript
  • Mitotic inducer, protein phosphatase [Cell division and chromosome partitioning].

CDC25C

• refseq_CDC25C.F2 refseq_CDC25C.R2 141 360
• NCBIGene 36.3 995
• Multiple exon skipping, size difference: 124
• Exclusion in the protein causing a frameshift, Exclusion in the protein (no frameshift)
• Reference transcript: NM_001790

• Changed! cd Cdc25 120aa 4e-45 in ref transcript
  • Cdc25 phosphatases are members of the Rhodanese Homology Domain superfamily. They activate the cell division kinases throughout the cell cycle progression. Cdc25 phosphatases dephosphorylate phosphotyrosine and phosphothreonine residues, in order to activate their Cdk/cyclin substrates. Cdc25A phosphatase functions to regulate S phase entry and Cdc25B is required for G2/M phase transition of the cell cycle. The Cdc25 domain binds oxyanions at the catalytic site and has the signature motif (H/YCxxxxxR).
• Changed! pfam M-inducer_phosp 180aa 1e-43 in ref transcript
  • M-phase inducer phosphatase. This family represents a region within eukaryotic M-phase inducer phosphatases (EC:3.1.3.48), which also contain the pfam00581 domain. These proteins are involved in the control of mitosis.
• Changed! pfam Rhodanese 107aa 6e-22 in ref transcript
  • Rhodanese-like domain. Rhodanese has an internal duplication. This Pfam represents a single copy of this duplicated domain. The domain is found as a single copy in other proteins, including phosphatases and ubiquitin C-terminal hydrolases.
• Changed! COG MIH1 241aa 1e-35 in ref transcript
  • Mitotic inducer, protein phosphatase [Cell division and chromosome partitioning].

CDC25C

• refseq_CDC25C.F3 refseq_CDC25C.R3 281 500
• NCBIGene 36.3 995
• Multiple exon skipping, size difference: 124
• Exclusion in the protein causing a frameshift, Exclusion in the protein (no frameshift)
• Reference transcript: NM_001790

• Changed! cd Cdc25 120aa 4e-45 in ref transcript
  • Cdc25 phosphatases are members of the Rhodanese Homology Domain superfamily. They activate the cell division kinases throughout the cell cycle progression. Cdc25 phosphatases dephosphorylate phosphotyrosine and phosphothreonine residues, in order to activate their Cdk/cyclin substrates. Cdc25A phosphatase functions to regulate S phase entry and Cdc25B is required for G2/M phase transition of the cell cycle. The Cdc25 domain binds oxyanions at the catalytic site and has the signature motif (H/YCxxxxxR).
• Changed! pfam M-inducer_phosp 180aa 1e-43 in ref transcript
  • M-phase inducer phosphatase. This family represents a region within eukaryotic M-phase inducer phosphatases (EC:3.1.3.48), which also contain the pfam00581 domain. These proteins are involved in the control of mitosis.
• Changed! pfam Rhodanese 107aa 6e-22 in ref transcript
  • Rhodanese-like domain. Rhodanese has an internal duplication. This Pfam represents a single copy of this duplicated domain. The domain is found as a single copy in other proteins, including phosphatases and ubiquitin C-terminal hydrolases.
• Changed! COG MIH1 241aa 1e-35 in ref transcript
  • Mitotic inducer, protein phosphatase [Cell division and chromosome partitioning].

CDC2L1

• refseq_CDC2L1.F2 refseq_CDC2L1.R5 134 167
• NCBIGene 36.3 984
• Alternative 5-prime and 3-prime, size difference: 33
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_033486

• cd S_TKc 287aa 3e-68 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• smart S_TKc 276aa 1e-68 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• PTZ PTZ00024 295aa 4e-55 in ref transcript
  • cyclin-dependent protein kinase; Provisional.

CDC2L1

• refseq_CDC2L1.F3 refseq_CDC2L1.R3 106 133
• NCBIGene 36.3 984
• Alternative 3-prime, size difference: 27
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_033486

• cd S_TKc 287aa 3e-68 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• smart S_TKc 276aa 1e-68 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• PTZ PTZ00024 295aa 4e-55 in ref transcript
  • cyclin-dependent protein kinase; Provisional.

CDC2L2

• refseq_CDC2L2.F3 refseq_CDC2L2.R3 128 244
• NCBIGene 36.2 985
• Alternative 5-prime, size difference: 116
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_033531

• Changed! cd S_TKc 287aa 1e-68 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• Changed! smart S_TKc 276aa 5e-69 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• Changed! PTZ PTZ00024 295aa 4e-55 in ref transcript
  • cyclin-dependent protein kinase; Provisional.

CDC2L5

• refseq_CDC2L5.F1 refseq_CDC2L5.R1 141 321
• NCBIGene 36.3 8621
• Alternative 3-prime, size difference: 180
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_003718

• cd S_TKc 295aa 4e-72 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• pfam Pkinase 294aa 2e-74 in ref transcript
  • Protein kinase domain.
• PTZ PTZ00024 301aa 2e-47 in ref transcript
  • cyclin-dependent protein kinase; Provisional.

CDC42

• refseq_CDC42.F1 refseq_CDC42.R1 235 361
• NCBIGene 36.3 998
• Single exon skipping, size difference: 126
• Exclusion in 5'UTR
• Reference transcript: NM_001039802

• cd Cdc42 175aa 1e-104 in ref transcript
  • Cdc42 subfamily. Cdc42 is an essential GTPase that belongs to the Rho family of Ras-like GTPases. These proteins act as molecular switches by responding to exogenous and/or endogenous signals and relaying those signals to activate downstream components of a biological pathway. Cdc42 transduces signals to the actin cytoskeleton to initiate and maintain polarized growth and to mitogen-activated protein morphogenesis. In the budding yeast Saccharomyces cerevisiae, Cdc42 plays an important role in multiple actin-dependent morphogenetic events such as bud emergence, mating-projection formation, and pseudohyphal growth. In mammalian cells, Cdc42 regulates a variety of actin-dependent events and induces the JNK/SAPK protein kinase cascade, which leads to the activation of transcription factors within the nucleus. Cdc42 mediates these processes through interactions with a myriad of downstream effectors, whose number and regulation we are just starting to understand. In addition, Cdc42 has been implicated in a number of human diseases through interactions with its regulators and downstream effectors. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.
• smart RHO 174aa 5e-94 in ref transcript
  • Rho (Ras homology) subfamily of Ras-like small GTPases. Members of this subfamily of Ras-like small GTPases include Cdc42 and Rac, as well as Rho isoforms.
• COG COG1100 183aa 2e-30 in ref transcript
  • GTPase SAR1 and related small G proteins [General function prediction only].

CDC42SE1

• refseq_CDC42SE1.F2 refseq_CDC42SE1.R2 100 236
• NCBIGene 36.3 56882
• Single exon skipping, size difference: 136
• Exclusion in 5'UTR
• Reference transcript: NM_001038707

CDC42SE2

• refseq_CDC42SE2.F1 refseq_CDC42SE2.R1 232 401
• NCBIGene 36.3 56990
• Single exon skipping, size difference: 169
• Exclusion in 5'UTR
• Reference transcript: NM_020240

• cd CRIB 41aa 1e-06 in ref transcript
  • PAK (p21 activated kinase) Binding Domain (PBD), binds Cdc42p- and/or Rho-like small GTPases; also known as the Cdc42/Rac interactive binding (CRIB) motif; has been shown to inhibit transcriptional activation and cell transformation mediated by the Ras-Rac pathway. CRIB-containing effector proteins are functionally diverse and include serine/threonine kinases, tyrosine kinases, actin-binding proteins, and adapter molecules.
• pfam PBD 15aa 0.002 in ref transcript
  • P21-Rho-binding domain. Small domains that bind Cdc42p- and/or Rho-like small GTPases. Also known as the Cdc42/Rac interactive binding (CRIB).

NUF2

• refseq_CDCA1.F1 refseq_CDCA1.R1 243 389
• NCBIGene 36.3 83540
• Alternative 5-prime, size difference: 146
• Exclusion in 5'UTR
• Reference transcript: NM_145697

• pfam Nuf2 148aa 3e-62 in ref transcript
  • Nuf2 family. Members of this family are components of the mitotic spindle. It has been shown that Nuf2 from yeast is part of a complex called the Ndc80p complex. This complex is thought to bind to the microtubules of the spindle. An arabidopsis protein has been included in this family that has previously not been identified as a member of this family. The match is not strong, but in common with other members of this family contains coiled-coil to the C terminus of this region.
• pfam SMC_N 307aa 4e-10 in ref transcript
  • RecF/RecN/SMC N terminal domain. This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.
• COG Smc 316aa 4e-07 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].

CDCA7

• refseq_CDCA7.F1 refseq_CDCA7.R1 152 389
• NCBIGene 36.3 83879
• Single exon skipping, size difference: 237
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_031942

• pfam zf-4CXXC_R1 101aa 6e-51 in ref transcript
  • Zinc-finger domain of monoamine-oxidase A repressor R1. R1 is a transcription factor repressor that inhibits monoamine oxidase A gene expression. This domain is a four-CXXC zinc finger putative DNA-binding domain found at the C-terminal end of R1. The domain carries 12 cysteines of which four pairs are of the CXXC type.

CDH24

• refseq_CDH24.F1 refseq_CDH24.R1 112 226
• NCBIGene 36.3 64403
• Single exon skipping, size difference: 114
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_022478

• Changed! cd CA 192aa 2e-37 in ref transcript
  • Cadherin repeat domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion; these domains occur as repeats in the extracellular regions which are thought to mediate cell-cell contact when bound to calcium; plays a role in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-,CNR-,proto-,and FAT-family cadherin, desmocollin, and desmoglein, exists as monomers or dimers (hetero- and homo-); two copies of the repeat are present here.
• cd CA 186aa 2e-36 in ref transcript
• cd CA 214aa 4e-34 in ref transcript
• Changed! cd CA 237aa 2e-25 in ref transcript
• pfam Cadherin_C 150aa 9e-23 in ref transcript
  • Cadherin cytoplasmic region. Cadherins are vital in cell-cell adhesion during tissue differentiation. Cadherins are linked to the cytoskeleton by catenins. Catenins bind to the cytoplasmic tail of the cadherin. Cadherins cluster to form foci of homophilic binding units. A key determinant to the strength of the binding that it is mediated by cadherins is the juxtamembrane region of the cadherin. This region induces clustering and also binds to the protein p120ctn.
• smart CA 79aa 1e-16 in ref transcript
  • Cadherin repeats. Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. Cadherin domains occur as repeats in the extracellular regions which are thought to mediate cell-cell contact when bound to calcium.
• pfam Cadherin 103aa 1e-15 in ref transcript
  • Cadherin domain.
• Changed! pfam Cadherin 77aa 3e-15 in ref transcript
• pfam Cadherin 81aa 1e-11 in ref transcript
• Changed! smart CA 116aa 1e-10 in ref transcript
• pfam Cadherin 95aa 9e-05 in ref transcript
• Changed! cd CA 208aa 3e-39 in modified transcript
• Changed! cd CA 199aa 6e-30 in modified transcript
• Changed! pfam Cadherin 90aa 2e-16 in modified transcript

CDK10

• refseq_CDK10.F3 refseq_CDK10.R3 195 329
• NCBIGene 36.3 8558
• Alternative 3-prime, size difference: 134
• Exclusion of the stop codon
• Reference transcript: NM_052988

• cd S_TKc 286aa 1e-62 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• pfam Pkinase 285aa 5e-62 in ref transcript
  • Protein kinase domain.
• Changed! PTZ PTZ00024 296aa 2e-52 in ref transcript
  • cyclin-dependent protein kinase; Provisional.
• Changed! PTZ PTZ00024 293aa 6e-50 in modified transcript

CDK10

• refseq_CDK10.F5 refseq_CDK10.R6 109 257
• NCBIGene 36.2 8558
• Exon skipping and alternative 3-prime or 5-prime, size difference: 148
• Exclusion in 5'UTR, Exclusion in 5'UTR
• Reference transcript: NM_003674

• cd S_TKc 252aa 3e-49 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• pfam Pkinase 251aa 2e-51 in ref transcript
  • Protein kinase domain.
• PTZ PTZ00024 259aa 2e-44 in ref transcript
  • cyclin-dependent protein kinase; Provisional.

CDK2

• refseq_CDK2.F2 refseq_CDK2.R2 187 289
• NCBIGene 36.3 1017
• Single exon skipping, size difference: 102
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001798

• Changed! cd S_TKc 284aa 1e-81 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• Changed! pfam Pkinase 283aa 2e-86 in ref transcript
  • Protein kinase domain.
• Changed! PTZ PTZ00024 285aa 3e-57 in ref transcript
  • cyclin-dependent protein kinase; Provisional.
• Changed! cd S_TKc 250aa 4e-60 in modified transcript
• Changed! pfam Pkinase 249aa 2e-62 in modified transcript
• Changed! PTZ PTZ00024 251aa 1e-35 in modified transcript

CDK5RAP1

• refseq_CDK5RAP1.F2 refseq_CDK5RAP1.R2 113 261
• NCBIGene 36.3 51654
• Alternative 3-prime, size difference: 148
• Exclusion of the protein initiation site
• Reference transcript: NM_016408

• TIGR TIGR00089 472aa 1e-121 in ref transcript
  • This subfamily is aparrently a part of a larger superfamily of enzymes utilizing both a 4Fe4S cluster and S-adenosyl methionine (SAM) to initiate radical reactions. MiaB acts on a particular isoprenylated Adenine base of certain tRNAs causing thiolation at an aromatic carbon, and probably also transferring a methyl grouyp from SAM to the thiol. The particular substrate of the three other clades is unknown but may be very closely related.
• COG MiaB 476aa 1e-114 in ref transcript
  • 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis].

CDK5RAP2

• refseq_CDK5RAP2.F1 refseq_CDK5RAP2.R1 113 350
• NCBIGene 36.3 55755
• Single exon skipping, size difference: 237
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_018249

• pfam Microtub_assoc 75aa 3e-15 in ref transcript
  • Microtubule associated. This presumed domain has been identified in two microtubule associated proteins in Schizosaccharomyces pombe, Mto1 and Pcp1. Mto1 has been identified in association with spindle pole body and non-spindle pole body microtubules. The pericentrin homolog Pcp1 is also associated with the fungal centrosome or spindle pole body (SPB).
• TIGR SMC_prok_B 306aa 5e-10 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• Changed! TIGR SMC_prok_B 259aa 1e-05 in ref transcript
• pfam SMC_N 625aa 3e-04 in ref transcript
  • RecF/RecN/SMC N terminal domain. This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.
• COG Smc 363aa 4e-12 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].
• Changed! COG Smc 270aa 0.001 in ref transcript
• Changed! TIGR SMC_prok_B 182aa 0.001 in modified transcript

CDKN2B

• refseq_CDKN2B.F2 refseq_CDKN2B.R2 170 293
• NCBIGene 36.3 1030
• Alternative 5-prime, size difference: 123
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_004936

• Changed! cd ANK 115aa 1e-15 in ref transcript
  • ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats.
• Changed! PTZ PTZ00322 81aa 9e-06 in ref transcript
  • 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase; Provisional.
• Changed! cd ANK 37aa 7e-04 in modified transcript

CEACAM1

• refseq_CEACAM1.F1 refseq_CEACAM1.R1 115 168
• NCBIGene 36.3 634
• Single exon skipping, size difference: 53
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_001712

• cd IGcam 72aa 3e-07 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• cd IGcam 75aa 5e-05 in ref transcript
• cd IGcam 71aa 0.003 in ref transcript
• pfam V-set 106aa 3e-11 in ref transcript
  • Immunoglobulin V-set domain. This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.
• smart IGc2 62aa 2e-09 in ref transcript
  • Immunoglobulin C-2 Type.
• smart IG_like 61aa 1e-08 in ref transcript
  • Immunoglobulin like. IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
• smart IG_like 78aa 1e-05 in ref transcript

CENPM

• refseq_CENPM.F2 refseq_CENPM.R2 145 237
• NCBIGene 36.3 79019
• Single exon skipping, size difference: 92
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_024053

CENTG2

• refseq_CENTG2.F2 refseq_CENTG2.R2 166 325
• NCBIGene 36.3 116987
• Single exon skipping, size difference: 159
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001037131

• cd Centaurin_gamma 158aa 4e-90 in ref transcript
  • Centaurin gamma. The centaurins (alpha, beta, gamma, and delta) are large, multi-domain proteins that all contain an ArfGAP domain and ankyrin repeats, and in some cases, numerous additional domains. Centaurin gamma contains an additional GTPase domain near its N-terminus. The specific function of this GTPase domain has not been well characterized, but centaurin gamma 2 (CENTG2) may play a role in the development of autism. Centaurin gamma 1 is also called PIKE (phosphatidyl inositol (PI) 3-kinase enhancer) and centaurin gamma 2 is also known as AGAP (ArfGAP protein with a GTPase-like domain, ankyrin repeats and a Pleckstrin homology domain) or GGAP. Three isoforms of PIKE have been identified. PIKE-S (short) and PIKE-L (long) are brain-specific isoforms, with PIKE-S restricted to the nucleus and PIKE-L found in multiple cellular compartments. A third isoform, PIKE-A was identified in human glioblastoma brain cancers and has been found in various tissues. GGAP has been shown to have high GTPase activity due to a direct intramolecular interaction between the N-terminal GTPase domain and the C-terminal ArfGAP domain. In human tissue, AGAP mRNA was detected in skeletal muscle, kidney, placenta, brain, heart, colon, and lung. Reduced expression levels were also observed in the spleen, liver, and small intestine.
• cd PH_centaurin 64aa 9e-16 in ref transcript
  • Centaurin Pleckstrin homology (PH) domain. Centaurin beta and gamma consist of a PH domain, an ArfGAP domain and three ankyrin repeats. Centaurain gamma also has an N-terminal Ras homology domain. Centaurin alpha has a different domain architecture and its PH domain is in a different subfamily. Centaurin can bind to phosphatidlyinositol (3,4,5)P3. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
• cd ANK 90aa 3e-11 in ref transcript
  • ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats.
• cd PH_centaurin 42aa 2e-05 in ref transcript
• pfam ArfGap 117aa 7e-37 in ref transcript
  • Putative GTPase activating protein for Arf. Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs.
• pfam Miro 108aa 3e-22 in ref transcript
  • Miro-like protein. Mitochondrial Rho proteins (Miro-1 and Miro-2), are atypical Rho GTPases. They have a unique domain organisation, with tandem GTP-binding domains and two EF hand domains (pfam00036), that may bind calcium. They are also larger than classical small GTPases. It has been proposed that they are involved in mitochondrial homeostasis and apoptosis.
• pfam Ank 32aa 7e-06 in ref transcript
  • Ankyrin repeat. There's no clear separation between noise and signal on the HMM search Ankyrin repeats generally consist of a beta, alpha, alpha, beta order of secondary structures. The repeats associate to form a higher order structure.
• smart PH 65aa 9e-05 in ref transcript
  • Pleckstrin homology domain. Domain commonly found in eukaryotic signalling proteins. The domain family possesses multiple functions including the abilities to bind inositol phosphates, and various proteins. PH domains have been found to possess inserted domains (such as in PLC gamma, syntrophins) and to be inserted within other domains. Mutations in Brutons tyrosine kinase (Btk) within its PH domain cause X-linked agammaglobulinaemia (XLA) in patients. Point mutations cluster into the positively charged end of the molecule around the predicted binding site for phosphatidylinositol lipids.
• smart PH 40aa 0.001 in ref transcript
• COG COG5347 118aa 3e-24 in ref transcript
  • GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion].
• COG COG1100 170aa 6e-08 in ref transcript
  • GTPase SAR1 and related small G proteins [General function prediction only].
• PTZ PTZ00322 107aa 6e-07 in ref transcript
  • 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase; Provisional.

CERKL

• refseq_CERKL.F2 refseq_CERKL.R2 113 191
• NCBIGene 36.3 375298
• Single exon skipping, size difference: 78
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001030311

• Changed! pfam DAGK_cat 165aa 2e-15 in ref transcript
  • Diacylglycerol kinase catalytic domain. Diacylglycerol (DAG) is a second messenger that acts as a protein kinase C activator. The catalytic domain is assumed from the finding of bacterial homologues. YegS is the Escherichia coli protein in this family whose crystal structure reveals an active site in the inter-domain cleft formed by four conserved sequence motifs, revealing a novel metal-binding site. The residues of this site are conserved across the family.
• Changed! COG LCB5 384aa 3e-16 in ref transcript
  • Sphingosine kinase and enzymes related to eukaryotic diacylglycerol kinase [Lipid metabolism / General function prediction only].
• Changed! pfam DAGK_cat 139aa 1e-11 in modified transcript
• Changed! COG LCB5 358aa 7e-13 in modified transcript

CES2

• refseq_CES2.F1 refseq_CES2.R1 117 165
• NCBIGene 36.3 8824
• Alternative 5-prime, size difference: 48
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_003869

• Changed! cd Esterase_lipase 490aa 1e-134 in ref transcript
  • Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These catalytic residues are responsible for the nucleophilic attack on the carbonyl carbon atom of the ester bond. In contrast with other alpha/beta hydrolase fold family members, p-nitrobenzyl esterase and acetylcholine esterase have a Glu instead of Asp at the active site carboxylate.
• Changed! pfam COesterase 510aa 1e-171 in ref transcript
  • Carboxylesterase.
• Changed! COG PnbA 510aa 7e-90 in ref transcript
  • Carboxylesterase type B [Lipid metabolism].
• Changed! cd Esterase_lipase 474aa 1e-128 in modified transcript
• Changed! pfam COesterase 494aa 1e-164 in modified transcript
• Changed! COG PnbA 494aa 3e-84 in modified transcript

CGGBP1

• refseq_CGGBP1.F1 refseq_CGGBP1.R1 199 301
• NCBIGene 36.3 8545
• Single exon skipping, size difference: 102
• Exclusion in 5'UTR
• Reference transcript: NM_001008390

TPPP3

• refseq_CGI-38.F1 refseq_CGI-38.R1 149 240
• NCBIGene 36.3 51673
• Single exon skipping, size difference: 91
• Exclusion in 5'UTR
• Reference transcript: NM_016140

• pfam p25-alpha 165aa 2e-60 in ref transcript
  • p25-alpha. This family encodes a 25 kDa protein that is phosphorylated by a Ser/Thr-Pro kinase. It has been described as a brain specific protein, but it is found in Tetrahymena thermophila.

CHAT

• refseq_CHAT.F1 refseq_CHAT.R1 128 300
• NCBIGene 36.3 1103
• Single exon skipping, size difference: 172
• Exclusion in 5'UTR
• Reference transcript: NM_020985

• pfam Carn_acyltransf 590aa 0.0 in ref transcript
  • Choline/Carnitine o-acyltransferase.

CHCHD7

• refseq_CHCHD7.F1 refseq_CHCHD7.R1 105 125
• NCBIGene 36.3 79145
• Alternative 5-prime, size difference: 20
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_001011668

• Changed! pfam CHCH 36aa 0.008 in ref transcript
  • CHCH domain. we have identified a conserved motif in the LOC118487 protein that we have called the CHCH motif. Alignment of this protein with related members showed the presence of three subgroups of proteins, which are called the S (Small), N (N-terminal extended) and C (C-terminal extended) subgroups. All three sub-groups of proteins have in common that they contain a predicted conserved [coiled coil 1]-[helix 1]-[coiled coil 2]-[helix 2] domain (CHCH domain). Within each helix of the CHCH domain, there are two cysteines present in a C-X9-C motif. The N-group contains an additional double helix domain, and each helix contains the C-X9-C motif. This family contains a number of characterised proteins: Cox19 protein - a nuclear gene of Saccharomyces cerevisiae, codes for an 11-kDa protein (Cox19p) required for expression of cytochrome oxidase. Because cox19 mutants are able to synthesise the mitochondrial and nuclear gene products of cytochrome oxidase, Cox19p probably functions post-translationally during assembly of the enzyme. Cox19p is present in the cytoplasm and mitochondria, where it exists as a soluble intermembrane protein. This dual location is similar to what was previously reported for Cox17p, a low molecular weight copper protein thought to be required for maturation of the CuA centre of subunit 2 of cytochrome oxidase. Cox19p have four conserved potential metal ligands, these are three cysteines and one histidine. Mrp10 - belongs to the class of yeast mitochondrial ribosomal proteins that are essential for translation. Eukaryotic NADH-ubiquinone oxidoreductase 19 kDa (NDUFA8) subunit. The CHCH domain was previously called DUF657.

CHCHD7

• refseq_CHCHD7.F3 refseq_CHCHD7.R3 133 177
• NCBIGene 36.3 79145
• Alternative 3-prime, size difference: 44
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_001011668

• Changed! pfam CHCH 36aa 0.008 in ref transcript
  • CHCH domain. we have identified a conserved motif in the LOC118487 protein that we have called the CHCH motif. Alignment of this protein with related members showed the presence of three subgroups of proteins, which are called the S (Small), N (N-terminal extended) and C (C-terminal extended) subgroups. All three sub-groups of proteins have in common that they contain a predicted conserved [coiled coil 1]-[helix 1]-[coiled coil 2]-[helix 2] domain (CHCH domain). Within each helix of the CHCH domain, there are two cysteines present in a C-X9-C motif. The N-group contains an additional double helix domain, and each helix contains the C-X9-C motif. This family contains a number of characterised proteins: Cox19 protein - a nuclear gene of Saccharomyces cerevisiae, codes for an 11-kDa protein (Cox19p) required for expression of cytochrome oxidase. Because cox19 mutants are able to synthesise the mitochondrial and nuclear gene products of cytochrome oxidase, Cox19p probably functions post-translationally during assembly of the enzyme. Cox19p is present in the cytoplasm and mitochondria, where it exists as a soluble intermembrane protein. This dual location is similar to what was previously reported for Cox17p, a low molecular weight copper protein thought to be required for maturation of the CuA centre of subunit 2 of cytochrome oxidase. Cox19p have four conserved potential metal ligands, these are three cysteines and one histidine. Mrp10 - belongs to the class of yeast mitochondrial ribosomal proteins that are essential for translation. Eukaryotic NADH-ubiquinone oxidoreductase 19 kDa (NDUFA8) subunit. The CHCH domain was previously called DUF657.

CHD3

• refseq_CHD3.F1 refseq_CHD3.R1 160 262
• NCBIGene 36.3 1107
• Single exon skipping, size difference: 102
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001005271

• cd HELICc 109aa 8e-21 in ref transcript
  • Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process.
• cd DEXDc 159aa 1e-16 in ref transcript
  • DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
• cd CHROMO 56aa 4e-06 in ref transcript
  • Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence implicates the chromo domain in the binding activity of these proteins to methylated histone tails and maybe RNA. May occur as single instance, in a tandem arrangement or followd by a related "chromo shadow" domain.
• cd CHROMO 45aa 4e-04 in ref transcript
• cd BAH_plant_2 24aa 0.008 in ref transcript
  • BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
• pfam CHDCT2 173aa 8e-92 in ref transcript
  • CHDCT2 (NUC038) domain. The CHDCT2 C-terminal domain is found in PHD/RING finger and chromo domain-associated CHD-like helicases.
• pfam SNF2_N 287aa 1e-62 in ref transcript
  • SNF2 family N-terminal domain. This domain is found in proteins involved in a variety of processes including transcription regulation (e.g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as well as a variety of other proteins with little functional information (e.g., lodestar, ETL1).
• pfam DUF1086 133aa 5e-61 in ref transcript
  • Domain of Unknown Function (DUF1086). This family consists of several eukaryotic domains of unknown function which are present in chromodomain helicase DNA binding proteins. This domain is often found in conjunction with pfam00176, pfam00271, pfam06465, pfam00385 and pfam00628.
• pfam CHDNT 55aa 7e-23 in ref transcript
  • CHDNT (NUC034) domain. The CHDNT domain is found in PHD/RING finger and chromo domain-associated helicases.
• pfam Helicase_C 81aa 3e-19 in ref transcript
  • Helicase conserved C-terminal domain. The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.
• pfam DUF1087 46aa 4e-16 in ref transcript
  • Domain of Unknown Function (DUF1087). Members of this family are found in various chromatin remodelling factors and transposases. Their exact function is, as yet, unknown.
• pfam PHD 45aa 8e-12 in ref transcript
  • PHD-finger. PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
• pfam PHD 43aa 8e-12 in ref transcript
• pfam Chromo 51aa 1e-08 in ref transcript
  • 'chromo' (CHRromatin Organisation MOdifier) domain.
• smart CHROMO 77aa 2e-05 in ref transcript
  • Chromatin organization modifier domain.
• COG HepA 501aa 2e-74 in ref transcript
  • Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair].
• COG TNG2 51aa 0.004 in ref transcript
  • Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics].

CHI3L2

• refseq_CHI3L2.F2 refseq_CHI3L2.R2 150 180
• NCBIGene 36.3 1117
• Single exon skipping, size difference: 30
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_004000

• cd GH18_chitolectin_chitotriosidase 359aa 1e-152 in ref transcript
  • This conserved domain family includes a large number of catalytically inactive chitinase-like lectins (chitolectins) including YKL-39, YKL-40 (HCGP39), YM1, oviductin, and AMCase (acidic mammalian chitinase), as well as catalytically active chitotriosidases. The conserved domain is an eight-stranded alpha/beta barrel fold belonging to the family 18 glycosyl hydrolases. The fold has a pronounced active-site cleft at the C-terminal end of the beta-barrel. The chitolectins lack a key active site glutamate (the proton donor required for hydrolytic activity) but retain highly conserved residues involved in oligosaccharide binding. Chitotriosidase is a chitinolytic enzyme expressed in maturing macrophages, which suggests that it plays a part in antimicrobial defense. Chitotriosidase hydrolyzes chitotriose, as well as colloidal chitin to yield chitobiose and is therefore considered an exochitinase. Chitotriosidase occurs in two major forms, the large form being converted to the small form by either RNA or post-translational processing. Although the small form, containing the chitinase domain alone, is sufficient for the chitinolytic activity, the additional C-terminal chitin-binding domain of the large form plays a role in processing colloidal chitin. The chitotriosidase gene is nonessential in humans, as about 35% of the population are heterozygous and 6% homozygous for an inactivated form of the gene. HCGP39 is a 39-kDa human cartilage glycoprotein thought to play a role in connective tissue remodeling and defense against pathogens.
• smart Glyco_18 338aa 2e-94 in ref transcript
  • Glycosyl hydrolase family 18.
• COG ChiA 340aa 6e-39 in ref transcript
  • Chitinase [Carbohydrate transport and metabolism].

CHIA

• refseq_CHIA.F2 refseq_CHIA.R2 100 162
• NCBIGene 36.2 27159
• Multiple exon skipping, size difference: 62
• Exclusion in 5'UTR, Exclusion in 5'UTR
• Reference transcript: NM_201653

• cd GH18_chitolectin_chitotriosidase 279aa 1e-134 in ref transcript
  • This conserved domain family includes a large number of catalytically inactive chitinase-like lectins (chitolectins) including YKL-39, YKL-40 (HCGP39), YM1, oviductin, and AMCase (acidic mammalian chitinase), as well as catalytically active chitotriosidases. The conserved domain is an eight-stranded alpha/beta barrel fold belonging to the family 18 glycosyl hydrolases. The fold has a pronounced active-site cleft at the C-terminal end of the beta-barrel. The chitolectins lack a key active site glutamate (the proton donor required for hydrolytic activity) but retain highly conserved residues involved in oligosaccharide binding. Chitotriosidase is a chitinolytic enzyme expressed in maturing macrophages, which suggests that it plays a part in antimicrobial defense. Chitotriosidase hydrolyzes chitotriose, as well as colloidal chitin to yield chitobiose and is therefore considered an exochitinase. Chitotriosidase occurs in two major forms, the large form being converted to the small form by either RNA or post-translational processing. Although the small form, containing the chitinase domain alone, is sufficient for the chitinolytic activity, the additional C-terminal chitin-binding domain of the large form plays a role in processing colloidal chitin. The chitotriosidase gene is nonessential in humans, as about 35% of the population are heterozygous and 6% homozygous for an inactivated form of the gene. HCGP39 is a 39-kDa human cartilage glycoprotein thought to play a role in connective tissue remodeling and defense against pathogens.
• smart Glyco_18 257aa 3e-80 in ref transcript
  • Glycosyl hydrolase family 18.
• smart ChtBD2 48aa 3e-09 in ref transcript
  • Chitin-binding domain type 2.
• COG ChiA 257aa 1e-37 in ref transcript
  • Chitinase [Carbohydrate transport and metabolism].

CHKA

• refseq_CHKA.F1 refseq_CHKA.R1 121 175
• NCBIGene 36.3 1119
• Single exon skipping, size difference: 54
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001277

• Changed! cd ChoK_euk 317aa 1e-91 in ref transcript
  • Choline Kinase (ChoK) in eukaryotes. The ChoK subfamily is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs), RIO kinases, actin-fragmin kinase (AFK), and phosphoinositide 3-kinase (PI3K). It is composed of bacterial and eukaryotic choline kinases, as well as eukaryotic ethanolamine kinase. ChoK catalyzes the transfer of the gamma-phosphoryl group from ATP (or CTP) to its substrate, choline, producing phosphorylcholine (PCho), a precursor to the biosynthesis of two major membrane phospholipids, phosphatidylcholine (PC) and sphingomyelin (SM). Although choline is the preferred substrate, ChoK also shows substantial activity towards ethanolamine and its N-methylated derivatives. ChoK plays an important role in cell signaling pathways and the regulation of cell growth. Along with PCho, it is involved in malignant transformation through Ras oncogenes in various human cancers such as breast, lung, colon, prostate, neuroblastoma, and hepatic lymphoma. In mammalian cells, there are three ChoK isoforms (A-1, A-2, and B) which are active in homo or heterodimeric forms.
• Changed! pfam Choline_kinase 236aa 4e-62 in ref transcript
  • Choline/ethanolamine kinase. Choline kinase catalyses the committed step in the synthesis of phosphatidylcholine by the CDP-choline pathway. This alignment covers the protein kinase portion of the protein. The divergence of this family makes it very difficult to create a model that specifically predicts choline/ethanolamine kinases only.
• Changed! PTZ PTZ00296 361aa 6e-36 in ref transcript
  • choline kinase; Provisional.
• Changed! cd ChoK_euk 299aa 1e-93 in modified transcript
• Changed! pfam Choline_kinase 218aa 3e-64 in modified transcript
• Changed! PTZ PTZ00296 343aa 1e-36 in modified transcript

CHRFAM7A

• refseq_CHRFAM7A.F2 refseq_CHRFAM7A.R2 146 210
• NCBIGene 36.3 89832
• Single exon skipping, size difference: 64
• Exclusion of the protein initiation site
• Reference transcript: NM_139320

• Changed! TIGR LIC 373aa 1e-107 in ref transcript
  • selective while glycine receptors are anion selective).
• Changed! TIGR LIC 307aa 3e-78 in modified transcript

CHRM2

• refseq_CHRM2.F1 refseq_CHRM2.R1 130 186
• NCBIGene 36.3 1129
• Alternative 5-prime, size difference: 56
• Exclusion in 5'UTR
• Reference transcript: NM_001006632

• pfam 7tm_1 174aa 7e-36 in ref transcript
  • 7 transmembrane receptor (rhodopsin family). This family contains, amongst other G-protein-coupled receptors (GCPRs), members of the opsin family, which have been considered to be typical members of the rhodopsin superfamily. They share several motifs, mainly the seven transmembrane helices, GCPRs of the rhodopsin superfamily. All opsins bind a chromophore, such as 11-cis-retinal. The function of most opsins other than the photoisomerases is split into two steps: light absorption and G-protein activation. Photoisomerases, on the other hand, are not coupled to G-proteins - they are thought to generate and supply the chromophore that is used by visual opsins.
• pfam 7tm_1 81aa 9e-06 in ref transcript

CHRM2

• refseq_CHRM2.F3 refseq_CHRM2.R3 108 186
• NCBIGene 36.3 1129
• Single exon skipping, size difference: 78
• Exclusion in 5'UTR
• Reference transcript: NM_001006626

• pfam 7tm_1 174aa 7e-36 in ref transcript
  • 7 transmembrane receptor (rhodopsin family). This family contains, amongst other G-protein-coupled receptors (GCPRs), members of the opsin family, which have been considered to be typical members of the rhodopsin superfamily. They share several motifs, mainly the seven transmembrane helices, GCPRs of the rhodopsin superfamily. All opsins bind a chromophore, such as 11-cis-retinal. The function of most opsins other than the photoisomerases is split into two steps: light absorption and G-protein activation. Photoisomerases, on the other hand, are not coupled to G-proteins - they are thought to generate and supply the chromophore that is used by visual opsins.
• pfam 7tm_1 81aa 9e-06 in ref transcript

CHRNA1

• refseq_CHRNA1.F1 refseq_CHRNA1.R1 116 191
• NCBIGene 36.3 1134
• Single exon skipping, size difference: 75
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001039523

• Changed! pfam Neur_chan_LBD 233aa 3e-70 in ref transcript
  • Neurotransmitter-gated ion-channel ligand binding domain. This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.
• Changed! pfam Neur_chan_memb 209aa 7e-45 in ref transcript
  • Neurotransmitter-gated ion-channel transmembrane region. This family includes the four transmembrane helices that form the ion channel.
• Changed! pfam Neur_chan_LBD 208aa 4e-74 in modified transcript
• Changed! TIGR LIC 427aa 1e-65 in modified transcript
  • selective while glycine receptors are anion selective).

NLRP3

• refseq_CIAS1.F1 refseq_CIAS1.R1 125 296
• NCBIGene 36.3 114548
• Single exon skipping, size difference: 171
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001079821

• Changed! cd LRR_RI 317aa 6e-50 in ref transcript
  • Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1).
• Changed! cd LRR_RI 207aa 1e-07 in ref transcript
• pfam NACHT 170aa 1e-41 in ref transcript
  • NACHT domain. This NTPase domain is found in apoptosis proteins as well as those involved in MHC transcription activation. This family is closely related to pfam00931.
• pfam PAAD_DAPIN 84aa 6e-21 in ref transcript
  • PAAD/DAPIN/Pyrin domain. This domain is predicted to contain 6 alpha helices and to have the same fold as the pfam00531 domain. This similarity may mean that this is a protein-protein interaction domain.
• smart LRR_RI 28aa 0.001 in ref transcript
  • Leucine rich repeat, ribonuclease inhibitor type.
• Changed! smart LRR_RI 28aa 0.002 in ref transcript
• Changed! COG RNA1 230aa 0.003 in ref transcript
  • Ran GTPase-activating protein (RanGAP) involved in mRNA processing and transport [Signal transduction mechanisms / RNA processing and modification].
• Changed! cd LRR_RI 320aa 5e-54 in modified transcript

NLRP3

• refseq_CIAS1.F3 refseq_CIAS1.R3 215 386
• NCBIGene 36.3 114548
• Single exon skipping, size difference: 171
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001079821

• Changed! cd LRR_RI 317aa 6e-50 in ref transcript
  • Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1).
• Changed! cd LRR_RI 207aa 1e-07 in ref transcript
• pfam NACHT 170aa 1e-41 in ref transcript
  • NACHT domain. This NTPase domain is found in apoptosis proteins as well as those involved in MHC transcription activation. This family is closely related to pfam00931.
• pfam PAAD_DAPIN 84aa 6e-21 in ref transcript
  • PAAD/DAPIN/Pyrin domain. This domain is predicted to contain 6 alpha helices and to have the same fold as the pfam00531 domain. This similarity may mean that this is a protein-protein interaction domain.
• smart LRR_RI 28aa 0.001 in ref transcript
  • Leucine rich repeat, ribonuclease inhibitor type.
• smart LRR_RI 28aa 0.002 in ref transcript
• Changed! COG RNA1 230aa 0.003 in ref transcript
  • Ran GTPase-activating protein (RanGAP) involved in mRNA processing and transport [Signal transduction mechanisms / RNA processing and modification].
• Changed! cd LRR_RI 320aa 2e-48 in modified transcript
• Changed! COG RNA1 114aa 0.001 in modified transcript

CKAP5

• refseq_CKAP5.F2 refseq_CKAP5.R2 183 363
• NCBIGene 36.3 9793
• Single exon skipping, size difference: 180
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001008938

CKLF

• refseq_CKLF.F1 refseq_CKLF.R1 173 269
• NCBIGene 36.3 51192
• Single exon skipping, size difference: 96
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_016951

• Changed! pfam MARVEL 118aa 3e-05 in ref transcript
  • Membrane-associating domain. MARVEL domain-containing proteins are often found in lipid-associating proteins - such as Occludin and MAL family proteins. It may be part of the machinery of membrane apposition events, such as transport vesicle biogenesis.

CKLF

• refseq_CKLF.F3 refseq_CKLF.R3 206 365
• NCBIGene 36.3 51192
• Single exon skipping, size difference: 159
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_016951

• Changed! pfam MARVEL 118aa 3e-05 in ref transcript
  • Membrane-associating domain. MARVEL domain-containing proteins are often found in lipid-associating proteins - such as Occludin and MAL family proteins. It may be part of the machinery of membrane apposition events, such as transport vesicle biogenesis.

CLCN3

• refseq_CLCN3.F2 refseq_CLCN3.R2 286 362
• NCBIGene 36.3 1182
• Single exon skipping, size difference: 76
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_173872

• cd ClC_3_like 435aa 1e-176 in ref transcript
  • ClC-3-like chloride channel proteins. This CD includes ClC-3, ClC-4, ClC-5 and ClC-Y1. ClC-3 was initially cloned from rat kidney. Expression of ClC-3 produces outwardly-rectifying Cl currents that are inhibited by protein kinase C activation. It has been suggested that ClC-3 may be a ubiquitous swelling-activated Cl channel that has very similar characteristics to those of native volume-regulated Cl currents. The function of ClC-4 is unclear. Studies of human ClC-4 have revealed that it gives rise to Cl currents that rapidly activate at positive voltages, and are sensitive to extracellular pH, with currents decreasing when pH falls below 6.5. ClC-4 is broadly distributed, especially in brain and heart. ClC-5 is predominantly expressed in the kidney, but can be found in the brain and liver. Mutations in the ClC-5 gene cause certain hereditary diseases, including Dent's disease, an X-chromosome linked syndrome characterised by proteinuria, hypercalciuria, and kidney stones (nephrolithiasis), leading to progressive renal failure. These proteins belong to the ClC superfamily of chloride ion channels, which share the unique double-barreled architecture and voltage-dependent gating mechanism. The gating is conferred by the permeating anion itself, acting as the gating charge. This domain is found in the eukaryotic halogen ion (Cl- and I-) channel proteins, that perform a variety of functions including cell volume regulation, the membrane potential stabilization, transepithelial chloride transport and charge compensation necessary for the acidification of intracellular organelles.
• Changed! cd CBS_pair_EriC_assoc_euk_bac 139aa 4e-24 in ref transcript
  • This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the EriC CIC-type chloride channels in eukaryotes and bacteria. These ion channels are proteins with a seemingly simple task of allowing the passive flow of chloride ions across biological membranes. CIC-type chloride channels come from all kingdoms of life, have several gene families, and can be gated by voltage. The members of the CIC-type chloride channel are double-barreled: two proteins forming homodimers at a broad interface formed by four helices from each protein. The two pores are not found at this interface, but are completely contained within each subunit, as deduced from the mutational analyses, unlike many other channels, in which four or five identical or structurally related subunits jointly form one pore. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain in CLC chloride channel family members have been associated with classic Bartter syndrome, Osteopetrosis, Dent's disease, idiopathic generalized epilepsy, and myotonia.
• pfam Voltage_CLC 403aa 1e-62 in ref transcript
  • Voltage gated chloride channel. This family of ion channels contains 10 or 12 transmembrane helices. Each protein forms a single pore. It has been shown that some members of this family form homodimers. In terms of primary structure, they are unrelated to known cation channels or other types of anion channels. Three ClC subfamilies are found in animals. ClC-1 is involved in setting and restoring the resting membrane potential of skeletal muscle, while other channels play important parts in solute concentration mechanisms in the kidney. These proteins contain two pfam00571 domains.
• Changed! pfam CBS 149aa 3e-10 in ref transcript
  • CBS domain pair. CBS domains are small intracellular modules that pair together to form a stable globular domain. This family represents a pair of CBS domains, that has been termed a Bateman domain. CBS domains have been shown to bind ligands with an adenosyl group such as AMP, ATP and S-AdoMet. CBS domains are found attached to a wide range of other protein domains suggesting that CBS domains may play a regulatory role making proteins sensitive to adenosyl carrying ligands. The region containing the CBS domains in Cystathionine-beta synthase is involved in regulation by S-AdoMet. CBS domain pairs from AMPK bind AMP or ATP. The CBS domains from IMPDH and the chloride channel CLC2 bind ATP.
• COG EriC 455aa 3e-38 in ref transcript
  • Chloride channel protein EriC [Inorganic ion transport and metabolism].
• Changed! COG TlyC 153aa 0.001 in ref transcript
  • Hemolysins and related proteins containing CBS domains [General function prediction only].
• Changed! cd CBS_pair_EriC_assoc_euk_bac 139aa 3e-26 in modified transcript
• Changed! pfam CBS 150aa 1e-11 in modified transcript
• Changed! COG COG0517 54aa 3e-05 in modified transcript
  • FOG: CBS domain [General function prediction only].
• Changed! COG COG4109 164aa 7e-05 in modified transcript
  • Predicted transcriptional regulator containing CBS domains [Transcription].

CLCN6

• refseq_CLCN6.F1 refseq_CLCN6.R1 134 301
• NCBIGene 36.3 1185
• Single exon skipping, size difference: 167
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_001286

• Changed! cd ClC_6_like 322aa 1e-105 in ref transcript
  • ClC-6-like chloride channel proteins. This CD includes ClC-6, ClC-7 and ClC-B, C, D in plants. Proteins in this family are ubiquitous in eukarotes and their functions are unclear. They are expressed in intracellular organelles membranes. This family belongs to the ClC superfamily of chloride ion channels, which share the unique double-barreled architecture and voltage-dependent gating mechanism. The gating is conferred by the permeating anion itself, acting as the gating charge. ClC chloride ion channel superfamily perform a variety of functions including cellular excitability regulation, cell volume regulation, membrane potential stabilization, acidification of intracellular organelles, signal transduction, and transepithelial transport in animals.
• Changed! cd ClC_6_like 112aa 5e-39 in ref transcript
• Changed! cd CBS_pair_EriC_assoc_euk_bac 54aa 2e-13 in ref transcript
  • This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the EriC CIC-type chloride channels in eukaryotes and bacteria. These ion channels are proteins with a seemingly simple task of allowing the passive flow of chloride ions across biological membranes. CIC-type chloride channels come from all kingdoms of life, have several gene families, and can be gated by voltage. The members of the CIC-type chloride channel are double-barreled: two proteins forming homodimers at a broad interface formed by four helices from each protein. The two pores are not found at this interface, but are completely contained within each subunit, as deduced from the mutational analyses, unlike many other channels, in which four or five identical or structurally related subunits jointly form one pore. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain in CLC chloride channel family members have been associated with classic Bartter syndrome, Osteopetrosis, Dent's disease, idiopathic generalized epilepsy, and myotonia.
• Changed! pfam Voltage_CLC 231aa 4e-28 in ref transcript
  • Voltage gated chloride channel. This family of ion channels contains 10 or 12 transmembrane helices. Each protein forms a single pore. It has been shown that some members of this family form homodimers. In terms of primary structure, they are unrelated to known cation channels or other types of anion channels. Three ClC subfamilies are found in animals. ClC-1 is involved in setting and restoring the resting membrane potential of skeletal muscle, while other channels play important parts in solute concentration mechanisms in the kidney. These proteins contain two pfam00571 domains.
• Changed! pfam Voltage_CLC 129aa 2e-15 in ref transcript
• Changed! pfam CBS 58aa 3e-08 in ref transcript
  • CBS domain pair. CBS domains are small intracellular modules that pair together to form a stable globular domain. This family represents a pair of CBS domains, that has been termed a Bateman domain. CBS domains have been shown to bind ligands with an adenosyl group such as AMP, ATP and S-AdoMet. CBS domains are found attached to a wide range of other protein domains suggesting that CBS domains may play a regulatory role making proteins sensitive to adenosyl carrying ligands. The region containing the CBS domains in Cystathionine-beta synthase is involved in regulation by S-AdoMet. CBS domain pairs from AMPK bind AMP or ATP. The CBS domains from IMPDH and the chloride channel CLC2 bind ATP.
• Changed! smart CBS 48aa 0.009 in ref transcript
  • Domain in cystathionine beta-synthase and other proteins. Domain present in all 3 forms of cellular life. Present in two copies in inosine monophosphate dehydrogenase, of which one is disordered in the crystal structure [3]. A number of disease states are associated with CBS-containing proteins including homocystinuria, Becker's and Thomsen disease.
• Changed! COG EriC 287aa 2e-13 in ref transcript
  • Chloride channel protein EriC [Inorganic ion transport and metabolism].
• Changed! COG EriC 111aa 3e-09 in ref transcript
• Changed! PRK PRK05567 58aa 3e-05 in ref transcript
  • inositol-5'-monophosphate dehydrogenase; Reviewed.
• Changed! cd ClC_6_like 270aa 7e-85 in modified transcript
• Changed! pfam Voltage_CLC 175aa 2e-20 in modified transcript
• Changed! COG EriC 239aa 2e-09 in modified transcript

CLDN15

• refseq_CLDN15.F1 refseq_CLDN15.R1 252 392
• NCBIGene 36.2 24146
• Single exon skipping, size difference: 140
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_014343

• Changed! pfam PMP22_Claudin 169aa 5e-16 in ref transcript
  • PMP-22/EMP/MP20/Claudin family.

CLEC10A

• refseq_CLEC10A.F1 refseq_CLEC10A.R1 156 228
• NCBIGene 36.3 10462
• Alternative 3-prime, size difference: 81
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_182906

• cd CLECT_DC-SIGN_like 125aa 8e-41 in ref transcript
  • CLECT_DC-SIGN_like: C-type lectin-like domain (CTLD) of the type found in human dendritic cell (DC)-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN) and the related receptor, DC-SIGN receptor (DC-SIGNR). This group also contains proteins similar to hepatic asialoglycoprotein receptor (ASGP-R) and langerin in human. These proteins are type II membrane proteins with a CTLD ectodomain. CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. DC-SIGN is thought to mediate the initial contact between dendritic cells and resting T cells, and may also mediate the rolling of DCs on epithelium. DC-SIGN and DC-SIGNR bind to oligosaccharides present on human tissues, as well as, on pathogens including parasites, bacteria, and viruses. DC-SIGN and DC-SIGNR bind to HIV enhancing viral infection of T cells. DC-SIGN and DC-SIGNR are homotetrameric, and contain four CTLDs stabilized by a coiled coil of alpha helices. The hepatic ASGP-R is an endocytic recycling receptor which binds and internalizes desialylated glycoproteins having a terminal galactose or N-acetylgalactosamine residues on their N-linked carbohydrate chains, via the clathrin-coated pit mediated endocytic pathway, and delivers them to lysosomes for degradation. It has been proposed that glycoproteins bearing terminal Sia (sialic acid) alpha2, 6GalNAc and Sia alpha2, 6Gal are endogenous ligands for ASGP-R and that ASGP-R participates in regulating the relative concentration of serum glycoproteins bearing alpha 2,6-linked Sia. The human ASGP-R is a hetero-oligomer composed of two subunits, both of which are found within this group. Langerin is expressed in a subset of dendritic leukocytes, the Langerhans cells (LC). Langerin induces the formation of Birbeck Granules (BGs) and associates with these BGs following internalization. Langerin binds, in a calcium-dependent manner, to glyco-conjugates containing mannose and related sugars mediating their uptake and degradation. Langerin molecules oligomerize as trimers with three CTLDs held together by a coiled-coil of alpha helices.
• pfam Lectin_C 108aa 1e-28 in ref transcript
  • Lectin C-type domain. This family includes both long and short form C-type.
• Changed! pfam Lectin_N 165aa 2e-26 in ref transcript
  • Hepatic lectin, N-terminal domain.
• Changed! pfam Lectin_N 138aa 2e-30 in modified transcript

CLEC10A

• refseq_CLEC10A.F1 refseq_CLEC10A.R3 109 190
• NCBIGene 36.3 10462
• Alternative 3-prime, size difference: 81
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_182906

• cd CLECT_DC-SIGN_like 125aa 8e-41 in ref transcript
  • CLECT_DC-SIGN_like: C-type lectin-like domain (CTLD) of the type found in human dendritic cell (DC)-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN) and the related receptor, DC-SIGN receptor (DC-SIGNR). This group also contains proteins similar to hepatic asialoglycoprotein receptor (ASGP-R) and langerin in human. These proteins are type II membrane proteins with a CTLD ectodomain. CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. DC-SIGN is thought to mediate the initial contact between dendritic cells and resting T cells, and may also mediate the rolling of DCs on epithelium. DC-SIGN and DC-SIGNR bind to oligosaccharides present on human tissues, as well as, on pathogens including parasites, bacteria, and viruses. DC-SIGN and DC-SIGNR bind to HIV enhancing viral infection of T cells. DC-SIGN and DC-SIGNR are homotetrameric, and contain four CTLDs stabilized by a coiled coil of alpha helices. The hepatic ASGP-R is an endocytic recycling receptor which binds and internalizes desialylated glycoproteins having a terminal galactose or N-acetylgalactosamine residues on their N-linked carbohydrate chains, via the clathrin-coated pit mediated endocytic pathway, and delivers them to lysosomes for degradation. It has been proposed that glycoproteins bearing terminal Sia (sialic acid) alpha2, 6GalNAc and Sia alpha2, 6Gal are endogenous ligands for ASGP-R and that ASGP-R participates in regulating the relative concentration of serum glycoproteins bearing alpha 2,6-linked Sia. The human ASGP-R is a hetero-oligomer composed of two subunits, both of which are found within this group. Langerin is expressed in a subset of dendritic leukocytes, the Langerhans cells (LC). Langerin induces the formation of Birbeck Granules (BGs) and associates with these BGs following internalization. Langerin binds, in a calcium-dependent manner, to glyco-conjugates containing mannose and related sugars mediating their uptake and degradation. Langerin molecules oligomerize as trimers with three CTLDs held together by a coiled-coil of alpha helices.
• pfam Lectin_C 108aa 1e-28 in ref transcript
  • Lectin C-type domain. This family includes both long and short form C-type.
• Changed! pfam Lectin_N 165aa 2e-26 in ref transcript
  • Hepatic lectin, N-terminal domain.
• Changed! pfam Lectin_N 138aa 2e-30 in modified transcript

CLEC2D

• refseq_CLEC2D.F1 refseq_CLEC2D.R1 161 243
• NCBIGene 36.3 29121
• Single exon skipping, size difference: 82
• Exclusion in 5'UTR
• Reference transcript: NM_001004419

• pfam Nucleoplasmin 52aa 6e-17 in ref transcript
  • Nucleoplasmin. Nucleoplasmins are also known as chromatin decondensation proteins. They bind to core histones and transfer DNA to them in a reaction that requires ATP. This is thought to play a role in the assembly of regular nucleosomal arrays.

CLEC2D

• refseq_CLEC2D.F3 refseq_CLEC2D.R3 107 182
• NCBIGene 36.2 29121
• Alternative 5-prime, size difference: 75
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_001004419

• Changed! cd CLECT_NK_receptors_like 97aa 9e-25 in ref transcript
  • CLECT_NK_receptors_like: C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs), including proteins similar to oxidized low density lipoprotein (OxLDL) receptor (LOX-1), CD94, CD69, NKG2-A and -D, osteoclast inhibitory lectin (OCIL), dendritic cell-associated C-type lectin-1 (dectin-1), human myeloid inhibitory C-type lectin-like receptor (MICL), mast cell-associated functional antigen (MAFA), killer cell lectin-like receptors: subfamily F, member 1 (KLRF1) and subfamily B, member 1 (KLRB1), and lys49 receptors. CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. NKRs are variously associated with activation or inhibition of natural killer (NK) cells. Activating NKRs stimulate cytolysis by NK cells of virally infected or transformed cells; inhibitory NKRs block cytolysis upon recognition of markers of healthy self cells. Most Lys49 receptors are inhibitory; some are stimulatory. OCIL inhibits NK cell function via binding to the receptor NKRP1D. Murine OCIL in addition to inhibiting NK cell function inhibits osteoclast differentiation. MAFA clusters with the type I Fc epsilon receptor (FcepsilonRI) and inhibits the mast cells secretory response to FcepsilonRI stimulus. CD72 is a negative regulator of B cell receptor signaling. NKG2D is an activating receptor for stress-induced antigens; human NKG2D ligands include the stress induced MHC-I homologs, MICA, MICB, and ULBP family of glycoproteins Several NKRs have a carbohydrate-binding capacity which is not mediated through calcium ions (e.g. OCIL binds a range of high molecular weight sulfated glycosaminoglycans including dextran sulfate, fucoidan, and gamma-carrageenan sugars). Dectin-1 binds fungal beta-glucans and in involved in the innate immune responses to fungal pathogens. MAFA binds saccharides having terminal alpha-D mannose residues in a calcium-dependent manner. LOX-1 is the major receptor for OxLDL in endothelial cells and thought to play a role in the pathology of atherosclerosis. Some NKRs exist as homodimers (e.g.Lys49, NKG2D, CD69, LOX-1) and some as heterodimers (e.g. CD94/NKG2A). Dectin-1 can function as a monomer in vitro.
• Changed! smart CLECT 78aa 2e-16 in ref transcript
  • C-type lectin (CTL) or carbohydrate-recognition domain (CRD). Many of these domains function as calcium-dependent carbohydrate binding modules.
• Changed! cd CLECT_NK_receptors_like 45aa 1e-11 in modified transcript
• Changed! smart CLECT 45aa 2e-09 in modified transcript

CLEC4A

• refseq_CLEC4A.F1 refseq_CLEC4A.R1 130 229
• NCBIGene 36.3 50856
• Single exon skipping, size difference: 99
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_016184

• cd CLECT_DC-SIGN_like 127aa 8e-40 in ref transcript
  • CLECT_DC-SIGN_like: C-type lectin-like domain (CTLD) of the type found in human dendritic cell (DC)-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN) and the related receptor, DC-SIGN receptor (DC-SIGNR). This group also contains proteins similar to hepatic asialoglycoprotein receptor (ASGP-R) and langerin in human. These proteins are type II membrane proteins with a CTLD ectodomain. CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. DC-SIGN is thought to mediate the initial contact between dendritic cells and resting T cells, and may also mediate the rolling of DCs on epithelium. DC-SIGN and DC-SIGNR bind to oligosaccharides present on human tissues, as well as, on pathogens including parasites, bacteria, and viruses. DC-SIGN and DC-SIGNR bind to HIV enhancing viral infection of T cells. DC-SIGN and DC-SIGNR are homotetrameric, and contain four CTLDs stabilized by a coiled coil of alpha helices. The hepatic ASGP-R is an endocytic recycling receptor which binds and internalizes desialylated glycoproteins having a terminal galactose or N-acetylgalactosamine residues on their N-linked carbohydrate chains, via the clathrin-coated pit mediated endocytic pathway, and delivers them to lysosomes for degradation. It has been proposed that glycoproteins bearing terminal Sia (sialic acid) alpha2, 6GalNAc and Sia alpha2, 6Gal are endogenous ligands for ASGP-R and that ASGP-R participates in regulating the relative concentration of serum glycoproteins bearing alpha 2,6-linked Sia. The human ASGP-R is a hetero-oligomer composed of two subunits, both of which are found within this group. Langerin is expressed in a subset of dendritic leukocytes, the Langerhans cells (LC). Langerin induces the formation of Birbeck Granules (BGs) and associates with these BGs following internalization. Langerin binds, in a calcium-dependent manner, to glyco-conjugates containing mannose and related sugars mediating their uptake and degradation. Langerin molecules oligomerize as trimers with three CTLDs held together by a coiled-coil of alpha helices.
• smart CLECT 126aa 7e-26 in ref transcript
  • C-type lectin (CTL) or carbohydrate-recognition domain (CRD). Many of these domains function as calcium-dependent carbohydrate binding modules.

CLEC4A

• refseq_CLEC4A.F3 refseq_CLEC4A.R3 122 242
• NCBIGene 36.3 50856
• Single exon skipping, size difference: 117
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_016184

• cd CLECT_DC-SIGN_like 127aa 8e-40 in ref transcript
  • CLECT_DC-SIGN_like: C-type lectin-like domain (CTLD) of the type found in human dendritic cell (DC)-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN) and the related receptor, DC-SIGN receptor (DC-SIGNR). This group also contains proteins similar to hepatic asialoglycoprotein receptor (ASGP-R) and langerin in human. These proteins are type II membrane proteins with a CTLD ectodomain. CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. DC-SIGN is thought to mediate the initial contact between dendritic cells and resting T cells, and may also mediate the rolling of DCs on epithelium. DC-SIGN and DC-SIGNR bind to oligosaccharides present on human tissues, as well as, on pathogens including parasites, bacteria, and viruses. DC-SIGN and DC-SIGNR bind to HIV enhancing viral infection of T cells. DC-SIGN and DC-SIGNR are homotetrameric, and contain four CTLDs stabilized by a coiled coil of alpha helices. The hepatic ASGP-R is an endocytic recycling receptor which binds and internalizes desialylated glycoproteins having a terminal galactose or N-acetylgalactosamine residues on their N-linked carbohydrate chains, via the clathrin-coated pit mediated endocytic pathway, and delivers them to lysosomes for degradation. It has been proposed that glycoproteins bearing terminal Sia (sialic acid) alpha2, 6GalNAc and Sia alpha2, 6Gal are endogenous ligands for ASGP-R and that ASGP-R participates in regulating the relative concentration of serum glycoproteins bearing alpha 2,6-linked Sia. The human ASGP-R is a hetero-oligomer composed of two subunits, both of which are found within this group. Langerin is expressed in a subset of dendritic leukocytes, the Langerhans cells (LC). Langerin induces the formation of Birbeck Granules (BGs) and associates with these BGs following internalization. Langerin binds, in a calcium-dependent manner, to glyco-conjugates containing mannose and related sugars mediating their uptake and degradation. Langerin molecules oligomerize as trimers with three CTLDs held together by a coiled-coil of alpha helices.
• smart CLECT 126aa 7e-26 in ref transcript
  • C-type lectin (CTL) or carbohydrate-recognition domain (CRD). Many of these domains function as calcium-dependent carbohydrate binding modules.

CLEC4C

• refseq_CLEC4C.F1 refseq_CLEC4C.R1 254 347
• NCBIGene 36.3 170482
• Single exon skipping, size difference: 93
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_130441

• cd CLECT_DC-SIGN_like 126aa 3e-38 in ref transcript
  • CLECT_DC-SIGN_like: C-type lectin-like domain (CTLD) of the type found in human dendritic cell (DC)-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN) and the related receptor, DC-SIGN receptor (DC-SIGNR). This group also contains proteins similar to hepatic asialoglycoprotein receptor (ASGP-R) and langerin in human. These proteins are type II membrane proteins with a CTLD ectodomain. CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. DC-SIGN is thought to mediate the initial contact between dendritic cells and resting T cells, and may also mediate the rolling of DCs on epithelium. DC-SIGN and DC-SIGNR bind to oligosaccharides present on human tissues, as well as, on pathogens including parasites, bacteria, and viruses. DC-SIGN and DC-SIGNR bind to HIV enhancing viral infection of T cells. DC-SIGN and DC-SIGNR are homotetrameric, and contain four CTLDs stabilized by a coiled coil of alpha helices. The hepatic ASGP-R is an endocytic recycling receptor which binds and internalizes desialylated glycoproteins having a terminal galactose or N-acetylgalactosamine residues on their N-linked carbohydrate chains, via the clathrin-coated pit mediated endocytic pathway, and delivers them to lysosomes for degradation. It has been proposed that glycoproteins bearing terminal Sia (sialic acid) alpha2, 6GalNAc and Sia alpha2, 6Gal are endogenous ligands for ASGP-R and that ASGP-R participates in regulating the relative concentration of serum glycoproteins bearing alpha 2,6-linked Sia. The human ASGP-R is a hetero-oligomer composed of two subunits, both of which are found within this group. Langerin is expressed in a subset of dendritic leukocytes, the Langerhans cells (LC). Langerin induces the formation of Birbeck Granules (BGs) and associates with these BGs following internalization. Langerin binds, in a calcium-dependent manner, to glyco-conjugates containing mannose and related sugars mediating their uptake and degradation. Langerin molecules oligomerize as trimers with three CTLDs held together by a coiled-coil of alpha helices.
• smart CLECT 125aa 2e-24 in ref transcript
  • C-type lectin (CTL) or carbohydrate-recognition domain (CRD). Many of these domains function as calcium-dependent carbohydrate binding modules.

CLEC4M

• refseq_CLEC4M.F1 refseq_CLEC4M.R1 156 219
• NCBIGene 36.3 10332
• Exon skipping and alternative 3-prime or 5-prime, size difference: 63
• Inclusion in the protein (no stop codon or frameshift), Exclusion in the protein (no frameshift)
• Reference transcript: NM_214675

• cd CLECT_DC-SIGN_like 124aa 5e-42 in ref transcript
  • CLECT_DC-SIGN_like: C-type lectin-like domain (CTLD) of the type found in human dendritic cell (DC)-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN) and the related receptor, DC-SIGN receptor (DC-SIGNR). This group also contains proteins similar to hepatic asialoglycoprotein receptor (ASGP-R) and langerin in human. These proteins are type II membrane proteins with a CTLD ectodomain. CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. DC-SIGN is thought to mediate the initial contact between dendritic cells and resting T cells, and may also mediate the rolling of DCs on epithelium. DC-SIGN and DC-SIGNR bind to oligosaccharides present on human tissues, as well as, on pathogens including parasites, bacteria, and viruses. DC-SIGN and DC-SIGNR bind to HIV enhancing viral infection of T cells. DC-SIGN and DC-SIGNR are homotetrameric, and contain four CTLDs stabilized by a coiled coil of alpha helices. The hepatic ASGP-R is an endocytic recycling receptor which binds and internalizes desialylated glycoproteins having a terminal galactose or N-acetylgalactosamine residues on their N-linked carbohydrate chains, via the clathrin-coated pit mediated endocytic pathway, and delivers them to lysosomes for degradation. It has been proposed that glycoproteins bearing terminal Sia (sialic acid) alpha2, 6GalNAc and Sia alpha2, 6Gal are endogenous ligands for ASGP-R and that ASGP-R participates in regulating the relative concentration of serum glycoproteins bearing alpha 2,6-linked Sia. The human ASGP-R is a hetero-oligomer composed of two subunits, both of which are found within this group. Langerin is expressed in a subset of dendritic leukocytes, the Langerhans cells (LC). Langerin induces the formation of Birbeck Granules (BGs) and associates with these BGs following internalization. Langerin binds, in a calcium-dependent manner, to glyco-conjugates containing mannose and related sugars mediating their uptake and degradation. Langerin molecules oligomerize as trimers with three CTLDs held together by a coiled-coil of alpha helices.
• smart CLECT 123aa 6e-30 in ref transcript
  • C-type lectin (CTL) or carbohydrate-recognition domain (CRD). Many of these domains function as calcium-dependent carbohydrate binding modules.
• TIGR SMC_prok_B 182aa 1e-07 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• Changed! PRK PRK03918 172aa 4e-06 in ref transcript
  • chromosome segregation protein; Provisional.
• Changed! PRK PRK05771 186aa 2e-05 in modified transcript
  • V-type ATP synthase subunit I; Validated.

CLEC4M

• refseq_CLEC4M.F3 refseq_CLEC4M.R3 183 296
• NCBIGene 36.3 10332
• Single exon skipping, size difference: 113
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_214675

• Changed! cd CLECT_DC-SIGN_like 124aa 5e-42 in ref transcript
  • CLECT_DC-SIGN_like: C-type lectin-like domain (CTLD) of the type found in human dendritic cell (DC)-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN) and the related receptor, DC-SIGN receptor (DC-SIGNR). This group also contains proteins similar to hepatic asialoglycoprotein receptor (ASGP-R) and langerin in human. These proteins are type II membrane proteins with a CTLD ectodomain. CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. DC-SIGN is thought to mediate the initial contact between dendritic cells and resting T cells, and may also mediate the rolling of DCs on epithelium. DC-SIGN and DC-SIGNR bind to oligosaccharides present on human tissues, as well as, on pathogens including parasites, bacteria, and viruses. DC-SIGN and DC-SIGNR bind to HIV enhancing viral infection of T cells. DC-SIGN and DC-SIGNR are homotetrameric, and contain four CTLDs stabilized by a coiled coil of alpha helices. The hepatic ASGP-R is an endocytic recycling receptor which binds and internalizes desialylated glycoproteins having a terminal galactose or N-acetylgalactosamine residues on their N-linked carbohydrate chains, via the clathrin-coated pit mediated endocytic pathway, and delivers them to lysosomes for degradation. It has been proposed that glycoproteins bearing terminal Sia (sialic acid) alpha2, 6GalNAc and Sia alpha2, 6Gal are endogenous ligands for ASGP-R and that ASGP-R participates in regulating the relative concentration of serum glycoproteins bearing alpha 2,6-linked Sia. The human ASGP-R is a hetero-oligomer composed of two subunits, both of which are found within this group. Langerin is expressed in a subset of dendritic leukocytes, the Langerhans cells (LC). Langerin induces the formation of Birbeck Granules (BGs) and associates with these BGs following internalization. Langerin binds, in a calcium-dependent manner, to glyco-conjugates containing mannose and related sugars mediating their uptake and degradation. Langerin molecules oligomerize as trimers with three CTLDs held together by a coiled-coil of alpha helices.
• Changed! smart CLECT 123aa 6e-30 in ref transcript
  • C-type lectin (CTL) or carbohydrate-recognition domain (CRD). Many of these domains function as calcium-dependent carbohydrate binding modules.
• TIGR SMC_prok_B 182aa 1e-07 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• PRK PRK03918 172aa 4e-06 in ref transcript
  • chromosome segregation protein; Provisional.
• Changed! cd CLECT_DC-SIGN_like 45aa 5e-13 in modified transcript
• Changed! smart CLECT 45aa 7e-11 in modified transcript

CLEC7A

• refseq_CLEC7A.F1 refseq_CLEC7A.R1 247 366
• NCBIGene 36.3 64581
• Single exon skipping, size difference: 119
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_197947

• Changed! cd CLECT_NK_receptors_like 124aa 2e-27 in ref transcript
  • CLECT_NK_receptors_like: C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs), including proteins similar to oxidized low density lipoprotein (OxLDL) receptor (LOX-1), CD94, CD69, NKG2-A and -D, osteoclast inhibitory lectin (OCIL), dendritic cell-associated C-type lectin-1 (dectin-1), human myeloid inhibitory C-type lectin-like receptor (MICL), mast cell-associated functional antigen (MAFA), killer cell lectin-like receptors: subfamily F, member 1 (KLRF1) and subfamily B, member 1 (KLRB1), and lys49 receptors. CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. NKRs are variously associated with activation or inhibition of natural killer (NK) cells. Activating NKRs stimulate cytolysis by NK cells of virally infected or transformed cells; inhibitory NKRs block cytolysis upon recognition of markers of healthy self cells. Most Lys49 receptors are inhibitory; some are stimulatory. OCIL inhibits NK cell function via binding to the receptor NKRP1D. Murine OCIL in addition to inhibiting NK cell function inhibits osteoclast differentiation. MAFA clusters with the type I Fc epsilon receptor (FcepsilonRI) and inhibits the mast cells secretory response to FcepsilonRI stimulus. CD72 is a negative regulator of B cell receptor signaling. NKG2D is an activating receptor for stress-induced antigens; human NKG2D ligands include the stress induced MHC-I homologs, MICA, MICB, and ULBP family of glycoproteins Several NKRs have a carbohydrate-binding capacity which is not mediated through calcium ions (e.g. OCIL binds a range of high molecular weight sulfated glycosaminoglycans including dextran sulfate, fucoidan, and gamma-carrageenan sugars). Dectin-1 binds fungal beta-glucans and in involved in the innate immune responses to fungal pathogens. MAFA binds saccharides having terminal alpha-D mannose residues in a calcium-dependent manner. LOX-1 is the major receptor for OxLDL in endothelial cells and thought to play a role in the pathology of atherosclerosis. Some NKRs exist as homodimers (e.g.Lys49, NKG2D, CD69, LOX-1) and some as heterodimers (e.g. CD94/NKG2A). Dectin-1 can function as a monomer in vitro.
• Changed! smart CLECT 123aa 1e-18 in ref transcript
  • C-type lectin (CTL) or carbohydrate-recognition domain (CRD). Many of these domains function as calcium-dependent carbohydrate binding modules.
• Changed! cd CLECT_NK_receptors_like 45aa 9e-10 in modified transcript
• Changed! smart CLECT 45aa 2e-08 in modified transcript

CLEC7A

• refseq_CLEC7A.F3 refseq_CLEC7A.R3 158 296
• NCBIGene 36.3 64581
• Single exon skipping, size difference: 138
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_197947

• cd CLECT_NK_receptors_like 124aa 2e-27 in ref transcript
  • CLECT_NK_receptors_like: C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs), including proteins similar to oxidized low density lipoprotein (OxLDL) receptor (LOX-1), CD94, CD69, NKG2-A and -D, osteoclast inhibitory lectin (OCIL), dendritic cell-associated C-type lectin-1 (dectin-1), human myeloid inhibitory C-type lectin-like receptor (MICL), mast cell-associated functional antigen (MAFA), killer cell lectin-like receptors: subfamily F, member 1 (KLRF1) and subfamily B, member 1 (KLRB1), and lys49 receptors. CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. NKRs are variously associated with activation or inhibition of natural killer (NK) cells. Activating NKRs stimulate cytolysis by NK cells of virally infected or transformed cells; inhibitory NKRs block cytolysis upon recognition of markers of healthy self cells. Most Lys49 receptors are inhibitory; some are stimulatory. OCIL inhibits NK cell function via binding to the receptor NKRP1D. Murine OCIL in addition to inhibiting NK cell function inhibits osteoclast differentiation. MAFA clusters with the type I Fc epsilon receptor (FcepsilonRI) and inhibits the mast cells secretory response to FcepsilonRI stimulus. CD72 is a negative regulator of B cell receptor signaling. NKG2D is an activating receptor for stress-induced antigens; human NKG2D ligands include the stress induced MHC-I homologs, MICA, MICB, and ULBP family of glycoproteins Several NKRs have a carbohydrate-binding capacity which is not mediated through calcium ions (e.g. OCIL binds a range of high molecular weight sulfated glycosaminoglycans including dextran sulfate, fucoidan, and gamma-carrageenan sugars). Dectin-1 binds fungal beta-glucans and in involved in the innate immune responses to fungal pathogens. MAFA binds saccharides having terminal alpha-D mannose residues in a calcium-dependent manner. LOX-1 is the major receptor for OxLDL in endothelial cells and thought to play a role in the pathology of atherosclerosis. Some NKRs exist as homodimers (e.g.Lys49, NKG2D, CD69, LOX-1) and some as heterodimers (e.g. CD94/NKG2A). Dectin-1 can function as a monomer in vitro.
• smart CLECT 123aa 1e-18 in ref transcript
  • C-type lectin (CTL) or carbohydrate-recognition domain (CRD). Many of these domains function as calcium-dependent carbohydrate binding modules.

CLK1

• refseq_CLK1.F1 refseq_CLK1.R1 109 200
• NCBIGene 36.2 1195
• Single exon skipping, size difference: 91
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_004071

• Changed! cd S_TKc 318aa 1e-52 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• Changed! pfam Pkinase 317aa 4e-60 in ref transcript
  • Protein kinase domain.
• Changed! PTZ PTZ00284 332aa 1e-52 in ref transcript
  • protein kinase; Provisional.

CLK2

• refseq_CLK2.F1 refseq_CLK2.R1 228 313
• NCBIGene 36.2 1196
• Single exon skipping, size difference: 85
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_003993

• Changed! cd S_TKc 318aa 1e-46 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• Changed! pfam Pkinase 317aa 3e-53 in ref transcript
  • Protein kinase domain.
• Changed! PTZ PTZ00284 331aa 6e-49 in ref transcript
  • protein kinase; Provisional.

CLK3

• refseq_CLK3.F2 refseq_CLK3.R2 197 294
• NCBIGene 36.3 1198
• Single exon skipping, size difference: 97
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_003992

• Changed! cd S_TKc 318aa 8e-45 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• Changed! smart S_TKc 307aa 4e-49 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• Changed! PTZ PTZ00284 341aa 3e-46 in ref transcript
  • protein kinase; Provisional.

CLSTN1

• refseq_CLSTN1.F1 refseq_CLSTN1.R1 165 195
• NCBIGene 36.3 22883
• Single exon skipping, size difference: 30
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001009566

• Changed! cd CA 218aa 7e-21 in ref transcript
  • Cadherin repeat domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion; these domains occur as repeats in the extracellular regions which are thought to mediate cell-cell contact when bound to calcium; plays a role in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-,CNR-,proto-,and FAT-family cadherin, desmocollin, and desmoglein, exists as monomers or dimers (hetero- and homo-); two copies of the repeat are present here.
• smart CA 76aa 1e-07 in ref transcript
  • Cadherin repeats. Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. Cadherin domains occur as repeats in the extracellular regions which are thought to mediate cell-cell contact when bound to calcium.
• pfam Cadherin 89aa 3e-05 in ref transcript
  • Cadherin domain.
• Changed! cd CA 208aa 6e-22 in modified transcript

CLTA

• refseq_CLTA.F2 refseq_CLTA.R2 287 377
• NCBIGene 36.3 1211
• Multiple exon skipping, size difference: 90
• Exclusion in the protein (no frameshift), Exclusion in the protein (no frameshift)
• Reference transcript: NM_007096

• Changed! pfam Clathrin_lg_ch 220aa 2e-69 in ref transcript
  • Clathrin light chain.
• Changed! pfam Clathrin_lg_ch 190aa 7e-58 in modified transcript

CLTB

• refseq_CLTB.F1 refseq_CLTB.R1 219 273
• NCBIGene 36.3 1212
• Single exon skipping, size difference: 54
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_007097

• Changed! pfam Clathrin_lg_ch 201aa 2e-71 in ref transcript
  • Clathrin light chain.
• Changed! pfam Clathrin_lg_ch 183aa 1e-59 in modified transcript

CLTCL1

• refseq_CLTCL1.F1 refseq_CLTCL1.R1 186 357
• NCBIGene 36.2 8218
• Single exon skipping, size difference: 171
• Exclusion in 3'UTR
• Reference transcript: NM_007098

• pfam Clathrin 143aa 1e-33 in ref transcript
  • Region in Clathrin and VPS. Each region is about 140 amino acids long. The regions are composed of multiple alpha helical repeats. They occur in the arm region of the Clathrin heavy chain.
• pfam Clathrin 140aa 8e-33 in ref transcript
• pfam Clathrin 146aa 9e-32 in ref transcript
• pfam Clathrin 143aa 8e-27 in ref transcript
• pfam Clathrin 74aa 8e-11 in ref transcript
• pfam Clathrin-link 24aa 2e-04 in ref transcript
  • Clathrin, heavy-chain linker. Members of this family adopt a structure consisting of alpha-alpha superhelix. They are predominantly found in clathrin, where they act as a heavy-chain linker domain.

CMTM3

• refseq_CMTM3.F2 refseq_CMTM3.R2 139 245
• NCBIGene 36.3 123920
• Alternative 5-prime, size difference: 106
• Exclusion in 5'UTR
• Reference transcript: NM_144601

• pfam MARVEL 55aa 2e-04 in ref transcript
  • Membrane-associating domain. MARVEL domain-containing proteins are often found in lipid-associating proteins - such as Occludin and MAL family proteins. It may be part of the machinery of membrane apposition events, such as transport vesicle biogenesis.

CMTM5

• refseq_CMTM5.F1 refseq_CMTM5.R1 204 297
• NCBIGene 36.3 116173
• Single exon skipping, size difference: 93
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_138460

• Changed! pfam MARVEL 61aa 3e-05 in ref transcript
  • Membrane-associating domain. MARVEL domain-containing proteins are often found in lipid-associating proteins - such as Occludin and MAL family proteins. It may be part of the machinery of membrane apposition events, such as transport vesicle biogenesis.
• Changed! pfam MARVEL 53aa 2e-04 in modified transcript

CMTM7

• refseq_CMTM7.F2 refseq_CMTM7.R2 159 258
• NCBIGene 36.3 112616
• Single exon skipping, size difference: 99
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_138410

• Changed! pfam MARVEL 124aa 7e-10 in ref transcript
  • Membrane-associating domain. MARVEL domain-containing proteins are often found in lipid-associating proteins - such as Occludin and MAL family proteins. It may be part of the machinery of membrane apposition events, such as transport vesicle biogenesis.
• Changed! pfam MARVEL 82aa 6e-06 in modified transcript

CNIH

• refseq_CNIH.F1 refseq_CNIH.R1 121 234
• NCBIGene 36.2 10175
• Single exon skipping, size difference: 113
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_005776

• Changed! pfam Cornichon 117aa 2e-39 in ref transcript
  • Cornichon protein.
• Changed! pfam Cornichon 45aa 1e-07 in modified transcript

CNN2

• refseq_CNN2.F1 refseq_CNN2.R1 226 343
• NCBIGene 36.3 1265
• Single exon skipping, size difference: 117
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_004368

• Changed! cd CH 101aa 1e-16 in ref transcript
  • Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav).
• Changed! pfam CH 102aa 8e-18 in ref transcript
  • Calponin homology (CH) domain. The CH domain is found in both cytoskeletal proteins and signal transduction proteins. The CH domain is involved in actin binding in some members of the family. However in calponins there is evidence that the CH domain is not involved in its actin binding activity. Most proteins have two copies of the CH domain, however some proteins such as calponin have only a single copy.
• Changed! pfam Calponin 26aa 1e-05 in ref transcript
  • Calponin family repeat.
• pfam Calponin 26aa 3e-04 in ref transcript
• pfam Calponin 25aa 0.001 in ref transcript
• Changed! COG SCP1 167aa 2e-20 in ref transcript
  • Calponin [Cytoskeleton].
• Changed! cd CH 100aa 8e-17 in modified transcript
• Changed! pfam CH 100aa 7e-18 in modified transcript
• Changed! pfam Calponin 23aa 9e-04 in modified transcript
• Changed! COG SCP1 168aa 5e-16 in modified transcript

CNNM2

• refseq_CNNM2.F1 refseq_CNNM2.R1 151 217
• NCBIGene 36.3 54805
• Single exon skipping, size difference: 66
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_017649

• cd CBS_pair_CorC_HlyC_assoc 106aa 2e-16 in ref transcript
  • This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the CorC_HlyC domain. CorC_HlyC is a transporter associated domain. This small domain is found in Na+/H+ antiporters, in proteins involved in magnesium and cobalt efflux, and in association with some proteins of unknown function. The function of the CorC_HlyC domain is uncertain but it might be involved in modulating transport of ion substrates. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. The second CBS domain in this CD is degenerate.
• TIGR GldE 326aa 7e-29 in ref transcript
  • Members of this protein family are exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). GldC is a protein linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Flavobacterium johnsoniae and Cytophaga hutchinsonii. GldE was discovered because of its adjacency to GldD in F. johnsonii. Overexpression of GldE partially supresses the effects of a GldB point mutant suggesting that GldB and GldE interact. Gliding motility appears closely linked to chitin utilization in the model species Flavobacterium johnsoniae. Not all Bacteroidetes with members of this protein family appear to have all of the genes associated with gliding motility and in fact some do not appear to express the gliding phenotype.
• COG TlyC 331aa 9e-37 in ref transcript
  • Hemolysins and related proteins containing CBS domains [General function prediction only].

CNNM3

• refseq_CNNM3.F2 refseq_CNNM3.R2 276 420
• NCBIGene 36.3 26505
• Single exon skipping, size difference: 144
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_017623

• Changed! cd CBS_pair_CorC_HlyC_assoc 122aa 8e-19 in ref transcript
  • This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the CorC_HlyC domain. CorC_HlyC is a transporter associated domain. This small domain is found in Na+/H+ antiporters, in proteins involved in magnesium and cobalt efflux, and in association with some proteins of unknown function. The function of the CorC_HlyC domain is uncertain but it might be involved in modulating transport of ion substrates. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. The second CBS domain in this CD is degenerate.
• Changed! TIGR GldE 143aa 8e-20 in ref transcript
  • Members of this protein family are exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). GldC is a protein linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Flavobacterium johnsoniae and Cytophaga hutchinsonii. GldE was discovered because of its adjacency to GldD in F. johnsonii. Overexpression of GldE partially supresses the effects of a GldB point mutant suggesting that GldB and GldE interact. Gliding motility appears closely linked to chitin utilization in the model species Flavobacterium johnsoniae. Not all Bacteroidetes with members of this protein family appear to have all of the genes associated with gliding motility and in fact some do not appear to express the gliding phenotype.
• Changed! COG TlyC 250aa 1e-22 in ref transcript
  • Hemolysins and related proteins containing CBS domains [General function prediction only].
• Changed! cd CBS_pair_CorC_HlyC_assoc 87aa 5e-10 in modified transcript
• Changed! TIGR GldE 95aa 5e-09 in modified transcript
• Changed! COG TlyC 191aa 2e-12 in modified transcript

CNTFR

• refseq_CNTFR.F1 refseq_CNTFR.R1 144 255
• NCBIGene 36.3 1271
• Single exon skipping, size difference: 111
• Exclusion in 5'UTR
• Reference transcript: NM_147164

• cd FN3 97aa 1e-06 in ref transcript
  • Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.
• smart IGc2 58aa 2e-07 in ref transcript
  • Immunoglobulin C-2 Type.
• pfam fn3 91aa 1e-04 in ref transcript
  • Fibronectin type III domain.

CNTN1

• refseq_CNTN1.F1 refseq_CNTN1.R1 134 167
• NCBIGene 36.3 1272
• Single exon skipping, size difference: 33
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001843

• cd IGcam 88aa 2e-12 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• cd IGcam 86aa 8e-12 in ref transcript
• cd IGcam 76aa 9e-11 in ref transcript
• cd FN3 88aa 3e-10 in ref transcript
  • Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.
• cd IGcam 86aa 6e-10 in ref transcript
• cd FN3 91aa 1e-07 in ref transcript
• cd FN3 93aa 6e-07 in ref transcript
• cd IGcam 96aa 4e-06 in ref transcript
• cd IGcam 69aa 0.002 in ref transcript
• cd FN3 85aa 0.005 in ref transcript
• smart IGc2 60aa 2e-14 in ref transcript
  • Immunoglobulin C-2 Type.
• smart IG_like 81aa 2e-11 in ref transcript
  • Immunoglobulin like. IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
• pfam fn3 83aa 8e-11 in ref transcript
  • Fibronectin type III domain.
• pfam I-set 78aa 3e-10 in ref transcript
  • Immunoglobulin I-set domain.
• smart IG_like 68aa 5e-09 in ref transcript
• smart IG_like 91aa 2e-07 in ref transcript
• pfam fn3 84aa 3e-07 in ref transcript
• smart FN3 91aa 2e-04 in ref transcript
  • Fibronectin type 3 domain. One of three types of internal repeat within the plasma protein, fibronectin. The tenth fibronectin type III repeat contains a RGD cell recognition sequence in a flexible loop between 2 strands. Type III modules are present in both extracellular and intracellular proteins.
• pfam fn3 81aa 0.007 in ref transcript
• smart IG_like 73aa 0.009 in ref transcript

CNTROB

• refseq_CNTROB.F1 refseq_CNTROB.R1 183 249
• NCBIGene 36.3 116840
• Alternative 5-prime, size difference: 66
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001037144

COG5

• refseq_COG5.F1 refseq_COG5.R1 183 246
• NCBIGene 36.3 10466
• Single exon skipping, size difference: 63
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_006348

• pfam COG5 124aa 4e-26 in ref transcript
  • Golgi transport complex subunit 5. The COG complex, the peripheral membrane oligomeric protein complex involved in intra-Golgi protein trafficking, consists of eight subunits arranged in two lobes bridged by Cog1. Cog5 is in the smaller, B lobe, bound in with Cog6-8, and is itself bound to Cog1 as well as, strongly, to Cog7.

COL11A2

• refseq_COL11A2.F1 refseq_COL11A2.R1 108 288
• NCBIGene 36.3 1302
• Single exon skipping, size difference: 180
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_080680

• cd LamG 152aa 1e-05 in ref transcript
  • Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules.
• smart COLFI 196aa 6e-85 in ref transcript
  • Fibrillar collagens C-terminal domain. Found at C-termini of fibrillar collagens: Ephydatia muelleri procollagen EMF1alpha, vertebrate collagens alpha(1)III, alpha(1)II, alpha(2)V etc.
• smart TSPN 183aa 7e-56 in ref transcript
  • Thrombospondin N-terminal -like domains. Heparin-binding and cell adhesion domain of thrombospondin.

COL13A1

• refseq_COL13A1.F1 refseq_COL13A1.R1 126 213
• NCBIGene 36.3 1305
• Single exon skipping, size difference: 87
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_005203

• Changed! pfam Collagen 63aa 0.007 in modified transcript
  • Collagen triple helix repeat (20 copies). Members of this family belong to the collagen superfamily. Collagens are generally extracellular structural proteins involved in formation of connective tissue structure. The alignment contains 20 copies of the G-X-Y repeat that forms a triple helix. The first position of the repeat is glycine, the second and third positions can be any residue but are frequently proline and hydroxyproline. Collagens are post translationally modified by proline hydroxylase to form the hydroxyproline residues. Defective hydroxylation is the cause of scurvy. Some members of the collagen superfamily are not involved in connective tissue structure but share the same triple helical structure.

COL13A1

• refseq_COL13A1.F3 refseq_COL13A1.R3 155 221
• NCBIGene 36.3 1305
• Single exon skipping, size difference: 66
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_005203

COL13A1

• refseq_COL13A1.F4 refseq_COL13A1.R4 93 150
• NCBIGene 36.3 1305
• Single exon skipping, size difference: 57
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_005203

COL13A1

• refseq_COL13A1.F6 refseq_COL13A1.R6 92 143
• NCBIGene 36.3 1305
• Single exon skipping, size difference: 51
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_005203

COL2A1

• refseq_COL2A1.F1 refseq_COL2A1.R1 129 336
• NCBIGene 36.3 1280
• Single exon skipping, size difference: 207
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001844

• smart COLFI 236aa 1e-115 in ref transcript
  • Fibrillar collagens C-terminal domain. Found at C-termini of fibrillar collagens: Ephydatia muelleri procollagen EMF1alpha, vertebrate collagens alpha(1)III, alpha(1)II, alpha(2)V etc.
• Changed! pfam VWC 56aa 2e-18 in ref transcript
  • von Willebrand factor type C domain. The high cutoff was used to prevent overlap with pfam00094.
• pfam Collagen 59aa 1e-04 in ref transcript
  • Collagen triple helix repeat (20 copies). Members of this family belong to the collagen superfamily. Collagens are generally extracellular structural proteins involved in formation of connective tissue structure. The alignment contains 20 copies of the G-X-Y repeat that forms a triple helix. The first position of the repeat is glycine, the second and third positions can be any residue but are frequently proline and hydroxyproline. Collagens are post translationally modified by proline hydroxylase to form the hydroxyproline residues. Defective hydroxylation is the cause of scurvy. Some members of the collagen superfamily are not involved in connective tissue structure but share the same triple helical structure.

COL4A3

• refseq_COL4A3.F1 refseq_COL4A3.R1 182 355
• NCBIGene 36.3 1285
• Single exon skipping, size difference: 173
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_000091

• pfam C4 110aa 6e-54 in ref transcript
  • C-terminal tandem repeated domain in type 4 procollagen. Duplicated domain in C-terminus of type 4 collagens. Mutations in alpha-5 collagen IV are associated with X-linked Alport syndrome.
• Changed! pfam C4 113aa 5e-47 in ref transcript
• Changed! pfam C4 31aa 2e-10 in modified transcript

COL4A3BP

• refseq_COL4A3BP.F1 refseq_COL4A3BP.R1 195 273
• NCBIGene 36.3 10087
• Single exon skipping, size difference: 78
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_005713

• cd PH_GPBP 90aa 3e-42 in ref transcript
  • Goodpasture antigen binding protein (GPBP) Pleckstrin homology (PH) domain. The GPBP protein is a kinase that phosphorylates an N-terminal region of the alpha 3 chain of type IV collagen , which is commonly known as the goodpasture antigen. It has has an N-terminal PH domain and a C-terminal START domain. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinsases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes.
• Changed! cd START 220aa 1e-25 in ref transcript
  • START(STeroidogenic Acute Regulatory (STAR) related lipid Transfer) Domain. These domains are 200-210 amino acid in length and occur in proteins involved in lipid transport (phosphatidylcholine) and metabolism, signal transduction, and transcriptional regulation. The most striking feature of the START domain structure is a predominantly hydrophobic tunnel extending nearly the entire protein and used to binding a single molecule of large lipophilic compounds, like cholesterol.
• smart START 202aa 3e-18 in ref transcript
  • in StAR and phosphatidylcholine transfer protein. putative lipid-binding domain in StAR and phosphatidylcholine transfer protein.
• pfam PH 92aa 3e-13 in ref transcript
  • PH domain. PH stands for pleckstrin homology.
• Changed! cd START 224aa 7e-26 in modified transcript

COL6A2

• refseq_COL6A2.F2 refseq_COL6A2.R2 142 435
• NCBIGene 36.3 1292
• Alternative 3-prime, size difference: 293
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_058174

• cd vWA_collagen_alpha_1-VI-type 192aa 1e-51 in ref transcript
  • VWA_collagen alpha(VI) type: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different collagen types identified thus far. Collagens are centrally involved in the formation of fibrillar and microfibrillar networks of the extracellular matrix, basement membranes as well as other structures of the extracellular matrix. Some collagens have about 15-18 vWA domains in them. The VWA domains present in these collagens mediate protein-protein interactions.
• cd vWA_collagen_alpha_1-VI-type 189aa 1e-46 in ref transcript
• pfam VWA 187aa 2e-29 in ref transcript
  • von Willebrand factor type A domain.
• smart VWA 169aa 1e-18 in ref transcript
  • von Willebrand factor (vWF) type A domain. VWA domains in extracellular eukaryotic proteins mediate adhesion via metal ion-dependent adhesion sites (MIDAS). Intracellular VWA domains and homologues in prokaryotes have recently been identified. The proposed VWA domains in integrin beta subunits have recently been substantiated using sequence-based methods.
• pfam Collagen 46aa 8e-06 in ref transcript
  • Collagen triple helix repeat (20 copies). Members of this family belong to the collagen superfamily. Collagens are generally extracellular structural proteins involved in formation of connective tissue structure. The alignment contains 20 copies of the G-X-Y repeat that forms a triple helix. The first position of the repeat is glycine, the second and third positions can be any residue but are frequently proline and hydroxyproline. Collagens are post translationally modified by proline hydroxylase to form the hydroxyproline residues. Defective hydroxylation is the cause of scurvy. Some members of the collagen superfamily are not involved in connective tissue structure but share the same triple helical structure.
• pfam Collagen 62aa 4e-05 in ref transcript
• pfam Collagen 88aa 6e-05 in ref transcript

COL8A1

• refseq_COL8A1.F1 refseq_COL8A1.R1 119 181
• NCBIGene 36.3 1295
• Single exon skipping, size difference: 62
• Exclusion in 5'UTR
• Reference transcript: NM_001850

• smart C1Q 136aa 9e-55 in ref transcript
  • Complement component C1q domain. Globular domain found in many collagens and eponymously in complement C1q. When part of full length proteins these domains form a 'bouquet' due to the multimerization of heterotrimers. The C1q fold is similar to that of tumour necrosis factor.

COLEC11

• refseq_COLEC11.F1 refseq_COLEC11.R1 100 179
• NCBIGene 36.3 78989
• Single exon skipping, size difference: 79
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_024027

• Changed! cd CLECT_collectin_like 116aa 5e-45 in ref transcript
  • CLECT_collectin_like: C-type lectin-like domain (CTLD) of the type found in human collectins including lung surfactant proteins A and D, mannose- or mannan binding lectin (MBL), and CL-L1 (collectin liver 1). CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. The CTLDs of these collectins bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, or apoptotic cells) and mediate functions associated with killing and phagocytosis. MBPs recognize high mannose oligosaccharides in a calcium dependent manner, bind to a broad range of pathogens, and trigger cell killing by activating the complement pathway. MBP also acts directly as an opsonin. SP-A and SP-D in addition to functioning as host defense components, are components of pulmonary surfactant which play a role in surfactant homeostasis. Pulmonary surfactant is a phospholipid-protein complex which reduces the surface tension within the lungs. SP-A binds the major surfactant lipid: dipalmitoylphosphatidylcholine (DPPC). SP-D binds two minor components of surfactant that contain sugar moieties: glucosylceramide and phosphatidylinositol (PI). MBP and SP-A, -D monomers are homotrimers with an N-terminal collagen region and three CTLDs. Multiple homotrimeric units associate to form supramolecular complexes. MBL deficiency results in an increased susceptibility to a large number of different infections and to inflammatory disease, such as rheumatoid arthritis.
• Changed! pfam Lectin_C 108aa 2e-19 in ref transcript
  • Lectin C-type domain. This family includes both long and short form C-type.

COLQ

• refseq_COLQ.F1 refseq_COLQ.R1 142 169
• NCBIGene 36.3 8292
• Single exon skipping, size difference: 27
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_005677

• TIGR myxo_disulf_rpt 25aa 5e-04 in ref transcript
  • This model represents a sequence region shared between several proteins of Myxococcus xanthus DK 1622 and some eukaryotic proteins that include human pappalysin-1. The region of about 40 amino acids contains several conserved Cys residues presumed to form disulfide bonds. The region appears in up to 13 repeats in Myxococcus.
• pfam Collagen 63aa 0.004 in ref transcript
  • Collagen triple helix repeat (20 copies). Members of this family belong to the collagen superfamily. Collagens are generally extracellular structural proteins involved in formation of connective tissue structure. The alignment contains 20 copies of the G-X-Y repeat that forms a triple helix. The first position of the repeat is glycine, the second and third positions can be any residue but are frequently proline and hydroxyproline. Collagens are post translationally modified by proline hydroxylase to form the hydroxyproline residues. Defective hydroxylation is the cause of scurvy. Some members of the collagen superfamily are not involved in connective tissue structure but share the same triple helical structure.

COLQ

• refseq_COLQ.F4 refseq_COLQ.R4 136 276
• NCBIGene 36.2 8292
• Single exon skipping, size difference: 140
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_005677

• Changed! TIGR myxo_disulf_rpt 25aa 5e-04 in ref transcript
  • This model represents a sequence region shared between several proteins of Myxococcus xanthus DK 1622 and some eukaryotic proteins that include human pappalysin-1. The region of about 40 amino acids contains several conserved Cys residues presumed to form disulfide bonds. The region appears in up to 13 repeats in Myxococcus.
• Changed! pfam Collagen 63aa 0.004 in ref transcript
  • Collagen triple helix repeat (20 copies). Members of this family belong to the collagen superfamily. Collagens are generally extracellular structural proteins involved in formation of connective tissue structure. The alignment contains 20 copies of the G-X-Y repeat that forms a triple helix. The first position of the repeat is glycine, the second and third positions can be any residue but are frequently proline and hydroxyproline. Collagens are post translationally modified by proline hydroxylase to form the hydroxyproline residues. Defective hydroxylation is the cause of scurvy. Some members of the collagen superfamily are not involved in connective tissue structure but share the same triple helical structure.

COMMD6

• refseq_COMMD6.F1 refseq_COMMD6.R1 147 186
• NCBIGene 36.3 170622
• Single exon skipping, size difference: 39
• Exclusion in 5'UTR
• Reference transcript: NM_203497

COP1

• refseq_COP1.F1 refseq_COP1.R1 333 396
• NCBIGene 36.3 114769
• Single exon skipping, size difference: 63
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_001017534

• pfam CARD 88aa 7e-19 in ref transcript
  • Caspase recruitment domain. Motif contained in proteins involved in apoptotic signaling. Predicted to possess a DEATH (pfam00531) domain-like fold.

COPE

• refseq_COPE.F1 refseq_COPE.R1 222 378
• NCBIGene 36.3 11316
• Single exon skipping, size difference: 156
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_007263

• Changed! cd TPR 83aa 0.007 in ref transcript
  • Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here.
• Changed! pfam Coatomer_E 291aa 1e-109 in ref transcript
  • Coatomer epsilon subunit. This family represents the epsilon subunit of the coatomer complex, which is involved in the regulation of intracellular protein trafficking between the endoplasmic reticulum and the Golgi complex.
• Changed! pfam Coatomer_E 239aa 5e-75 in modified transcript

COPS8

• refseq_COPS8.F1 refseq_COPS8.R1 191 256
• NCBIGene 36.3 10920
• Single exon skipping, size difference: 65
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_006710

• Changed! pfam PCI_Csn8 175aa 3e-60 in ref transcript
  • COP9 signalosome, subunit CSN8. This PCI_Csn8 domain is conserved from plants to humans. It is a signature protein motif found in components of CSN (COP9 signalosome). It functions as a structural scaffold for subunit-subunit interactions within the complex and is a key regulator of photomorphogenic development.

COQ6

• refseq_COQ6.F1 refseq_COQ6.R1 168 227
• NCBIGene 36.3 51004
• Single exon skipping, size difference: 59
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_182476

• Changed! TIGR COQ6 428aa 0.0 in ref transcript
  • This model represents the monooxygenase responsible for the 4-hydroxylateion of the phenol ring in the aerobic biosynthesis of ubiquinone.
• Changed! PRK PRK08850 390aa 3e-61 in ref transcript
  • 2-octaprenyl-6-methoxyphenol hydroxylase; Validated.
• Changed! TIGR COQ6 67aa 2e-14 in modified transcript

ENOX2

• refseq_COVA1.F2 refseq_COVA1.R2 184 273
• NCBIGene 36.3 10495
• Single exon skipping, size difference: 89
• Exclusion of the protein initiation site
• Reference transcript: NM_182314

• cd RRM 58aa 1e-06 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• pfam RRM_1 58aa 3e-07 in ref transcript
  • RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain). The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have a N terminus rrm which is included in the seed. There is a second region towards the C terminus that has some features of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.
• COG COG0724 79aa 0.001 in ref transcript
  • RNA-binding proteins (RRM domain) [General function prediction only].

CPB2

• refseq_CPB2.F1 refseq_CPB2.R1 100 211
• NCBIGene 36.3 1361
• Single exon skipping, size difference: 111
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001872

• Changed! cd M14_CPB2 302aa 1e-170 in ref transcript
  • Peptidase M14 Carboxypeptidase (CP) B2 (CPB2, also known as plasma carboxypeptidase B, carboxypeptidase U, and CPU), belongs to the carboxpeptidase A/B subfamily of the M14 family of metallocarboxypeptidases (MCPs). The M14 family are zinc-binding CPs which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. CPB2 enzyme displays B-like activity; it only cleaves the basic residues lysine or arginine. It is produced and secreted by the liver as the inactive precursor, procarboxypeptidase U or PCPB2, commonly referred to as thrombin-activatable fibrinolysis inhibitor (TAFI). It circulates in plasma as a zymogen bound to plasminogen, and the active enzyme, TAFIa, inhibits fibrinolysis. It is highly regulated, increased TAFI concentrations are thought to increase the risk of thrombosis and coronary artery disease by reducing fibrinolytic activity while low TAFI levels have been correlated with chronic liver disease.
• Changed! smart Zn_pept 283aa 2e-92 in ref transcript
  • Zn_pept.
• pfam Propep_M14 78aa 2e-20 in ref transcript
  • Carboxypeptidase activation peptide. Carboxypeptidases are found in abundance in pancreatic secretions. The pro-segment moiety (activation peptide) accounts for up to a quarter of the total length of the peptidase, and is responsible for modulation of folding and activity of the pro-enzyme.
• Changed! COG COG2866 310aa 3e-08 in ref transcript
  • Predicted carboxypeptidase [Amino acid transport and metabolism].
• Changed! cd M14_CPB2 265aa 1e-145 in modified transcript
• Changed! smart Zn_pept 246aa 3e-76 in modified transcript

CPEB2

• refseq_CPEB2.F2 refseq_CPEB2.R2 316 406
• NCBIGene 36.3 132864
• Single exon skipping, size difference: 90
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_182485

• cd RRM 88aa 1e-09 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• cd RRM 79aa 0.002 in ref transcript
• smart RRM_2 63aa 9e-08 in ref transcript
  • RNA recognition motif.
• Changed! COG COG0724 176aa 1e-04 in ref transcript
  • RNA-binding proteins (RRM domain) [General function prediction only].
• Changed! COG COG0724 272aa 3e-04 in modified transcript

CPM

• refseq_CPM.F1 refseq_CPM.R1 102 120
• NCBIGene 36.3 1368
• Alternative 5-prime, size difference: 18
• Exclusion in 5'UTR
• Reference transcript: NM_198320

• cd M14_CPM 376aa 0.0 in ref transcript
  • Peptidase M14 Carboxypeptidase (CP) M (CPM) belongs to the N/E subfamily of the M14 family of metallocarboxypeptidases (MCPs).The M14 family are zinc-binding CPs which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. CPM is an extracellular glycoprotein, bound to cell membranes via a glycosyl-phosphatidylinositol on the C-terminus of the protein. It specifically removes C-terminal basic residues such as lysine and arginine from peptides and proteins. The highest levels of CPM have been found in human lung and placenta, but significant amounts are present in kidney, blood vessels, intestine, brain, and peripheral nerves. CPM has also been found in soluble form in various body fluids, including amniotic fluid, seminal plasma and urine. Due to its wide distribution in a variety of tissues, it is believed that it plays an important role in the control of peptide hormones and growth factor activity on the cell surface and in the membrane-localized degradation of extracellular proteins, for example it hydrolyses the C-terminal arginine of epidermal growth factor (EGF) resulting in des-Arg-EGF which binds to the EGF receptor (EGFR) with an equal or greater affinity than native EGF. CPM is a required processing enzyme that generates specific agonists for the B1 receptor.
• smart Zn_pept 273aa 8e-69 in ref transcript
  • Zn_pept.
• COG COG2866 138aa 1e-04 in ref transcript
  • Predicted carboxypeptidase [Amino acid transport and metabolism].
• COG PcaH 71aa 0.002 in ref transcript
  • Protocatechuate 3,4-dioxygenase beta subunit [Secondary metabolites biosynthesis, transport, and catabolism].

CPNE1

• refseq_CPNE1.F1 refseq_CPNE1.R1 152 295
• NCBIGene 36.3 8904
• Single exon skipping, size difference: 143
• Exclusion in 5'UTR
• Reference transcript: NM_152930

• cd vWA_copine_like 259aa 4e-88 in ref transcript
  • VWA Copine: Copines are phospholipid-binding proteins originally identified in paramecium. They are found in human and orthologues have been found in C. elegans and Arabidopsis Thaliana. None have been found in D. Melanogaster or S. Cereviciae. Phylogenetic distribution suggests that copines have been lost in some eukaryotes. No functional properties have been assigned to the VWA domains present in copines. The members of this subgroup contain a functional MIDAS motif based on their preferential binding to magnesium and manganese. However, the MIDAS motif is not totally conserved, in most cases the MIDAS consists of the sequence DxTxS instead of the motif DxSxS that is found in most cases. The C2 domains present in copines mediate phospholipid binding.
• cd C2 109aa 7e-15 in ref transcript
  • Protein kinase C conserved region 2 (CalB); Ca2+-binding motif present in phospholipases, protein kinases C, and synaptotagmins (among others). Some do not appear to contain Ca2+-binding sites. Particular C2s appear to bind phospholipids, inositol polyphosphates,and intracellular proteins. Synaptotagmin and PLC C2s are permuted in sequence with respect to N- and C-terminal beta strands.
• cd C2 99aa 2e-10 in ref transcript
• pfam Copine 148aa 4e-65 in ref transcript
  • Copine. This family represents a conserved region approximately 180 residues long within eukaryotic copines. Copines are Ca(2+)-dependent phospholipid-binding proteins that are thought to be involved in membrane-trafficking, and may also be involved in cell division and growth.
• pfam C2 85aa 3e-14 in ref transcript
  • C2 domain.
• smart C2 97aa 3e-10 in ref transcript
  • Protein kinase C conserved region 2 (CalB). Ca2+-binding motif present in phospholipases, protein kinases C, and synaptotamins (among others). Some do not appear to contain Ca2+-binding sites. Particular C2s appear to bind phospholipids, inositol polyphosphates, and intracellular proteins. Unusual occurrence in perforin. Synaptotagmin and PLC C2s are permuted in sequence with respect to N- and C-terminal beta strands. SMART detects C2 domains using one or both of two profiles.
• COG COG5038 94aa 3e-07 in ref transcript
  • Ca2+-dependent lipid-binding protein, contains C2 domain [General function prediction only].

CPNE1

• refseq_CPNE1.F3 refseq_CPNE1.R3 180 212
• NCBIGene 36.3 8904
• Alternative 3-prime, size difference: 32
• Inclusion in 5'UTR
• Reference transcript: NM_152931

• cd vWA_copine_like 259aa 4e-88 in ref transcript
  • VWA Copine: Copines are phospholipid-binding proteins originally identified in paramecium. They are found in human and orthologues have been found in C. elegans and Arabidopsis Thaliana. None have been found in D. Melanogaster or S. Cereviciae. Phylogenetic distribution suggests that copines have been lost in some eukaryotes. No functional properties have been assigned to the VWA domains present in copines. The members of this subgroup contain a functional MIDAS motif based on their preferential binding to magnesium and manganese. However, the MIDAS motif is not totally conserved, in most cases the MIDAS consists of the sequence DxTxS instead of the motif DxSxS that is found in most cases. The C2 domains present in copines mediate phospholipid binding.
• cd C2 109aa 7e-15 in ref transcript
  • Protein kinase C conserved region 2 (CalB); Ca2+-binding motif present in phospholipases, protein kinases C, and synaptotagmins (among others). Some do not appear to contain Ca2+-binding sites. Particular C2s appear to bind phospholipids, inositol polyphosphates,and intracellular proteins. Synaptotagmin and PLC C2s are permuted in sequence with respect to N- and C-terminal beta strands.
• cd C2 99aa 2e-10 in ref transcript
• pfam Copine 148aa 4e-65 in ref transcript
  • Copine. This family represents a conserved region approximately 180 residues long within eukaryotic copines. Copines are Ca(2+)-dependent phospholipid-binding proteins that are thought to be involved in membrane-trafficking, and may also be involved in cell division and growth.
• pfam C2 85aa 3e-14 in ref transcript
  • C2 domain.
• smart C2 97aa 3e-10 in ref transcript
  • Protein kinase C conserved region 2 (CalB). Ca2+-binding motif present in phospholipases, protein kinases C, and synaptotamins (among others). Some do not appear to contain Ca2+-binding sites. Particular C2s appear to bind phospholipids, inositol polyphosphates, and intracellular proteins. Unusual occurrence in perforin. Synaptotagmin and PLC C2s are permuted in sequence with respect to N- and C-terminal beta strands. SMART detects C2 domains using one or both of two profiles.
• COG COG5038 94aa 3e-07 in ref transcript
  • Ca2+-dependent lipid-binding protein, contains C2 domain [General function prediction only].

CPNE7

• refseq_CPNE7.F1 refseq_CPNE7.R1 140 365
• NCBIGene 36.3 27132
• Multiple exon skipping, size difference: 225
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_014427

• cd vWA_copine_like 258aa 4e-84 in ref transcript
  • VWA Copine: Copines are phospholipid-binding proteins originally identified in paramecium. They are found in human and orthologues have been found in C. elegans and Arabidopsis Thaliana. None have been found in D. Melanogaster or S. Cereviciae. Phylogenetic distribution suggests that copines have been lost in some eukaryotes. No functional properties have been assigned to the VWA domains present in copines. The members of this subgroup contain a functional MIDAS motif based on their preferential binding to magnesium and manganese. However, the MIDAS motif is not totally conserved, in most cases the MIDAS consists of the sequence DxTxS instead of the motif DxSxS that is found in most cases. The C2 domains present in copines mediate phospholipid binding.
• Changed! cd C2 98aa 5e-11 in ref transcript
  • Protein kinase C conserved region 2 (CalB); Ca2+-binding motif present in phospholipases, protein kinases C, and synaptotagmins (among others). Some do not appear to contain Ca2+-binding sites. Particular C2s appear to bind phospholipids, inositol polyphosphates,and intracellular proteins. Synaptotagmin and PLC C2s are permuted in sequence with respect to N- and C-terminal beta strands.
• cd C2 87aa 9e-09 in ref transcript
• pfam Copine 148aa 2e-70 in ref transcript
  • Copine. This family represents a conserved region approximately 180 residues long within eukaryotic copines. Copines are Ca(2+)-dependent phospholipid-binding proteins that are thought to be involved in membrane-trafficking, and may also be involved in cell division and growth.
• Changed! pfam C2 87aa 2e-11 in ref transcript
  • C2 domain.
• pfam C2 86aa 1e-10 in ref transcript
• Changed! COG COG5038 151aa 6e-04 in ref transcript
  • Ca2+-dependent lipid-binding protein, contains C2 domain [General function prediction only].
• Changed! cd C2 100aa 3e-11 in modified transcript
• Changed! smart C2 98aa 2e-11 in modified transcript
  • Protein kinase C conserved region 2 (CalB). Ca2+-binding motif present in phospholipases, protein kinases C, and synaptotamins (among others). Some do not appear to contain Ca2+-binding sites. Particular C2s appear to bind phospholipids, inositol polyphosphates, and intracellular proteins. Unusual occurrence in perforin. Synaptotagmin and PLC C2s are permuted in sequence with respect to N- and C-terminal beta strands. SMART detects C2 domains using one or both of two profiles.
• Changed! COG COG5038 112aa 0.001 in modified transcript

CPSF3L

• refseq_CPSF3L.F2 refseq_CPSF3L.R2 211 277
• NCBIGene 36.2 54973
• Alternative 3-prime, size difference: 66
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_017871

• Changed! TIGR arCOG00543 443aa 5e-86 in ref transcript
  • This family of proteins is universal in the archaea and consistsof an N-terminal type-1 KH-domain (pfam00013) a central beta-lactamase-domain (pfam00753) with a C-terminal motif associated with RNA metabolism (pfam07521). KH-domains are associated with RNA-binding, so taken together, this protein is a likely metal-dependent RNAase. This family was defined in as arCOG01782.
• Changed! COG YSH1 443aa 1e-94 in ref transcript
  • Predicted exonuclease of the beta-lactamase fold involved in RNA processing [Translation, ribosomal structure and biogenesis].
• Changed! TIGR arCOG00543 421aa 9e-80 in modified transcript
• Changed! COG YSH1 421aa 3e-83 in modified transcript

CPVL

• refseq_CPVL.F2 refseq_CPVL.R2 185 273
• NCBIGene 36.3 54504
• Alternative 5-prime, size difference: 88
• Exclusion in 5'UTR
• Reference transcript: NM_019029

• pfam Peptidase_S10 400aa 2e-97 in ref transcript
  • Serine carboxypeptidase.
• COG COG2939 383aa 1e-35 in ref transcript
  • Carboxypeptidase C (cathepsin A) [Amino acid transport and metabolism].

CR2

• refseq_CR2.F1 refseq_CR2.R1 145 322
• NCBIGene 36.3 1380
• Single exon skipping, size difference: 177
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001006658

• cd CCP 58aa 1e-09 in ref transcript
  • Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR); The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function.
• Changed! cd CCP 58aa 9e-09 in ref transcript
• cd CCP 68aa 1e-08 in ref transcript
• cd CCP 58aa 2e-08 in ref transcript
• cd CCP 57aa 6e-08 in ref transcript
• cd CCP 61aa 6e-08 in ref transcript
• cd CCP 58aa 9e-08 in ref transcript
• cd CCP 57aa 2e-07 in ref transcript
• cd CCP 61aa 2e-07 in ref transcript
• cd CCP 68aa 6e-07 in ref transcript
• cd CCP 57aa 4e-06 in ref transcript
• cd CCP 57aa 1e-05 in ref transcript
• cd CCP 39aa 5e-05 in ref transcript
• smart CCP 57aa 1e-11 in ref transcript
  • Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR). The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. A missense mutation in seventh CCP domain causes deficiency of the b subunit of factor XIII.
• smart CCP 67aa 6e-11 in ref transcript
• Changed! smart CCP 57aa 1e-10 in ref transcript
• smart CCP 57aa 8e-10 in ref transcript
• smart CCP 61aa 1e-09 in ref transcript
• smart CCP 57aa 2e-09 in ref transcript
• smart CCP 51aa 7e-09 in ref transcript
• pfam Sushi 60aa 9e-09 in ref transcript
  • Sushi domain (SCR repeat).
• smart CCP 56aa 2e-08 in ref transcript
• smart CCP 67aa 2e-08 in ref transcript
• smart CCP 56aa 6e-07 in ref transcript
• pfam Sushi 56aa 1e-06 in ref transcript
• smart CCP 57aa 1e-05 in ref transcript
• pfam Sushi 57aa 5e-04 in ref transcript
• Changed! cd CCP 58aa 0.010 in modified transcript

CRAT

• refseq_CRAT.F2 refseq_CRAT.R2 139 385
• NCBIGene 36.2 1384
• Exon skipping and alternative 3-prime or 5-prime, size difference: 246
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_000755

• Changed! pfam Carn_acyltransf 582aa 0.0 in ref transcript
  • Choline/Carnitine o-acyltransferase.
• Changed! pfam Carn_acyltransf 250aa 1e-107 in modified transcript
• Changed! pfam Carn_acyltransf 248aa 2e-94 in modified transcript

CREB1

• refseq_CREB1.F1 refseq_CREB1.R1 151 193
• NCBIGene 36.3 1385
• Single exon skipping, size difference: 42
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_134442

• pfam pKID 29aa 3e-10 in ref transcript
  • pKID domain. CBP and P300 bind to the pKID (phosphorylated kinase-inducible-domain) domain of CREB.
• pfam bZIP_1 57aa 2e-06 in ref transcript
  • bZIP transcription factor. The Pfam entry includes the basic region and the leucine zipper region.

CRELD1

• refseq_CRELD1.F1 refseq_CRELD1.R1 168 362
• NCBIGene 36.3 78987
• Single exon skipping, size difference: 194
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_001031717

• smart EGF_CA 32aa 0.003 in ref transcript
  • Calcium-binding EGF-like domain.
• pfam EGF_CA 28aa 0.006 in ref transcript
  • Calcium binding EGF domain.

CREM

• refseq_CREM.F1 refseq_CREM.R1 306 495
• NCBIGene 36.3 1390
• Single exon skipping, size difference: 189
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_182769

• Changed! pfam pKID 41aa 6e-11 in ref transcript
  • pKID domain. CBP and P300 bind to the pKID (phosphorylated kinase-inducible-domain) domain of CREB.
• pfam bZIP_1 53aa 8e-07 in ref transcript
  • bZIP transcription factor. The Pfam entry includes the basic region and the leucine zipper region.
• Changed! pfam pKID 37aa 4e-10 in modified transcript

CREM

• refseq_CREM.F2 refseq_CREM.R2 106 204
• NCBIGene 36.3 1390
• Single exon skipping, size difference: 98
• Exclusion of the protein initiation site
• Reference transcript: NM_183013

• pfam pKID 41aa 2e-10 in ref transcript
  • pKID domain. CBP and P300 bind to the pKID (phosphorylated kinase-inducible-domain) domain of CREB.
• pfam bZIP_1 53aa 1e-04 in ref transcript
  • bZIP transcription factor. The Pfam entry includes the basic region and the leucine zipper region.

CREM

• refseq_CREM.F5 refseq_CREM.R4 185 221
• NCBIGene 36.3 1390
• Single exon skipping, size difference: 36
• Exclusion of the protein initiation site
• Reference transcript: NM_182723

• pfam bZIP_1 53aa 3e-04 in ref transcript
  • bZIP transcription factor. The Pfam entry includes the basic region and the leucine zipper region.

CREM

• refseq_CREM.F7 refseq_CREM.R5 153 251
• NCBIGene 36.3 1390
• Single exon skipping, size difference: 98
• Exclusion of the protein initiation site
• Reference transcript: NM_181571

• pfam pKID 41aa 9e-11 in ref transcript
  • pKID domain. CBP and P300 bind to the pKID (phosphorylated kinase-inducible-domain) domain of CREB.
• pfam bZIP_1 53aa 4e-06 in ref transcript
  • bZIP transcription factor. The Pfam entry includes the basic region and the leucine zipper region.

CREM

• refseq_CREM.F8 refseq_CREM.R6 98 500
• NCBIGene 36.3 1390
• Alternative 3-prime, size difference: 402
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_181571

• pfam pKID 41aa 9e-11 in ref transcript
  • pKID domain. CBP and P300 bind to the pKID (phosphorylated kinase-inducible-domain) domain of CREB.
• Changed! pfam bZIP_1 53aa 4e-06 in ref transcript
  • bZIP transcription factor. The Pfam entry includes the basic region and the leucine zipper region.
• Changed! pfam bZIP_1 53aa 3e-06 in modified transcript

CRISP1

• refseq_CRISP1.F1 refseq_CRISP1.R1 258 347
• NCBIGene 36.3 167
• Single exon skipping, size difference: 89
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_001131

• cd SCP_CRISP 139aa 3e-51 in ref transcript
  • SCP_CRISP: SCP-like extracellular protein domain, CRISP-like sub-family. The wider family of SCP containing proteins includes plant pathogenesis-related protein 1 (PR-1), CRISPs, mammalian cysteine-rich secretory proteins, which combine SCP with a C-terminal cysteine rich domain, and allergen 5 from vespid venom. Involvement of CRISP in response to pathogens, fertilization, and sperm maturation have been proposed. One member, Tex31 from the venom duct of Conus textile, has been shown to possess proteolytic activity sensitive to serine protease inhibitors. SCP has also been proposed to be a Ca++ chelating serine protease. The Ca++-chelating function would fit with various signaling processes that members of this family, such as the CRISPs, are involved in, and is supported by sequence and structural evidence of a conserved pocket containing two histidines and a glutamate. It also may explain how helothermine, a toxic peptide secreted by the beaded lizard, blocks Ca++ transporting ryanodine receptors. One member, DE or CRISP-1, has been shown to mediate gamete fusion by binding to the egg surface; a sequence motif in the SCP domain plays a role in that binding.
• smart SCP 139aa 1e-31 in ref transcript
  • SCP / Tpx-1 / Ag5 / PR-1 / Sc7 family of extracellular domains. Human glioma pathogenesis-related protein GliPR and the plant pathogenesis-related protein represent functional links between plant defense systems and human immune system. This family has no known function.
• Changed! pfam Crisp 55aa 3e-18 in ref transcript
  • Crisp. This domain is found on Crisp proteins which contain pfam00188 and has been termed the Crisp domain. It is found in the mammalian reproductive tract and the venom of reptiles, and has been shown to regulate ryanodine receptor Ca2+ signalling. It contains 10 conserved cysteines which are all involved in disulphide bonds and is structurally related to the ion channel inhibitor toxins BgK and ShK.
• Changed! cd SCP_CRISP 140aa 1e-51 in modified transcript

CRK

• refseq_CRK.F1 refseq_CRK.R1 156 326
• NCBIGene 36.3 1398
• Alternative 5-prime, size difference: 170
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_016823

• cd SH2 106aa 2e-17 in ref transcript
  • Src homology 2 domains; Signal transduction, involved in recognition of phosphorylated tyrosine (pTyr). SH2 domains typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites.
• cd SH3 54aa 1e-12 in ref transcript
  • Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
• Changed! cd SH3 55aa 0.009 in ref transcript
• smart SH2 97aa 9e-18 in ref transcript
  • Src homology 2 domains. Src homology 2 domains bind phosphotyrosine-containing polypeptides via 2 surface pockets. Specificity is provided via interaction with residues that are distinct from the phosphotyrosine. Only a single occurrence of a SH2 domain has been found in S. cerevisiae.
• smart SH3 58aa 1e-14 in ref transcript
  • Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.
• Changed! pfam SH3_2 55aa 5e-11 in ref transcript
  • Variant SH3 domain. SH3 (Src homology 3) domains are often indicative of a protein involved in signal transduction related to cytoskeletal organisation. First described in the Src cytoplasmic tyrosine kinase. The structure is a partly opened beta barrel.

MED23

• refseq_CRSP3.F1 refseq_CRSP3.R1 102 120
• NCBIGene 36.3 9439
• Single exon skipping, size difference: 18
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_004830

CRTC1

• refseq_CRTC1.F2 refseq_CRTC1.R2 100 187
• NCBIGene 36.2 23373
• Single exon skipping, size difference: 87
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_015321

CS

• refseq_CS.F1 refseq_CS.R1 149 232
• NCBIGene 36.3 1431
• Single exon skipping, size difference: 83
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_004077

• Changed! cd ScCit1-2_like 427aa 0.0 in ref transcript
  • Saccharomyces cerevisiae (Sc) citrate synthases Cit1-2_like. Citrate synthases (CS) catalyzes the condensation of acetyl coenzyme A (AcCoA) with oxaloacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). Some CS proteins function as 2-methylcitrate synthase (2MCS). 2MCS catalyzes the condensation of propionyl-coenzyme A (PrCoA) and OAA to form 2-methylcitrate and CoA during propionate metabolism. The overall CS reaction is thought to proceed through three partial reactions and involves both closed and open conformational forms of the enzyme: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, and c) the hydrolysis of citryl-CoA to produce citrate and CoA. There are two types of CSs: type I CS and type II CSs. Type I CSs are found in eukarya, gram-positive bacteria, archaea, and in some gram-negative bacteria and are homodimers with both subunits participating in the active site. Type II CSs are unique to gram-negative bacteria and are homohexamers of identical subunits (approximated as a trimer of dimers). ScCit1 is a nuclear-encoded mitochondrial CS with highly specificity for AcCoA. In addition to its CS function, ScCit1 plays a part in the construction of the TCA cycle metabolon. Yeast cells deleted for Cit1 are hyper-susceptible to apoptosis induced by heat and aging stress. ScCit2 is a peroxisomal CS involved in the glyoxylate cycle; in addition to having activity with AcCoA, it may have activity with PrCoA. Chicken and pig heart CS, two Arabidopsis thaliana (Ath) CSs, CSY4 and -5, and Aspergillus niger (An) CS also belong to this group. Ath CSY4 has a mitochondrial targeting sequence; AthCSY5 has no identifiable targeting sequence. AnCS encoded by the citA gene has both an N-terminal mitochondrial import signal and a C-terminal peroxisiomal target sequence; it is not known if both these signals are functional in vivo. This group contains proteins which functions exclusively as either a CS or a 2MCS, as well as those with relaxed specificity which have dual functions as both a CS and a 2MCS.
• Changed! TIGR cit_synth_euk 428aa 0.0 in ref transcript
  • This model includes both mitochondrial and peroxisomal forms of citrate synthase. Citrate synthase is the entry point to the TCA cycle from acetyl-CoA. Peroxisomal forms, such as a member from yeast (recognized by the C-terminal targeting motif SKL) act in the glyoxylate cycle. Eukaryotic homologs excluded by the high trusted cutoff of this model include a Tetrahymena thermophila citrate synthase that doubles as a filament protein, a putative citrate synthase from Plasmodium falciparum (no TCA cycle), and a methylcitrate synthase from Aspergillus nidulans.
• Changed! PRK PRK09569 428aa 1e-148 in ref transcript
  • type I citrate synthase; Reviewed.

CSAG1

• refseq_CSAG1.F1 refseq_CSAG1.R1 100 316
• NCBIGene 36.3 158511
• Single exon skipping, size difference: 216
• Exclusion in 5'UTR
• Reference transcript: NM_153478

CSDE1

• refseq_CSDE1.F1 refseq_CSDE1.R1 260 353
• NCBIGene 36.3 7812
• Single exon skipping, size difference: 93
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001007553

• cd CSP_CDS 61aa 6e-08 in ref transcript
  • Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein. CSP expression is up-regulated by an abrupt drop in growth temperature. CSP's are also expressed under normal condition at lower level. The function of cold-shock proteins is not fully understood. They preferentially bind poly-pyrimidine region of single-stranded RNA and DNA. CSP's are thought to bind mRNA and regulate ribosomal translation, mRNA degradation, and the rate of transcription termination. The human Y-box protein, which contains a CSD, regulates transcription and translation of genes that contain the Y-box sequence in their promoters. This specific ssDNA-binding properties of CSD are required for the binding of Y-box protein to the promoter's Y-box sequence, thereby regulating transcription.
• cd CSP_CDS 50aa 1e-06 in ref transcript
• cd CSP_CDS 53aa 0.003 in ref transcript
• Changed! cd CSP_CDS 54aa 0.010 in ref transcript
• pfam CSD 63aa 3e-13 in ref transcript
  • 'Cold-shock' DNA-binding domain.
• smart CSP 64aa 5e-12 in ref transcript
  • Cold shock protein domain. RNA-binding domain that functions as a RNA-chaperone in bacteria and is involved in regulating translation in eukaryotes. Contains sub-family of RNA-binding domains in the Rho transcription termination factor.
• pfam CSD 65aa 4e-11 in ref transcript
• Changed! pfam CSD 62aa 3e-10 in ref transcript
• smart CSP 64aa 9e-10 in ref transcript
• TIGR 3_prime_RNase 174aa 3e-04 in ref transcript
  • This model is defined to identify a pair of paralogous 3-prime exoribonucleases in E. coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterized originally as required for the expression of virulence genes, but is now recognized as the exoribonuclease RNase R (Rnr). Its paralog in E. coli and H. influenzae is designated exoribonuclease II (Rnb). Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cutoff to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3-prime exoribonucleases.
• COG CspC 64aa 7e-06 in ref transcript
  • Cold shock proteins [Transcription].
• Changed! smart CSP 61aa 3e-10 in modified transcript

CSF3R

• refseq_CSF3R.F1 refseq_CSF3R.R1 170 251
• NCBIGene 36.3 1441
• Alternative 3-prime, size difference: 81
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_156039

• cd FN3 81aa 1e-04 in ref transcript
  • Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.
• cd FN3 91aa 0.002 in ref transcript
• cd FN3 79aa 0.007 in ref transcript
• pfam Lep_receptor_Ig 90aa 5e-27 in ref transcript
  • Ig-like C2-type domain. This domain is a ligand-binding immunoglobulin-like domain. The two cysteine residues form a disulphide bridge.
• smart FN3 81aa 7e-06 in ref transcript
  • Fibronectin type 3 domain. One of three types of internal repeat within the plasma protein, fibronectin. The tenth fibronectin type III repeat contains a RGD cell recognition sequence in a flexible loop between 2 strands. Type III modules are present in both extracellular and intracellular proteins.
• pfam fn3 85aa 0.002 in ref transcript
  • Fibronectin type III domain.

CSF3R

• refseq_CSF3R.F4 refseq_CSF3R.R4 122 216
• NCBIGene 36.3 1441
• Single exon skipping, size difference: 94
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_156039

• cd FN3 81aa 1e-04 in ref transcript
  • Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.
• cd FN3 91aa 0.002 in ref transcript
• cd FN3 79aa 0.007 in ref transcript
• pfam Lep_receptor_Ig 90aa 5e-27 in ref transcript
  • Ig-like C2-type domain. This domain is a ligand-binding immunoglobulin-like domain. The two cysteine residues form a disulphide bridge.
• smart FN3 81aa 7e-06 in ref transcript
  • Fibronectin type 3 domain. One of three types of internal repeat within the plasma protein, fibronectin. The tenth fibronectin type III repeat contains a RGD cell recognition sequence in a flexible loop between 2 strands. Type III modules are present in both extracellular and intracellular proteins.
• pfam fn3 85aa 0.002 in ref transcript
  • Fibronectin type III domain.

CSMD3

• refseq_CSMD3.F1 refseq_CSMD3.R1 100 412
• NCBIGene 36.3 114788
• Single exon skipping, size difference: 312
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_198123

• cd CUB 108aa 3e-26 in ref transcript
  • CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.
• cd CUB 108aa 3e-25 in ref transcript
• cd CUB 108aa 2e-23 in ref transcript
• cd CUB 107aa 4e-23 in ref transcript
• cd CUB 108aa 6e-23 in ref transcript
• cd CUB 109aa 1e-21 in ref transcript
• cd CUB 107aa 1e-20 in ref transcript
• cd CUB 108aa 7e-20 in ref transcript
• cd CUB 109aa 8e-18 in ref transcript
• cd CUB 109aa 1e-17 in ref transcript
• cd CUB 107aa 4e-17 in ref transcript
• cd CUB 108aa 4e-16 in ref transcript
• Changed! cd CUB 85aa 2e-14 in ref transcript
• cd CCP 59aa 6e-09 in ref transcript
  • Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR); The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function.
• cd CCP 55aa 7e-09 in ref transcript
• cd CCP 55aa 1e-08 in ref transcript
• cd CCP 55aa 2e-08 in ref transcript
• cd CCP 56aa 2e-08 in ref transcript
• cd CCP 57aa 4e-08 in ref transcript
• cd CCP 54aa 4e-08 in ref transcript
• cd CCP 54aa 4e-08 in ref transcript
• cd CCP 55aa 6e-08 in ref transcript
• cd CCP 54aa 2e-07 in ref transcript
• cd CCP 55aa 4e-07 in ref transcript
• cd CCP 59aa 5e-07 in ref transcript
• cd CCP 55aa 5e-07 in ref transcript
• cd CUB 108aa 1e-06 in ref transcript
• cd CCP 57aa 1e-06 in ref transcript
• cd CCP 57aa 1e-06 in ref transcript
• cd CCP 59aa 2e-06 in ref transcript
• cd CCP 54aa 3e-06 in ref transcript
• cd CCP 58aa 8e-06 in ref transcript
• cd CCP 56aa 9e-06 in ref transcript
• cd CCP 62aa 2e-05 in ref transcript
• cd CCP 59aa 3e-05 in ref transcript
• cd CCP 58aa 3e-05 in ref transcript
• cd CCP 59aa 4e-05 in ref transcript
• cd CCP 57aa 1e-04 in ref transcript
• cd CCP 60aa 3e-04 in ref transcript
• cd CCP 58aa 4e-04 in ref transcript
• cd CCP 59aa 4e-04 in ref transcript
• cd CCP 58aa 0.001 in ref transcript
• pfam CUB 106aa 3e-26 in ref transcript
  • CUB domain.
• pfam CUB 106aa 1e-25 in ref transcript
• pfam CUB 106aa 4e-23 in ref transcript
• pfam CUB 106aa 4e-23 in ref transcript
• pfam CUB 101aa 3e-22 in ref transcript
• pfam CUB 106aa 8e-21 in ref transcript
• pfam CUB 107aa 4e-20 in ref transcript
• pfam CUB 109aa 9e-20 in ref transcript
• pfam CUB 106aa 5e-19 in ref transcript
• pfam CUB 108aa 7e-18 in ref transcript
• smart CUB 98aa 2e-17 in ref transcript
  • Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. This domain is found mostly among developmentally-regulated proteins. Spermadhesins contain only this domain.
• pfam CUB 106aa 5e-16 in ref transcript
• pfam CUB 102aa 5e-14 in ref transcript
• smart CCP 54aa 7e-10 in ref transcript
  • Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR). The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. A missense mutation in seventh CCP domain causes deficiency of the b subunit of factor XIII.
• smart CCP 58aa 3e-09 in ref transcript
• smart CCP 54aa 6e-09 in ref transcript
• smart CCP 55aa 7e-09 in ref transcript
• smart CCP 56aa 1e-08 in ref transcript
• smart CCP 54aa 1e-08 in ref transcript
• smart CCP 54aa 1e-08 in ref transcript
• smart CCP 55aa 6e-08 in ref transcript
• smart CCP 54aa 8e-08 in ref transcript
• pfam CUB 106aa 1e-07 in ref transcript
• smart CCP 54aa 1e-07 in ref transcript
• smart CCP 56aa 1e-07 in ref transcript
• pfam Sushi 58aa 1e-07 in ref transcript
  • Sushi domain (SCR repeat).
• smart CCP 54aa 2e-07 in ref transcript
• smart CCP 61aa 2e-07 in ref transcript
• smart CCP 54aa 3e-07 in ref transcript
• smart CCP 54aa 4e-07 in ref transcript
• smart CCP 56aa 6e-07 in ref transcript
• smart CCP 58aa 1e-06 in ref transcript
• smart CCP 58aa 1e-06 in ref transcript
• smart CCP 56aa 3e-06 in ref transcript
• smart CCP 57aa 4e-06 in ref transcript
• pfam Sushi 58aa 7e-06 in ref transcript
• pfam Sushi 57aa 3e-05 in ref transcript
• smart CCP 58aa 5e-05 in ref transcript
• smart CCP 56aa 7e-05 in ref transcript
• smart CCP 59aa 2e-04 in ref transcript
• smart CCP 58aa 4e-04 in ref transcript
• smart CCP 58aa 0.001 in ref transcript
• Changed! cd CUB 86aa 2e-14 in modified transcript

CSMD3

• refseq_CSMD3.F2 refseq_CSMD3.R2 155 350
• NCBIGene 36.3 114788
• Single exon skipping, size difference: 195
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_198123

• cd CUB 108aa 3e-26 in ref transcript
  • CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.
• cd CUB 108aa 3e-25 in ref transcript
• cd CUB 108aa 2e-23 in ref transcript
• cd CUB 107aa 4e-23 in ref transcript
• cd CUB 108aa 6e-23 in ref transcript
• cd CUB 109aa 1e-21 in ref transcript
• cd CUB 107aa 1e-20 in ref transcript
• cd CUB 108aa 7e-20 in ref transcript
• cd CUB 109aa 8e-18 in ref transcript
• cd CUB 109aa 1e-17 in ref transcript
• cd CUB 107aa 4e-17 in ref transcript
• cd CUB 108aa 4e-16 in ref transcript
• cd CUB 85aa 2e-14 in ref transcript
• cd CCP 59aa 6e-09 in ref transcript
  • Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR); The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function.
• cd CCP 55aa 7e-09 in ref transcript
• cd CCP 55aa 1e-08 in ref transcript
• cd CCP 55aa 2e-08 in ref transcript
• cd CCP 56aa 2e-08 in ref transcript
• cd CCP 57aa 4e-08 in ref transcript
• cd CCP 54aa 4e-08 in ref transcript
• cd CCP 54aa 4e-08 in ref transcript
• cd CCP 55aa 6e-08 in ref transcript
• cd CCP 54aa 2e-07 in ref transcript
• cd CCP 55aa 4e-07 in ref transcript
• cd CCP 59aa 5e-07 in ref transcript
• cd CCP 55aa 5e-07 in ref transcript
• cd CUB 108aa 1e-06 in ref transcript
• cd CCP 57aa 1e-06 in ref transcript
• cd CCP 57aa 1e-06 in ref transcript
• cd CCP 59aa 2e-06 in ref transcript
• cd CCP 54aa 3e-06 in ref transcript
• cd CCP 58aa 8e-06 in ref transcript
• cd CCP 56aa 9e-06 in ref transcript
• Changed! cd CCP 62aa 2e-05 in ref transcript
• cd CCP 59aa 3e-05 in ref transcript
• cd CCP 58aa 3e-05 in ref transcript
• cd CCP 59aa 4e-05 in ref transcript
• cd CCP 57aa 1e-04 in ref transcript
• cd CCP 60aa 3e-04 in ref transcript
• cd CCP 58aa 4e-04 in ref transcript
• cd CCP 59aa 4e-04 in ref transcript
• cd CCP 58aa 0.001 in ref transcript
• pfam CUB 106aa 3e-26 in ref transcript
  • CUB domain.
• pfam CUB 106aa 1e-25 in ref transcript
• pfam CUB 106aa 4e-23 in ref transcript
• pfam CUB 106aa 4e-23 in ref transcript
• pfam CUB 101aa 3e-22 in ref transcript
• pfam CUB 106aa 8e-21 in ref transcript
• pfam CUB 107aa 4e-20 in ref transcript
• pfam CUB 109aa 9e-20 in ref transcript
• pfam CUB 106aa 5e-19 in ref transcript
• pfam CUB 108aa 7e-18 in ref transcript
• smart CUB 98aa 2e-17 in ref transcript
  • Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. This domain is found mostly among developmentally-regulated proteins. Spermadhesins contain only this domain.
• pfam CUB 106aa 5e-16 in ref transcript
• pfam CUB 102aa 5e-14 in ref transcript
• smart CCP 54aa 7e-10 in ref transcript
  • Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR). The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. A missense mutation in seventh CCP domain causes deficiency of the b subunit of factor XIII.
• smart CCP 58aa 3e-09 in ref transcript
• smart CCP 54aa 6e-09 in ref transcript
• smart CCP 55aa 7e-09 in ref transcript
• smart CCP 56aa 1e-08 in ref transcript
• smart CCP 54aa 1e-08 in ref transcript
• smart CCP 54aa 1e-08 in ref transcript
• smart CCP 55aa 6e-08 in ref transcript
• smart CCP 54aa 8e-08 in ref transcript
• pfam CUB 106aa 1e-07 in ref transcript
• smart CCP 54aa 1e-07 in ref transcript
• smart CCP 56aa 1e-07 in ref transcript
• pfam Sushi 58aa 1e-07 in ref transcript
  • Sushi domain (SCR repeat).
• smart CCP 54aa 2e-07 in ref transcript
• Changed! smart CCP 61aa 2e-07 in ref transcript
• smart CCP 54aa 3e-07 in ref transcript
• smart CCP 54aa 4e-07 in ref transcript
• smart CCP 56aa 6e-07 in ref transcript
• smart CCP 58aa 1e-06 in ref transcript
• smart CCP 58aa 1e-06 in ref transcript
• smart CCP 56aa 3e-06 in ref transcript
• smart CCP 57aa 4e-06 in ref transcript
• pfam Sushi 58aa 7e-06 in ref transcript
• pfam Sushi 57aa 3e-05 in ref transcript
• smart CCP 58aa 5e-05 in ref transcript
• smart CCP 56aa 7e-05 in ref transcript
• smart CCP 59aa 2e-04 in ref transcript
• smart CCP 58aa 4e-04 in ref transcript
• smart CCP 58aa 0.001 in ref transcript

CSNK1A1

• refseq_CSNK1A1.F2 refseq_CSNK1A1.R2 138 222
• NCBIGene 36.3 1452
• Single exon skipping, size difference: 84
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001025105

• Changed! cd S_TKc 292aa 1e-31 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• Changed! pfam Pkinase 240aa 2e-30 in ref transcript
  • Protein kinase domain.
• Changed! COG SPS1 239aa 5e-22 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].
• Changed! cd S_TKc 264aa 1e-34 in modified transcript
• Changed! pfam Pkinase 212aa 3e-32 in modified transcript
• Changed! COG SPS1 211aa 2e-25 in modified transcript

CSNK1D

• refseq_CSNK1D.F2 refseq_CSNK1D.R2 238 302
• NCBIGene 36.3 1453
• Single exon skipping, size difference: 64
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_001893

• cd S_TKc 264aa 7e-42 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• pfam Pkinase 253aa 4e-42 in ref transcript
  • Protein kinase domain.
• COG SPS1 277aa 1e-26 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].

CSNK1G3

• refseq_CSNK1G3.F1 refseq_CSNK1G3.R1 122 146
• NCBIGene 36.3 1456
• Single exon skipping, size difference: 24
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001044723

• cd S_TKc 265aa 6e-37 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• pfam Pkinase 257aa 3e-37 in ref transcript
  • Protein kinase domain.
• COG SPS1 325aa 4e-27 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].

CSNK1G3

• refseq_CSNK1G3.F3 refseq_CSNK1G3.R3 333 405
• NCBIGene 36.3 1456
• Single exon skipping, size difference: 96
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001044723

• cd S_TKc 265aa 6e-37 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• pfam Pkinase 257aa 3e-37 in ref transcript
  • Protein kinase domain.
• Changed! COG SPS1 325aa 4e-27 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].
• Changed! COG SPS1 349aa 2e-27 in modified transcript

CSNK2A1

• refseq_CSNK2A1.F2 refseq_CSNK2A1.R2 225 342
• NCBIGene 36.3 1457
• Single exon skipping, size difference: 117
• Exclusion in 5'UTR
• Reference transcript: NM_177559

• cd S_TKc 287aa 4e-46 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• pfam Pkinase 286aa 1e-57 in ref transcript
  • Protein kinase domain.
• COG SPS1 287aa 3e-26 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].

CST11

• refseq_CST11.F1 refseq_CST11.R1 227 332
• NCBIGene 36.3 140880
• Single exon skipping, size difference: 105
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_130794

• Changed! cd CY 92aa 3e-09 in ref transcript
  • Cystatin-like domain; Cystatins are a family of cysteine protease inhibitors that occur mainly as single domain proteins. However some extracellular proteins such as kininogen, His-rich glycoprotein and fetuin also contain these domains.
• Changed! smart CY 83aa 5e-11 in ref transcript
  • Cystatin-like domain. Cystatins are a family of cysteine protease inhibitors that occur mainly as single domain proteins. However some extracellular proteins such as kininogen, His-rich glycoprotein and fetuin also contain these domains.
• Changed! smart CY 26aa 0.003 in modified transcript

CSTF1

• refseq_CSTF1.F2 refseq_CSTF1.R2 117 219
• NCBIGene 36.3 1477
• Alternative 5-prime, size difference: 102
• Exclusion in 5'UTR
• Reference transcript: NM_001033522

• cd WD40 325aa 1e-44 in ref transcript
  • WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.
• pfam WD40 36aa 2e-06 in ref transcript
  • WD domain, G-beta repeat.
• pfam WD40 30aa 7e-04 in ref transcript
• COG COG2319 345aa 5e-21 in ref transcript
  • FOG: WD40 repeat [General function prediction only].

CSTF1

• refseq_CSTF1.F3 refseq_CSTF1.R1 149 324
• NCBIGene 36.3 1477
• Alternative 5-prime, size difference: 175
• Exclusion in 5'UTR
• Reference transcript: NM_001324

• cd WD40 325aa 1e-44 in ref transcript
  • WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.
• pfam WD40 36aa 2e-06 in ref transcript
  • WD domain, G-beta repeat.
• pfam WD40 30aa 7e-04 in ref transcript
• COG COG2319 345aa 5e-21 in ref transcript
  • FOG: WD40 repeat [General function prediction only].

CTBP1

• refseq_CTBP1.F1 refseq_CTBP1.R1 186 381
• NCBIGene 36.3 1487
• Single exon skipping, size difference: 195
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_001328

• Changed! pfam 2-Hacid_dh 291aa 2e-58 in ref transcript
  • D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain. This family represents the largest portion of the catalytic domain of 2-hydroxyacid dehydrogenases as the NAD binding domain is inserted within the structural domain.
• Changed! COG LdhA 296aa 3e-61 in ref transcript
  • Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only].

CTDSPL

• refseq_CTDSPL.F2 refseq_CTDSPL.R2 144 177
• NCBIGene 36.3 10217
• Single exon skipping, size difference: 33
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001008392

• Changed! TIGR HIF-SF_euk 160aa 5e-72 in ref transcript
  • This domain is related to domains found in FCP1-like phosphatases (TIGR02250), and together both are detected by the pfam03031.
• COG FCP1 176aa 7e-47 in ref transcript
  • TFIIF-interacting CTD phosphatases, including NLI-interacting factor [Transcription].
• Changed! pfam NIF 165aa 6e-72 in modified transcript
  • NLI interacting factor-like phosphatase. This family contains a number of NLI interacting factor isoforms and also an N-terminal regions of RNA polymerase II CTC phosphatase and FCP1 serine phosphatase. This region has been identified as the minimal phosphatase domain.

CTF8

• refseq_CTF8.F1 refseq_CTF8.R1 149 207
• NCBIGene 36.3 54921
• Single exon skipping, size difference: 58
• Exclusion in 5'UTR
• Reference transcript: NM_001039690

CTLA4

• refseq_CTLA4.F2 refseq_CTLA4.R2 213 323
• NCBIGene 36.3 1493
• Single exon skipping, size difference: 110
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_005214

• smart IGv 74aa 2e-06 in ref transcript
  • Immunoglobulin V-Type.

CTNNBIP1

• refseq_CTNNBIP1.F1 refseq_CTNNBIP1.R1 187 221
• NCBIGene 36.3 56998
• Single exon skipping, size difference: 34
• Exclusion in 5'UTR
• Reference transcript: NM_020248

CTSE

• refseq_CTSE.F1 refseq_CTSE.R1 109 251
• NCBIGene 36.3 1510
• Single exon skipping, size difference: 142
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_001910

• Changed! cd Cathespin_E 316aa 1e-176 in ref transcript
  • Cathepsin E, non-lysosomal aspartic protease. Cathepsin E is an intracellular, non-lysosomal aspartic protease expressed in a variety of cells and tissues. The protease has proposed physiological roles in antigen presentation by the MHC class II system, in the biogenesis of the vasoconstrictor peptide endothelin, and in neurodegeneration associated with brain ischemia and aging. Cathepsin E is the only A1 aspartic protease that exists as a homodimer with a disulfide bridge linking the two monomers. Like many other aspartic proteases, it is synthesized as a zymogen which is catalytically inactive towards its natural substrates at neutral pH and which auto-activates in an acidic environment. The overall structure follows the general fold of aspartic proteases of the A1 family, it is composed of two structurally similar beta barrel lobes, each lobe contributing an aspartic acid residue to form a catalytic dyad that acts to cleave the substrate peptide bond. The catalytic Asp residues are contained in an Asp-Thr-Gly-Ser/thr motif in both N- and C-terminal lobes of the enzyme. The aspartic acid residues act together to allow a water molecule to attack the peptide bond. One aspartic acid residue (in its deprotonated form) activates the attacking water molecule, whereas the other aspartic acid residue (in its protonated form) polarizes the peptide carbonyl, increasing its susceptibility to attack. This family of aspartate proteases is classified by MEROPS as the peptidase family A1 (pepsin A, clan AA).
• Changed! pfam Asp 318aa 1e-128 in ref transcript
  • Eukaryotic aspartyl protease. Aspartyl (acid) proteases include pepsins, cathepsins, and renins. Two-domain structure, probably arising from ancestral duplication. This family does not include the retroviral nor retrotransposon proteases (pfam00077), which are much smaller and appear to be homologous to a single domain of the eukaryotic asp proteases.
• pfam A1_Propeptide 29aa 5e-05 in ref transcript
  • A1 Propeptide. Most eukaryotic endopeptidases (Merops Family A1) are synthesised with signal and propeptides. The animal pepsin-like endopeptidase propeptides form a distinct family of propeptides, which contain a conserved motif approximately 30 residues long. In pepsinogen A, the first 11 residues of the mature pepsin sequence are displaced by residues of the propeptide. The propeptide contains two helices that block the active site cleft, in particular the conserved Asp11 residue, in pepsin, hydrogen bonds to a conserved Arg residues in the propeptide. This hydrogen bond stabilises the propeptide conformation and is probably responsible for triggering the conversion of pepsinogen to pepsin under acidic conditions.
• Changed! PTZ PTZ00165 368aa 2e-67 in ref transcript
  • aspartyl protease; Provisional.
• Changed! cd Cathespin_E 186aa 1e-101 in modified transcript
• Changed! pfam Asp 185aa 3e-77 in modified transcript
• Changed! PTZ PTZ00165 238aa 4e-40 in modified transcript

CTSL1

• refseq_CTSL.F2 refseq_CTSL.R2 224 369
• NCBIGene 36.3 1514
• Alternative 5-prime, size difference: 145
• Exclusion in 5'UTR
• Reference transcript: NM_001912

• cd Peptidase_C1A 217aa 4e-83 in ref transcript
  • Peptidase C1A subfamily (MEROPS database nomenclature); composed of cysteine peptidases (CPs) similar to papain, including the mammalian CPs (cathepsins B, C, F, H, L, K, O, S, V, X and W). Papain is an endopeptidase with specific substrate preferences, primarily for bulky hydrophobic or aromatic residues at the S2 subsite, a hydrophobic pocket in papain that accommodates the P2 sidechain of the substrate (the second residue away from the scissile bond). Most members of the papain subfamily are endopeptidases. Some exceptions to this rule can be explained by specific details of the catalytic domains like the occluding loop in cathepsin B which confers an additional carboxydipeptidyl activity and the mini-chain of cathepsin H resulting in an N-terminal exopeptidase activity. Papain-like CPs have different functions in various organisms. Plant CPs are used to mobilize storage proteins in seeds. Parasitic CPs act extracellularly to help invade tissues and cells, to hatch or to evade the host immune system. Mammalian CPs are primarily lysosomal enzymes with the exception of cathepsin W, which is retained in the endoplasmic reticulum. They are responsible for protein degradation in the lysosome. Papain-like CPs are synthesized as inactive proenzymes with N-terminal propeptide regions, which are removed upon activation. In addition to its inhibitory role, the propeptide is required for proper folding of the newly synthesized enzyme and its stabilization in denaturing pH conditions. Residues within the propeptide region also play a role in the transport of the proenzyme to lysosomes or acidified vesicles. Also included in this subfamily are proteins classified as non-peptidase homologs, which lack peptidase activity or have missing active site residues.
• pfam Peptidase_C1 219aa 9e-99 in ref transcript
  • Papain family cysteine protease.
• pfam Inhibitor_I29 60aa 1e-14 in ref transcript
  • Cathepsin propeptide inhibitor domain (I29). This domain is found at the N-terminus of some C1 peptidases such as Cathepsin L where it acts as a propeptide. There are also a number of proteins that are composed solely of multiple copies of this domain such as the peptidase inhibitor salarin. This family is classified as I29 by MEROPS.
• PTZ PTZ00203 288aa 1e-44 in ref transcript
  • cathepsin L protease; Provisional.

CTTN

• refseq_CTTN.F1 refseq_CTTN.R1 123 234
• NCBIGene 36.3 2017
• Single exon skipping, size difference: 111
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_005231

• cd SH3 53aa 7e-14 in ref transcript
  • Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
• smart SH3 53aa 3e-16 in ref transcript
  • Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.
• pfam HS1_rep 37aa 5e-12 in ref transcript
  • Repeat in HS1/Cortactin. The function of this repeat is unknown. Seven copies are found in cortactin and four copies are found in HS1. The repeats are always found amino terminal to an SH3 domain pfam00018.
• pfam HS1_rep 37aa 2e-11 in ref transcript
• pfam HS1_rep 37aa 6e-11 in ref transcript
• Changed! pfam HS1_rep 37aa 2e-10 in ref transcript
• Changed! pfam HS1_rep 35aa 4e-10 in ref transcript
• pfam HS1_rep 37aa 1e-09 in ref transcript
• Changed! pfam HS1_rep 37aa 3e-11 in modified transcript

CYB5A

• refseq_CYB5A.F1 refseq_CYB5A.R1 124 148
• NCBIGene 36.3 1528
• Single exon skipping, size difference: 24
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_148923

• pfam Cyt-b5 75aa 1e-24 in ref transcript
  • Cytochrome b5-like Heme/Steroid binding domain. This family includes heme binding domains from a diverse range of proteins. This family also includes proteins that bind to steroids. The family includes progesterone receptors. Many members of this subfamily are membrane anchored by an N-terminal transmembrane alpha helix. This family also includes a domain in some chitin synthases. There is no known ligand for this domain in the chitin synthases.
• COG CYB5 81aa 6e-16 in ref transcript
  • Cytochrome b involved in lipid metabolism [Energy production and conversion / Lipid metabolism].

CLIP2

• refseq_CYLN2.F1 refseq_CYLN2.R1 257 362
• NCBIGene 36.3 7461
• Single exon skipping, size difference: 105
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_003388

• pfam CAP_GLY 66aa 1e-26 in ref transcript
  • CAP-Gly domain. Cytoskeleton-associated proteins (CAPs) are involved in the organisation of microtubules and transportation of vesicles and organelles along the cytoskeletal network. A conserved motif, CAP-Gly, has been identified in a number of CAPs, including CLIP-170 and dynactins. The crystal structure of Caenorhabditis elegans F53F4.3 protein CAP-Gly domain was recently solved. The domain contains three beta-strands. The most conserved sequence, GKNDG, is located in two consecutive sharp turns on the surface, forming the entrance to a groove.
• pfam CAP_GLY 66aa 2e-24 in ref transcript
• Changed! TIGR SMC_prok_B 354aa 2e-08 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• Changed! pfam Myosin_tail_1 592aa 2e-07 in ref transcript
  • Myosin tail. The myosin molecule is a multi-subunit complex made up of two heavy chains and four light chains it is a fundamental contractile protein found in all eukaryote cell types. This family consists of the coiled-coil myosin heavy chain tail region. The coiled-coil is composed of the tail from two molecules of myosin. These can then assemble into the macromolecular thick filament. The coiled-coil region provides the structural backbone the thick filament.
• COG NIP100 61aa 5e-13 in ref transcript
  • Dynactin complex subunit involved in mitotic spindle partitioning in anaphase B [Cell division and chromosome partitioning].
• COG NIP100 62aa 5e-12 in ref transcript
• Changed! COG Smc 657aa 6e-10 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].
• Changed! TIGR SMC_prok_B 313aa 8e-09 in modified transcript
• Changed! TIGR SMC_prok_B 217aa 2e-07 in modified transcript
• Changed! pfam Myosin_tail_1 557aa 2e-07 in modified transcript
• Changed! COG Smc 399aa 2e-08 in modified transcript
• Changed! COG Smc 350aa 2e-06 in modified transcript

CYP11B1

• refseq_CYP11B1.F2 refseq_CYP11B1.R2 173 371
• NCBIGene 36.3 1584
• Single exon skipping, size difference: 198
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000497

• Changed! pfam p450 448aa 2e-93 in ref transcript
  • Cytochrome P450. Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyse regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures.
• Changed! COG CypX 460aa 5e-29 in ref transcript
  • Cytochrome P450 [Secondary metabolites biosynthesis, transport, and catabolism].
• Changed! pfam p450 359aa 1e-66 in modified transcript
• Changed! COG CypX 360aa 1e-15 in modified transcript

CYP19A1

• refseq_CYP19A1.F1 refseq_CYP19A1.R1 232 341
• NCBIGene 36.3 1588
• Single exon skipping, size difference: 109
• Exclusion in 5'UTR
• Reference transcript: NM_031226

• pfam p450 424aa 1e-90 in ref transcript
  • Cytochrome P450. Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyse regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures.
• COG CypX 415aa 2e-29 in ref transcript
  • Cytochrome P450 [Secondary metabolites biosynthesis, transport, and catabolism].

CYP20A1

• refseq_CYP20A1.F1 refseq_CYP20A1.R1 303 382
• NCBIGene 36.2 57404
• Single exon skipping, size difference: 79
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_177538

• Changed! pfam p450 375aa 1e-26 in ref transcript
  • Cytochrome P450. Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyse regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures.
• Changed! COG CypX 238aa 4e-13 in ref transcript
  • Cytochrome P450 [Secondary metabolites biosynthesis, transport, and catabolism].
• Changed! pfam p450 46aa 2e-05 in modified transcript

CYP2A7

• refseq_CYP2A7.F1 refseq_CYP2A7.R1 147 300
• NCBIGene 36.3 1549
• Exon skipping and alternative 3-prime or 5-prime, size difference: 153
• Inclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_000764

• Changed! pfam p450 458aa 1e-131 in ref transcript
  • Cytochrome P450. Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyse regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures.
• Changed! COG CypX 429aa 2e-32 in ref transcript
  • Cytochrome P450 [Secondary metabolites biosynthesis, transport, and catabolism].
• Changed! pfam p450 378aa 1e-105 in modified transcript
• Changed! COG CypX 233aa 2e-27 in modified transcript

CYP2D6

• refseq_CYP2D6.F1 refseq_CYP2D6.R1 218 371
• NCBIGene 36.3 1565
• Single exon skipping, size difference: 153
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000106

• Changed! pfam p450 436aa 1e-120 in ref transcript
  • Cytochrome P450. Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyse regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures.
• Changed! COG CypX 415aa 1e-31 in ref transcript
  • Cytochrome P450 [Secondary metabolites biosynthesis, transport, and catabolism].
• Changed! pfam p450 385aa 1e-101 in modified transcript
• Changed! COG CypX 263aa 1e-26 in modified transcript

DAP3

• refseq_DAP3.F2 refseq_DAP3.R2 202 271
• NCBIGene 36.3 7818
• Alternative 5-prime, size difference: 69
• Exclusion in 5'UTR
• Reference transcript: NM_033657

• pfam DAP3 296aa 8e-93 in ref transcript
  • Mitochondrial ribosomal death-associated protein 3. This is a family of conserved proteins which were originally described as death-associated-protein-3 (DAP-3). The proteins carry a P-loop DNA-binding motif, and induce apoptosis. DAP3 has been shown to be a pro-apoptotic factor in the mitochondrial matrix and to be crucial for mitochondrial biogenesis and so has also been designated as MRP-S29 (mitochondrial ribosomal protein subunit 29).

DAZAP1

• refseq_DAZAP1.F1 refseq_DAZAP1.R1 189 278
• NCBIGene 36.3 26528
• Single exon skipping, size difference: 89
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_018959

• cd RRM 74aa 1e-17 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• cd RRM 70aa 1e-15 in ref transcript
• smart RRM 70aa 8e-18 in ref transcript
  • RNA recognition motif.
• smart RRM 70aa 2e-16 in ref transcript
• TIGR SF-CC1 174aa 4e-15 in ref transcript
  • A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed.
• COG COG0724 172aa 2e-14 in ref transcript
  • RNA-binding proteins (RRM domain) [General function prediction only].

DCHS2

• refseq_DCHS2.F2 refseq_DCHS2.R2 100 136
• NCBIGene 36.2 54798
• Single exon skipping, size difference: 36
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_017639

• cd CA 199aa 1e-48 in ref transcript
  • Cadherin repeat domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion; these domains occur as repeats in the extracellular regions which are thought to mediate cell-cell contact when bound to calcium; plays a role in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-,CNR-,proto-,and FAT-family cadherin, desmocollin, and desmoglein, exists as monomers or dimers (hetero- and homo-); two copies of the repeat are present here.
• cd CA 197aa 4e-45 in ref transcript
• cd CA 198aa 2e-40 in ref transcript
• cd CA 194aa 2e-39 in ref transcript
• cd CA 209aa 4e-39 in ref transcript
• cd CA 206aa 1e-38 in ref transcript
• cd CA 196aa 2e-38 in ref transcript
• cd CA 200aa 2e-37 in ref transcript
• cd CA 239aa 7e-34 in ref transcript
• cd CA 195aa 2e-33 in ref transcript
• cd CA 189aa 3e-33 in ref transcript
• cd CA 201aa 1e-32 in ref transcript
• cd CA 192aa 3e-32 in ref transcript
• cd CA 201aa 2e-30 in ref transcript
• Changed! cd CA 167aa 1e-26 in ref transcript
• cd CA 207aa 5e-25 in ref transcript
• cd CA 197aa 2e-24 in ref transcript
• cd CA 193aa 2e-20 in ref transcript
• smart CA 79aa 7e-23 in ref transcript
  • Cadherin repeats. Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. Cadherin domains occur as repeats in the extracellular regions which are thought to mediate cell-cell contact when bound to calcium.
• smart CA 79aa 5e-21 in ref transcript
• smart CA 78aa 1e-19 in ref transcript
• smart CA 79aa 1e-18 in ref transcript
• pfam Cadherin 91aa 3e-17 in ref transcript
  • Cadherin domain.
• smart CA 77aa 3e-16 in ref transcript
• pfam Cadherin 89aa 6e-16 in ref transcript
• smart CA 90aa 1e-15 in ref transcript
• smart CA 73aa 8e-15 in ref transcript
• smart CA 68aa 1e-13 in ref transcript
• smart CA 75aa 2e-12 in ref transcript
• pfam Cadherin 79aa 4e-12 in ref transcript
• Changed! smart CA 94aa 4e-11 in ref transcript
• pfam Cadherin 95aa 2e-10 in ref transcript
• pfam Cadherin 89aa 5e-10 in ref transcript
• pfam Cadherin 90aa 6e-10 in ref transcript
• smart CA 121aa 7e-10 in ref transcript
• smart CA 70aa 3e-09 in ref transcript
• smart CA 67aa 1e-07 in ref transcript
• pfam Cadherin 81aa 2e-06 in ref transcript
• pfam Cadherin 51aa 1e-04 in ref transcript
• Changed! cd CA 155aa 6e-28 in modified transcript
• Changed! smart CA 82aa 2e-12 in modified transcript

DCHS2

• refseq_DCHS2.F4 refseq_DCHS2.R4 103 388
• NCBIGene 36.2 54798
• Multiple exon skipping, size difference: 285
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_017639

• cd CA 199aa 1e-48 in ref transcript
  • Cadherin repeat domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion; these domains occur as repeats in the extracellular regions which are thought to mediate cell-cell contact when bound to calcium; plays a role in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-,CNR-,proto-,and FAT-family cadherin, desmocollin, and desmoglein, exists as monomers or dimers (hetero- and homo-); two copies of the repeat are present here.
• cd CA 197aa 4e-45 in ref transcript
• cd CA 198aa 2e-40 in ref transcript
• cd CA 194aa 2e-39 in ref transcript
• cd CA 209aa 4e-39 in ref transcript
• cd CA 206aa 1e-38 in ref transcript
• cd CA 196aa 2e-38 in ref transcript
• cd CA 200aa 2e-37 in ref transcript
• cd CA 239aa 7e-34 in ref transcript
• cd CA 195aa 2e-33 in ref transcript
• cd CA 189aa 3e-33 in ref transcript
• cd CA 201aa 1e-32 in ref transcript
• cd CA 192aa 3e-32 in ref transcript
• cd CA 201aa 2e-30 in ref transcript
• Changed! cd CA 167aa 1e-26 in ref transcript
• cd CA 207aa 5e-25 in ref transcript
• cd CA 197aa 2e-24 in ref transcript
• cd CA 193aa 2e-20 in ref transcript
• smart CA 79aa 7e-23 in ref transcript
  • Cadherin repeats. Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. Cadherin domains occur as repeats in the extracellular regions which are thought to mediate cell-cell contact when bound to calcium.
• smart CA 79aa 5e-21 in ref transcript
• smart CA 78aa 1e-19 in ref transcript
• smart CA 79aa 1e-18 in ref transcript
• pfam Cadherin 91aa 3e-17 in ref transcript
  • Cadherin domain.
• smart CA 77aa 3e-16 in ref transcript
• pfam Cadherin 89aa 6e-16 in ref transcript
• smart CA 90aa 1e-15 in ref transcript
• smart CA 73aa 8e-15 in ref transcript
• smart CA 68aa 1e-13 in ref transcript
• smart CA 75aa 2e-12 in ref transcript
• pfam Cadherin 79aa 4e-12 in ref transcript
• smart CA 94aa 4e-11 in ref transcript
• pfam Cadherin 95aa 2e-10 in ref transcript
• pfam Cadherin 89aa 5e-10 in ref transcript
• pfam Cadherin 90aa 6e-10 in ref transcript
• smart CA 121aa 7e-10 in ref transcript
• smart CA 70aa 3e-09 in ref transcript
• smart CA 67aa 1e-07 in ref transcript
• pfam Cadherin 81aa 2e-06 in ref transcript
• Changed! pfam Cadherin 51aa 1e-04 in ref transcript
• Changed! cd CA 207aa 2e-32 in modified transcript
• Changed! cd CA 197aa 3e-31 in modified transcript
• Changed! smart CA 71aa 3e-09 in modified transcript

DCHS2

• refseq_DCHS2.F6 refseq_DCHS2.R6 162 294
• NCBIGene 36.2 54798
• Single exon skipping, size difference: 132
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_017639

• cd CA 199aa 1e-48 in ref transcript
  • Cadherin repeat domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion; these domains occur as repeats in the extracellular regions which are thought to mediate cell-cell contact when bound to calcium; plays a role in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-,CNR-,proto-,and FAT-family cadherin, desmocollin, and desmoglein, exists as monomers or dimers (hetero- and homo-); two copies of the repeat are present here.
• cd CA 197aa 4e-45 in ref transcript
• cd CA 198aa 2e-40 in ref transcript
• cd CA 194aa 2e-39 in ref transcript
• cd CA 209aa 4e-39 in ref transcript
• cd CA 206aa 1e-38 in ref transcript
• cd CA 196aa 2e-38 in ref transcript
• cd CA 200aa 2e-37 in ref transcript
• Changed! cd CA 239aa 7e-34 in ref transcript
• cd CA 195aa 2e-33 in ref transcript
• cd CA 189aa 3e-33 in ref transcript
• cd CA 201aa 1e-32 in ref transcript
• cd CA 192aa 3e-32 in ref transcript
• cd CA 201aa 2e-30 in ref transcript
• cd CA 167aa 1e-26 in ref transcript
• cd CA 207aa 5e-25 in ref transcript
• cd CA 197aa 2e-24 in ref transcript
• cd CA 193aa 2e-20 in ref transcript
• smart CA 79aa 7e-23 in ref transcript
  • Cadherin repeats. Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. Cadherin domains occur as repeats in the extracellular regions which are thought to mediate cell-cell contact when bound to calcium.
• smart CA 79aa 5e-21 in ref transcript
• smart CA 78aa 1e-19 in ref transcript
• smart CA 79aa 1e-18 in ref transcript
• pfam Cadherin 91aa 3e-17 in ref transcript
  • Cadherin domain.
• smart CA 77aa 3e-16 in ref transcript
• pfam Cadherin 89aa 6e-16 in ref transcript
• smart CA 90aa 1e-15 in ref transcript
• smart CA 73aa 8e-15 in ref transcript
• smart CA 68aa 1e-13 in ref transcript
• smart CA 75aa 2e-12 in ref transcript
• pfam Cadherin 79aa 4e-12 in ref transcript
• smart CA 94aa 4e-11 in ref transcript
• pfam Cadherin 95aa 2e-10 in ref transcript
• pfam Cadherin 89aa 5e-10 in ref transcript
• pfam Cadherin 90aa 6e-10 in ref transcript
• Changed! smart CA 121aa 7e-10 in ref transcript
• smart CA 70aa 3e-09 in ref transcript
• smart CA 67aa 1e-07 in ref transcript
• pfam Cadherin 81aa 2e-06 in ref transcript
• pfam Cadherin 51aa 1e-04 in ref transcript
• Changed! cd CA 195aa 8e-40 in modified transcript
• Changed! cd CA 199aa 3e-32 in modified transcript
• Changed! smart CA 77aa 3e-16 in modified transcript

DCLRE1C

• refseq_DCLRE1C.F1 refseq_DCLRE1C.R1 116 172
• NCBIGene 36.3 64421
• Single exon skipping, size difference: 56
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_001033855

• Changed! pfam DRMBL 99aa 2e-16 in ref transcript
  • DNA repair metallo-beta-lactamase. The metallo-beta-lactamase fold contains five sequence motifs. The first four motifs are found in pfam00753 and are common to all metallo-beta-lactamases. The fifth motif appears to be specific to function. This entry represents the fifth motif from metallo-beta-lactamases involved in DNA repair.
• Changed! smart Lactamase_B 115aa 3e-08 in ref transcript
  • Metallo-beta-lactamase superfamily. Apart from the beta-lactamases a number of other proteins contain this domain PUBMED:7588620. These proteins include thiolesterases, members of the glyoxalase II family, that catalyse the hydrolysis of S-D-lactoyl-glutathione to form glutathione and D-lactic acid and a competence protein that is essential for natural transformation in Neisseria gonorrhoeae and could be a transporter involved in DNA uptake. Except for the competence protein these proteins bind two zinc ions per molecule as cofactor.
• Changed! COG YSH1 175aa 1e-11 in ref transcript
  • Predicted exonuclease of the beta-lactamase fold involved in RNA processing [Translation, ribosomal structure and biogenesis].
• Changed! smart Lactamase_B 62aa 0.002 in modified transcript
• Changed! COG COG0595 79aa 0.009 in modified transcript
  • Predicted hydrolase of the metallo-beta-lactamase superfamily [General function prediction only].

DCLRE1C

• refseq_DCLRE1C.F3 refseq_DCLRE1C.R3 172 257
• NCBIGene 36.3 64421
• Single exon skipping, size difference: 85
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_001033855

• Changed! pfam DRMBL 99aa 2e-16 in ref transcript
  • DNA repair metallo-beta-lactamase. The metallo-beta-lactamase fold contains five sequence motifs. The first four motifs are found in pfam00753 and are common to all metallo-beta-lactamases. The fifth motif appears to be specific to function. This entry represents the fifth motif from metallo-beta-lactamases involved in DNA repair.
• Changed! smart Lactamase_B 115aa 3e-08 in ref transcript
  • Metallo-beta-lactamase superfamily. Apart from the beta-lactamases a number of other proteins contain this domain PUBMED:7588620. These proteins include thiolesterases, members of the glyoxalase II family, that catalyse the hydrolysis of S-D-lactoyl-glutathione to form glutathione and D-lactic acid and a competence protein that is essential for natural transformation in Neisseria gonorrhoeae and could be a transporter involved in DNA uptake. Except for the competence protein these proteins bind two zinc ions per molecule as cofactor.
• Changed! COG YSH1 175aa 1e-11 in ref transcript
  • Predicted exonuclease of the beta-lactamase fold involved in RNA processing [Translation, ribosomal structure and biogenesis].

DCN

• refseq_DCN.F2 refseq_DCN.R2 102 429
• NCBIGene 36.3 1634
• Multiple exon skipping, size difference: 327
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_001920

• Changed! cd LRR_RI 217aa 0.002 in ref transcript
  • Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1).
• Changed! pfam LRRNT 24aa 1e-05 in ref transcript
  • Leucine rich repeat N-terminal domain. Leucine Rich Repeats pfam00560 are short sequence motifs present in a number of proteins with diverse functions and cellular locations. Leucine Rich Repeats are often flanked by cysteine rich domains. This domain is often found at the N-terminus of tandem leucine rich repeats.
• Changed! COG COG4886 150aa 5e-05 in ref transcript
  • Leucine-rich repeat (LRR) protein [Function unknown].
• Changed! smart LRRNT 24aa 9e-04 in modified transcript
  • Leucine rich repeat N-terminal domain.
• Changed! COG COG4886 134aa 6e-05 in modified transcript

DCTD

• refseq_DCTD.F2 refseq_DCTD.R2 101 124
• NCBIGene 36.3 1635
• Alternative 5-prime, size difference: 23
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_001012732

• Changed! cd deoxycytidylate_deaminase 122aa 1e-37 in ref transcript
  • Deoxycytidylate deaminase domain. Deoxycytidylate deaminase catalyzes the deamination of dCMP to dUMP, providing the nucleotide substrate for thymidylate synthase. The enzyme binds Zn++, which is required for catalytic activity. The activity of the enzyme is allosterically regulated by the ratio of dCTP to dTTP not only in eukaryotic cells but also in T-even phage-infected Escherichia coli, with dCTP acting as an activator and dTTP as an inhibitor.
• Changed! pfam dCMP_cyt_deam_1 115aa 4e-24 in ref transcript
  • Cytidine and deoxycytidylate deaminase zinc-binding region.
• Changed! COG ComEB 152aa 1e-32 in ref transcript
  • Deoxycytidylate deaminase [Nucleotide transport and metabolism].

DCTN3

• refseq_DCTN3.F1 refseq_DCTN3.R1 303 400
• NCBIGene 36.3 11258
• Alternative 3-prime, size difference: 97
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_007234

• Changed! pfam Dynactin_p22 172aa 1e-82 in ref transcript
  • Dynactin subunit p22. This family contains p22, the smallest subunit of dynactin, a complex that binds to cytoplasmic dynein and is a required activator for cytoplasmic dynein-mediated vesicular transport. Dynactin localises to the cleavage furrow and to the midbodies of dividing cells, suggesting that it may function in cytokinesis. Family members are approximately 170 residues long and seem to be restricted to mammals.
• Changed! pfam Dynactin_p22 137aa 6e-70 in modified transcript

DCUN1D4

• refseq_DCUN1D4.F1 refseq_DCUN1D4.R1 374 479
• NCBIGene 36.3 23142
• Single exon skipping, size difference: 105
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001040402

• Changed! pfam DUF298 113aa 3e-33 in ref transcript
  • Domain of unknown function (DUF298). Members of this family contain a basic helix-loop-helix leucine zipper motif. This domain is implicated in some aspect of neddylation of the cullin 3 family and has a possible role in the regulation of the protein modifier Nedd8 E3 ligase. Neddylation is the process by which the C-terminal glycine of the ubiquitin-like protein Nedd8 is covalently linked to lysine residues in a protein through an isopeptide bond.
• Changed! pfam DUF298 78aa 2e-18 in modified transcript

DDO

• refseq_DDO.F1 refseq_DDO.R1 165 342
• NCBIGene 36.3 8528
• Single exon skipping, size difference: 177
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_003649

• TIGR thiamin_ThiO 152aa 2e-09 in ref transcript
  • This family consists of the homotetrameric, FAD-dependent glycine oxidase ThiO, from species such as Bacillus subtilis that use glycine in thiamine biosynthesis. In general, members of this family will not be found in species such as E. coli that instead use tyrosine and the ThiH protein.
• Changed! pfam DAO 309aa 2e-09 in ref transcript
  • FAD dependent oxidoreductase. This family includes various FAD dependent oxidoreductases: Glycerol-3-phosphate dehydrogenase EC:1.1.99.5, Sarcosine oxidase beta subunit EC:1.5.3.1, D-alanine oxidase EC:1.4.99.1, D-aspartate oxidase EC:1.4.3.1.
• Changed! COG DadA 150aa 1e-04 in ref transcript
  • Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism].
• Changed! COG DadA 193aa 1e-04 in modified transcript

DDR2

• refseq_DDR2.F2 refseq_DDR2.R2 171 251
• NCBIGene 36.3 4921
• Single exon skipping, size difference: 80
• Exclusion in 5'UTR
• Reference transcript: NM_001014796

• cd PTKc_DDR2 295aa 0.0 in ref transcript
  • Catalytic Domain of the Protein Tyrosine Kinase, Discoidin Domain Receptor 2. Protein Tyrosine Kinase (PTK) family; mammalian Discoidin domain receptor 2 (DDR2) and homologs; catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. DDR2 is a member of the DDR subfamily, which are receptor tyr kinases (RTKs) containing an extracellular discoidin homology domain, a transmembrane segment, an extended juxtamembrane region, and an intracellular catalytic domain. The binding of the ligand, collagen, to DDRs results in a slow but sustained receptor activation. DDR2 binds mostly to fibrillar collagens. More recently, it has been reported to also bind collagen X. DDR2 is widely expressed in many tissues with the highest levels found in skeletal muscle, skin, kidney and lung. It is important in cell proliferation and development. Mice, with a deletion of DDR2, suffer from dwarfism and delayed healing of epidermal wounds. DDR2 also contributes to collagen (type I) regulation by inhibiting fibrillogenesis and altering the morphology of collagen fibers. It is also expressed in immature dendritic cells (DCs), where it plays a role in DC activation and function.
• cd FA58C 153aa 2e-37 in ref transcript
  • Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes.
• smart TyrKc 287aa 1e-105 in ref transcript
  • Tyrosine kinase, catalytic domain. Phosphotransferases. Tyrosine-specific kinase subfamily.
• smart FA58C 156aa 2e-32 in ref transcript
  • Coagulation factor 5/8 C-terminal domain, discoidin domain. Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes.
• COG SPS1 289aa 1e-20 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].

DDX11

• refseq_DDX11.F1 refseq_DDX11.R1 122 272
• NCBIGene 36.3 1663
• Single exon skipping, size difference: 150
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_152438

• Changed! TIGR rad3 596aa 1e-101 in ref transcript
  • All proteins in this family for which funcitons are known are DNA-DNA helicases that funciton in the initiation of transcription and nucleotide excision repair as part of the TFIIH complex. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
• smart DEXDc3 68aa 6e-25 in ref transcript
  • DEAD-like helicases superfamily.
• Changed! COG DinG 590aa 3e-29 in ref transcript
  • Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair].
• COG DinG 53aa 8e-10 in ref transcript
• Changed! TIGR rad3 546aa 7e-88 in modified transcript
• Changed! COG DinG 540aa 2e-23 in modified transcript

DDX19B

• refseq_DDX19B.F1 refseq_DDX19B.R1 264 357
• NCBIGene 36.3 11269
• Single exon skipping, size difference: 93
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_007242

• Changed! cd DEADc 203aa 2e-51 in ref transcript
  • DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP- binding region.
• cd HELICc 136aa 2e-26 in ref transcript
  • Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process.
• Changed! pfam DEAD 166aa 4e-32 in ref transcript
  • DEAD/DEAH box helicase. Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.
• pfam Helicase_C 83aa 2e-22 in ref transcript
  • Helicase conserved C-terminal domain. The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.
• TIGR recQ_fam 201aa 6e-07 in ref transcript
  • This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
• Changed! COG SrmB 399aa 8e-84 in ref transcript
  • Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis].
• Changed! cd DEADc 166aa 7e-40 in modified transcript
• Changed! pfam DEAD 159aa 2e-30 in modified transcript
• Changed! COG SrmB 348aa 1e-73 in modified transcript

DDX19B

• refseq_DDX19B.F3 refseq_DDX19B.R3 219 322
• NCBIGene 36.3 11269
• Multiple exon skipping, size difference: 103
• Exclusion in the protein causing a frameshift, Exclusion in the protein (no frameshift)
• Reference transcript: NM_007242

• Changed! cd DEADc 203aa 2e-51 in ref transcript
  • DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP- binding region.
• Changed! cd HELICc 136aa 2e-26 in ref transcript
  • Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process.
• Changed! pfam DEAD 166aa 4e-32 in ref transcript
  • DEAD/DEAH box helicase. Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.
• Changed! pfam Helicase_C 83aa 2e-22 in ref transcript
  • Helicase conserved C-terminal domain. The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.
• Changed! TIGR recQ_fam 201aa 6e-07 in ref transcript
  • This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
• Changed! COG SrmB 399aa 8e-84 in ref transcript
  • Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis].

DDX42

• refseq_DDX42.F1 refseq_DDX42.R1 113 184
• NCBIGene 36.3 11325
• Single exon skipping, size difference: 71
• Exclusion in 5'UTR
• Reference transcript: NM_007372

• cd DEADc 205aa 2e-73 in ref transcript
  • DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP- binding region.
• cd HELICc 126aa 5e-28 in ref transcript
  • Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process.
• pfam DEAD 172aa 1e-56 in ref transcript
  • DEAD/DEAH box helicase. Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.
• smart HELICc 82aa 2e-24 in ref transcript
  • helicase superfamily c-terminal domain.
• TIGR recG 309aa 1e-06 in ref transcript
• PTZ PTZ00110 445aa 1e-116 in ref transcript
  • helicase; Provisional.

DDX47

• refseq_DDX47.F2 refseq_DDX47.R2 162 309
• NCBIGene 36.3 51202
• Single exon skipping, size difference: 147
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_016355

• cd DEADc 202aa 5e-66 in ref transcript
  • DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP- binding region.
• Changed! cd HELICc 130aa 3e-28 in ref transcript
  • Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process.
• pfam DEAD 168aa 3e-48 in ref transcript
  • DEAD/DEAH box helicase. Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.
• Changed! pfam Helicase_C 78aa 2e-23 in ref transcript
  • Helicase conserved C-terminal domain. The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.
• Changed! TIGR recQ_fam 373aa 4e-18 in ref transcript
  • This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
• Changed! COG SrmB 424aa 1e-103 in ref transcript
  • Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis].
• Changed! cd HELICc 67aa 9e-17 in modified transcript
• Changed! pfam Helicase_C 60aa 9e-17 in modified transcript
• Changed! COG SrmB 375aa 2e-84 in modified transcript

DDX52

• refseq_DDX52.F1 refseq_DDX52.R1 247 362
• NCBIGene 36.3 11056
• Single exon skipping, size difference: 115
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_007010

• Changed! cd DEADc 208aa 1e-41 in ref transcript
  • DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP- binding region.
• Changed! cd HELICc 124aa 2e-27 in ref transcript
  • Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process.
• Changed! pfam DEAD 173aa 2e-37 in ref transcript
  • DEAD/DEAH box helicase. Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.
• Changed! pfam Helicase_C 77aa 3e-24 in ref transcript
  • Helicase conserved C-terminal domain. The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.
• Changed! TIGR recQ 349aa 1e-09 in ref transcript
  • The ATP-dependent DNA helicase RecQ of E. coli is about 600 residues long. This model represents bacterial proteins with a high degree of similarity in domain architecture and in primary sequence to E. coli RecQ. The model excludes eukaryotic and archaeal proteins with RecQ-like regions, as well as more distantly related bacterial helicases related to RecQ.
• Changed! COG SrmB 398aa 7e-80 in ref transcript
  • Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis].

DEDD

• refseq_DEDD.F1 refseq_DEDD.R1 168 201
• NCBIGene 36.3 9191
• Single exon skipping, size difference: 33
• Exclusion in 5'UTR
• Reference transcript: NM_032998

• cd DED 78aa 7e-11 in ref transcript
  • Death effector domain. DED is part of a superfamily of death domains which also includes death-domain (DD) and caspase recruitment domain (CARD). Protein-protein interactions involving these domains occur through homotypic interactions, such as DED-DED. Caspases are the primary executioners of apoptosis via proteolytic cascades, and upstream caspases such as caspase-8 and caspase-9 are activated by signaling complexes such as the death inducing signaling complex (DISC) and the apoptosome. Binding of caspases to specific adaptor molecules via DED or CARD domains leads to autoactivation of caspases.
• pfam DED 85aa 3e-15 in ref transcript
  • Death effector domain.

DEFB119

• refseq_DEFB119.F1 refseq_DEFB119.R1 224 264
• NCBIGene 36.3 245932
• Single exon skipping, size difference: 40
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_153289

DGKH

• refseq_DGKH.F2 refseq_DGKH.R2 109 240
• NCBIGene 36.3 160851
• Single exon skipping, size difference: 131
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_178009

• Changed! cd SAM 62aa 2e-14 in ref transcript
  • Sterile alpha motif.; Widespread domain in signalling and nuclear proteins. In EPH-related tyrosine kinases, appears to mediate cell-cell initiated signal transduction via the binding of SH2-containing proteins to a conserved tyrosine that is phosphorylated. In many cases mediates homodimerization.
• cd PH 89aa 5e-13 in ref transcript
  • Pleckstrin homology (PH) domain. PH domains are only found in eukaryotes. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes.
• cd C1 50aa 5e-12 in ref transcript
  • Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
• cd C1 51aa 4e-06 in ref transcript
• smart DAGKa 158aa 3e-68 in ref transcript
  • Diacylglycerol kinase accessory domain (presumed). Diacylglycerol (DAG) is a second messenger that acts as a protein kinase C activator. DAG can be produced from the hydrolysis of phosphatidylinositol 4,5-bisphosphate (PIP2) by a phosphoinositide-specific phospholipase C and by the degradation of phosphatidylcholine (PC) by a phospholipase C or the concerted actions of phospholipase D and phosphatidate phosphohydrolase. This domain might either be an accessory domain or else contribute to the catalytic domain. Bacterial homologues are known.
• smart DAGKc 123aa 2e-41 in ref transcript
  • Diacylglycerol kinase catalytic domain (presumed). Diacylglycerol (DAG) is a second messenger that acts as a protein kinase C activator. DAG can be produced from the hydrolysis of phosphatidylinositol 4,5-bisphosphate (PIP2) by a phosphoinositide-specific phospholipase C and by the degradation of phosphatidylcholine (PC) by a phospholipase C or the concerted actions of phospholipase D and phosphatidate phosphohydrolase. This domain is presumed to be the catalytic domain. Bacterial homologues areknown.
• smart PH 91aa 2e-14 in ref transcript
  • Pleckstrin homology domain. Domain commonly found in eukaryotic signalling proteins. The domain family possesses multiple functions including the abilities to bind inositol phosphates, and various proteins. PH domains have been found to possess inserted domains (such as in PLC gamma, syntrophins) and to be inserted within other domains. Mutations in Brutons tyrosine kinase (Btk) within its PH domain cause X-linked agammaglobulinaemia (XLA) in patients. Point mutations cluster into the positively charged end of the molecule around the predicted binding site for phosphatidylinositol lipids.
• Changed! smart SAM 64aa 7e-14 in ref transcript
  • Sterile alpha motif. Widespread domain in signalling and nuclear proteins. In EPH-related tyrosine kinases, appears to mediate cell-cell initiated signal transduction via the binding of SH2-containing proteins to a conserved tyrosine that is phosphorylated. In many cases mediates homodimerisation.
• smart C1 50aa 6e-12 in ref transcript
  • Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
• smart C1 45aa 2e-06 in ref transcript
• COG LCB5 122aa 3e-07 in ref transcript
  • Sphingosine kinase and enzymes related to eukaryotic diacylglycerol kinase [Lipid metabolism / General function prediction only].

DGUOK

• refseq_DGUOK.F1 refseq_DGUOK.R1 120 384
• NCBIGene 36.3 1716
• Multiple exon skipping, size difference: 264
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_080916

• Changed! cd dNK 215aa 2e-48 in ref transcript
  • Deoxyribonucleoside kinase (dNK) catalyzes the phosphorylation of deoxyribonucleosides to yield corresponding monophosphates (dNMPs). This family consists of various deoxynucleoside kinases including deoxyribo- cytidine (EC 2.7.1.74), guanosine (EC 2.7.1.113), adenosine (EC 2.7.1.76), and thymidine (EC 2.7.1.21) kinases. They are key enzymes in the salvage of deoxyribonucleosides originating from extra- or intracellular breakdown of DNA.
• Changed! pfam dNK 158aa 2e-44 in ref transcript
  • Deoxynucleoside kinase. This family consists of various deoxynucleoside kinases cytidine EC:2.7.1.74, guanosine EC:2.7.1.113, adenosine EC:2.7.1.76 and thymidine kinase EC:2.7.1.21 (which also phosphorylates deoxyuridine and deoxycytosine.) These enzymes catalyse the production of deoxynucleotide 5'-monophosphate from a deoxynucleoside. Using ATP and yielding ADP in the process.
• Changed! COG COG1428 239aa 3e-22 in ref transcript
  • Deoxynucleoside kinases [Nucleotide transport and metabolism].
• Changed! cd dNK 117aa 4e-21 in modified transcript
• Changed! pfam dNK 47aa 6e-06 in modified transcript
• Changed! COG COG1428 144aa 6e-08 in modified transcript

DHODH

• refseq_DHODH.F1 refseq_DHODH.R1 100 402
• NCBIGene 36.2 1723
• Multiple exon skipping, size difference: 302
• Exclusion in the protein causing a frameshift, Exclusion in the protein (no frameshift)
• Reference transcript: NM_001361

• Changed! cd DHOD_2_like 331aa 1e-125 in ref transcript
  • Dihydroorotate dehydrogenase (DHOD) class 2. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires FMN as co-factor. DHOD divides into class 1 and class 2 based on their amino acid sequences, their cellular location and their natural electron acceptor used to reoxidize the flavin group. Members of class 1 are cytosolic enzymes and multimers, while class 2 enzymes are membrane associated, monomeric and use respiratory quinones as their physiological electron acceptors.
• Changed! TIGR pyrD_sub2 335aa 1e-136 in ref transcript
  • The subfamilies 1 and 2 share extensive homology, particularly toward the C-terminus. This subfamily has a longer N-terminal region.
• Changed! PRK PRK05286 330aa 1e-123 in ref transcript
  • dihydroorotate dehydrogenase 2; Reviewed.
• Changed! cd DHOD_2_like 125aa 2e-49 in modified transcript
• Changed! TIGR pyrD_sub2 124aa 1e-54 in modified transcript
• Changed! PRK PRK05286 120aa 1e-47 in modified transcript

DHPS

• refseq_DHPS.F2 refseq_DHPS.R2 111 279
• NCBIGene 36.3 1725
• Exon skipping and alternative 3-prime or 5-prime, size difference: 168
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_001930

• Changed! pfam DS 315aa 1e-149 in ref transcript
  • Deoxyhypusine synthase. Eukaryotic initiation factor 5A (eIF-5A) contains an unusual amino acid, hypusine [N epsilon-(4-aminobutyl-2-hydroxy)lysine]. The first step in the post-translational formation of hypusine is catalysed by the enzyme deoxyhypusine synthase (DS) EC:1.1.1.249. The modified version of eIF-5A, and DS, are required for eukaryotic cell proliferation.
• Changed! COG DYS1 331aa 1e-101 in ref transcript
  • Deoxyhypusine synthase [Posttranslational modification, protein turnover, chaperones].
• Changed! pfam DS 259aa 1e-105 in modified transcript
• Changed! COG DYS1 275aa 7e-67 in modified transcript

DHX30

• refseq_DHX30.F1 refseq_DHX30.R1 163 192
• NCBIGene 36.3 22907
• Single exon skipping, size difference: 29
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_138615

• Changed! cd DEXDc 142aa 2e-16 in ref transcript
  • DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
• Changed! cd HELICc 128aa 1e-05 in ref transcript
  • Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process.
• Changed! TIGR DEAH_box_HrpA 541aa 8e-86 in ref transcript
  • This model represents HrpA, one of two related but uncharacterized DEAH-box ATP-dependent helicases in many Proteobacteria and a few high-GC Gram-positive bacteria. HrpA is about 1300 amino acids long, while its paralog HrpB, also uncharacterized, is about 800 amino acids long. Related characterized eukarotic proteins are RNA helicases associated with pre-mRNA processing.
• Changed! pfam DUF1605 123aa 1e-04 in ref transcript
  • Domain of unknown function (DUF1605). This family is found towards the C-terminus of the DEAD-box helicases (pfam00270). In these helicases it apparently always found in association with pfam04408. There do seem to be a couple of instances where it occurs by itself.
• Changed! COG HrpA 650aa 1e-122 in ref transcript
  • HrpA-like helicases [DNA replication, recombination, and repair].

DHX34

• refseq_DHX34.F1 refseq_DHX34.R1 103 178
• NCBIGene 36.2 9704
• Single exon skipping, size difference: 75
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_014681

• cd DEXDc 136aa 1e-18 in ref transcript
  • DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
• cd HELICc 94aa 2e-05 in ref transcript
  • Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process.
• TIGR DEAH_box_HrpA 474aa 1e-101 in ref transcript
  • This model represents HrpA, one of two related but uncharacterized DEAH-box ATP-dependent helicases in many Proteobacteria and a few high-GC Gram-positive bacteria. HrpA is about 1300 amino acids long, while its paralog HrpB, also uncharacterized, is about 800 amino acids long. Related characterized eukarotic proteins are RNA helicases associated with pre-mRNA processing.
• Changed! pfam DUF1605 100aa 0.001 in ref transcript
  • Domain of unknown function (DUF1605). This family is found towards the C-terminus of the DEAD-box helicases (pfam00270). In these helicases it apparently always found in association with pfam04408. There do seem to be a couple of instances where it occurs by itself.
• COG HrpA 505aa 1e-131 in ref transcript
  • HrpA-like helicases [DNA replication, recombination, and repair].

DIABLO

• refseq_DIABLO.F1 refseq_DIABLO.R1 130 262
• NCBIGene 36.3 56616
• Single exon skipping, size difference: 132
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_019887

• Changed! pfam Smac_DIABLO 234aa 1e-100 in ref transcript
  • Second Mitochondria-derived Activator of Caspases. Second Mitochondria-derived Activator of Caspases promotes apoptosis by activating caspases in the cytochrome c/Apaf-1/caspase-9 pathway, and by opposing the inhibitory activity of inhibitor of apoptosis proteins (XIAP-BIR3). The protein assumes an elongated three-helix bundle structure, and forms a dimer in solution.
• Changed! pfam Smac_DIABLO 190aa 3e-73 in modified transcript

DIO1

• refseq_DIO1.F1 refseq_DIO1.R1 189 333
• NCBIGene 36.3 1733
• Single exon skipping, size difference: 144
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_001039715

• Changed! pfam T4_deiodinase 168aa 5e-55 in ref transcript
  • Iodothyronine deiodinase. Iodothyronine deiodinase converts thyroxine (T4) to 3,5,3'-triiodothyronine (T3).
• Changed! pfam T4_deiodinase 93aa 2e-28 in modified transcript

DIO1

• refseq_DIO1.F3 refseq_DIO1.R3 154 346
• NCBIGene 36.3 1733
• Alternative 5-prime, size difference: 192
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000792

• Changed! pfam T4_deiodinase 93aa 2e-28 in ref transcript
  • Iodothyronine deiodinase. Iodothyronine deiodinase converts thyroxine (T4) to 3,5,3'-triiodothyronine (T3).
• Changed! pfam T4_deiodinase 13aa 0.005 in modified transcript

DIO1

• refseq_DIO1.F4 refseq_DIO1.R4 102 302
• NCBIGene 36.3 1733
• Single exon skipping, size difference: 200
• Exclusion in 3'UTR
• Reference transcript: NM_000792

• pfam T4_deiodinase 93aa 2e-28 in ref transcript
  • Iodothyronine deiodinase. Iodothyronine deiodinase converts thyroxine (T4) to 3,5,3'-triiodothyronine (T3).

DIO2

• refseq_DIO2.F1 refseq_DIO2.R1 180 288
• NCBIGene 36.3 1734
• Single exon skipping, size difference: 108
• Exclusion in 5'UTR
• Reference transcript: NM_001007023

DISC1

• refseq_DISC1.F2 refseq_DISC1.R2 208 274
• NCBIGene 36.3 27185
• Alternative 5-prime, size difference: 66
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_018662

STAG3L1

• refseq_DKFZP434A0131.F1 refseq_DKFZP434A0131.R1 112 236
• NCBIGene 36.3 54441
• Single exon skipping, size difference: 124
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_018991

• Changed! COG IRR1 114aa 1e-08 in ref transcript
  • Cohesin [Cell division and chromosome partitioning].

FAM149A

• refseq_DKFZP564J102.F2 refseq_DKFZP564J102.R2 102 129
• NCBIGene 36.3 25854
• Alternative 3-prime, size difference: 27
• Inclusion in 5'UTR
• Reference transcript: NM_001006655

DKFZP586H2123

• refseq_DKFZP586H2123.F2 refseq_DKFZP586H2123.R2 130 181
• NCBIGene 36.3 25891
• Single exon skipping, size difference: 51
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_015430

• cd Tryp_SPc 258aa 3e-28 in ref transcript
  • Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
• cd CUB 107aa 5e-25 in ref transcript
  • CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.
• cd CCP 64aa 2e-07 in ref transcript
  • Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR); The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function.
• cd EGF_CA 33aa 7e-04 in ref transcript
  • Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements.
• smart Tryp_SPc 255aa 1e-27 in ref transcript
  • Trypsin-like serine protease. Many of these are synthesised as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. A few, however, are active as single chain molecules, and others are inactive due to substitutions of the catalytic triad residues.
• smart CUB 92aa 5e-23 in ref transcript
  • Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. This domain is found mostly among developmentally-regulated proteins. Spermadhesins contain only this domain.
• smart CCP 63aa 4e-08 in ref transcript
  • Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR). The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. A missense mutation in seventh CCP domain causes deficiency of the b subunit of factor XIII.
• smart EGF_CA 33aa 0.002 in ref transcript
  • Calcium-binding EGF-like domain.
• smart CCP 35aa 0.003 in ref transcript
• COG COG5640 259aa 5e-07 in ref transcript
  • Secreted trypsin-like serine protease [Posttranslational modification, protein turnover, chaperones].

DKFZP686M0199

• refseq_DKFZP686M0199.F1 refseq_DKFZP686M0199.R1 152 250
• NCBIGene 36.2 653238
• Single exon skipping, size difference: 98
• Exclusion in 5'UTR
• Reference transcript: XM_001130651

• cd vWA_transcription_factor_IIH_type 181aa 1e-75 in ref transcript
  • Transcription factors IIH type: TFIIH is a multiprotein complex that is one of the five general transcription factors that binds RNA polymerase II holoenzyme. Orthologues of these genes are found in all completed eukaryotic genomes and all these proteins contain a VWA domain. The p44 subunit of TFIIH functions as a DNA helicase in RNA polymerase II transcription initiation and DNA repair, and its transcriptional activity is dependent on its C-terminal Zn-binding domains. The function of the vWA domain is unclear, but may be involved in complex assembly. The MIDAS motif is not conserved in this sub-group.
• pfam Ssl1 249aa 1e-117 in ref transcript
  • Ssl1-like. Ssl1-like proteins are 40kDa subunits of the Transcription factor II H complex.
• TIGR ssl1 101aa 3e-41 in ref transcript
  • This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
• COG SSL1 375aa 6e-76 in ref transcript
  • RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair].

ZMIZ2

• refseq_DKFZp761I2123.F2 refseq_DKFZp761I2123.R2 261 339
• NCBIGene 36.3 83637
• Single exon skipping, size difference: 78
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_031449

• pfam zf-MIZ 49aa 6e-21 in ref transcript
  • MIZ/SP-RING zinc finger. This domain has SUMO (small ubiquitin-like modifier) ligase activity and is involved in DNA repair and chromosome organisation.
• TIGR PABP-1234 81aa 5e-04 in ref transcript
  • There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, and of unknown tissue range.

DLEC1

• refseq_DLEC1.F1 refseq_DLEC1.R1 141 265
• NCBIGene 36.3 9940
• Single exon skipping, size difference: 124
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_007337

DLX1

• refseq_DLX1.F2 refseq_DLX1.R2 161 361
• NCBIGene 36.3 1745
• Single exon skipping, size difference: 200
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_178120

• Changed! cd homeodomain 57aa 3e-15 in ref transcript
  • Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
• Changed! pfam Homeobox 57aa 9e-21 in ref transcript
  • Homeobox domain.
• Changed! COG COG5576 78aa 1e-06 in ref transcript
  • Homeodomain-containing transcription factor [Transcription].

DMD

• refseq_DMD.F1 refseq_DMD.R1 219 362
• NCBIGene 36.3 1756
• Alternative 5-prime, size difference: 143
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_004011

• Changed! cd ZZ_dystrophin 49aa 2e-23 in ref transcript
  • Zinc finger, ZZ type. Zinc finger present in dystrophin and dystrobrevin. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dystrophin attaches actin filaments to an integral membrane glycoprotein complex in muscle cells. The ZZ domain in dystrophin has been shown to be essential for binding to the membrane protein beta-dystroglycan.
• Changed! cd SPEC 217aa 8e-14 in ref transcript
  • Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here.
• Changed! cd SPEC 216aa 4e-11 in ref transcript
• Changed! cd SPEC 244aa 5e-10 in ref transcript
• Changed! cd SPEC 209aa 4e-09 in ref transcript
• Changed! cd SPEC 111aa 1e-06 in ref transcript
• Changed! cd WW 30aa 1e-05 in ref transcript
  • Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
• Changed! cd SPEC 189aa 2e-05 in ref transcript
• Changed! cd SPEC 210aa 3e-05 in ref transcript
• Changed! cd SPEC 226aa 4e-04 in ref transcript
• Changed! pfam efhand_1 121aa 8e-45 in ref transcript
  • EF hand. Members of this family adopt a helix-loop-helix motif, as per other EF hand domains. However, since they do not contain the canonical pattern of calcium binding residues found in many EF hand domains, they do not bind calcium ions. The main function of this domain is the provision of specificity in beta-dystroglycan recognition, though in dystrophin it serves an additional role: stabilisation of the WW domain (pfam00397), enhancing dystroglycan binding.
• Changed! pfam efhand_2 92aa 4e-40 in ref transcript
  • EF-hand. Members of this family adopt a helix-loop-helix motif, as per other EF hand domains. However, since they do not contain the canonical pattern of calcium binding residues found in many EF hand domains, they do not bind calcium ions. The main function of this domain is the provision of specificity in beta-dystroglycan recognition, though in dystrophin it serves an additional role: stabilisation of the WW domain (pfam00397), enhancing dystroglycan binding.
• Changed! pfam ZZ 46aa 1e-18 in ref transcript
  • Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300. ZZ in dystrophin binds calmodulin. Putative zinc finger; binding not yet shown. Four to six cysteine residues in its sequence are responsible for coordinating zinc ions, to reinforce the structure.
• Changed! smart SPEC 101aa 9e-09 in ref transcript
  • Spectrin repeats.
• Changed! pfam Spectrin 107aa 2e-08 in ref transcript
  • Spectrin repeat. Spectrin repeats are found in several proteins involved in cytoskeletal structure. These include spectrin, alpha-actinin and dystrophin. The sequence repeat used in this family is taken from the structural repeat in reference. The spectrin repeat forms a three helix bundle. The second helix is interrupted by proline in some sequences. The repeats are defined by a characteristic tryptophan (W) residue at position 17 in helix A and a leucine (L) at 2 residues from the carboxyl end of helix C.
• Changed! smart SPEC 102aa 5e-08 in ref transcript
• Changed! smart SPEC 110aa 6e-07 in ref transcript
• Changed! TIGR SMC_prok_B 582aa 6e-07 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• Changed! smart WW 32aa 4e-06 in ref transcript
  • Domain with 2 conserved Trp (W) residues. Also known as the WWP or rsp5 domain. Binds proline-rich polypeptides.
• Changed! pfam Spectrin 117aa 2e-05 in ref transcript
• Changed! TIGR SMC_prok_B 278aa 8e-05 in ref transcript
• Changed! COG SbcC 548aa 1e-08 in ref transcript
  • ATPase involved in DNA repair [DNA replication, recombination, and repair].
• Changed! PRK PRK00409 138aa 4e-04 in ref transcript
  • recombination and DNA strand exchange inhibitor protein; Reviewed.

DMD

• refseq_DMD.F3 refseq_DMD.R3 166 198
• NCBIGene 36.3 1756
• Single exon skipping, size difference: 32
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_004006

• cd ZZ_dystrophin 49aa 3e-23 in ref transcript
  • Zinc finger, ZZ type. Zinc finger present in dystrophin and dystrobrevin. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dystrophin attaches actin filaments to an integral membrane glycoprotein complex in muscle cells. The ZZ domain in dystrophin has been shown to be essential for binding to the membrane protein beta-dystroglycan.
• cd CH 106aa 6e-16 in ref transcript
  • Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav).
• cd SPEC 217aa 7e-14 in ref transcript
  • Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here.
• cd SPEC 218aa 5e-13 in ref transcript
• cd SPEC 216aa 3e-11 in ref transcript
• cd SPEC 244aa 5e-10 in ref transcript
• cd SPEC 209aa 4e-09 in ref transcript
• cd CH 104aa 6e-09 in ref transcript
• cd SPEC 207aa 7e-09 in ref transcript
• cd SPEC 215aa 1e-07 in ref transcript
• cd SPEC 111aa 1e-06 in ref transcript
• cd SPEC 183aa 5e-06 in ref transcript
• cd SPEC 207aa 5e-06 in ref transcript
• cd SPEC 189aa 2e-05 in ref transcript
• cd SPEC 210aa 3e-05 in ref transcript
• cd WW 30aa 4e-05 in ref transcript
  • Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
• cd SPEC 226aa 4e-04 in ref transcript
• cd SPEC 208aa 0.004 in ref transcript
• pfam efhand_1 121aa 1e-44 in ref transcript
  • EF hand. Members of this family adopt a helix-loop-helix motif, as per other EF hand domains. However, since they do not contain the canonical pattern of calcium binding residues found in many EF hand domains, they do not bind calcium ions. The main function of this domain is the provision of specificity in beta-dystroglycan recognition, though in dystrophin it serves an additional role: stabilisation of the WW domain (pfam00397), enhancing dystroglycan binding.
• pfam efhand_2 92aa 7e-40 in ref transcript
  • EF-hand. Members of this family adopt a helix-loop-helix motif, as per other EF hand domains. However, since they do not contain the canonical pattern of calcium binding residues found in many EF hand domains, they do not bind calcium ions. The main function of this domain is the provision of specificity in beta-dystroglycan recognition, though in dystrophin it serves an additional role: stabilisation of the WW domain (pfam00397), enhancing dystroglycan binding.
• pfam ZZ 46aa 2e-18 in ref transcript
  • Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300. ZZ in dystrophin binds calmodulin. Putative zinc finger; binding not yet shown. Four to six cysteine residues in its sequence are responsible for coordinating zinc ions, to reinforce the structure.
• smart CH 100aa 4e-18 in ref transcript
  • Calponin homology domain. Actin binding domains present in duplicate at the N-termini of spectrin-like proteins (including dystrophin, alpha-actinin). These domains cross-link actin filaments into bundles and networks. A calponin homology domain is predicted in yeasst Cdc24p.
• smart CH 101aa 4e-11 in ref transcript
• TIGR SMC_prok_B 595aa 6e-09 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• smart SPEC 101aa 1e-08 in ref transcript
  • Spectrin repeats.
• pfam Spectrin 107aa 2e-08 in ref transcript
  • Spectrin repeat. Spectrin repeats are found in several proteins involved in cytoskeletal structure. These include spectrin, alpha-actinin and dystrophin. The sequence repeat used in this family is taken from the structural repeat in reference. The spectrin repeat forms a three helix bundle. The second helix is interrupted by proline in some sequences. The repeats are defined by a characteristic tryptophan (W) residue at position 17 in helix A and a leucine (L) at 2 residues from the carboxyl end of helix C.
• smart SPEC 103aa 5e-08 in ref transcript
• smart SPEC 102aa 6e-08 in ref transcript
• pfam Spectrin 105aa 1e-07 in ref transcript
• smart SPEC 110aa 8e-07 in ref transcript
• smart WW 32aa 1e-05 in ref transcript
  • Domain with 2 conserved Trp (W) residues. Also known as the WWP or rsp5 domain. Binds proline-rich polypeptides.
• pfam Spectrin 117aa 3e-05 in ref transcript
• TIGR SMC_prok_B 278aa 8e-05 in ref transcript
• smart SPEC 101aa 3e-04 in ref transcript
• smart SPEC 98aa 0.003 in ref transcript
• pfam Spectrin 66aa 0.007 in ref transcript
• TIGR SMC_prok_B 391aa 0.010 in ref transcript
• COG SAC6 225aa 6e-25 in ref transcript
  • Ca2+-binding actin-bundling protein fimbrin/plastin (EF-Hand superfamily) [Cytoskeleton].
• COG SbcC 643aa 3e-09 in ref transcript
  • ATPase involved in DNA repair [DNA replication, recombination, and repair].
• PRK PRK00409 138aa 5e-04 in ref transcript
  • recombination and DNA strand exchange inhibitor protein; Reviewed.

DMD

• refseq_DMD.F5 refseq_DMD.R5 270 354
• NCBIGene 36.3 1756
• Alternative 5-prime, size difference: 84
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_004009

• Changed! cd ZZ_dystrophin 49aa 3e-23 in ref transcript
  • Zinc finger, ZZ type. Zinc finger present in dystrophin and dystrobrevin. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dystrophin attaches actin filaments to an integral membrane glycoprotein complex in muscle cells. The ZZ domain in dystrophin has been shown to be essential for binding to the membrane protein beta-dystroglycan.
• Changed! cd CH 106aa 5e-16 in ref transcript
  • Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav).
• Changed! cd SPEC 217aa 8e-14 in ref transcript
  • Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here.
• Changed! cd SPEC 218aa 5e-13 in ref transcript
• Changed! cd SPEC 216aa 3e-11 in ref transcript
• Changed! cd SPEC 244aa 5e-10 in ref transcript
• Changed! cd SPEC 209aa 4e-09 in ref transcript
• Changed! cd CH 104aa 6e-09 in ref transcript
• Changed! cd SPEC 207aa 8e-09 in ref transcript
• Changed! cd SPEC 215aa 1e-07 in ref transcript
• Changed! cd SPEC 111aa 1e-06 in ref transcript
• Changed! cd SPEC 183aa 5e-06 in ref transcript
• Changed! cd SPEC 207aa 5e-06 in ref transcript
• Changed! cd SPEC 189aa 2e-05 in ref transcript
• Changed! cd SPEC 210aa 3e-05 in ref transcript
• Changed! cd WW 30aa 3e-05 in ref transcript
  • Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
• Changed! cd SPEC 226aa 4e-04 in ref transcript
• Changed! cd SPEC 208aa 0.004 in ref transcript
• Changed! pfam efhand_1 121aa 1e-44 in ref transcript
  • EF hand. Members of this family adopt a helix-loop-helix motif, as per other EF hand domains. However, since they do not contain the canonical pattern of calcium binding residues found in many EF hand domains, they do not bind calcium ions. The main function of this domain is the provision of specificity in beta-dystroglycan recognition, though in dystrophin it serves an additional role: stabilisation of the WW domain (pfam00397), enhancing dystroglycan binding.
• Changed! pfam efhand_2 92aa 6e-40 in ref transcript
  • EF-hand. Members of this family adopt a helix-loop-helix motif, as per other EF hand domains. However, since they do not contain the canonical pattern of calcium binding residues found in many EF hand domains, they do not bind calcium ions. The main function of this domain is the provision of specificity in beta-dystroglycan recognition, though in dystrophin it serves an additional role: stabilisation of the WW domain (pfam00397), enhancing dystroglycan binding.
• Changed! pfam ZZ 46aa 2e-18 in ref transcript
  • Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300. ZZ in dystrophin binds calmodulin. Putative zinc finger; binding not yet shown. Four to six cysteine residues in its sequence are responsible for coordinating zinc ions, to reinforce the structure.
• Changed! smart CH 100aa 4e-18 in ref transcript
  • Calponin homology domain. Actin binding domains present in duplicate at the N-termini of spectrin-like proteins (including dystrophin, alpha-actinin). These domains cross-link actin filaments into bundles and networks. A calponin homology domain is predicted in yeasst Cdc24p.
• Changed! smart CH 101aa 4e-11 in ref transcript
• Changed! TIGR SMC_prok_B 595aa 6e-09 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• Changed! smart SPEC 101aa 1e-08 in ref transcript
  • Spectrin repeats.
• Changed! pfam Spectrin 107aa 2e-08 in ref transcript
  • Spectrin repeat. Spectrin repeats are found in several proteins involved in cytoskeletal structure. These include spectrin, alpha-actinin and dystrophin. The sequence repeat used in this family is taken from the structural repeat in reference. The spectrin repeat forms a three helix bundle. The second helix is interrupted by proline in some sequences. The repeats are defined by a characteristic tryptophan (W) residue at position 17 in helix A and a leucine (L) at 2 residues from the carboxyl end of helix C.
• Changed! smart SPEC 103aa 5e-08 in ref transcript
• Changed! smart SPEC 102aa 6e-08 in ref transcript
• Changed! pfam Spectrin 105aa 1e-07 in ref transcript
• Changed! smart SPEC 110aa 8e-07 in ref transcript
• Changed! smart WW 32aa 1e-05 in ref transcript
  • Domain with 2 conserved Trp (W) residues. Also known as the WWP or rsp5 domain. Binds proline-rich polypeptides.
• Changed! pfam Spectrin 117aa 3e-05 in ref transcript
• Changed! TIGR SMC_prok_B 278aa 8e-05 in ref transcript
• Changed! smart SPEC 101aa 3e-04 in ref transcript
• Changed! smart SPEC 98aa 0.003 in ref transcript
• Changed! pfam Spectrin 66aa 0.007 in ref transcript
• Changed! COG SAC6 225aa 6e-25 in ref transcript
  • Ca2+-binding actin-bundling protein fimbrin/plastin (EF-Hand superfamily) [Cytoskeleton].
• Changed! COG SbcC 643aa 3e-09 in ref transcript
  • ATPase involved in DNA repair [DNA replication, recombination, and repair].
• Changed! PRK PRK00409 138aa 5e-04 in ref transcript
  • recombination and DNA strand exchange inhibitor protein; Reviewed.

DMD

• refseq_DMD.F7 refseq_DMD.R7 116 155
• NCBIGene 36.3 1756
• Single exon skipping, size difference: 39
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_004006

• cd ZZ_dystrophin 49aa 3e-23 in ref transcript
  • Zinc finger, ZZ type. Zinc finger present in dystrophin and dystrobrevin. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dystrophin attaches actin filaments to an integral membrane glycoprotein complex in muscle cells. The ZZ domain in dystrophin has been shown to be essential for binding to the membrane protein beta-dystroglycan.
• cd CH 106aa 6e-16 in ref transcript
  • Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav).
• cd SPEC 217aa 7e-14 in ref transcript
  • Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here.
• cd SPEC 218aa 5e-13 in ref transcript
• cd SPEC 216aa 3e-11 in ref transcript
• cd SPEC 244aa 5e-10 in ref transcript
• cd SPEC 209aa 4e-09 in ref transcript
• cd CH 104aa 6e-09 in ref transcript
• cd SPEC 207aa 7e-09 in ref transcript
• cd SPEC 215aa 1e-07 in ref transcript
• cd SPEC 111aa 1e-06 in ref transcript
• cd SPEC 183aa 5e-06 in ref transcript
• cd SPEC 207aa 5e-06 in ref transcript
• cd SPEC 189aa 2e-05 in ref transcript
• cd SPEC 210aa 3e-05 in ref transcript
• cd WW 30aa 4e-05 in ref transcript
  • Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
• cd SPEC 226aa 4e-04 in ref transcript
• cd SPEC 208aa 0.004 in ref transcript
• pfam efhand_1 121aa 1e-44 in ref transcript
  • EF hand. Members of this family adopt a helix-loop-helix motif, as per other EF hand domains. However, since they do not contain the canonical pattern of calcium binding residues found in many EF hand domains, they do not bind calcium ions. The main function of this domain is the provision of specificity in beta-dystroglycan recognition, though in dystrophin it serves an additional role: stabilisation of the WW domain (pfam00397), enhancing dystroglycan binding.
• pfam efhand_2 92aa 7e-40 in ref transcript
  • EF-hand. Members of this family adopt a helix-loop-helix motif, as per other EF hand domains. However, since they do not contain the canonical pattern of calcium binding residues found in many EF hand domains, they do not bind calcium ions. The main function of this domain is the provision of specificity in beta-dystroglycan recognition, though in dystrophin it serves an additional role: stabilisation of the WW domain (pfam00397), enhancing dystroglycan binding.
• pfam ZZ 46aa 2e-18 in ref transcript
  • Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300. ZZ in dystrophin binds calmodulin. Putative zinc finger; binding not yet shown. Four to six cysteine residues in its sequence are responsible for coordinating zinc ions, to reinforce the structure.
• smart CH 100aa 4e-18 in ref transcript
  • Calponin homology domain. Actin binding domains present in duplicate at the N-termini of spectrin-like proteins (including dystrophin, alpha-actinin). These domains cross-link actin filaments into bundles and networks. A calponin homology domain is predicted in yeasst Cdc24p.
• smart CH 101aa 4e-11 in ref transcript
• TIGR SMC_prok_B 595aa 6e-09 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• smart SPEC 101aa 1e-08 in ref transcript
  • Spectrin repeats.
• pfam Spectrin 107aa 2e-08 in ref transcript
  • Spectrin repeat. Spectrin repeats are found in several proteins involved in cytoskeletal structure. These include spectrin, alpha-actinin and dystrophin. The sequence repeat used in this family is taken from the structural repeat in reference. The spectrin repeat forms a three helix bundle. The second helix is interrupted by proline in some sequences. The repeats are defined by a characteristic tryptophan (W) residue at position 17 in helix A and a leucine (L) at 2 residues from the carboxyl end of helix C.
• smart SPEC 103aa 5e-08 in ref transcript
• smart SPEC 102aa 6e-08 in ref transcript
• pfam Spectrin 105aa 1e-07 in ref transcript
• smart SPEC 110aa 8e-07 in ref transcript
• smart WW 32aa 1e-05 in ref transcript
  • Domain with 2 conserved Trp (W) residues. Also known as the WWP or rsp5 domain. Binds proline-rich polypeptides.
• pfam Spectrin 117aa 3e-05 in ref transcript
• TIGR SMC_prok_B 278aa 8e-05 in ref transcript
• smart SPEC 101aa 3e-04 in ref transcript
• smart SPEC 98aa 0.003 in ref transcript
• pfam Spectrin 66aa 0.007 in ref transcript
• Changed! TIGR SMC_prok_B 391aa 0.010 in ref transcript
• COG SAC6 225aa 6e-25 in ref transcript
  • Ca2+-binding actin-bundling protein fimbrin/plastin (EF-Hand superfamily) [Cytoskeleton].
• COG SbcC 643aa 3e-09 in ref transcript
  • ATPase involved in DNA repair [DNA replication, recombination, and repair].
• PRK PRK00409 138aa 5e-04 in ref transcript
  • recombination and DNA strand exchange inhibitor protein; Reviewed.

DNAJC21

• refseq_DNAJA5.F1 refseq_DNAJA5.R1 216 351
• NCBIGene 36.3 134218
• Single exon skipping, size difference: 135
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_194283

• cd DnaJ 56aa 1e-17 in ref transcript
  • DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification.
• TIGR DnaJ_bact 88aa 2e-25 in ref transcript
  • This model represents bacterial forms of DnaJ, part of the DnaK-DnaJ-GrpE chaperone system. The three components typically are encoded by consecutive genes. DnaJ homologs occur in many genomes, typically not near DnaK and GrpE-like genes; most such genes are not included by this family. Eukaryotic (mitochondrial and chloroplast) forms are not included in the scope of this family.
• smart ZnF_U1 30aa 8e-04 in ref transcript
  • U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
• COG DnaJ 75aa 8e-23 in ref transcript
  • DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones].
• Changed! COG ZUO1 264aa 4e-12 in ref transcript
  • Ribosome-associated chaperone zuotin [Translation, ribosomal structure and biogenesis / Posttranslational modification, protein turnover, chaperones].
• Changed! COG ZUO1 245aa 9e-12 in modified transcript

DNAJC19

• refseq_DNAJC19.F1 refseq_DNAJC19.R1 137 189
• NCBIGene 36.2 131118
• Single exon skipping, size difference: 52
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_145261

• Changed! cd DnaJ 45aa 5e-07 in ref transcript
  • DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification.
• Changed! smart DnaJ 46aa 2e-07 in ref transcript
  • DnaJ molecular chaperone homology domain.
• Changed! PTZ PTZ00100 58aa 4e-20 in ref transcript
  • DnaJ chaperone protein; Provisional.

DNASE1L1

• refseq_DNASE1L1.F1 refseq_DNASE1L1.R1 111 369
• NCBIGene 36.3 1774
• Single exon skipping, size difference: 258
• Exclusion in 5'UTR
• Reference transcript: NM_001009932

• smart DNaseIc 272aa 1e-114 in ref transcript
  • deoxyribonuclease I. Deoxyribonuclease I catalyzes the endonucleolytic cleavage of double-stranded DNA. The enzyme is secreted outside the cell and also involved in apoptosis in the nucleus.

DNM1

• refseq_DNM1.F2 refseq_DNM1.R2 159 196
• NCBIGene 36.3 1759
• Single exon skipping, size difference: 37
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_004408

• cd PH_dynamin 110aa 1e-50 in ref transcript
  • Dynamin pleckstrin homology (PH) domain. Dynamin is a GTPase that regulates endocytic vesicle formation. It has an N-terminal GTPase domain, followed by a PH domain, a GTPase effector domain and a C-terminal proline arginine rich domain. Dynamin-like proteins, which are found in metazoa, plants and yeast have the same domain architecture as dynamin, but lack the PH domain. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
• smart DYNc 240aa 1e-130 in ref transcript
  • Dynamin, GTPase. Large GTPases that mediate vesicle trafficking. Dynamin participates in the endocytic uptake of receptors, associated ligands, and plasma membrane following an exocytic event.
• pfam Dynamin_M 294aa 1e-118 in ref transcript
  • Dynamin central region. This region lies between the GTPase domain, see pfam00350, and the pleckstrin homology (PH) domain, see pfam00169.
• pfam GED 92aa 2e-22 in ref transcript
  • Dynamin GTPase effector domain.
• smart PH 104aa 2e-05 in ref transcript
  • Pleckstrin homology domain. Domain commonly found in eukaryotic signalling proteins. The domain family possesses multiple functions including the abilities to bind inositol phosphates, and various proteins. PH domains have been found to possess inserted domains (such as in PLC gamma, syntrophins) and to be inserted within other domains. Mutations in Brutons tyrosine kinase (Btk) within its PH domain cause X-linked agammaglobulinaemia (XLA) in patients. Point mutations cluster into the positively charged end of the molecule around the predicted binding site for phosphatidylinositol lipids.
• COG COG0699 424aa 5e-34 in ref transcript
  • Predicted GTPases (dynamin-related) [General function prediction only].

DPAGT1

• refseq_DPAGT1.F1 refseq_DPAGT1.R1 194 315
• NCBIGene 36.3 1798
• Single exon skipping, size difference: 121
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_001382

• Changed! cd GT_GPT_euk 289aa 1e-113 in ref transcript
  • UDP-GlcNAc:dolichol-P GlcNAc-1-P transferase (GPT) catalyzes the transfer of GlcNAc-1-P from UDP-GlcNAc to dolichol-P to form GlcNAc-P-P-dolichol. The reaction is the first step in the assembly of dolichol-linked oligosaccharide intermediates and is essential for eukaryotic N-glycosylation. GPT activity has been identified in all eukaryotic cells examined to date. A series of six conserved motifs designated A through F, ranging in length from 5 to 13 amino acid residues, has been identified in this family. They have been determined to be important for stable expression, substrate binding, or catalytic activities.
• Changed! pfam Glycos_transf_4 178aa 1e-44 in ref transcript
  • Glycosyl transferase family 4.
• Changed! COG Rfe 196aa 1e-18 in ref transcript
  • UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N- acetylglucosamine-1-phosphate transferase [Cell envelope biogenesis, outer membrane].
• Changed! cd GT_GPT_euk 26aa 0.008 in modified transcript

DPP8

• refseq_DPP8.F1 refseq_DPP8.R1 218 354
• NCBIGene 36.3 54878
• Single exon skipping, size difference: 136
• Inclusion in 5'UTR
• Reference transcript: NM_130434

• pfam DPPIV_N 421aa 7e-72 in ref transcript
  • Dipeptidyl peptidase IV (DPP IV) N-terminal region. This family is an alignment of the region to the N-terminal side of the active site. The Prosite motif does not correspond to this Pfam entry.
• pfam Peptidase_S9 206aa 9e-53 in ref transcript
  • Prolyl oligopeptidase family.
• COG DAP2 330aa 7e-48 in ref transcript
  • Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism].

DPP8

• refseq_DPP8.F3 refseq_DPP8.R3 184 337
• NCBIGene 36.3 54878
• Single exon skipping, size difference: 153
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_197960

• pfam DPPIV_N 421aa 4e-72 in ref transcript
  • Dipeptidyl peptidase IV (DPP IV) N-terminal region. This family is an alignment of the region to the N-terminal side of the active site. The Prosite motif does not correspond to this Pfam entry.
• Changed! pfam Peptidase_S9 206aa 6e-53 in ref transcript
  • Prolyl oligopeptidase family.
• Changed! COG DAP2 330aa 4e-48 in ref transcript
  • Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism].
• Changed! pfam Peptidase_S9 155aa 7e-25 in modified transcript
• Changed! COG DAP2 279aa 1e-27 in modified transcript

DRD2

• refseq_DRD2.F1 refseq_DRD2.R1 276 363
• NCBIGene 36.3 1813
• Single exon skipping, size difference: 87
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000795

• pfam 7tm_1 131aa 8e-23 in ref transcript
  • 7 transmembrane receptor (rhodopsin family). This family contains, amongst other G-protein-coupled receptors (GCPRs), members of the opsin family, which have been considered to be typical members of the rhodopsin superfamily. They share several motifs, mainly the seven transmembrane helices, GCPRs of the rhodopsin superfamily. All opsins bind a chromophore, such as 11-cis-retinal. The function of most opsins other than the photoisomerases is split into two steps: light absorption and G-protein activation. Photoisomerases, on the other hand, are not coupled to G-proteins - they are thought to generate and supply the chromophore that is used by visual opsins.
• pfam 7tm_1 68aa 7e-17 in ref transcript

DSC1

• refseq_DSC1.F2 refseq_DSC1.R2 251 297
• NCBIGene 36.3 1823
• Single exon skipping, size difference: 46
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_024421

• cd CA 201aa 1e-34 in ref transcript
  • Cadherin repeat domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion; these domains occur as repeats in the extracellular regions which are thought to mediate cell-cell contact when bound to calcium; plays a role in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-,CNR-,proto-,and FAT-family cadherin, desmocollin, and desmoglein, exists as monomers or dimers (hetero- and homo-); two copies of the repeat are present here.
• cd CA 209aa 2e-34 in ref transcript
• cd CA 182aa 6e-23 in ref transcript
• cd CA 212aa 4e-21 in ref transcript
• pfam Cadherin 97aa 4e-20 in ref transcript
  • Cadherin domain.
• pfam Cadherin_pro 81aa 4e-17 in ref transcript
  • Cadherin prodomain like. Cadherins are a family of proteins that mediate calcium dependent cell-cell adhesion. They are activated through cleavage of a prosequence in the late Golgi. This domain corresponds to the folded region of the prosequence, and is termed the prodomain. The prodomain shows structural resemblance to the cadherin domain, but lacks all the features known to be important for cadherin-cadherin interactions.
• pfam Cadherin 95aa 9e-16 in ref transcript
• pfam Cadherin 83aa 3e-13 in ref transcript
• pfam Cadherin 91aa 2e-11 in ref transcript
• pfam Cadherin 86aa 0.002 in ref transcript

DSC2

• refseq_DSC2.F1 refseq_DSC2.R1 217 263
• NCBIGene 36.3 1824
• Single exon skipping, size difference: 46
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_024422

• cd CA 210aa 5e-32 in ref transcript
  • Cadherin repeat domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion; these domains occur as repeats in the extracellular regions which are thought to mediate cell-cell contact when bound to calcium; plays a role in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-,CNR-,proto-,and FAT-family cadherin, desmocollin, and desmoglein, exists as monomers or dimers (hetero- and homo-); two copies of the repeat are present here.
• cd CA 209aa 2e-24 in ref transcript
• cd CA 196aa 2e-22 in ref transcript
• pfam Cadherin 104aa 8e-14 in ref transcript
  • Cadherin domain.
• smart CA 86aa 9e-14 in ref transcript
  • Cadherin repeats. Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. Cadherin domains occur as repeats in the extracellular regions which are thought to mediate cell-cell contact when bound to calcium.
• pfam Cadherin_pro 81aa 2e-13 in ref transcript
  • Cadherin prodomain like. Cadherins are a family of proteins that mediate calcium dependent cell-cell adhesion. They are activated through cleavage of a prosequence in the late Golgi. This domain corresponds to the folded region of the prosequence, and is termed the prodomain. The prodomain shows structural resemblance to the cadherin domain, but lacks all the features known to be important for cadherin-cadherin interactions.
• pfam Cadherin 93aa 6e-13 in ref transcript
• pfam Cadherin 95aa 1e-11 in ref transcript
• Changed! pfam Cadherin_C 45aa 0.002 in ref transcript
  • Cadherin cytoplasmic region. Cadherins are vital in cell-cell adhesion during tissue differentiation. Cadherins are linked to the cytoskeleton by catenins. Catenins bind to the cytoplasmic tail of the cadherin. Cadherins cluster to form foci of homophilic binding units. A key determinant to the strength of the binding that it is mediated by cadherins is the juxtamembrane region of the cadherin. This region induces clustering and also binds to the protein p120ctn.

DSCAM

• refseq_DSCAM.F1 refseq_DSCAM.R1 141 332
• NCBIGene 36.2 1826
• Alternative 5-prime and 3-prime, size difference: 191
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_001389

• cd FN3 91aa 1e-12 in ref transcript
  • Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.
• cd IGcam 94aa 1e-12 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• cd IGcam 77aa 3e-12 in ref transcript
• cd IGcam 91aa 2e-11 in ref transcript
• cd IGcam 88aa 2e-11 in ref transcript
• cd IGcam 70aa 1e-09 in ref transcript
• cd FN3 98aa 3e-09 in ref transcript
• cd IGcam 90aa 1e-08 in ref transcript
• cd IGcam 95aa 5e-08 in ref transcript
• cd FN3 86aa 6e-08 in ref transcript
• cd FN3 94aa 2e-07 in ref transcript
• cd FN3 74aa 1e-05 in ref transcript
• cd IGcam 64aa 3e-04 in ref transcript
• cd IGcam 90aa 0.002 in ref transcript
• cd FN3 73aa 0.005 in ref transcript
• pfam I-set 76aa 5e-13 in ref transcript
  • Immunoglobulin I-set domain.
• pfam fn3 84aa 1e-12 in ref transcript
  • Fibronectin type III domain.
• pfam I-set 95aa 1e-11 in ref transcript
• pfam I-set 79aa 3e-11 in ref transcript
• pfam I-set 85aa 5e-11 in ref transcript
• smart IGc2 65aa 1e-09 in ref transcript
  • Immunoglobulin C-2 Type.
• smart FN3 88aa 2e-09 in ref transcript
  • Fibronectin type 3 domain. One of three types of internal repeat within the plasma protein, fibronectin. The tenth fibronectin type III repeat contains a RGD cell recognition sequence in a flexible loop between 2 strands. Type III modules are present in both extracellular and intracellular proteins.
• smart IGc2 58aa 8e-09 in ref transcript
• pfam fn3 87aa 2e-08 in ref transcript
• smart IG_like 90aa 2e-08 in ref transcript
  • Immunoglobulin like. IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
• pfam fn3 79aa 8e-08 in ref transcript
• pfam fn3 69aa 9e-06 in ref transcript

PSMG1

• refseq_DSCR2.F1 refseq_DSCR2.R1 214 277
• NCBIGene 36.3 8624
• Single exon skipping, size difference: 63
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_003720

DSTN

• refseq_DSTN.F1 refseq_DSTN.R1 152 284
• NCBIGene 36.3 11034
• Single exon skipping, size difference: 132
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_006870

• Changed! cd ADF 150aa 6e-32 in ref transcript
  • Actin depolymerisation factor/cofilin -like domains; present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
• Changed! smart ADF 135aa 4e-35 in ref transcript
  • Actin depolymerisation factor/cofilin -like domains. Severs actin filaments and binds to actin monomers.
• Changed! PTZ PTZ00152 131aa 1e-05 in ref transcript
  • actin depolymerizing factor; Provisional.

DTNA

• refseq_DTNA.F1 refseq_DTNA.R1 273 351
• NCBIGene 36.3 1837
• Single exon skipping, size difference: 78
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_032980

• PRK PRK05431 71aa 7e-05 in ref transcript
  • seryl-tRNA synthetase; Provisional.
• COG COG3264 191aa 0.005 in ref transcript
  • Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane].

DTNA

• refseq_DTNA.F3 refseq_DTNA.R3 142 226
• NCBIGene 36.3 1837
• Single exon skipping, size difference: 84
• Exclusion in 5'UTR
• Reference transcript: NM_001390

• cd ZZ_dystrophin 49aa 1e-20 in ref transcript
  • Zinc finger, ZZ type. Zinc finger present in dystrophin and dystrobrevin. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dystrophin attaches actin filaments to an integral membrane glycoprotein complex in muscle cells. The ZZ domain in dystrophin has been shown to be essential for binding to the membrane protein beta-dystroglycan.
• pfam efhand_1 127aa 6e-50 in ref transcript
  • EF hand. Members of this family adopt a helix-loop-helix motif, as per other EF hand domains. However, since they do not contain the canonical pattern of calcium binding residues found in many EF hand domains, they do not bind calcium ions. The main function of this domain is the provision of specificity in beta-dystroglycan recognition, though in dystrophin it serves an additional role: stabilisation of the WW domain (pfam00397), enhancing dystroglycan binding.
• pfam efhand_2 89aa 2e-35 in ref transcript
  • EF-hand. Members of this family adopt a helix-loop-helix motif, as per other EF hand domains. However, since they do not contain the canonical pattern of calcium binding residues found in many EF hand domains, they do not bind calcium ions. The main function of this domain is the provision of specificity in beta-dystroglycan recognition, though in dystrophin it serves an additional role: stabilisation of the WW domain (pfam00397), enhancing dystroglycan binding.
• smart ZnF_ZZ 45aa 3e-13 in ref transcript
  • Zinc-binding domain, present in Dystrophin, CREB-binding protein. Putative zinc-binding domain present in dystrophin-like proteins, and CREB-binding protein/p300 homologues. The ZZ in dystrophin appears to bind calmodulin. A missense mutation of one of the conserved cysteines in dystrophin results in a patient with Duchenne muscular dystrophy [3].
• pfam Cast 103aa 0.005 in ref transcript
  • RIM-binding protein of the cytomatrix active zone. This is a family of proteins that form part of the CAZ (cytomatrix at the active zone) complex which is involved in determining the site of synaptic vesicle fusion. The C-terminus is a PDZ-binding motif that binds directly to RIM (a small G protein Rab-3A effector). The family also contains four coiled-coil domains.
• PRK PRK05431 71aa 1e-04 in ref transcript
  • seryl-tRNA synthetase; Provisional.
• COG COG3264 191aa 0.004 in ref transcript
  • Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane].

DTNA

• refseq_DTNA.F4 refseq_DTNA.R1 100 193
• NCBIGene 36.3 1837
• Single exon skipping, size difference: 93
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001390

• cd ZZ_dystrophin 49aa 1e-20 in ref transcript
  • Zinc finger, ZZ type. Zinc finger present in dystrophin and dystrobrevin. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dystrophin attaches actin filaments to an integral membrane glycoprotein complex in muscle cells. The ZZ domain in dystrophin has been shown to be essential for binding to the membrane protein beta-dystroglycan.
• pfam efhand_1 127aa 6e-50 in ref transcript
  • EF hand. Members of this family adopt a helix-loop-helix motif, as per other EF hand domains. However, since they do not contain the canonical pattern of calcium binding residues found in many EF hand domains, they do not bind calcium ions. The main function of this domain is the provision of specificity in beta-dystroglycan recognition, though in dystrophin it serves an additional role: stabilisation of the WW domain (pfam00397), enhancing dystroglycan binding.
• pfam efhand_2 89aa 2e-35 in ref transcript
  • EF-hand. Members of this family adopt a helix-loop-helix motif, as per other EF hand domains. However, since they do not contain the canonical pattern of calcium binding residues found in many EF hand domains, they do not bind calcium ions. The main function of this domain is the provision of specificity in beta-dystroglycan recognition, though in dystrophin it serves an additional role: stabilisation of the WW domain (pfam00397), enhancing dystroglycan binding.
• smart ZnF_ZZ 45aa 3e-13 in ref transcript
  • Zinc-binding domain, present in Dystrophin, CREB-binding protein. Putative zinc-binding domain present in dystrophin-like proteins, and CREB-binding protein/p300 homologues. The ZZ in dystrophin appears to bind calmodulin. A missense mutation of one of the conserved cysteines in dystrophin results in a patient with Duchenne muscular dystrophy [3].
• Changed! pfam Cast 103aa 0.005 in ref transcript
  • RIM-binding protein of the cytomatrix active zone. This is a family of proteins that form part of the CAZ (cytomatrix at the active zone) complex which is involved in determining the site of synaptic vesicle fusion. The C-terminus is a PDZ-binding motif that binds directly to RIM (a small G protein Rab-3A effector). The family also contains four coiled-coil domains.
• PRK PRK05431 71aa 1e-04 in ref transcript
  • seryl-tRNA synthetase; Provisional.
• COG COG3264 191aa 0.004 in ref transcript
  • Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane].
• Changed! TIGR SMC_prok_B 77aa 0.006 in modified transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.

DTNB

• refseq_DTNB.F1 refseq_DTNB.R1 114 204
• NCBIGene 36.3 1838
• Single exon skipping, size difference: 90
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_021907

• cd ZZ_dystrophin 49aa 4e-18 in ref transcript
  • Zinc finger, ZZ type. Zinc finger present in dystrophin and dystrobrevin. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dystrophin attaches actin filaments to an integral membrane glycoprotein complex in muscle cells. The ZZ domain in dystrophin has been shown to be essential for binding to the membrane protein beta-dystroglycan.
• pfam efhand_1 127aa 3e-47 in ref transcript
  • EF hand. Members of this family adopt a helix-loop-helix motif, as per other EF hand domains. However, since they do not contain the canonical pattern of calcium binding residues found in many EF hand domains, they do not bind calcium ions. The main function of this domain is the provision of specificity in beta-dystroglycan recognition, though in dystrophin it serves an additional role: stabilisation of the WW domain (pfam00397), enhancing dystroglycan binding.
• pfam efhand_2 89aa 3e-37 in ref transcript
  • EF-hand. Members of this family adopt a helix-loop-helix motif, as per other EF hand domains. However, since they do not contain the canonical pattern of calcium binding residues found in many EF hand domains, they do not bind calcium ions. The main function of this domain is the provision of specificity in beta-dystroglycan recognition, though in dystrophin it serves an additional role: stabilisation of the WW domain (pfam00397), enhancing dystroglycan binding.
• smart ZnF_ZZ 45aa 3e-11 in ref transcript
  • Zinc-binding domain, present in Dystrophin, CREB-binding protein. Putative zinc-binding domain present in dystrophin-like proteins, and CREB-binding protein/p300 homologues. The ZZ in dystrophin appears to bind calmodulin. A missense mutation of one of the conserved cysteines in dystrophin results in a patient with Duchenne muscular dystrophy [3].
• TIGR SMC_prok_B 66aa 0.008 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• PRK PRK05431 65aa 0.003 in ref transcript
  • seryl-tRNA synthetase; Provisional.

DTNB

• refseq_DTNB.F2 refseq_DTNB.R2 115 205
• NCBIGene 36.3 1838
• Single exon skipping, size difference: 90
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_021907

• cd ZZ_dystrophin 49aa 4e-18 in ref transcript
  • Zinc finger, ZZ type. Zinc finger present in dystrophin and dystrobrevin. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dystrophin attaches actin filaments to an integral membrane glycoprotein complex in muscle cells. The ZZ domain in dystrophin has been shown to be essential for binding to the membrane protein beta-dystroglycan.
• pfam efhand_1 127aa 3e-47 in ref transcript
  • EF hand. Members of this family adopt a helix-loop-helix motif, as per other EF hand domains. However, since they do not contain the canonical pattern of calcium binding residues found in many EF hand domains, they do not bind calcium ions. The main function of this domain is the provision of specificity in beta-dystroglycan recognition, though in dystrophin it serves an additional role: stabilisation of the WW domain (pfam00397), enhancing dystroglycan binding.
• pfam efhand_2 89aa 3e-37 in ref transcript
  • EF-hand. Members of this family adopt a helix-loop-helix motif, as per other EF hand domains. However, since they do not contain the canonical pattern of calcium binding residues found in many EF hand domains, they do not bind calcium ions. The main function of this domain is the provision of specificity in beta-dystroglycan recognition, though in dystrophin it serves an additional role: stabilisation of the WW domain (pfam00397), enhancing dystroglycan binding.
• smart ZnF_ZZ 45aa 3e-11 in ref transcript
  • Zinc-binding domain, present in Dystrophin, CREB-binding protein. Putative zinc-binding domain present in dystrophin-like proteins, and CREB-binding protein/p300 homologues. The ZZ in dystrophin appears to bind calmodulin. A missense mutation of one of the conserved cysteines in dystrophin results in a patient with Duchenne muscular dystrophy [3].
• TIGR SMC_prok_B 66aa 0.008 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• PRK PRK05431 65aa 0.003 in ref transcript
  • seryl-tRNA synthetase; Provisional.

DTNB

• refseq_DTNB.F5 refseq_DTNB.R5 110 164
• NCBIGene 36.3 1838
• Single exon skipping, size difference: 54
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_021907

• cd ZZ_dystrophin 49aa 4e-18 in ref transcript
  • Zinc finger, ZZ type. Zinc finger present in dystrophin and dystrobrevin. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dystrophin attaches actin filaments to an integral membrane glycoprotein complex in muscle cells. The ZZ domain in dystrophin has been shown to be essential for binding to the membrane protein beta-dystroglycan.
• pfam efhand_1 127aa 3e-47 in ref transcript
  • EF hand. Members of this family adopt a helix-loop-helix motif, as per other EF hand domains. However, since they do not contain the canonical pattern of calcium binding residues found in many EF hand domains, they do not bind calcium ions. The main function of this domain is the provision of specificity in beta-dystroglycan recognition, though in dystrophin it serves an additional role: stabilisation of the WW domain (pfam00397), enhancing dystroglycan binding.
• pfam efhand_2 89aa 3e-37 in ref transcript
  • EF-hand. Members of this family adopt a helix-loop-helix motif, as per other EF hand domains. However, since they do not contain the canonical pattern of calcium binding residues found in many EF hand domains, they do not bind calcium ions. The main function of this domain is the provision of specificity in beta-dystroglycan recognition, though in dystrophin it serves an additional role: stabilisation of the WW domain (pfam00397), enhancing dystroglycan binding.
• smart ZnF_ZZ 45aa 3e-11 in ref transcript
  • Zinc-binding domain, present in Dystrophin, CREB-binding protein. Putative zinc-binding domain present in dystrophin-like proteins, and CREB-binding protein/p300 homologues. The ZZ in dystrophin appears to bind calmodulin. A missense mutation of one of the conserved cysteines in dystrophin results in a patient with Duchenne muscular dystrophy [3].
• TIGR SMC_prok_B 66aa 0.008 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• PRK PRK05431 65aa 0.003 in ref transcript
  • seryl-tRNA synthetase; Provisional.

DTNBP1

• refseq_DTNBP1.F1 refseq_DTNBP1.R1 226 271
• NCBIGene 36.3 84062
• Alternative 3-prime, size difference: 45
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_032122

• Changed! pfam Dysbindin 121aa 7e-16 in ref transcript
  • Dysbindin (Dystrobrevin binding protein 1). Dysbindin is an evolutionary conserved 40-kDa coiled-coil-containing protein that binds to alpha- and beta-dystrobrevin in muscle and brain. Dystrophin and alpha-dystrobrevin are co-immunoprecipitated with dysbindin, indicating that dysbindin is DPC-associated in muscle. Dysbindin co-localises with alpha-dystrobrevin at the sarcolemma and is up-regulated in dystrophin-deficient muscle. In the brain, dysbindin is found primarily in axon bundles and especially in certain axon terminals, notably mossy fibre synaptic terminals in the cerebellum and hippocampus. Dysbindin may have implications for the molecular pathology of Duchenne muscular dystrophy and may provide an alternative route for anchoring dystrobrevin and the DPC to the muscle membrane. Genetic variation in the human dysbindin gene is also thought to be associated with Schizophrenia.

DUOX1

• refseq_DUOX1.F2 refseq_DUOX1.R2 127 319
• NCBIGene 36.3 53905
• Single exon skipping, size difference: 192
• Exclusion in 5'UTR
• Reference transcript: NM_017434

• cd NOX_Duox_like_FAD_NADP 180aa 9e-45 in ref transcript
  • NADPH oxidase (NOX) catalyzes the generation of reactive oxygen species (ROS) such as superoxide and hydrogen peroxide. ROS were originally identified as bactericidal agents in phagocytes, but are now also implicated in cell signaling and metabolism. NOX has a 6-alpha helix heme-binding transmembrane domain fused to a flavoprotein with the nucleotide binding domain located in the cytoplasm. Duox enzymes link a peroxidase domain to the NOX domain via a single transmembrane and EF-hand Ca2+ binding sites. The flavoprotein module has a ferredoxin like FAD/NADPH binding domain. In classical phagocytic NOX2, electron transfer occurs from NADPH to FAD to the heme of cytb to oxygen leading to superoxide formation.
• cd EFh 62aa 1e-11 in ref transcript
  • EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers.
• cd EFh 62aa 8e-05 in ref transcript
• cd NOX_Duox_like_FAD_NADP 36aa 0.007 in ref transcript
• pfam An_peroxidase 528aa 1e-139 in ref transcript
  • Animal haem peroxidase.
• pfam NAD_binding_6 155aa 2e-27 in ref transcript
  • Ferric reductase NAD binding domain.
• pfam FAD_binding_8 97aa 4e-17 in ref transcript
  • FAD-binding domain.
• pfam Ferric_reduct 70aa 7e-08 in ref transcript
  • Ferric reductase like transmembrane component. This family includes a common region in the transmembrane proteins mammalian cytochrome B-245 heavy chain (gp91-phox), ferric reductase transmembrane component in yeast and respiratory burst oxidase from mouse-ear cress. This may be a family of flavocytochromes capable of moving electrons across the plasma membrane. The Frp1 protein from S. pombe is a ferric reductase component and is required for cell surface ferric reductase activity, mutants in frp1 are deficient in ferric iron uptake. Cytochrome B-245 heavy chain is a FAD-dependent dehydrogenase it is also has electron transferase activity which reduces molecular oxygen to superoxide anion, a precursor in the production of microbicidal oxidants. Mutations in the sequence of cytochrome B-245 heavy chain (gp91-phox) lead to the X-linked chronic granulomatous disease. The bacteriocidal ability of phagocytic cells is reduced and is characterised by the absence of a functional plasma membrane associated NADPH oxidase. The chronic granulomatous disease gene codes for the beta chain of cytochrome B-245 and cytochrome B-245 is missing from patients with the disease.
• smart EFh 25aa 4e-04 in ref transcript
  • EF-hand, calcium binding motif. EF-hands are calcium-binding motifs that occur at least in pairs. Links between disease states and genes encoding EF-hands, particularly the S100 subclass, are emerging. Each motif consists of a 12 residue loop flanked on either side by a 12 residue alpha-helix. EF-hands undergo a conformational change unpon binding calcium ions.
• smart EFh 25aa 0.002 in ref transcript
• COG FRQ1 171aa 2e-11 in ref transcript
  • Ca2+-binding protein (EF-Hand superfamily) [Signal transduction mechanisms / Cytoskeleton / Cell division and chromosome partitioning / General function prediction only].
• COG UbiB 195aa 3e-10 in ref transcript
  • 2-polyprenylphenol hydroxylase and related flavodoxin oxidoreductases [Coenzyme metabolism / Energy production and conversion].

DUSP13

• refseq_DUSP13.F1 refseq_DUSP13.R1 144 352
• NCBIGene 36.2 51207
• Single exon skipping, size difference: 208
• Exclusion of the protein initiation site
• Reference transcript: NM_001007271

• cd DSPc 144aa 2e-32 in ref transcript
  • Dual specificity phosphatases (DSP); Ser/Thr and Tyr protein phosphatases. Structurally similar to tyrosine-specific phosphatases but with a shallower active site cleft and a distinctive active site signature motif, HCxxGxxR. Characterized as VHR- or Cdc25-like.
• smart DSPc 143aa 4e-26 in ref transcript
  • Dual specificity phosphatase, catalytic domain.
• COG CDC14 140aa 1e-07 in ref transcript
  • Predicted protein-tyrosine phosphatase [Signal transduction mechanisms].

DUT

• refseq_DUT.F1 refseq_DUT.R1 103 419
• NCBIGene 36.3 1854
• Alternative 5-prime, size difference: 316
• Exclusion of the protein initiation site
• Reference transcript: NM_001025248

• TIGR dut 138aa 5e-60 in ref transcript
  • Changed role from 132 to 123. RTD.
• COG Dut 134aa 1e-36 in ref transcript
  • dUTPase [Nucleotide transport and metabolism].
• Changed! PRK PRK07764 117aa 0.006 in ref transcript
  • DNA polymerase III subunits gamma and tau; Validated.

DYRK1A

• refseq_DYRK1A.F2 refseq_DYRK1A.R2 143 170
• NCBIGene 36.3 1859
• Alternative 3-prime, size difference: 27
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001396

• cd S_TKc 322aa 6e-56 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• smart S_TKc 230aa 2e-54 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• smart S_TKc 28aa 4e-04 in ref transcript
• PTZ PTZ00284 225aa 9e-30 in ref transcript
  • protein kinase; Provisional.

DYRK1A

• refseq_DYRK1A.F3 refseq_DYRK1A.R3 133 264
• NCBIGene 36.3 1859
• Alternative 5-prime, size difference: 131
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_001396

• Changed! cd S_TKc 322aa 6e-56 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• smart S_TKc 230aa 2e-54 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• smart S_TKc 28aa 4e-04 in ref transcript
• PTZ PTZ00284 225aa 9e-30 in ref transcript
  • protein kinase; Provisional.
• Changed! cd S_TKc 241aa 9e-54 in modified transcript

DYRK1A

• refseq_DYRK1A.F5 refseq_DYRK1A.R5 101 273
• NCBIGene 36.3 1859
• Alternative 3-prime, size difference: 172
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_101395

• cd S_TKc 241aa 9e-54 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• smart S_TKc 230aa 2e-52 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• smart S_TKc 28aa 7e-04 in ref transcript
• PTZ PTZ00284 225aa 4e-30 in ref transcript
  • protein kinase; Provisional.

DYRK2

• refseq_DYRK2.F1 refseq_DYRK2.R1 198 347
• NCBIGene 36.3 8445
• Single exon skipping, size difference: 149
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_006482

• Changed! cd S_TKc 237aa 4e-60 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• Changed! cd STKc_Cdc7_like 30aa 3e-04 in ref transcript
  • Serine/threonine kinases (STKs), cell division control protein 7 (Cdc7)-like subfamily, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The Cdc7-like subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. Members of this subfamily include Schizosaccharomyces pombe Cdc7, Saccharomyces cerevisiae Cdc15, Arabidopsis thaliana mitogen-activated protein kinase (MAPK) kinase kinase (MAPKKK) epsilon, and related proteins. MAPKKKs phosphorylate and activate MAPK kinases (MAPKKs or MKKs or MAP2Ks), which in turn phosphorylate and activate MAPKs during signaling cascades that are important in mediating cellular responses to extracellular signals. Fission yeast Cdc7 is essential for cell division by playing a key role in the initiation of septum formation and cytokinesis. Budding yeast Cdc15 functions to coordinate mitotic exit with cytokinesis. Arabidopsis MAPKKK epsilon is required for pollen development in the plasma membrane.
• Changed! smart S_TKc 304aa 2e-63 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• Changed! COG SPS1 335aa 6e-31 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].

DYRK3

• refseq_DYRK3.F1 refseq_DYRK3.R1 260 354
• NCBIGene 36.3 8444
• Single exon skipping, size difference: 94
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_003582

• Changed! cd S_TKc 315aa 1e-60 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• Changed! smart S_TKc 304aa 8e-65 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• Changed! COG SPS1 315aa 4e-28 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].

DYX1C1

• refseq_DYX1C1.F1 refseq_DYX1C1.R1 181 287
• NCBIGene 36.3 161582
• Single exon skipping, size difference: 106
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_130810

• cd p23_DYX1C1_like 78aa 3e-31 in ref transcript
  • p23_like domain found in proteins similar to dyslexia susceptibility 1 (DYX1) candidate 1 (C1) protein, DYX1C1. The human gene encoding this protein is a positional candidate gene for developmental dyslexia (DD), it is located on 15q21.3 by the DYX1 DD susceptibility locus (15q15-21). Independent association studies have reported conflicting results. However, association of short-term memory, which plays a role in DD, with a variant within the DYX1C1 gene has been reported. Most proteins belonging to this group contain a C-terminal tetratricopeptide repeat (TPR) protein binding region.
• Changed! cd TPR 106aa 5e-05 in ref transcript
  • Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here.
• pfam CS 70aa 7e-12 in ref transcript
  • CS domain. The CS and CHORD (pfam04968) are fused into a single polypeptide chain in metazoans but are found in separate proteins in plants; this is thought to be indicative of an interaction between CS and CHORD. It has been suggested that the CS domain is a binding module for HSP90, implying that CS domain-containing proteins are involved in recruiting heat shock proteins to multiprotein assemblies.
• Changed! TIGR 3a0801s09 121aa 4e-06 in ref transcript
• Changed! TIGR 3a0801s09 75aa 0.009 in modified transcript

DZIP1

• refseq_DZIP1.F1 refseq_DZIP1.R1 148 205
• NCBIGene 36.3 22873
• Single exon skipping, size difference: 57
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_198968

EBF2

• refseq_EBF2.F1 refseq_EBF2.R1 109 178
• NCBIGene 36.2 64641
• Single exon skipping, size difference: 69
• Exclusion in the protein (no frameshift)
• Reference transcript: XM_927203

• cd IPT_COE 85aa 3e-43 in ref transcript
  • IPT domain of the COE family (Col/Olf-1/EBF) of non-basic, helix-loop-helix (HLH)-containing transcription factors. COE family proteins are all transcription factors and play an important role in variety of developmental processes. Mouse EBF is involved in the regulation of the early stages of B-cell differentiation, Drosophila collier is a regulator of the head patterning, and a related protein in Xenopus is involved in primary neurogenesis. All COE family members have a well conserved DNA binding domain that contains an atypical Zn finger motif. The function of the IPT domain is unknown.
• pfam TIG 83aa 5e-09 in ref transcript
  • IPT/TIG domain. This family consists of a domain that has an immunoglobulin like fold. These domains are found in cell surface receptors such as Met and Ron as well as in intracellular transcription factors where it is involved in DNA binding. CAUTION: This family does not currently recognise a significant number of members.

ECM1

• refseq_ECM1.F2 refseq_ECM1.R2 100 475
• NCBIGene 36.3 1893
• Single exon skipping, size difference: 375
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_004425

• Changed! pfam ECM1 279aa 1e-120 in ref transcript
  • Extracellular matrix protein 1 (ECM1). This family consists of several eukaryotic extracellular matrix protein 1 (ECM1) sequences. ECM1 has been shown to regulate endochondral bone formation, stimulate the proliferation of endothelial cells and induce angiogenesis. Mutations in the ECM1 gene can cause lipoid proteinosis, a disorder which causes generalised thickening of skin, mucosae and certain viscera. Classical features include beaded eyelid papules and laryngeal infiltration leading to hoarseness.
• Changed! pfam ECM1 242aa 1e-97 in ref transcript
• Changed! pfam ECM1 415aa 0.0 in modified transcript

EFEMP1

• refseq_EFEMP1.F1 refseq_EFEMP1.R1 165 206
• NCBIGene 36.3 2202
• Single exon skipping, size difference: 41
• Exclusion in 5'UTR
• Reference transcript: NM_001039348

• cd vWA_Matrilin 40aa 2e-04 in ref transcript
  • VWA_Matrilin: In cartilaginous plate, extracellular matrix molecules mediate cell-matrix and matrix-matrix interactions thereby providing tissue integrity. Some members of the matrilin family are expressed specifically in developing cartilage rudiments. The matrilin family consists of at least four members. All the members of the matrilin family contain VWA domains, EGF-like domains and a heptad repeat coiled-coiled domain at the carboxy terminus which is responsible for the oligomerization of the matrilins. The VWA domains have been shown to be essential for matrilin network formation by interacting with matrix ligands.
• cd vWA_Matrilin 42aa 0.001 in ref transcript
• cd vWA_Matrilin 33aa 0.004 in ref transcript
• cd vWA_Matrilin 40aa 0.004 in ref transcript
• pfam EGF_CA 34aa 3e-06 in ref transcript
  • Calcium binding EGF domain.
• smart EGF_CA 31aa 4e-05 in ref transcript
  • Calcium-binding EGF-like domain.
• smart EGF_CA 40aa 0.002 in ref transcript

EFNA1

• refseq_EFNA1.F1 refseq_EFNA1.R1 320 386
• NCBIGene 36.3 1942
• Single exon skipping, size difference: 66
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_004428

• Changed! pfam Ephrin 135aa 4e-61 in ref transcript
  • Ephrin.
• Changed! pfam Ephrin 119aa 4e-53 in modified transcript

EFNA4

• refseq_EFNA4.F1 refseq_EFNA4.R1 143 289
• NCBIGene 36.3 1945
• Alternative 3-prime, size difference: 146
• Exclusion of the stop codon
• Reference transcript: NM_005227

• pfam Ephrin 131aa 3e-43 in ref transcript
  • Ephrin.

EFS

• refseq_EFS.F1 refseq_EFS.R1 101 380
• NCBIGene 36.3 10278
• Single exon skipping, size difference: 279
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_005864

• Changed! cd SH3 56aa 9e-11 in ref transcript
  • Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
• Changed! smart SH3 57aa 6e-13 in ref transcript
  • Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.

EGFLAM

• refseq_EGFLAM.F1 refseq_EGFLAM.R1 199 389
• NCBIGene 36.3 133584
• Single exon skipping, size difference: 190
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_152403

• Changed! cd LamG 154aa 5e-26 in ref transcript
  • Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules.
• Changed! cd LamG 138aa 9e-25 in ref transcript
• Changed! cd LamG 151aa 3e-23 in ref transcript
• cd FN3 98aa 3e-13 in ref transcript
  • Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.
• cd FN3 93aa 2e-12 in ref transcript
• Changed! cd EGF_CA 29aa 1e-04 in ref transcript
  • Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements.
• Changed! cd EGF_CA 43aa 2e-04 in ref transcript
• Changed! pfam Laminin_G_2 126aa 6e-29 in ref transcript
  • Laminin G domain. This family includes the Thrombospondin N-terminal-like domain, a Laminin G subfamily.
• Changed! smart LamG 133aa 4e-27 in ref transcript
  • Laminin G domain.
• Changed! smart LamG 135aa 2e-22 in ref transcript
• pfam fn3 87aa 8e-13 in ref transcript
  • Fibronectin type III domain.
• pfam fn3 91aa 1e-09 in ref transcript
• Changed! pfam EGF 28aa 7e-04 in ref transcript
  • EGF-like domain. There is no clear separation between noise and signal. pfam00053 is very similar, but has 8 instead of 6 conserved cysteines. Includes some cytokine receptors. The EGF domain misses the N-terminus regions of the Ca2+ binding EGF domains (this is the main reason of discrepancy between Swiss-Prot domain start/end and Pfam). The family is hard to model due to many similar but different sub-types of EGF domains. Pfam certainly misses a number of EGF domains.
• Changed! pfam EGF 32aa 0.004 in ref transcript
• Changed! cd LamG 112aa 3e-15 in modified transcript
• Changed! smart LamG 91aa 2e-12 in modified transcript

EHMT2

• refseq_EHMT2.F1 refseq_EHMT2.R1 117 219
• NCBIGene 36.3 10919
• Single exon skipping, size difference: 102
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_006709

• cd ANK 120aa 3e-29 in ref transcript
  • ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats.
• cd ANK 126aa 2e-28 in ref transcript
• pfam SET 127aa 2e-36 in ref transcript
  • SET domain. SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure.
• smart PreSET 100aa 4e-27 in ref transcript
  • N-terminal to some SET domains. A Cys-rich putative Zn2+-binding domain that occurs N-terminal to some SET domains. Function is unknown. Unpublished.
• TIGR trp 177aa 1e-08 in ref transcript
  • after chronic exposure to capsaicin. (McCleskey and Gold, 1999).
• pfam Ank 31aa 4e-06 in ref transcript
  • Ankyrin repeat. There's no clear separation between noise and signal on the HMM search Ankyrin repeats generally consist of a beta, alpha, alpha, beta order of secondary structures. The repeats associate to form a higher order structure.
• COG COG2940 242aa 3e-20 in ref transcript
  • Proteins containing SET domain [General function prediction only].
• COG Arp 156aa 1e-17 in ref transcript
  • FOG: Ankyrin repeat [General function prediction only].
• COG Arp 158aa 1e-13 in ref transcript

EI24

• refseq_EI24.F1 refseq_EI24.R1 159 271
• NCBIGene 36.3 9538
• Single exon skipping, size difference: 112
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_001007277

• Changed! pfam EI24 154aa 6e-44 in ref transcript
  • Etoposide-induced protein 2.4 (EI24). This family contains a number of eukaryotic etoposide-induced 2.4 (EI24) proteins approximately 350 residues long. In cells treated with the cytotoxic drug etoposide, EI24 is induced by p53. It has been suggested to play an important role in negative cell growth control.
• Changed! pfam EI24 212aa 2e-66 in modified transcript

EIF2C3

• refseq_EIF2C3.F1 refseq_EIF2C3.R1 187 324
• NCBIGene 36.3 192669
• Single exon skipping, size difference: 137
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_024852

• Changed! cd Piwi_ago-like 426aa 1e-173 in ref transcript
  • Piwi_ago-like: PIWI domain, Argonaute-like subfamily. Argonaute is the central component of the RNA-induced silencing complex (RISC) and related complexes. The PIWI domain is the C-terminal portion of Argonaute and consists of two subdomains, one of which provides the 5' anchoring of the guide RNA and the other, the catalytic site for slicing.
• Changed! cd PAZ_argonaute_like 121aa 1e-32 in ref transcript
  • PAZ domain, argonaute_like subfamily. Argonaute is part of the RNA-induced silencing complex (RISC), and is an endonuclease that plays a key role in the RNA interference pathway. The PAZ domain has been named after the proteins Piwi,Argonaut, and Zwille. PAZ is found in two families of proteins that are essential components of RNA-mediated gene-silencing pathways, including RNA interference, the Piwi and Dicer families. PAZ functions as a nucleic acid binding domain, with a strong preference for single-stranded nucleic acids (RNA or DNA) or RNA duplexes with single-stranded 3' overhangs. It has been suggested that the PAZ domain provides a unique mode for the recognition of the two 3'-terminal nucleotides in single-stranded nucleic acids and buries the 3' OH group, and that it might recognize characteristic 3' overhangs in siRNAs within RISC (RNA-induced silencing) and other complexes.
• Changed! pfam Piwi 302aa 1e-103 in ref transcript
  • Piwi domain. This domain is found in the protein Piwi and its relatives. The function of this domain is the dsRNA guided hydrolysis of ssRNA. Determination of the crystal structure of Argonaute reveals that PIWI is an RNase H domain, and identifies Argonaute as Slicer, the enzyme that cleaves mRNA in the RNAi RISC complex. In addition, Mg+2 dependence and production of 3'-OH and 5' phosphate products are shared characteristics of RNaseH and RISC. The PIWI domain core has a tertiary structure belonging to the RNase H family of enzymes. RNase H fold proteins all have a five-stranded mixed beta-sheet surrounded by helices. By analogy to RNase H enzymes which cleave single-stranded RNA guided by the DNA strand in an RNA/DNA hybrid, the PIWI domain can be inferred to cleave single-stranded RNA, for example mRNA, guided by double stranded siRNA.
• Changed! pfam PAZ 117aa 4e-32 in ref transcript
  • PAZ domain. This domain is named PAZ after the proteins Piwi Argonaut and Zwille. This domain is found in two families of proteins that are involved in post-transcriptional gene silencing. These are the Piwi family and the Dicer family, that includes the Carpel factory protein. The function of the domains is unknown but has been suggested to mediate complex formation between proteins of the Piwi and Dicer families by hetero-dimerisation. The three-dimensional structure of this domain has been solved. The PAZ domain is composed of two subdomains. One subdomain is similar to the OB fold, albeit with a different topology. The OB-fold is well known as a single-stranded nucleic acid binding fold. The second subdomain is composed of a beta-hairpin followed by an alpha-helix. The PAZ domains shows low-affinity nucleic acid binding and appears to interact with the 3' ends of single-stranded regions of RNA in the cleft between the two subdomains. PAZ can bind the characteristic two-base 3' overhangs of siRNAs, indicating that although PAZ may not be a primary nucleic acid binding site in Dicer or RISC, it may contribute to the specific and productive incorporation of siRNAs and miRNAs into the RNAi pathway.
• Changed! pfam DUF1785 53aa 3e-16 in ref transcript
  • Domain of unknown function (DUF1785). This region is found in argonaute proteins and often co-occurs with pfam02179 and pfam02171.

EIF2C3

• refseq_EIF2C3.F4 refseq_EIF2C3.R4 233 354
• NCBIGene 36.3 192669
• Single exon skipping, size difference: 121
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_024852

• Changed! cd Piwi_ago-like 426aa 1e-173 in ref transcript
  • Piwi_ago-like: PIWI domain, Argonaute-like subfamily. Argonaute is the central component of the RNA-induced silencing complex (RISC) and related complexes. The PIWI domain is the C-terminal portion of Argonaute and consists of two subdomains, one of which provides the 5' anchoring of the guide RNA and the other, the catalytic site for slicing.
• Changed! cd PAZ_argonaute_like 121aa 1e-32 in ref transcript
  • PAZ domain, argonaute_like subfamily. Argonaute is part of the RNA-induced silencing complex (RISC), and is an endonuclease that plays a key role in the RNA interference pathway. The PAZ domain has been named after the proteins Piwi,Argonaut, and Zwille. PAZ is found in two families of proteins that are essential components of RNA-mediated gene-silencing pathways, including RNA interference, the Piwi and Dicer families. PAZ functions as a nucleic acid binding domain, with a strong preference for single-stranded nucleic acids (RNA or DNA) or RNA duplexes with single-stranded 3' overhangs. It has been suggested that the PAZ domain provides a unique mode for the recognition of the two 3'-terminal nucleotides in single-stranded nucleic acids and buries the 3' OH group, and that it might recognize characteristic 3' overhangs in siRNAs within RISC (RNA-induced silencing) and other complexes.
• Changed! pfam Piwi 302aa 1e-103 in ref transcript
  • Piwi domain. This domain is found in the protein Piwi and its relatives. The function of this domain is the dsRNA guided hydrolysis of ssRNA. Determination of the crystal structure of Argonaute reveals that PIWI is an RNase H domain, and identifies Argonaute as Slicer, the enzyme that cleaves mRNA in the RNAi RISC complex. In addition, Mg+2 dependence and production of 3'-OH and 5' phosphate products are shared characteristics of RNaseH and RISC. The PIWI domain core has a tertiary structure belonging to the RNase H family of enzymes. RNase H fold proteins all have a five-stranded mixed beta-sheet surrounded by helices. By analogy to RNase H enzymes which cleave single-stranded RNA guided by the DNA strand in an RNA/DNA hybrid, the PIWI domain can be inferred to cleave single-stranded RNA, for example mRNA, guided by double stranded siRNA.
• Changed! pfam PAZ 117aa 4e-32 in ref transcript
  • PAZ domain. This domain is named PAZ after the proteins Piwi Argonaut and Zwille. This domain is found in two families of proteins that are involved in post-transcriptional gene silencing. These are the Piwi family and the Dicer family, that includes the Carpel factory protein. The function of the domains is unknown but has been suggested to mediate complex formation between proteins of the Piwi and Dicer families by hetero-dimerisation. The three-dimensional structure of this domain has been solved. The PAZ domain is composed of two subdomains. One subdomain is similar to the OB fold, albeit with a different topology. The OB-fold is well known as a single-stranded nucleic acid binding fold. The second subdomain is composed of a beta-hairpin followed by an alpha-helix. The PAZ domains shows low-affinity nucleic acid binding and appears to interact with the 3' ends of single-stranded regions of RNA in the cleft between the two subdomains. PAZ can bind the characteristic two-base 3' overhangs of siRNAs, indicating that although PAZ may not be a primary nucleic acid binding site in Dicer or RISC, it may contribute to the specific and productive incorporation of siRNAs and miRNAs into the RNAi pathway.
• Changed! pfam DUF1785 53aa 3e-16 in ref transcript
  • Domain of unknown function (DUF1785). This region is found in argonaute proteins and often co-occurs with pfam02179 and pfam02171.

EIF3C

• refseq_EIF3S8.F1 refseq_EIF3S8.R1 189 238
• NCBIGene 36.3 8663
• Alternative 5-prime, size difference: 49
• Exclusion in 5'UTR
• Reference transcript: NM_001037808

• pfam eIF-3c_N 389aa 1e-168 in ref transcript
  • Eukaryotic translation initiation factor 3 subunit 8 N-terminus (eIF3c_N). The largest of the mammalian translation initiation factors, eIF3, consists of at least eight subunits ranging in mass from 35 to 170 kDa. eIF3 binds to the 40 S ribosome in an early step of translation initiation and promotes the binding of methionyl-tRNAi and mRNA.
• pfam eIF-3c_N 146aa 3e-52 in ref transcript
• smart PAM 89aa 8e-16 in ref transcript
  • PCI/PINT associated module.

EIF3B

• refseq_EIF3S9.F2 refseq_EIF3S9.R2 323 398
• NCBIGene 36.3 8662
• Alternative 3-prime, size difference: 75
• Inclusion in 3'UTR
• Reference transcript: NM_003751

• cd RRM 53aa 3e-06 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• pfam eIF2A 196aa 4e-69 in ref transcript
  • Eukaryotic translation initiation factor eIF2A. This is a family of eukaryotic translation initiation factors.
• smart RRM_2 73aa 1e-08 in ref transcript
  • RNA recognition motif.
• COG COG5354 459aa 2e-79 in ref transcript
  • Uncharacterized protein, contains Trp-Asp (WD) repeat [General function prediction only].

EIF4G1

• refseq_EIF4G1.F1 refseq_EIF4G1.R1 132 370
• NCBIGene 36.3 1981
• Multiple exon skipping, size difference: 238
• Exclusion in 5'UTR, Exclusion of the protein initiation site, Exclusion in the protein (no frameshift)
• Reference transcript: NM_198241

• pfam MIF4G 229aa 3e-45 in ref transcript
  • MIF4G domain. MIF4G is named after Middle domain of eukaryotic initiation factor 4G (eIF4G). Also occurs in NMD2p and CBP80. The domain is rich in alpha-helices and may contain multiple alpha-helical repeats. In eIF4G, this domain binds eIF4A, eIF3, RNA and DNA.
• pfam MA3 102aa 6e-27 in ref transcript
  • MA3 domain. Domain in DAP-5, eIF4G, MA-3 and other proteins. Highly alpha-helical. May contain repeats and/or regions similar to MIF4G domains.
• pfam W2 62aa 5e-16 in ref transcript
  • eIF4-gamma/eIF5/eIF2-epsilon. This domain of unknown function is found at the C-terminus of several translation initiation factors.

ELAVL3

• refseq_ELAVL3.F1 refseq_ELAVL3.R1 119 140
• NCBIGene 36.3 1995
• Alternative 3-prime, size difference: 21
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001420

• cd RRM 75aa 3e-18 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• cd RRM 75aa 1e-16 in ref transcript
• cd RRM 77aa 1e-12 in ref transcript
• Changed! TIGR ELAV_HUD_SF 331aa 1e-151 in ref transcript
  • These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
• COG COG0724 160aa 2e-14 in ref transcript
  • RNA-binding proteins (RRM domain) [General function prediction only].
• COG COG0724 81aa 2e-11 in ref transcript
• Changed! TIGR ELAV_HUD_SF 324aa 1e-150 in modified transcript
• Changed! COG COG0724 271aa 6e-11 in modified transcript

ELF2

• refseq_ELF2.F1 refseq_ELF2.R1 137 173
• NCBIGene 36.3 1998
• Alternative 3-prime, size difference: 36
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_201999

• smart ETS 83aa 7e-39 in ref transcript
  • erythroblast transformation specific domain. variation of the helix-turn-helix motif.

ELMO2

• refseq_ELMO2.F1 refseq_ELMO2.R1 132 236
• NCBIGene 36.3 63916
• Exon skipping and alternative 3-prime or 5-prime, size difference: 104
• Exclusion in 5'UTR, Exclusion in 5'UTR
• Reference transcript: NM_133171

• cd PH_PLC 68aa 1e-04 in ref transcript
  • Phospholipase C (PLC) pleckstrin homology (PH) domain. There are several isozymes of PLC (beta, gamma, delta, epsilon. zeta). While, PLC beta, gamma and delta all have N-terminal PH domains, lipid binding specificity is not conserved between them. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
• pfam ELMO_CED12 184aa 3e-49 in ref transcript
  • ELMO/CED-12 family. This family represents a conserved domain which is found in a number of eukaryotic proteins including CED-12, ELMO I and ELMO II. ELMO1 is a component of signalling pathways that regulate phagocytosis and cell migration and is the mammalian orthologue of the Caenorhabditis elegans gene, ced-12. CED-12 is required for the engulfment of dying cells and cell migration. In mammalian cells, ELMO1 interacts with Dock180 as part of the CrkII/Dock180/Rac pathway responsible for phagocytosis and cell migration. ELMO1 is ubiquitously expressed, although its expression is highest in the spleen, an organ rich in immune cells. ELMO1 has a PH domain and a polyproline sequence motif at its C terminus which are not present in this alignment.

EML1

• refseq_EML1.F1 refseq_EML1.R1 129 186
• NCBIGene 36.3 2009
• Single exon skipping, size difference: 57
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001008707

• cd WD40 389aa 3e-22 in ref transcript
  • WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.
• cd WD40 197aa 2e-09 in ref transcript
• pfam HELP 78aa 6e-36 in ref transcript
  • HELP motif. The HELP (Hydrophobic ELP) motif is found in EMAP and EMAP-like proteins (ELPs). The HELP motif contains a predicted transmembrane helix so probably does not form a globular domain. It is also not clear if these proteins localise to membranes. A preliminary study has shown that the N terminus of Sea urchin EMAP containing HELP is sufficient for microtubule binding in vitro (Eichenmuller et al In press).
• pfam WD40 49aa 0.009 in ref transcript
  • WD domain, G-beta repeat.
• COG COG2319 404aa 2e-16 in ref transcript
  • FOG: WD40 repeat [General function prediction only].

EMR2

• refseq_EMR2.F2 refseq_EMR2.R2 244 391
• NCBIGene 36.3 30817
• Single exon skipping, size difference: 147
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_013447

• cd EGF_CA 36aa 2e-05 in ref transcript
  • Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements.
• Changed! cd EGF_CA 37aa 2e-05 in ref transcript
• Changed! cd EGF_CA 34aa 5e-05 in ref transcript
• cd EGF_CA 35aa 0.002 in ref transcript
• pfam 7tm_2 253aa 9e-46 in ref transcript
  • 7 transmembrane receptor (Secretin family). This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling.
• smart GPS 51aa 9e-12 in ref transcript
  • G-protein-coupled receptor proteolytic site domain. Present in latrophilin/CL-1, sea urchin REJ and polycystin.
• Changed! pfam EGF_CA 48aa 4e-10 in ref transcript
  • Calcium binding EGF domain.
• Changed! pfam EGF_CA 35aa 1e-09 in ref transcript
• smart EGF_CA 33aa 3e-06 in ref transcript
  • Calcium-binding EGF-like domain.
• pfam EGF_CA 51aa 3e-05 in ref transcript
• Changed! cd EGF_CA 37aa 9e-06 in modified transcript
• Changed! pfam EGF_CA 35aa 5e-10 in modified transcript

EMR2

• refseq_EMR2.F3 refseq_EMR2.R3 175 208
• NCBIGene 36.3 30817
• Alternative 3-prime, size difference: 33
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_013447

• cd EGF_CA 36aa 2e-05 in ref transcript
  • Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements.
• cd EGF_CA 37aa 2e-05 in ref transcript
• cd EGF_CA 34aa 5e-05 in ref transcript
• cd EGF_CA 35aa 0.002 in ref transcript
• pfam 7tm_2 253aa 9e-46 in ref transcript
  • 7 transmembrane receptor (Secretin family). This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling.
• smart GPS 51aa 9e-12 in ref transcript
  • G-protein-coupled receptor proteolytic site domain. Present in latrophilin/CL-1, sea urchin REJ and polycystin.
• pfam EGF_CA 48aa 4e-10 in ref transcript
  • Calcium binding EGF domain.
• pfam EGF_CA 35aa 1e-09 in ref transcript
• smart EGF_CA 33aa 3e-06 in ref transcript
  • Calcium-binding EGF-like domain.
• pfam EGF_CA 51aa 3e-05 in ref transcript

EMR3

• refseq_EMR3.F1 refseq_EMR3.R1 212 253
• NCBIGene 36.2 84658
• Exon skipping and alternative 3-prime or 5-prime, size difference: 41
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_032571

• Changed! cd EGF_CA 38aa 3e-05 in ref transcript
  • Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements.
• Changed! pfam 7tm_2 253aa 6e-50 in ref transcript
  • 7 transmembrane receptor (Secretin family). This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling.
• Changed! pfam GPS 46aa 2e-09 in ref transcript
  • Latrophilin/CL-1-like GPS domain. Domain present in latrophilin/CL-1, sea urchin REJ and polycystin.
• smart EGF_CA 35aa 2e-05 in ref transcript
  • Calcium-binding EGF-like domain.

ENAH

• refseq_ENAH.F1 refseq_ENAH.R1 133 196
• NCBIGene 36.3 55740
• Single exon skipping, size difference: 63
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001008493

• cd Ena-Vasp 110aa 5e-54 in ref transcript
  • Enabled-VASP-type homology (EVH1) domain. The EVH1 domain binds to other proteins at proline rich sequences. It is found in proteins involved in cytoskeletal reorganization such as Enabled and VASP. Ena-VASP type EVH1 domains specifically recognize FPPPP motifs in the focal adhesion proteins zyxin and vinculin, and the ActA surface protein of Listeria monocytogenes. It has a PH-like fold, despite having minimal sequence similarity to PH or PTB domains.
• pfam WH1 107aa 2e-38 in ref transcript
  • WH1 domain. WASp Homology domain 1 (WH1) domain. WASP is the protein that is defective in Wiskott-Aldrich syndrome (WAS). The majority of point mutations occur within the amino- terminal WH1 domain. The metabotropic glutamate receptors mGluR1alpha and mGluR5 bind a protein called homer, which is a WH1 domain homologue. A subset of WH1 domains has been termed a "EVH1" domain and appear to bind a polyproline motif.
• pfam VASP_tetra 40aa 3e-13 in ref transcript
  • VASP tetramerisation domain. Vasodilator-stimulated phosphoprotein (VASP) is an actin cytoskeletal regulatory protein. This region corresponds to the tetramerisation domain which forms a right handed alpha helical coiled coil structure.

ENO3

• refseq_ENO3.F1 refseq_ENO3.R1 109 151
• NCBIGene 36.3 2027
• Alternative 5-prime, size difference: 42
• Exclusion in 5'UTR
• Reference transcript: NM_001976

• cd enolase 411aa 0.0 in ref transcript
  • Enolase: Enolases are homodimeric enzymes that catalyse the reversible dehydration of 2-phospho-D-glycerate to phosphoenolpyruvate as part of the glycolytic and gluconeogenesis pathways. The reaction is facilitated by the presence of metal ions.
• TIGR eno 427aa 1e-161 in ref transcript
  • Alternate name: enolase.
• PTZ PTZ00081 429aa 0.0 in ref transcript
  • enolase (2-phospho-D-glycerate hydrolase); Provisional.

ENSA

• refseq_ENSA.F1 refseq_ENSA.R1 239 287
• NCBIGene 36.3 2029
• Single exon skipping, size difference: 48
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_207042

• Changed! pfam Endosulfine 64aa 2e-05 in ref transcript
  • cAMP-regulated phosphoprotein/endosulfine conserved region. Conserved region found in both cAMP-regulated phosphoprotein 19 (ARPP-19) and Alpha/Beta endosulfine. No function has yet been assigned to ARPP-19. Endosulfine is the endogenous ligand for the ATP-dependent potassium (K ATP) channels which occupy a key position in the control of insulin release from the pancreatic beta cell by coupling cell polarity to metabolism. In both cases the region occupies the majority of the protein.
• Changed! pfam Endosulfine 48aa 1e-06 in modified transcript

ENTPD2

• refseq_ENTPD2.F1 refseq_ENTPD2.R1 133 202
• NCBIGene 36.3 954
• Alternative 3-prime, size difference: 69
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_203468

• Changed! pfam GDA1_CD39 419aa 2e-82 in ref transcript
  • GDA1/CD39 (nucleoside phosphatase) family.
• COG COG5371 212aa 1e-12 in ref transcript
  • Golgi nucleoside diphosphatase [Carbohydrate transport and metabolism / Posttranslational modification, protein turnover, chaperones].
• Changed! pfam GDA1_CD39 396aa 9e-77 in modified transcript

EPB41

• refseq_EPB41.F1 refseq_EPB41.R1 204 306
• NCBIGene 36.3 2035
• Single exon skipping, size difference: 102
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_203343

• cd FERM_C 94aa 1e-32 in ref transcript
  • The FERM_C domain is the third structural domain within the FERM domain. The FERM domain is found in the cytoskeletal-associated proteins such as ezrin, moesin, radixin, 4.1R, and merlin. These proteins provide a link between the membrane and cytoskeleton and are involved in signal transduction pathways. The FERM_C domain is also found in protein tyrosine phosphatases (PTPs) , the tryosine kinases FAKand JAK, in addition to other proteins involved in signaling. This domain is structuraly similar to the PH and PTB domains and consequently is capable of binding to both peptides and phospholipids at different sites.
• smart B41 157aa 1e-40 in ref transcript
  • Band 4.1 homologues. Also known as ezrin/radixin/moesin (ERM) protein domains. Present in myosins, ezrin, radixin, moesin, protein tyrosine phosphatases. Plasma membrane-binding domain. These proteins play structural and regulatory roles in the assembly and stabilization of specialized plasmamembrane domains. Some PDZ domain containing proteins bind one or more of this family. Now includes JAKs.
• Changed! pfam 4_1_CTD 115aa 3e-26 in ref transcript
  • 4.1 protein C-terminal domain (CTD). At the C-terminus of all known 4.1 proteins is a sequence domain unique to these proteins, known as the C-terminal domain (CTD). Mammalian CTDs are associated with a growing number of protein-protein interactions, although such activities have yet to be associated with invertebrate CTDs. Mammalian CTDs are generally defined by sequence alignment as encoded by exons 18-21. Comparison of known vertebrate 4.1 proteins with invertebrate 4.1 proteins indicates that mammalian 4.1 exon 19 represents a vertebrate adaptation that extends the sequence of the CTD with a Ser/Thr-rich sequence. The CTD was first described as a 22/24-kDa domain by chymotryptic digestion of erythrocyte 4.1 (4.1R). CTD is thought to represent an independent folding structure which has gained function since the divergence of vertebrates from invertebrates.
• pfam FERM_C 85aa 2e-20 in ref transcript
  • FERM C-terminal PH-like domain.
• pfam SAB 47aa 5e-14 in ref transcript
  • SAB domain. This presumed domain is found in proteins containing FERM domains pfam00373. This domain is found to bind to both spectrin and actin, hence the name SAB (Spectrin and Actin Binding) domain.
• pfam FA 45aa 5e-13 in ref transcript
  • FERM adjacent (FA). This region is found adjacent to Band 4.1 / FERM domains (pfam00373) in a subset of FERM containing protein. The region has been hypothesised to play a role in regulatory adaptation, based on similarity to other protein kinase substrates.
• Changed! pfam 4_1_CTD 81aa 7e-29 in modified transcript

EPB41

• refseq_EPB41.F3 refseq_EPB41.R3 313 393
• NCBIGene 36.3 2035
• Single exon skipping, size difference: 80
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_203343

• Changed! cd FERM_C 94aa 1e-32 in ref transcript
  • The FERM_C domain is the third structural domain within the FERM domain. The FERM domain is found in the cytoskeletal-associated proteins such as ezrin, moesin, radixin, 4.1R, and merlin. These proteins provide a link between the membrane and cytoskeleton and are involved in signal transduction pathways. The FERM_C domain is also found in protein tyrosine phosphatases (PTPs) , the tryosine kinases FAKand JAK, in addition to other proteins involved in signaling. This domain is structuraly similar to the PH and PTB domains and consequently is capable of binding to both peptides and phospholipids at different sites.
• Changed! smart B41 157aa 1e-40 in ref transcript
  • Band 4.1 homologues. Also known as ezrin/radixin/moesin (ERM) protein domains. Present in myosins, ezrin, radixin, moesin, protein tyrosine phosphatases. Plasma membrane-binding domain. These proteins play structural and regulatory roles in the assembly and stabilization of specialized plasmamembrane domains. Some PDZ domain containing proteins bind one or more of this family. Now includes JAKs.
• Changed! pfam 4_1_CTD 115aa 3e-26 in ref transcript
  • 4.1 protein C-terminal domain (CTD). At the C-terminus of all known 4.1 proteins is a sequence domain unique to these proteins, known as the C-terminal domain (CTD). Mammalian CTDs are associated with a growing number of protein-protein interactions, although such activities have yet to be associated with invertebrate CTDs. Mammalian CTDs are generally defined by sequence alignment as encoded by exons 18-21. Comparison of known vertebrate 4.1 proteins with invertebrate 4.1 proteins indicates that mammalian 4.1 exon 19 represents a vertebrate adaptation that extends the sequence of the CTD with a Ser/Thr-rich sequence. The CTD was first described as a 22/24-kDa domain by chymotryptic digestion of erythrocyte 4.1 (4.1R). CTD is thought to represent an independent folding structure which has gained function since the divergence of vertebrates from invertebrates.
• Changed! pfam FERM_C 85aa 2e-20 in ref transcript
  • FERM C-terminal PH-like domain.
• Changed! pfam SAB 47aa 5e-14 in ref transcript
  • SAB domain. This presumed domain is found in proteins containing FERM domains pfam00373. This domain is found to bind to both spectrin and actin, hence the name SAB (Spectrin and Actin Binding) domain.
• Changed! pfam FA 45aa 5e-13 in ref transcript
  • FERM adjacent (FA). This region is found adjacent to Band 4.1 / FERM domains (pfam00373) in a subset of FERM containing protein. The region has been hypothesised to play a role in regulatory adaptation, based on similarity to other protein kinase substrates.

EPB41

• refseq_EPB41.F4 refseq_EPB41.R4 253 358
• NCBIGene 36.3 2035
• Single exon skipping, size difference: 105
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_203343

• cd FERM_C 94aa 1e-32 in ref transcript
  • The FERM_C domain is the third structural domain within the FERM domain. The FERM domain is found in the cytoskeletal-associated proteins such as ezrin, moesin, radixin, 4.1R, and merlin. These proteins provide a link between the membrane and cytoskeleton and are involved in signal transduction pathways. The FERM_C domain is also found in protein tyrosine phosphatases (PTPs) , the tryosine kinases FAKand JAK, in addition to other proteins involved in signaling. This domain is structuraly similar to the PH and PTB domains and consequently is capable of binding to both peptides and phospholipids at different sites.
• Changed! smart B41 157aa 1e-40 in ref transcript
  • Band 4.1 homologues. Also known as ezrin/radixin/moesin (ERM) protein domains. Present in myosins, ezrin, radixin, moesin, protein tyrosine phosphatases. Plasma membrane-binding domain. These proteins play structural and regulatory roles in the assembly and stabilization of specialized plasmamembrane domains. Some PDZ domain containing proteins bind one or more of this family. Now includes JAKs.
• pfam 4_1_CTD 115aa 3e-26 in ref transcript
  • 4.1 protein C-terminal domain (CTD). At the C-terminus of all known 4.1 proteins is a sequence domain unique to these proteins, known as the C-terminal domain (CTD). Mammalian CTDs are associated with a growing number of protein-protein interactions, although such activities have yet to be associated with invertebrate CTDs. Mammalian CTDs are generally defined by sequence alignment as encoded by exons 18-21. Comparison of known vertebrate 4.1 proteins with invertebrate 4.1 proteins indicates that mammalian 4.1 exon 19 represents a vertebrate adaptation that extends the sequence of the CTD with a Ser/Thr-rich sequence. The CTD was first described as a 22/24-kDa domain by chymotryptic digestion of erythrocyte 4.1 (4.1R). CTD is thought to represent an independent folding structure which has gained function since the divergence of vertebrates from invertebrates.
• pfam FERM_C 85aa 2e-20 in ref transcript
  • FERM C-terminal PH-like domain.
• pfam SAB 47aa 5e-14 in ref transcript
  • SAB domain. This presumed domain is found in proteins containing FERM domains pfam00373. This domain is found to bind to both spectrin and actin, hence the name SAB (Spectrin and Actin Binding) domain.
• pfam FA 45aa 5e-13 in ref transcript
  • FERM adjacent (FA). This region is found adjacent to Band 4.1 / FERM domains (pfam00373) in a subset of FERM containing protein. The region has been hypothesised to play a role in regulatory adaptation, based on similarity to other protein kinase substrates.
• Changed! smart B41 192aa 2e-55 in modified transcript

EPB41

• refseq_EPB41.F5 refseq_EPB41.R5 96 113
• NCBIGene 36.3 2035
• Alternative 3-prime, size difference: 17
• Exclusion of the protein initiation site
• Reference transcript: NM_203343

• cd FERM_C 94aa 1e-32 in ref transcript
  • The FERM_C domain is the third structural domain within the FERM domain. The FERM domain is found in the cytoskeletal-associated proteins such as ezrin, moesin, radixin, 4.1R, and merlin. These proteins provide a link between the membrane and cytoskeleton and are involved in signal transduction pathways. The FERM_C domain is also found in protein tyrosine phosphatases (PTPs) , the tryosine kinases FAKand JAK, in addition to other proteins involved in signaling. This domain is structuraly similar to the PH and PTB domains and consequently is capable of binding to both peptides and phospholipids at different sites.
• smart B41 157aa 1e-40 in ref transcript
  • Band 4.1 homologues. Also known as ezrin/radixin/moesin (ERM) protein domains. Present in myosins, ezrin, radixin, moesin, protein tyrosine phosphatases. Plasma membrane-binding domain. These proteins play structural and regulatory roles in the assembly and stabilization of specialized plasmamembrane domains. Some PDZ domain containing proteins bind one or more of this family. Now includes JAKs.
• pfam 4_1_CTD 115aa 3e-26 in ref transcript
  • 4.1 protein C-terminal domain (CTD). At the C-terminus of all known 4.1 proteins is a sequence domain unique to these proteins, known as the C-terminal domain (CTD). Mammalian CTDs are associated with a growing number of protein-protein interactions, although such activities have yet to be associated with invertebrate CTDs. Mammalian CTDs are generally defined by sequence alignment as encoded by exons 18-21. Comparison of known vertebrate 4.1 proteins with invertebrate 4.1 proteins indicates that mammalian 4.1 exon 19 represents a vertebrate adaptation that extends the sequence of the CTD with a Ser/Thr-rich sequence. The CTD was first described as a 22/24-kDa domain by chymotryptic digestion of erythrocyte 4.1 (4.1R). CTD is thought to represent an independent folding structure which has gained function since the divergence of vertebrates from invertebrates.
• pfam FERM_C 85aa 2e-20 in ref transcript
  • FERM C-terminal PH-like domain.
• pfam SAB 47aa 5e-14 in ref transcript
  • SAB domain. This presumed domain is found in proteins containing FERM domains pfam00373. This domain is found to bind to both spectrin and actin, hence the name SAB (Spectrin and Actin Binding) domain.
• pfam FA 45aa 5e-13 in ref transcript
  • FERM adjacent (FA). This region is found adjacent to Band 4.1 / FERM domains (pfam00373) in a subset of FERM containing protein. The region has been hypothesised to play a role in regulatory adaptation, based on similarity to other protein kinase substrates.

EPB41L1

• refseq_EPB41L1.F2 refseq_EPB41L1.R2 186 222
• NCBIGene 36.3 2036
• Single exon skipping, size difference: 36
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_012156

• cd FERM_C 94aa 1e-31 in ref transcript
  • The FERM_C domain is the third structural domain within the FERM domain. The FERM domain is found in the cytoskeletal-associated proteins such as ezrin, moesin, radixin, 4.1R, and merlin. These proteins provide a link between the membrane and cytoskeleton and are involved in signal transduction pathways. The FERM_C domain is also found in protein tyrosine phosphatases (PTPs) , the tryosine kinases FAKand JAK, in addition to other proteins involved in signaling. This domain is structuraly similar to the PH and PTB domains and consequently is capable of binding to both peptides and phospholipids at different sites.
• smart B41 190aa 1e-54 in ref transcript
  • Band 4.1 homologues. Also known as ezrin/radixin/moesin (ERM) protein domains. Present in myosins, ezrin, radixin, moesin, protein tyrosine phosphatases. Plasma membrane-binding domain. These proteins play structural and regulatory roles in the assembly and stabilization of specialized plasmamembrane domains. Some PDZ domain containing proteins bind one or more of this family. Now includes JAKs.
• pfam 4_1_CTD 93aa 1e-24 in ref transcript
  • 4.1 protein C-terminal domain (CTD). At the C-terminus of all known 4.1 proteins is a sequence domain unique to these proteins, known as the C-terminal domain (CTD). Mammalian CTDs are associated with a growing number of protein-protein interactions, although such activities have yet to be associated with invertebrate CTDs. Mammalian CTDs are generally defined by sequence alignment as encoded by exons 18-21. Comparison of known vertebrate 4.1 proteins with invertebrate 4.1 proteins indicates that mammalian 4.1 exon 19 represents a vertebrate adaptation that extends the sequence of the CTD with a Ser/Thr-rich sequence. The CTD was first described as a 22/24-kDa domain by chymotryptic digestion of erythrocyte 4.1 (4.1R). CTD is thought to represent an independent folding structure which has gained function since the divergence of vertebrates from invertebrates.
• pfam FERM_C 89aa 1e-22 in ref transcript
  • FERM C-terminal PH-like domain.
• pfam FA 47aa 9e-13 in ref transcript
  • FERM adjacent (FA). This region is found adjacent to Band 4.1 / FERM domains (pfam00373) in a subset of FERM containing protein. The region has been hypothesised to play a role in regulatory adaptation, based on similarity to other protein kinase substrates.
• Changed! pfam SAB 44aa 4e-09 in ref transcript
  • SAB domain. This presumed domain is found in proteins containing FERM domains pfam00373. This domain is found to bind to both spectrin and actin, hence the name SAB (Spectrin and Actin Binding) domain.
• Changed! pfam SAB 43aa 2e-08 in modified transcript

EPB41L1

• refseq_EPB41L1.F3 refseq_EPB41L1.R3 117 201
• NCBIGene 36.3 2036
• Single exon skipping, size difference: 84
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_012156

• cd FERM_C 94aa 1e-31 in ref transcript
  • The FERM_C domain is the third structural domain within the FERM domain. The FERM domain is found in the cytoskeletal-associated proteins such as ezrin, moesin, radixin, 4.1R, and merlin. These proteins provide a link between the membrane and cytoskeleton and are involved in signal transduction pathways. The FERM_C domain is also found in protein tyrosine phosphatases (PTPs) , the tryosine kinases FAKand JAK, in addition to other proteins involved in signaling. This domain is structuraly similar to the PH and PTB domains and consequently is capable of binding to both peptides and phospholipids at different sites.
• smart B41 190aa 1e-54 in ref transcript
  • Band 4.1 homologues. Also known as ezrin/radixin/moesin (ERM) protein domains. Present in myosins, ezrin, radixin, moesin, protein tyrosine phosphatases. Plasma membrane-binding domain. These proteins play structural and regulatory roles in the assembly and stabilization of specialized plasmamembrane domains. Some PDZ domain containing proteins bind one or more of this family. Now includes JAKs.
• pfam 4_1_CTD 93aa 1e-24 in ref transcript
  • 4.1 protein C-terminal domain (CTD). At the C-terminus of all known 4.1 proteins is a sequence domain unique to these proteins, known as the C-terminal domain (CTD). Mammalian CTDs are associated with a growing number of protein-protein interactions, although such activities have yet to be associated with invertebrate CTDs. Mammalian CTDs are generally defined by sequence alignment as encoded by exons 18-21. Comparison of known vertebrate 4.1 proteins with invertebrate 4.1 proteins indicates that mammalian 4.1 exon 19 represents a vertebrate adaptation that extends the sequence of the CTD with a Ser/Thr-rich sequence. The CTD was first described as a 22/24-kDa domain by chymotryptic digestion of erythrocyte 4.1 (4.1R). CTD is thought to represent an independent folding structure which has gained function since the divergence of vertebrates from invertebrates.
• pfam FERM_C 89aa 1e-22 in ref transcript
  • FERM C-terminal PH-like domain.
• pfam FA 47aa 9e-13 in ref transcript
  • FERM adjacent (FA). This region is found adjacent to Band 4.1 / FERM domains (pfam00373) in a subset of FERM containing protein. The region has been hypothesised to play a role in regulatory adaptation, based on similarity to other protein kinase substrates.
• pfam SAB 44aa 4e-09 in ref transcript
  • SAB domain. This presumed domain is found in proteins containing FERM domains pfam00373. This domain is found to bind to both spectrin and actin, hence the name SAB (Spectrin and Actin Binding) domain.

EPHA5

• refseq_EPHA5.F1 refseq_EPHA5.R1 187 253
• NCBIGene 36.3 2044
• Single exon skipping, size difference: 66
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_004439

• cd PTKc_EphR_A 267aa 1e-169 in ref transcript
  • Catalytic Domain of the Protein Tyrosine Kinases, Class EphA Ephrin Receptors. Protein Tyrosine Kinase (PTK) family; Ephrin Receptor (EphR) subfamily; most class EphA receptors including EphA3, EphA4, EphA5, and EphA7, but excluding EphA1, EphA2 and EphA10; catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. EphRs comprise the largest subfamily of receptor tyr kinases (RTKs). In general, class EphA receptors bind GPI-anchored ephrin-A ligands. There are ten vertebrate EphA receptors (EphA1-10), which display promiscuous interactions with six ephrin-A ligands. One exception is EphA4, which also binds ephrins-B2/B3. EphRs contain an ephrin-binding domain and two fibronectin repeats extracellularly, a transmembrane segment, and a cytoplasmic tyr kinase domain. Binding of the ephrin ligand to EphR requires cell-cell contact since both are anchored to the plasma membrane. The resulting downstream signals occur bidirectionally in both EphR-expressing cells (forward signaling) and ephrin-expressing cells (reverse signaling). Ephrin/EphR interaction mainly results in cell-cell repulsion or adhesion, making it important in neural development and plasticity, cell morphogenesis, cell-fate determination, embryonic development, tissue patterning, and angiogenesis. EphARs and ephrin-A ligands are expressed in multiple areas of the developing brain, especially in the retina and tectum. They are part of a system controlling retinotectal mapping.
• cd SAM 60aa 7e-16 in ref transcript
  • Sterile alpha motif.; Widespread domain in signalling and nuclear proteins. In EPH-related tyrosine kinases, appears to mediate cell-cell initiated signal transduction via the binding of SH2-containing proteins to a conserved tyrosine that is phosphorylated. In many cases mediates homodimerization.
• cd FN3 91aa 9e-14 in ref transcript
  • Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.
• cd FN3 95aa 3e-05 in ref transcript
• pfam Pkinase_Tyr 258aa 1e-114 in ref transcript
  • Protein tyrosine kinase.
• pfam Ephrin_lbd 173aa 6e-97 in ref transcript
  • Ephrin receptor ligand binding domain. The Eph receptors, which bind to ephrins pfam00812 are a large family of receptor tyrosine kinases. This family represents the amino terminal domain which binds the ephrin ligand.
• pfam SAM_1 61aa 6e-19 in ref transcript
  • SAM domain (Sterile alpha motif). It has been suggested that SAM is an evolutionarily conserved protein binding domain that is involved in the regulation of numerous developmental processes in diverse eukaryotes. The SAM domain can potentially function as a protein interaction module through its ability to homo- and heterooligomerise with other SAM domains.
• smart FN3 81aa 1e-12 in ref transcript
  • Fibronectin type 3 domain. One of three types of internal repeat within the plasma protein, fibronectin. The tenth fibronectin type III repeat contains a RGD cell recognition sequence in a flexible loop between 2 strands. Type III modules are present in both extracellular and intracellular proteins.
• pfam fn3 90aa 2e-07 in ref transcript
  • Fibronectin type III domain.
• COG SPS1 295aa 3e-23 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].

EPN2

• refseq_EPN2.F1 refseq_EPN2.R1 213 384
• NCBIGene 36.3 22905
• Single exon skipping, size difference: 171
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_014964

• cd ENTH_epsin 123aa 2e-61 in ref transcript
  • ENTH domain, Epsin family; The epsin (Eps15 interactor) N-terminal homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to as an AP180 N-terminal homology (ANTH) domain. ENTH and ANTH (E/ANTH) domains are structurally similar to the VHS domain and are composed of a superhelix of eight alpha helices. E/ANTH domains bind both inositol phospholipids and proteins and contribute to the nucleation and formation of clathrin coats on membranes. ENTH domains also function in the development of membrane curvature through lipid remodeling during the formation of clathrin-coated vesicles. E/ANTH-bearing proteins have recently been shown to function with adaptor protein-1 and GGA adaptors at the trans-Golgi network, which suggests that E/ANTH domains are universal components of the machinery for clathrin-mediated membrane budding.
• pfam ENTH 124aa 1e-62 in ref transcript
  • ENTH domain. The ENTH (Epsin N-terminal homology) domain is found in proteins involved in endocytosis and cytoskeletal machinery. The function of the ENTH domain is unknown.

EPS8L3

• refseq_EPS8L3.F1 refseq_EPS8L3.R1 129 219
• NCBIGene 36.3 79574
• Alternative 3-prime, size difference: 90
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_139053

• cd EPS8 126aa 4e-46 in ref transcript
  • Epidermal growth factor receptor kinase substrate (EPS8) Phosphotyrosine-binding (PTB) domain. EPS8 is a regulator of Rac signaling. It consists of a PTB and an SH3 domain. PTB domains have a PH-like fold and are found in various eukaryotic signaling molecules. They were initially identified based upon their ability to recognize phosphorylated tyrosine residues. In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. More recent studies have found that some types of PTB domains can bind to peptides which are not tyrosine phosphorylated or lack tyrosine residues altogether.
• cd SH3 53aa 1e-09 in ref transcript
  • Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
• pfam PTB 120aa 2e-37 in ref transcript
  • Phosphotyrosine-binding domain. The phosphotyrosine-binding domain (PTB, also phosphotyrosine-interaction or PI domain) in the protein tensin tends to be found at the C-terminus. Tensin is a multi-domain protein that binds to actin filaments and functions as a focal-adhesion molecule (focal adhesions are regions of plasma membrane through which cells attach to the extracellular matrix). Human tensin has actin-binding sites, an SH2 (pfam00017) domain and a region similar to the tumour suppressor PTEN. The PTB domain interacts with the cytoplasmic tails of beta integrin by binding to an NPXY motif.
• smart SH3 57aa 3e-11 in ref transcript
  • Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.

EPSTI1

• refseq_EPSTI1.F2 refseq_EPSTI1.R2 164 196
• NCBIGene 36.3 94240
• Single exon skipping, size difference: 32
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_001002264

ERBB2IP

• refseq_ERBB2IP.F1 refseq_ERBB2IP.R1 178 385
• NCBIGene 36.3 55914
• Single exon skipping, size difference: 207
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_018695

• cd PDZ_signaling 60aa 3e-09 in ref transcript
  • PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of PDZ domains an N-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in proteases.
• cd LRR_RI 162aa 2e-04 in ref transcript
  • Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1).
• Changed! smart PDZ 90aa 4e-10 in ref transcript
  • Domain present in PSD-95, Dlg, and ZO-1/2. Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities.
• COG COG4886 348aa 3e-18 in ref transcript
  • Leucine-rich repeat (LRR) protein [Function unknown].
• COG Prc 60aa 4e-04 in ref transcript
  • Periplasmic protease [Cell envelope biogenesis, outer membrane].
• Changed! smart PDZ 90aa 6e-10 in modified transcript

ERG

• refseq_ERG.F1 refseq_ERG.R1 100 172
• NCBIGene 36.3 2078
• Single exon skipping, size difference: 72
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_182918

• pfam Ets 84aa 1e-36 in ref transcript
  • Ets-domain.
• smart SAM_PNT 83aa 1e-23 in ref transcript
  • SAM / Pointed domain. A subfamily of the SAM domain.

ERP29

• refseq_ERP29.F1 refseq_ERP29.R1 187 326
• NCBIGene 36.3 10961
• Single exon skipping, size difference: 139
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_006817

• Changed! cd PDI_a_ERp29_N 114aa 3e-46 in ref transcript
  • PDIa family, endoplasmic reticulum protein 29 (ERp29) subfamily; ERp29 is a ubiquitous ER-resident protein expressed in high levels in secretory cells. It forms homodimers and higher oligomers in vitro and in vivo. It contains a redox inactive TRX-like domain at the N-terminus, which is homologous to the redox active TRX (a) domains of PDI, and a C-terminal helical domain similar to the C-terminal domain of P5. The expression profile of ERp29 suggests a role in secretory protein production distinct from that of PDI. It has also been identified as a member of the thyroglobulin folding complex. The Drosophila homolog, Wind, is the product of windbeutel, an essential gene in the development of dorsal-ventral patterning. Wind is required for correct targeting of Pipe, a Golgi-resident type II transmembrane protein with homology to 2-O-sulfotransferase.
• Changed! cd ERp29c 94aa 3e-20 in ref transcript
  • ERp29 and ERp38, C-terminal domain; composed of the protein disulfide isomerase (PDI)-like proteins ERp29 and ERp38. ERp29 (also called ERp28) is a ubiquitous endoplasmic reticulum (ER)-resident protein expressed in high levels in secretory cells. It contains a redox inactive TRX-like domain at the N-terminus. The expression profile of ERp29 suggests a role in secretory protein production, distinct from that of PDI. It has also been identified as a member of the thyroglobulin folding complex and is essential in regulating the secretion of thyroglobulin. The Drosophila homolog, Wind, is the product of windbeutel, an essential gene in the development of dorsal-ventral patterning. Wind is required for correct targeting of Pipe, a Golgi-resident type II transmembrane protein with homology to 2-O-sulfotransferase. ERp38 is a P5-like protein, first isolated from alfalfa (the cDNA clone was named G1), which contains two redox active TRX domains at the N-terminus, like human P5. However, unlike human P5, ERp38 also contains a C-terminal domain with homology to the C-terminal domain of ERp29. It may be a glucose-regulated protein. The function of the all-helical C-terminal domain of ERp29 and ERp38 remains unclear. The C-terminal domain of Wind is thought to provide a distinct site required for interaction with its substrate, Pipe.
• Changed! pfam ERp29_N 123aa 1e-48 in ref transcript
  • ERp29, N-terminal domain. ERp29 is a ubiquitously expressed endoplasmic reticulum protein, and is involved in the processes of protein maturation and protein secretion in this organelle. The protein exists as a homodimer, with each monomer being composed of two domains. The N-terminal domain featured in this family is organised into a thioredoxin-like fold that resembles the a domain of human protein disulphide isomerase (PDI). However, this domain lacks the C-X-X-C motif required for the redox function of PDI; it is therefore thought that ERp29's function is similar to the chaperone function of PDI. The N-terminal domain is exclusively responsible for the homodimerisation of the protein, without covalent linkages or additional contacts with other domains.
• Changed! pfam ERp29 97aa 3e-23 in ref transcript
  • Endoplasmic reticulum protein ERp29, C-terminal domain. ERp29 is a ubiquitously expressed endoplasmic reticulum protein found in mammals. ERp29 is comprised of two domains. This domain, the C-terminal domain, has an all helical fold. ERp29 is thought to form part of the thyroglobulin folding complex.

ESRRG

• refseq_ESRRG.F1 refseq_ESRRG.R1 218 336
• NCBIGene 36.3 2104
• Single exon skipping, size difference: 118
• Exclusion in 5'UTR
• Reference transcript: NM_206594

• cd NR_LBD_ERR 220aa 1e-111 in ref transcript
  • The ligand binding domain of estrogen receptor-related nuclear receptors. The ligand binding domain of estrogen receptor-related receptors (ERRs): The family of estrogen receptor-related receptors (ERRs), a subfamily of nuclear receptors, is closely related to the estrogen receptor (ER) family, but it lacks the ability to bind estrogen. ERRs can interfere with the classic ER-mediated estrogen signaling pathway, positively or negatively. ERRs share target genes, co-regulators and promoters with the estrogen receptor (ER) family. There are three subtypes of ERRs: alpha, beta and gamma. ERRs bind at least two types of DNA sequence, the estrogen response element and another site, originally characterized as SF-1 (steroidogenic factor 1) response element. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, ERR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
• pfam Hormone_recep 181aa 2e-42 in ref transcript
  • Ligand-binding domain of nuclear hormone receptor. This all helical domain is involved in binding the hormone in these receptors.
• pfam zf-C4 76aa 9e-37 in ref transcript
  • Zinc finger, C4 type (two domains). In nearly all cases, this is the DNA binding domain of a nuclear hormone receptor. The alignment contains two Zinc finger domains that are too dissimilar to be aligned with each other.

EVI2A

• refseq_EVI2A.F2 refseq_EVI2A.R2 144 285
• NCBIGene 36.3 2123
• Single exon skipping, size difference: 141
• Exclusion of the protein initiation site
• Reference transcript: NM_001003927

• pfam EVI2A 227aa 1e-104 in ref transcript
  • Ectropic viral integration site 2A protein (EVI2A). This family contains several mammalian ectropic viral integration site 2A (EVI2A) proteins. The function of this protein is unknown although it is thought to be a membrane protein and may function as an oncogene in retrovirus induced myeloid tumours.

EWSR1

• refseq_EWSR1.F1 refseq_EWSR1.R1 174 393
• NCBIGene 36.3 2130
• Multiple exon skipping, size difference: 219
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_005243

• cd RRM 82aa 3e-13 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• smart RRM_2 81aa 1e-14 in ref transcript
  • RNA recognition motif.
• pfam zf-RanBP 31aa 2e-07 in ref transcript
  • Zn-finger in Ran binding protein and others.
• COG COG0724 93aa 2e-07 in ref transcript
  • RNA-binding proteins (RRM domain) [General function prediction only].

EXO1

• refseq_EXO1.F1 refseq_EXO1.R1 290 395
• NCBIGene 36.3 9156
• Single exon skipping, size difference: 105
• Exclusion in 5'UTR
• Reference transcript: NM_130398

• cd XPG 308aa 1e-73 in ref transcript
  • Xeroderma pigmentosum G N- and I-regions (XPGN, XPGI); contains the HhH2 motif; domain in nucleases. XPG is a eukaryotic enzyme that functions in nucleotide-excision repair and transcription-coupled repair of oxidative DNA damage. Functionally/structurally related to FEN-1; divalent metal ion-dependent exo- and endonuclease, and bacterial and bacteriophage 5'3' exonucleases.
• smart XPGN 83aa 1e-24 in ref transcript
  • Xeroderma pigmentosum G N-region. domain in nucleases.
• pfam XPG_I 92aa 1e-23 in ref transcript
  • XPG I-region.
• TIGR fen_arch 308aa 7e-17 in ref transcript
  • Endonuclease that cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA.
• PTZ PTZ00217 290aa 2e-27 in ref transcript
  • flap endonuclease-1; Provisional.

EXOC1

• refseq_EXOC1.F2 refseq_EXOC1.R2 161 317
• NCBIGene 36.3 55763
• Alternative 5-prime, size difference: 156
• Exclusion in 5'UTR
• Reference transcript: NM_001024924

• pfam Sec3 703aa 0.0 in ref transcript
  • Exocyst complex component Sec3. This entry is the conserved middle and C-terminus of the Sec3 protein. Sec3 binds to the C-terminal cytoplasmic domain of GLYT1 (glycine transporter protein 1). Sec3 is the exocyst component that is closest to the plasma membrane docking site and it serves as a spatial landmark in the plasma membrane for incoming secretory vesicles. Sec3 is recruited to the sites of polarised membrane growth through its interaction with Rho1p, a small GTP-binding protein.

EXOC7

• refseq_EXOC7.F2 refseq_EXOC7.R2 198 291
• NCBIGene 36.3 23265
• Single exon skipping, size difference: 93
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001013839

• pfam Exo70 367aa 2e-74 in ref transcript
  • Exo70 exocyst complex subunit. The Exo70 protein forms one subunit of the exocyst complex. First discovered in Saccharomyces cerevisiae, Exo70 and other exocyst proteins have been observed in several other eukaryotes, including humans. In Saccharomyces cerevisiae, the exocyst complex is involved in the late stages of exocytosis, and is localised at the tip of the bud, the major site of exocytosis in yeast. Exo70 interacts with the Rho3 GTPase. This interaction mediates one of the three known functions of Rho3 in cell polarity: vesicle docking and fusion with the plasma membrane (the other two functions are regulation of actin polarity and transport of exocytic vesicles from the mother cell to the bud). In humans, the functions of Exo70 and the exocyst complex are less well characterised: Exo70 is expressed in several tissues and is thought to also be involved in exocytosis.

EXOSC10

• refseq_EXOSC10.F1 refseq_EXOSC10.R1 159 234
• NCBIGene 36.3 5394
• Single exon skipping, size difference: 75
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001001998

• cd Rrp6p_like_exo 191aa 1e-108 in ref transcript
  • Yeast Rrp6p and its human homolog, the Polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100), are exosome-associated proteins involved in the degradation and processing of precursors to stable RNAs. Both proteins contain a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. The motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. PM/Scl-100, an autoantigen present in the nucleolar compartment of the cell, reacts with autoantibodies produced by about 50% of patients with polymyositis-scleroderma overlap syndrome.
• pfam 3_5_exonuc 169aa 8e-54 in ref transcript
  • 3'-5' exonuclease. This domain is responsible for the 3'-5' exonuclease proofreading activity of Escherichia coli DNA polymerase I (polI) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in Escherichia coli polI it is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D). Werner syndrome is a human genetic disorder causing premature aging; the WRN protein has helicase activity in the 3'-5' direction. The FFA-1 protein is required for formation of a replication foci and also has helicase activity; it is a homologue of the WRN protein. RNase D is a 3'-5' exonuclease involved in tRNA processing. Also found in this family is the autoantigen PM/Scl thought to be involved in polymyositis-scleroderma overlap syndrome.
• pfam PMC2NT 92aa 1e-26 in ref transcript
  • PMC2NT (NUC016) domain. This domain is found at the N-terminus of 3'-5' exonucleases with HRDC domains, and also in putative exosome components.
• smart HRDC 81aa 5e-18 in ref transcript
  • Helicase and RNase D C-terminal. Hypothetical role in nucleic acid binding. Mutations in the HRDC domain cause human disease.
• COG Rnd 290aa 5e-49 in ref transcript
  • Ribonuclease D [Translation, ribosomal structure and biogenesis].

EXOSC3

• refseq_EXOSC3.F1 refseq_EXOSC3.R1 226 378
• NCBIGene 36.3 51010
• Single exon skipping, size difference: 152
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_016042

• Changed! cd S1_Rrp40 86aa 3e-38 in ref transcript
  • S1_Rrp40: Rrp40 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
• Changed! COG RRP4 207aa 2e-24 in ref transcript
  • RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis].
• Changed! cd S1_Rrp40 52aa 1e-20 in modified transcript
• Changed! COG RRP4 91aa 1e-07 in modified transcript

EXOSC9

• refseq_EXOSC9.F1 refseq_EXOSC9.R1 208 259
• NCBIGene 36.3 5393
• Single exon skipping, size difference: 51
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001034194

• pfam RNase_PH 133aa 9e-10 in ref transcript
  • 3' exoribonuclease family, domain 1. This family includes 3'-5' exoribonucleases. Ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain. PNPase is involved in mRNA degradation in a 3'-5' direction. The exosome is a 3'-5' exoribonuclease complex that is required for 3' processing of the 5.8S rRNA. Three of its five protein components contain a copy of this domain. A hypothetical protein from S. pombe appears to belong to an uncharacterised subfamily. This subfamily is found in both eukaryotes and archaebacteria.
• pfam RNase_PH_C 66aa 0.002 in ref transcript
  • 3' exoribonuclease family, domain 2. This family includes 3'-5' exoribonucleases. Ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain. PNPase is involved in mRNA degradation in a 3'-5' direction. The exosome is a 3'-5' exoribonuclease complex that is required for 3' processing of the 5.8S rRNA. Three of its five protein components contain a copy of this domain. A hypothetical protein from S. pombe appears to belong to an uncharacterised subfamily. This subfamily is found in both eukaryotes and archaebacteria.
• COG COG2123 271aa 1e-55 in ref transcript
  • RNase PH-related exoribonuclease [Translation, ribosomal structure and biogenesis].

EXT2

• refseq_EXT2.F1 refseq_EXT2.R1 143 296
• NCBIGene 36.3 2132
• Multiple exon skipping, size difference: 153
• Exclusion in 5'UTR, Exclusion of the protein initiation site
• Reference transcript: NM_000401

• pfam Glyco_transf_64 246aa 1e-101 in ref transcript
  • Glycosyl transferase family 64 domain. Members of this family catalyse the transfer reaction of N-acetylglucosamine and N-acetylgalactosamine from the respective UDP-sugars to the non-reducing end of [glucuronic acid]beta 1-3[galactose]beta 1-O-naphthalenemethanol, an acceptor substrate analog of the natural common linker of various glycosylaminoglycans. They are also required for the biosynthesis of heparan-sulphate.
• pfam Exostosin 281aa 5e-54 in ref transcript
  • Exostosin family. The EXT family is a family of tumour suppressor genes. Mutations of EXT1 on 8q24.1, EXT2 on 11p11-13, and EXT3 on 19p have been associated with the autosomal dominant disorder known as hereditary multiple exostoses (HME). This is the most common known skeletal dysplasia. The chromosomal locations of other EXT genes suggest association with other forms of neoplasia. EXT1 and EXT2 have both been shown to encode a heparan sulphate polymerase with both D-glucuronyl (GlcA) and N-acetyl-D-glucosaminoglycan (GlcNAC) transferase activities. The nature of the defect in heparan sulphate biosynthesis in HME is unclear.

EXTL2

• refseq_EXTL2.F2 refseq_EXTL2.R2 183 219
• NCBIGene 36.3 2135
• Alternative 3-prime, size difference: 36
• Inclusion in 5'UTR
• Reference transcript: NM_001033025

• pfam Glyco_transf_64 256aa 3e-86 in ref transcript
  • Glycosyl transferase family 64 domain. Members of this family catalyse the transfer reaction of N-acetylglucosamine and N-acetylgalactosamine from the respective UDP-sugars to the non-reducing end of [glucuronic acid]beta 1-3[galactose]beta 1-O-naphthalenemethanol, an acceptor substrate analog of the natural common linker of various glycosylaminoglycans. They are also required for the biosynthesis of heparan-sulphate.

EYA1

• refseq_EYA1.F2 refseq_EYA1.R2 187 277
• NCBIGene 36.3 2138
• Single exon skipping, size difference: 90
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000503

• Changed! TIGR EYA-cons_domain 271aa 1e-126 in ref transcript
  • This domain is common to all eyes absent (EYA) homologs. Metazoan EYA's also contain a variable N-terminal domain consisting largely of low-complexity sequences.
• Changed! TIGR EYA-cons_domain 241aa 1e-107 in modified transcript

EYA1

• refseq_EYA1.F4 refseq_EYA1.R4 171 299
• NCBIGene 36.3 2138
• Single exon skipping, size difference: 128
• Exclusion of the protein initiation site
• Reference transcript: NM_172058

• TIGR EYA-cons_domain 271aa 1e-126 in ref transcript
  • This domain is common to all eyes absent (EYA) homologs. Metazoan EYA's also contain a variable N-terminal domain consisting largely of low-complexity sequences.

EYA4

• refseq_EYA4.F1 refseq_EYA4.R1 113 182
• NCBIGene 36.3 2070
• Single exon skipping, size difference: 69
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_172105

• TIGR EYA-cons_domain 272aa 1e-129 in ref transcript
  • This domain is common to all eyes absent (EYA) homologs. Metazoan EYA's also contain a variable N-terminal domain consisting largely of low-complexity sequences.

EZH2

• refseq_EZH2.F1 refseq_EZH2.R1 156 273
• NCBIGene 36.3 2146
• Single exon skipping, size difference: 117
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_004456

• pfam SET 124aa 3e-36 in ref transcript
  • SET domain. SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure.
• Changed! COG COG2940 208aa 4e-15 in ref transcript
  • Proteins containing SET domain [General function prediction only].
• Changed! COG COG2940 180aa 7e-15 in modified transcript

F11

• refseq_F11.F1 refseq_F11.R1 141 301
• NCBIGene 36.2 2160
• Single exon skipping, size difference: 160
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_000128

• Changed! cd Tryp_SPc 231aa 4e-76 in ref transcript
  • Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
• Changed! cd APPLE_Factor_XI_like 84aa 3e-09 in ref transcript
  • Subfamily of PAN/APPLE-like domains; present in plasma prekallikrein/coagulation factor XI, microneme antigen proteins, and a few prokaryotic proteins. PAN/APPLE domains fulfill diverse biological functions by mediating protein-protein or protein-carbohydrate interactions.
• cd APPLE_Factor_XI_like 85aa 4e-09 in ref transcript
• Changed! cd APPLE_Factor_XI_like 85aa 9e-09 in ref transcript
• Changed! cd APPLE_Factor_XI_like 85aa 2e-08 in ref transcript
• Changed! smart Tryp_SPc 232aa 3e-81 in ref transcript
  • Trypsin-like serine protease. Many of these are synthesised as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. A few, however, are active as single chain molecules, and others are inactive due to substitutions of the catalytic triad residues.
• Changed! smart APPLE 84aa 7e-25 in ref transcript
  • APPLE domain. Four-fold repeat in plasma kallikrein and coagulation factor XI. Factor XI apple 3 mediates binding to platelets. Factor XI apple 1 binds high-molecular-mass kininogen. Apple 4 in factor XI mediates dimer formation and binds to factor XIIa. Mutations in apple 4 cause factor XI deficiency, an inherited bleeding disorder.
• smart APPLE 84aa 1e-23 in ref transcript
• Changed! smart APPLE 84aa 6e-23 in ref transcript
• Changed! smart APPLE 84aa 4e-22 in ref transcript
• Changed! COG COG5640 239aa 4e-29 in ref transcript
  • Secreted trypsin-like serine protease [Posttranslational modification, protein turnover, chaperones].

F11R

• refseq_F11R.F1 refseq_F11R.R1 102 162
• NCBIGene 36.2 50848
• Alternative 5-prime and 3-prime, size difference: 60
• Exclusion in the protein (no frameshift), Exclusion in the protein (no frameshift)
• Reference transcript: NM_144503

• cd IGcam 83aa 1e-09 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• Changed! cd IGcam 91aa 2e-05 in ref transcript
• Changed! smart IG_like 90aa 2e-11 in ref transcript
  • Immunoglobulin like. IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
• smart IG_like 79aa 3e-07 in ref transcript
• Changed! cd IGcam 84aa 4e-05 in modified transcript
• Changed! smart IG_like 84aa 2e-11 in modified transcript

F11R

• refseq_F11R.F1 refseq_F11R.R4 159 279
• NCBIGene 36.2 50848
• Alternative 5-prime and 3-prime, size difference: 60
• Inclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_144503

• cd IGcam 83aa 1e-09 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• Changed! cd IGcam 91aa 2e-05 in ref transcript
• Changed! smart IG_like 90aa 2e-11 in ref transcript
  • Immunoglobulin like. IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
• smart IG_like 79aa 3e-07 in ref transcript
• Changed! cd IGcam 71aa 4e-04 in modified transcript
• Changed! smart IG_like 70aa 3e-07 in modified transcript

F11R

• refseq_F11R.F4 refseq_F11R.R5 143 177
• NCBIGene 36.2 50848
• Alternative 5-prime and 3-prime, size difference: 34
• Inclusion in 5'UTR, Exclusion in 5'UTR
• Reference transcript: NM_144503

• cd IGcam 83aa 1e-09 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• cd IGcam 91aa 2e-05 in ref transcript
• smart IG_like 90aa 2e-11 in ref transcript
  • Immunoglobulin like. IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
• smart IG_like 79aa 3e-07 in ref transcript

F11R

• refseq_F11R.F6 refseq_F11R.R7 115 193
• NCBIGene 36.2 50848
• Single exon skipping, size difference: 78
• Exclusion in 5'UTR
• Reference transcript: NM_144503

• cd IGcam 83aa 1e-09 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• cd IGcam 91aa 2e-05 in ref transcript
• smart IG_like 90aa 2e-11 in ref transcript
  • Immunoglobulin like. IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
• smart IG_like 79aa 3e-07 in ref transcript

BPTF

• refseq_FALZ.F1 refseq_FALZ.R1 100 478
• NCBIGene 36.3 2186
• Multiple exon skipping, size difference: 378
• Inclusion in the protein (no stop codon or frameshift), Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_182641

• cd Bromo_gcn5_like 101aa 1e-46 in ref transcript
  • Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates acetylation of histones at lysine residues; such acetylation is generally correlated with the activation of transcription. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
• cd BAH_plant_2 27aa 8e-04 in ref transcript
  • BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
• smart BROMO 102aa 1e-27 in ref transcript
  • bromo domain.
• pfam DDT 61aa 1e-20 in ref transcript
  • DDT domain. This domain is approximately 60 residues in length, and is predicted to be a DNA binding domain. The DDT domain is named after (DNA binding homeobox and Different Transcription factors). It is exclusively associated with nuclear domains, and is thought to be arranged into three alpha helices.
• pfam PHD 45aa 6e-10 in ref transcript
  • PHD-finger. PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
• smart PHD 47aa 5e-08 in ref transcript
  • PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RI NG finger and the FYV E finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BR OMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RI NG fingers misidentified as PHD fingers.
• COG COG5076 105aa 8e-14 in ref transcript
  • Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription].

FAM111A

• refseq_FAM111A.F1 refseq_FAM111A.R1 122 161
• NCBIGene 36.3 63901
• Alternative 3-prime, size difference: 39
• Inclusion in 5'UTR
• Reference transcript: NM_198847

FAM119B

• refseq_FAM119B.F2 refseq_FAM119B.R2 155 294
• NCBIGene 36.3 25895
• Single exon skipping, size difference: 139
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_015433

• Changed! pfam Methyltransf_16 159aa 5e-35 in ref transcript
  • Putative methyltransferase.
• Changed! COG COG3897 173aa 8e-08 in ref transcript
  • Predicted methyltransferase [General function prediction only].
• Changed! pfam Methyltransf_16 75aa 8e-12 in modified transcript
• Changed! COG COG3897 93aa 2e-05 in modified transcript

FAM13C1

• refseq_FAM13C1.F1 refseq_FAM13C1.R1 106 400
• NCBIGene 36.3 220965
• Multiple exon skipping, size difference: 294
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_198215

FAM14B

• refseq_FAM14B.F1 refseq_FAM14B.R1 174 220
• NCBIGene 36.3 122509
• Alternative 3-prime, size difference: 46
• Inclusion in 5'UTR
• Reference transcript: NM_206949

FAM19A3

• refseq_FAM19A3.F2 refseq_FAM19A3.R2 148 216
• NCBIGene 36.3 284467
• Alternative 3-prime, size difference: 68
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_001004440

FAM19A4

• refseq_FAM19A4.F1 refseq_FAM19A4.R1 266 348
• NCBIGene 36.3 151647
• Alternative 5-prime, size difference: 82
• Exclusion in 5'UTR
• Reference transcript: NM_182522

FAM3B

• refseq_FAM3B.F1 refseq_FAM3B.R1 208 352
• NCBIGene 36.3 54097
• Single exon skipping, size difference: 144
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_058186

FAM3C

• refseq_FAM3C.F1 refseq_FAM3C.R1 174 214
• NCBIGene 36.3 10447
• Alternative 5-prime and 3-prime, size difference: 40
• Inclusion in 5'UTR, Exclusion in 5'UTR
• Reference transcript: NM_014888

FAM48A

• refseq_FAM48A.F2 refseq_FAM48A.R2 111 215
• NCBIGene 36.3 55578
• Single exon skipping, size difference: 104
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_001014286

FAM48A

• refseq_FAM48A.F4 refseq_FAM48A.R4 126 205
• NCBIGene 36.3 55578
• Alternative 5-prime, size difference: 79
• Inclusion in 5'UTR
• Reference transcript: NM_001014286

FAM86A

• refseq_FAM86A.F1 refseq_FAM86A.R1 109 211
• NCBIGene 36.3 196483
• Single exon skipping, size difference: 102
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_201400

• pfam Methyltransf_16 152aa 1e-12 in ref transcript
  • Putative methyltransferase.
• COG COG3897 130aa 6e-04 in ref transcript
  • Predicted methyltransferase [General function prediction only].
• Changed! PRK PRK03910 88aa 0.003 in ref transcript
  • D-cysteine desulfhydrase; Validated.

FAM96A

• refseq_FAM96A.F2 refseq_FAM96A.R2 137 187
• NCBIGene 36.3 84191
• Single exon skipping, size difference: 50
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_032231

• Changed! pfam DUF59 78aa 0.001 in ref transcript
  • Domain of unknown function DUF59. This family includes prokaryotic proteins of unknown function. The family also includes PhaH from Pseudomonas putida. PhaH forms a complex with PhaF, PhaG and PhaI, which hydroxylates phenylacetic acid to 2-hydroxyphenylacetic acid. So members of this family may all be components of ring hydroxylating complexes.
• Changed! COG COG5133 118aa 1e-24 in ref transcript
  • Uncharacterized conserved protein [Function unknown].
• Changed! pfam DUF59 59aa 0.005 in modified transcript
• Changed! COG COG5133 58aa 8e-07 in modified transcript

FANCB

• refseq_FANCB.F2 refseq_FANCB.R2 142 263
• NCBIGene 36.3 2187
• Single exon skipping, size difference: 121
• Exclusion in 5'UTR
• Reference transcript: NM_001018113

FBF1

• refseq_FBF1.F1 refseq_FBF1.R1 163 205
• NCBIGene 36.2 85302
• Single exon skipping, size difference: 42
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: XM_932831

• TIGR SMC_prok_B 283aa 8e-09 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• COG Smc 294aa 1e-07 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].

FBLIM1

• refseq_FBLIM1.F1 refseq_FBLIM1.R1 121 412
• NCBIGene 36.3 54751
• Multiple exon skipping, size difference: 291
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_001024215

• pfam LIM 56aa 2e-10 in ref transcript
  • LIM domain. This family represents two copies of the LIM structural domain.
• pfam LIM 56aa 5e-05 in ref transcript

FBLN2

• refseq_FBLN2.F2 refseq_FBLN2.R2 124 265
• NCBIGene 36.3 2199
• Single exon skipping, size difference: 141
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001004019

• cd ANATO 61aa 2e-05 in ref transcript
  • Anaphylatoxin homologous domain; C3a, C4a and C5a anaphylatoxins are protein fragments generated enzymatically in serum during activation of complement molecules C3, C4, and C5. They induce smooth muscle contraction. These fragments are homologous to repeats in fibulins.
• cd ANATO 40aa 0.003 in ref transcript
• cd vWA_Matrilin 44aa 0.005 in ref transcript
  • VWA_Matrilin: In cartilaginous plate, extracellular matrix molecules mediate cell-matrix and matrix-matrix interactions thereby providing tissue integrity. Some members of the matrilin family are expressed specifically in developing cartilage rudiments. The matrilin family consists of at least four members. All the members of the matrilin family contain VWA domains, EGF-like domains and a heptad repeat coiled-coiled domain at the carboxy terminus which is responsible for the oligomerization of the matrilins. The VWA domains have been shown to be essential for matrilin network formation by interacting with matrix ligands.
• cd EGF_CA 34aa 0.005 in ref transcript
  • Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements.
• pfam EGF_CA 49aa 2e-05 in ref transcript
  • Calcium binding EGF domain.
• smart EGF_CA 43aa 8e-05 in ref transcript
  • Calcium-binding EGF-like domain.
• pfam EGF_CA 45aa 2e-04 in ref transcript
• smart EGF_CA 48aa 3e-04 in ref transcript
• smart EGF_CA 42aa 0.002 in ref transcript
• pfam ANATO 36aa 0.004 in ref transcript
  • Anaphylotoxin-like domain. C3a, C4a and C5a anaphylatoxins are protein fragments generated enzymatically in serum during activation of complement molecules C3, C4, and C5. They induce smooth muscle contraction. These fragments are homologous to a three-fold repeat in fibulins.
• Changed! pfam EGF_CA 43aa 0.005 in ref transcript
• Changed! pfam EGF_CA 43aa 0.005 in modified transcript

FBXL10

• refseq_FBXL10.F1 refseq_FBXL10.R1 193 307
• NCBIGene 36.3 84678
• Single exon skipping, size difference: 114
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_032590

• pfam JmjC 107aa 6e-09 in ref transcript
  • JmjC domain. The JmjC domain belongs to the Cupin superfamily. JmjC-domain proteins may be protein hydroxylases that catalyse a novel histone modification.
• pfam zf-CXXC 31aa 1e-08 in ref transcript
  • CXXC zinc finger domain. This domain contains eight conserved cysteine residues that bind to two zinc ions. The CXXC domain is found in a variety of chromatin-associated proteins. This domain binds to nonmethyl-CpG dinucleotides. The domain is characterised by two CGXCXXC repeats. The RecQ helicase has a single repeat that also binds to zinc, but this has not been included in this family. The DNA binding interface has been identified by NMR.
• smart JmjC 76aa 5e-05 in ref transcript
  • A domain family that is part of the cupin metalloenzyme superfamily. Probable enzymes, but of unknown functions, that regulate chromatin reorganisation processes (Clissold and Ponting, in press).
• pfam F-box 43aa 7e-04 in ref transcript
  • F-box domain. This domain is approximately 50 amino acids long, and is usually found in the N-terminal half of a variety of proteins. Two motifs that are commonly found associated with the F-box domain are the leucine rich repeats (LRRs; pfam00560 and pfam07723) and the WD repeat (pfam00400). The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression.

FBXL5

• refseq_FBXL5.F1 refseq_FBXL5.R1 267 371
• NCBIGene 36.3 26234
• Single exon skipping, size difference: 104
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_012161

• Changed! pfam F-box 45aa 5e-06 in ref transcript
  • F-box domain. This domain is approximately 50 amino acids long, and is usually found in the N-terminal half of a variety of proteins. Two motifs that are commonly found associated with the F-box domain are the leucine rich repeats (LRRs; pfam00560 and pfam07723) and the WD repeat (pfam00400). The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression.
• Changed! smart LRR_CC 25aa 0.005 in ref transcript
  • Leucine-rich repeat - CC (cysteine-containing) subfamily.

FBXL6

• refseq_FBXL6.F1 refseq_FBXL6.R1 100 118
• NCBIGene 36.3 26233
• Alternative 5-prime, size difference: 18
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_012162

FBXO21

• refseq_FBXO21.F1 refseq_FBXO21.R1 119 140
• NCBIGene 36.3 23014
• Alternative 3-prime, size difference: 21
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_033624

• TIGR yccV 98aa 1e-36 in ref transcript
  • This model describes the small protein from E. coli YccV and its homologs in other Proteobacteria. YccV is now described as a hemimethylated DNA binding protein. The model also describes a domain in longer eukaryotic proteins.
• COG COG2912 189aa 9e-18 in ref transcript
  • Uncharacterized conserved protein [Function unknown].
• COG COG3785 96aa 2e-06 in ref transcript
  • Uncharacterized conserved protein [Function unknown].

FBXO24

• refseq_FBXO24.F1 refseq_FBXO24.R1 127 169
• NCBIGene 36.3 26261
• Alternative 5-prime, size difference: 42
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_033506

• pfam F-box 47aa 9e-05 in ref transcript
  • F-box domain. This domain is approximately 50 amino acids long, and is usually found in the N-terminal half of a variety of proteins. Two motifs that are commonly found associated with the F-box domain are the leucine rich repeats (LRRs; pfam00560 and pfam07723) and the WD repeat (pfam00400). The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression.
• COG ATS1 167aa 3e-04 in ref transcript
  • Alpha-tubulin suppressor and related RCC1 domain-containing proteins [Cell division and chromosome partitioning / Cytoskeleton].

FBXO24

• refseq_FBXO24.F3 refseq_FBXO24.R3 225 347
• NCBIGene 36.3 26261
• Single exon skipping, size difference: 122
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_033506

• pfam F-box 47aa 9e-05 in ref transcript
  • F-box domain. This domain is approximately 50 amino acids long, and is usually found in the N-terminal half of a variety of proteins. Two motifs that are commonly found associated with the F-box domain are the leucine rich repeats (LRRs; pfam00560 and pfam07723) and the WD repeat (pfam00400). The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression.
• Changed! COG ATS1 167aa 3e-04 in ref transcript
  • Alpha-tubulin suppressor and related RCC1 domain-containing proteins [Cell division and chromosome partitioning / Cytoskeleton].

FBXO25

• refseq_FBXO25.F1 refseq_FBXO25.R1 142 169
• NCBIGene 36.3 26260
• Single exon skipping, size difference: 27
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_183421

FBXO25

• refseq_FBXO25.F4 refseq_FBXO25.R4 270 320
• NCBIGene 36.3 26260
• Single exon skipping, size difference: 50
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_183421

FBXO38

• refseq_FBXO38.F2 refseq_FBXO38.R2 146 371
• NCBIGene 36.3 81545
• Alternative 5-prime, size difference: 225
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_205836

FBXO44

• refseq_FBXO44.F1 refseq_FBXO44.R1 101 473
• NCBIGene 36.3 93611
• Single exon skipping, size difference: 372
• Exclusion in 5'UTR
• Reference transcript: NM_001014765

• pfam FBA 185aa 2e-69 in ref transcript
  • F-box associated region. Members of this family are associated with F-box domains, hence the name FBA. This domain is probably involved in binding other proteins that will be targeted for ubiquitination. The human F-box only protein 2 is involved in binding to N-glycosylated proteins.

FBXO44

• refseq_FBXO44.F3 refseq_FBXO44.R3 116 241
• NCBIGene 36.3 93611
• Exon skipping and alternative 3-prime or 5-prime, size difference: 125
• Exclusion in the protein causing a frameshift, Exclusion in the protein (no frameshift)
• Reference transcript: NM_001014765

• Changed! pfam FBA 185aa 2e-69 in ref transcript
  • F-box associated region. Members of this family are associated with F-box domains, hence the name FBA. This domain is probably involved in binding other proteins that will be targeted for ubiquitination. The human F-box only protein 2 is involved in binding to N-glycosylated proteins.
• Changed! pfam FBA 56aa 2e-13 in modified transcript

FBXW8

• refseq_FBXW8.F1 refseq_FBXW8.R1 158 356
• NCBIGene 36.3 26259
• Alternative 5-prime, size difference: 198
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_153348

• cd WD40 288aa 6e-14 in ref transcript
  • WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.
• pfam F-box 43aa 3e-06 in ref transcript
  • F-box domain. This domain is approximately 50 amino acids long, and is usually found in the N-terminal half of a variety of proteins. Two motifs that are commonly found associated with the F-box domain are the leucine rich repeats (LRRs; pfam00560 and pfam07723) and the WD repeat (pfam00400). The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression.
• COG COG2319 302aa 6e-12 in ref transcript
  • FOG: WD40 repeat [General function prediction only].

FCAR

• refseq_FCAR.F4 refseq_FCAR.R4 166 202
• NCBIGene 36.3 2204
• Single exon skipping, size difference: 36
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_002000

FCGR2B

• refseq_FCGR2B.F1 refseq_FCGR2B.R1 152 209
• NCBIGene 36.3 2213
• Single exon skipping, size difference: 57
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_004001

• cd IGcam 54aa 0.002 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• smart IG_like 78aa 4e-06 in ref transcript
  • Immunoglobulin like. IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
• smart IGc2 50aa 5e-05 in ref transcript
  • Immunoglobulin C-2 Type.

FCGR2C

• refseq_FCGR2C.F2 refseq_FCGR2C.R2 161 246
• NCBIGene 36.2 9103
• Single exon skipping, size difference: 85
• Inclusion in 5'UTR
• Reference transcript: NM_201563

FCN2

• refseq_FCN2.F1 refseq_FCN2.R1 206 320
• NCBIGene 36.3 2220
• Single exon skipping, size difference: 114
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_004108

• cd FReD 211aa 7e-82 in ref transcript
  • Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation.
• smart FBG 212aa 3e-86 in ref transcript
  • Fibrinogen-related domains (FReDs). Domain present at the C-termini of fibrinogen beta and gamma chains, and a variety of fibrinogen-related proteins, including tenascin and Drosophila scabrous.

FCN3

• refseq_FCN3.F1 refseq_FCN3.R1 146 179
• NCBIGene 36.3 8547
• Single exon skipping, size difference: 33
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_003665

• Changed! cd FReD 210aa 7e-77 in ref transcript
  • Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation.
• Changed! smart FBG 210aa 3e-74 in ref transcript
  • Fibrinogen-related domains (FReDs). Domain present at the C-termini of fibrinogen beta and gamma chains, and a variety of fibrinogen-related proteins, including tenascin and Drosophila scabrous.
• Changed! cd FReD 209aa 1e-75 in modified transcript
• Changed! smart FBG 209aa 4e-73 in modified transcript

FDXR

• refseq_FDXR.F2 refseq_FDXR.R2 102 120
• NCBIGene 36.3 2232
• Alternative 3-prime, size difference: 18
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_004110

• TIGR gltA 158aa 3e-15 in ref transcript
  • This protein is homologous to the small subunit of NADPH and NADH forms of glutamate synthase as found in eukaryotes and some bacteria. This protein is found in numerous species having no homolog of the glutamate synthase large subunit. The prototype of the family, from Pyrococcus sp. KOD1, was shown to be active as a homotetramer and to require NADPH.
• Changed! PTZ PTZ00188 236aa 1e-44 in ref transcript
  • adrenodoxin reductase; Provisional.
• Changed! COG GltD 451aa 3e-36 in ref transcript
  • NADPH-dependent glutamate synthase beta chain and related oxidoreductases [Amino acid transport and metabolism / General function prediction only].
• Changed! TIGR Se_ygfK 380aa 2e-09 in modified transcript
  • Members of this protein family are YgfK, predicted to be one subunit of a three-subunit, molybdopterin-containing selenate reductase. This enzyme is found, typically, in genomic regions associated with xanthine dehydrogenase homologs predicted to belong to the selenium-dependent molybdenum hydroxylases (SDMH). Therefore, the selenate reductase is suggested to play a role in furnishing selenide for SelD, the selenophosphate synthase.
• Changed! PTZ PTZ00188 230aa 2e-46 in modified transcript
• Changed! COG GltD 445aa 4e-38 in modified transcript

FECH

• refseq_FECH.F1 refseq_FECH.R1 100 118
• NCBIGene 36.3 2235
• Alternative 5-prime, size difference: 18
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001012515

• cd Ferrochelatase_C 138aa 7e-44 in ref transcript
  • Ferrochelatase, C-terminal domain: Ferrochelatase (protoheme ferrolyase or HemH) is the terminal enzyme of the heme biosynthetic pathway. It catalyzes the insertion of ferrous iron into the protoporphyrin IX ring yielding protoheme. This enzyme is ubiquitous in nature and widely distributed in bacteria and eukaryotes. Recently, some archaeal members have been identified. The oligomeric state of these enzymes varies depending on the presence of a dimerization motif at the C-terminus.
• cd Ferrochelatase_N 162aa 3e-41 in ref transcript
  • Ferrochelatase, N-terminal domain: Ferrochelatase (protoheme ferrolyase or HemH) is the terminal enzyme of the heme biosynthetic pathway. It catalyzes the insertion of ferrous iron into the protoporphyrin IX ring yielding protoheme. This enzyme is ubiquitous in nature and widely distributed in bacteria and eukaryotes. Recently, some archaeal members have been identified. The oligomeric state of these enzymes varies depending on the presence of a dimerization motif at the C-terminus.
• pfam Ferrochelatase 321aa 1e-122 in ref transcript
  • Ferrochelatase.
• Changed! PRK hemH 325aa 1e-89 in ref transcript
  • ferrochelatase; Reviewed.
• Changed! PRK hemH 322aa 9e-89 in modified transcript

FER1L3

• refseq_FER1L3.F1 refseq_FER1L3.R1 216 255
• NCBIGene 36.3 26509
• Single exon skipping, size difference: 39
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_013451

• cd C2 103aa 3e-15 in ref transcript
  • Protein kinase C conserved region 2 (CalB); Ca2+-binding motif present in phospholipases, protein kinases C, and synaptotagmins (among others). Some do not appear to contain Ca2+-binding sites. Particular C2s appear to bind phospholipids, inositol polyphosphates,and intracellular proteins. Synaptotagmin and PLC C2s are permuted in sequence with respect to N- and C-terminal beta strands.
• cd C2_1 114aa 5e-11 in ref transcript
  • Protein kinase C conserved region 2, subgroup 1; C2 Ca2+-binding motif present in phospholipases, protein kinases C, and synaptotagmins (amongst others); some PKCs lack calcium dependence. Particular C2s appear to bind phospholipids, inositol polyphosphates,and intracellular proteins. Two distinct C2 topologies generated by permutation of the sequence with respect to the N- and C-terminal beta strands are seen. In this subgroup, containing synaptotagmins, specific protein kinases C (PKC) subtypes and other proteins, the N-terminal beta strand occupies the position of what is the C-terminal strand in subgroup 2.
• Changed! cd C2 114aa 1e-10 in ref transcript
• cd C2 95aa 2e-07 in ref transcript
• cd C2 103aa 3e-06 in ref transcript
• cd C2 117aa 1e-04 in ref transcript
• pfam FerB 76aa 9e-38 in ref transcript
  • FerB (NUC096) domain. This is central domain B in proteins of the Ferlin family.
• pfam FerI 72aa 5e-32 in ref transcript
  • FerI (NUC094) domain. This domain is present in proteins of the Ferlin family. It is often located between two C2 domains.
• pfam FerA 66aa 1e-20 in ref transcript
  • FerA (NUC095) domain. This is central domain A in proteins of the Ferlin family.
• pfam C2 84aa 6e-15 in ref transcript
  • C2 domain.
• smart DysFN 57aa 3e-13 in ref transcript
  • Dysferlin domain, N-terminal region. Domain of unknown function present in yeast peroxisomal proteins, dysferlin, myoferlin and hypothetical proteins. Due to an insertion of a dysferlin domain within a second dysferlin domain we have chosen to predict these domains in two parts: the N-terminal region and the C-terminal region.
• pfam C2 89aa 4e-13 in ref transcript
• pfam C2 97aa 2e-11 in ref transcript
• smart DysFN 59aa 2e-11 in ref transcript
• pfam C2 84aa 2e-09 in ref transcript
• smart C2 94aa 1e-07 in ref transcript
  • Protein kinase C conserved region 2 (CalB). Ca2+-binding motif present in phospholipases, protein kinases C, and synaptotamins (among others). Some do not appear to contain Ca2+-binding sites. Particular C2s appear to bind phospholipids, inositol polyphosphates, and intracellular proteins. Unusual occurrence in perforin. Synaptotagmin and PLC C2s are permuted in sequence with respect to N- and C-terminal beta strands. SMART detects C2 domains using one or both of two profiles.
• smart C2 96aa 2e-04 in ref transcript
• COG COG5038 77aa 8e-07 in ref transcript
  • Ca2+-dependent lipid-binding protein, contains C2 domain [General function prediction only].
• COG COG5038 87aa 6e-05 in ref transcript
• COG COG5038 90aa 0.009 in ref transcript
• Changed! cd C2 106aa 5e-10 in modified transcript

FGF1

• refseq_FGF1.F2 refseq_FGF1.R2 288 395
• NCBIGene 36.3 2246
• Exon skipping and alternative 3-prime or 5-prime, size difference: 107
• Exclusion in the protein causing a frameshift, Exclusion in the protein (no frameshift)
• Reference transcript: NM_000800

• Changed! cd FGF 123aa 1e-38 in ref transcript
  • Acidic and basic fibroblast growth factor family; FGFs are mitogens, which stimulate growth or differentiation of cells of mesodermal or neuroectodermal origin. The family plays essential roles in patterning and differentiation during vertebrate embryogenesis, and has neurotrophic activities. FGFs have a high affinity for heparan sulfate proteoglycans and require heparan sulfate to activate one of four cell surface FGF receptors. Upon binding to FGF, the receptors dimerize and their intracellular tyrosine kinase domains become active. FGFs have internal pseudo-threefold symmetry (beta-trefoil topology).
• Changed! smart FGF 127aa 1e-44 in ref transcript
  • Acidic and basic fibroblast growth factor family. Mitogens that stimulate growth or differentiation of cells of mesodermal or neuroectodermal origin. The family play essential roles in patterning and differentiation during vertebrate embryogenesis, and have neurotrophic activities.
• Changed! cd FGF 29aa 1e-05 in modified transcript
• Changed! smart FGF 35aa 1e-06 in modified transcript

FGF5

• refseq_FGF5.F2 refseq_FGF5.R2 256 360
• NCBIGene 36.3 2250
• Single exon skipping, size difference: 104
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_004464

• Changed! cd FGF 129aa 6e-37 in ref transcript
  • Acidic and basic fibroblast growth factor family; FGFs are mitogens, which stimulate growth or differentiation of cells of mesodermal or neuroectodermal origin. The family plays essential roles in patterning and differentiation during vertebrate embryogenesis, and has neurotrophic activities. FGFs have a high affinity for heparan sulfate proteoglycans and require heparan sulfate to activate one of four cell surface FGF receptors. Upon binding to FGF, the receptors dimerize and their intracellular tyrosine kinase domains become active. FGFs have internal pseudo-threefold symmetry (beta-trefoil topology).
• Changed! smart FGF 134aa 4e-44 in ref transcript
  • Acidic and basic fibroblast growth factor family. Mitogens that stimulate growth or differentiation of cells of mesodermal or neuroectodermal origin. The family play essential roles in patterning and differentiation during vertebrate embryogenesis, and have neurotrophic activities.
• Changed! cd FGF 26aa 0.001 in modified transcript
• Changed! pfam FGF 37aa 2e-06 in modified transcript
  • Fibroblast growth factor. Fibroblast growth factors are a family of proteins involved in growth and differentiation in a wide range of contexts. They are found in a wide range of organisms, from nematodes to humans. Most share an internal core region of high similarity, conserved residues in which are involved in binding with their receptors. On binding, they cause dimerisation of their tyrosine kinase receptors leading to intracellular signalling. There are currently four known tyrosine kinase receptors for fibroblast growth factors. These receptors can each bind several different members of this family. Members of this family have a beta trefoil structure. Most have N-terminal signal peptides and are secreted. A few lack signal sequences but are secreted anyway; still others also lack the signal peptide but are found on the cell surface and within the extracellular matrix. A third group remain intracellular. They have central roles in development, regulating cell proliferation, migration and differentiation. On the other hand, they are important in tissue repair following injury in adult organisms.

FGFR1OP

• refseq_FGFR1OP.F1 refseq_FGFR1OP.R1 194 254
• NCBIGene 36.3 11116
• Single exon skipping, size difference: 60
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_007045

• pfam FOP_dimer 81aa 8e-35 in ref transcript
  • FOP N terminal dimerisation domain. Fibroblast growth factor receptor 1 (FGFR1) oncogene partner (FOP) is a centrosomal protein that is involved in anchoring microtubules to subcellular structures. This domain includes a Lis-homology motif. It forms an alpha helical bundle and is involved in dimerisation.

FGL1

• refseq_FGL1.F2 refseq_FGL1.R2 216 343
• NCBIGene 36.3 2267
• Single exon skipping, size difference: 127
• Exclusion in 5'UTR
• Reference transcript: NM_201553

• cd FReD 227aa 1e-83 in ref transcript
  • Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation.
• smart FBG 226aa 2e-90 in ref transcript
  • Fibrinogen-related domains (FReDs). Domain present at the C-termini of fibrinogen beta and gamma chains, and a variety of fibrinogen-related proteins, including tenascin and Drosophila scabrous.

FGL1

• refseq_FGL1.F3 refseq_FGL1.R1 114 241
• NCBIGene 36.3 2267
• Single exon skipping, size difference: 127
• Exclusion in 5'UTR
• Reference transcript: NM_201552

• cd FReD 227aa 1e-83 in ref transcript
  • Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation.
• smart FBG 226aa 2e-90 in ref transcript
  • Fibrinogen-related domains (FReDs). Domain present at the C-termini of fibrinogen beta and gamma chains, and a variety of fibrinogen-related proteins, including tenascin and Drosophila scabrous.

FHL2

• refseq_FHL2.F1 refseq_FHL2.R1 205 377
• NCBIGene 36.3 2274
• Multiple exon skipping, size difference: 172
• Inclusion in the protein (no stop codon or frameshift), Inclusion in the protein causing a frameshift
• Reference transcript: NM_001450

• Changed! pfam LIM 56aa 7e-06 in ref transcript
  • LIM domain. This family represents two copies of the LIM structural domain.
• Changed! smart LIM 38aa 3e-04 in ref transcript
  • Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
• Changed! pfam LIM 58aa 5e-04 in ref transcript
• Changed! smart LIM 41aa 0.008 in ref transcript

FHL2

• refseq_FHL2.F3 refseq_FHL2.R1 123 244
• NCBIGene 36.3 2274
• Single exon skipping, size difference: 121
• Exclusion in 5'UTR
• Reference transcript: NM_201555

• pfam LIM 56aa 5e-05 in ref transcript
  • LIM domain. This family represents two copies of the LIM structural domain.
• smart LIM 38aa 0.001 in ref transcript
  • Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
• pfam LIM 58aa 0.002 in ref transcript

FHL2

• refseq_FHL2.F5 refseq_FHL2.R4 187 315
• NCBIGene 36.3 2274
• Alternative 5-prime, size difference: 128
• Exclusion in 5'UTR
• Reference transcript: NM_201555

• pfam LIM 56aa 5e-05 in ref transcript
  • LIM domain. This family represents two copies of the LIM structural domain.
• smart LIM 38aa 0.001 in ref transcript
  • Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
• pfam LIM 58aa 0.002 in ref transcript

FIBP

• refseq_FIBP.F1 refseq_FIBP.R1 116 137
• NCBIGene 36.3 9158
• Alternative 5-prime, size difference: 21
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_198897

• Changed! pfam FIBP 363aa 1e-162 in ref transcript
  • Acidic fibroblast growth factor binding (FIBP). Acidic fibroblast growth factor (aFGF) intracellular binding protein (FIBP) is a protein found mainly in the nucleus that is thought to be involved in the intracellular function of aFGF.
• Changed! pfam FIBP 356aa 1e-164 in modified transcript

FKBP1B

• refseq_FKBP1B.F2 refseq_FKBP1B.R2 144 189
• NCBIGene 36.3 2281
• Alternative 3-prime, size difference: 45
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_004116

• Changed! pfam FKBP_C 95aa 6e-33 in ref transcript
  • FKBP-type peptidyl-prolyl cis-trans isomerase.
• Changed! COG FkpA 104aa 3e-30 in ref transcript
  • FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones].
• Changed! pfam FKBP_C 53aa 3e-17 in modified transcript
• Changed! COG FkpA 66aa 9e-14 in modified transcript

FKBP7

• refseq_FKBP7.F1 refseq_FKBP7.R1 113 227
• NCBIGene 36.2 51661
• Single exon skipping, size difference: 114
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_181342

• Changed! pfam FKBP_C 98aa 2e-28 in ref transcript
  • FKBP-type peptidyl-prolyl cis-trans isomerase.
• Changed! COG FkpA 97aa 1e-17 in ref transcript
  • FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones].
• Changed! pfam FKBP_C 81aa 3e-20 in modified transcript
• Changed! COG FkpA 103aa 1e-11 in modified transcript

FKRP

• refseq_FKRP.F2 refseq_FKRP.R2 173 392
• NCBIGene 36.3 79147
• Alternative 5-prime, size difference: 219
• Exclusion in 5'UTR
• Reference transcript: NM_001039885

• pfam LicD 141aa 2e-16 in ref transcript
  • LICD Protein Family. The LICD family of proteins show high sequence similarity and are involved in phosphorylcholine metabolism. There is evidence to show that LicD2 mutants have a reduced ability to take up choline, have decreased ability to adhere to host cells and are less virulent.
• COG COG3475 48aa 6e-08 in ref transcript
  • LPS biosynthesis protein [Cell envelope biogenesis, outer membrane].
• PRK ispDF 95aa 0.006 in ref transcript
  • bifunctional 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase/2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase protein; Provisional.

FLJ12949

• refseq_FLJ12949.F1 refseq_FLJ12949.R1 125 199
• NCBIGene 36.2 65095
• Single exon skipping, size difference: 74
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_023008

• Changed! pfam Kri1 202aa 5e-52 in ref transcript
  • KRI1-like family. The yeast member of this family (Kri1p) is found to be required for 40S ribosome biogenesis in the nucleolus.

FLJ20105

• refseq_FLJ20105.F2 refseq_FLJ20105.R2 241 359
• NCBIGene 36.2 54821
• Single exon skipping, size difference: 118
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_017669

• Changed! cd DEXDc 144aa 8e-17 in ref transcript
  • DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
• Changed! cd HELICc 134aa 3e-14 in ref transcript
  • Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process.
• Changed! pfam SNF2_N 286aa 3e-60 in ref transcript
  • SNF2 family N-terminal domain. This domain is found in proteins involved in a variety of processes including transcription regulation (e.g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as well as a variety of other proteins with little functional information (e.g., lodestar, ETL1).
• Changed! smart HELICc 84aa 5e-09 in ref transcript
  • helicase superfamily c-terminal domain.
• Changed! COG HepA 571aa 2e-66 in ref transcript
  • Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair].

DEF8

• refseq_FLJ20186.F1 refseq_FLJ20186.R1 139 264
• NCBIGene 36.3 54849
• Alternative 5-prime, size difference: 125
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_207514

• Changed! cd C1 51aa 0.001 in ref transcript
  • Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
• Changed! pfam C1_1 54aa 0.002 in ref transcript
  • Phorbol esters/diacylglycerol binding domain (C1 domain). This domain is also known as the Protein kinase C conserved region 1 (C1) domain.

FLJ21839

• refseq_FLJ21839.F1 refseq_FLJ21839.R1 200 247
• NCBIGene 36.2 60509
• Single exon skipping, size difference: 47
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_001035506

• cd M14_AGBL5_like 167aa 2e-83 in ref transcript
  • Peptidase M14-like domain of ATP/GTP binding protein_like (AGBL)-5, and related proteins. The Peptidase M14 family of metallocarboxypeptidases are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. This eukaryotic subgroup includes the human AGBL5 and the mouse cytosolic carboxypeptidase (CCP)-5. ATP/GTP binding protein (AGTPBP-1/Nna1)-like proteins are active metallopeptidases that are thought to act on cytosolic proteins such as alpha-tubulin, to remove a C-terminal tyrosine. Mutations in AGTPBP-1/Nna1 cause Purkinje cell degeneration (pcd). AGTPBP-1/Nna1 however does not belong to this subgroup. AGTPBP-1/Nna1-like proteins from the different phyla are highly diverse, but they all contain a unique N-terminal conserved domain right before the CP domain. It has been suggested that this N-terminal domain might act as a folding domain.
• cd M14_AGBL5_like 145aa 8e-65 in ref transcript
• pfam Peptidase_M14 79aa 1e-16 in ref transcript
  • Zinc carboxypeptidase.

FLJ22222

• refseq_FLJ22222.F2 refseq_FLJ22222.R2 193 406
• NCBIGene 36.3 79701
• Single exon skipping, size difference: 213
• Exclusion of the stop codon
• Reference transcript: NM_175902

• Changed! smart P4Hc 115aa 5e-05 in ref transcript
  • Prolyl 4-hydroxylase alpha subunit homologues. Mammalian enzymes catalyse hydroxylation of collagen, for example. Prokaryotic enzymes might catalyse hydroxylation of antibiotic peptides. These are 2-oxoglutarate-dependent dioxygenases, requiring 2-oxoglutarate and dioxygen as cosubstrates and ferrous iron as a cofactor.
• Changed! smart P4Hc 145aa 1e-14 in modified transcript

FLJ31033

• refseq_FLJ31033.F2 refseq_FLJ31033.R2 228 276
• NCBIGene 36.2 91351
• Alternative 5-prime, size difference: 48
• Exclusion in the protein (no frameshift)
• Reference transcript: XM_930988

• cd DEXDc 143aa 3e-11 in ref transcript
  • DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
• cd HELICc 103aa 1e-07 in ref transcript
  • Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process.
• pfam DEAD 155aa 3e-15 in ref transcript
  • DEAD/DEAH box helicase. Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.
• smart HELICc 77aa 8e-09 in ref transcript
  • helicase superfamily c-terminal domain.
• COG COG4581 123aa 1e-24 in ref transcript
  • Superfamily II RNA helicase [DNA replication, recombination, and repair].
• COG COG4581 176aa 2e-22 in ref transcript

FLJ31033

• refseq_FLJ31033.F4 refseq_FLJ31033.R4 111 207
• NCBIGene 36.2 91351
• Single exon skipping, size difference: 96
• Exclusion in the protein (no frameshift)
• Reference transcript: XM_930988

• Changed! cd DEXDc 143aa 3e-11 in ref transcript
  • DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
• cd HELICc 103aa 1e-07 in ref transcript
  • Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process.
• Changed! pfam DEAD 155aa 3e-15 in ref transcript
  • DEAD/DEAH box helicase. Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.
• smart HELICc 77aa 8e-09 in ref transcript
  • helicase superfamily c-terminal domain.
• Changed! COG COG4581 123aa 1e-24 in ref transcript
  • Superfamily II RNA helicase [DNA replication, recombination, and repair].
• Changed! COG COG4581 176aa 2e-22 in ref transcript
• Changed! cd DEXDc 61aa 6e-04 in modified transcript
• Changed! smart DEXDc 74aa 1e-05 in modified transcript
  • DEAD-like helicases superfamily.
• Changed! COG COG4581 299aa 9e-25 in modified transcript
• Changed! COG COG4581 144aa 3e-13 in modified transcript

FLJ44379

• refseq_FLJ44379.F1 refseq_FLJ44379.R1 311 401
• NCBIGene 36.2 132203
• Single exon skipping, size difference: 90
• Exclusion in the protein (no frameshift)
• Reference transcript: XM_059578

• Changed! cd S-100 115aa 2e-10 in ref transcript
  • S-100: S-100 domain, which represents the largest family within the superfamily of proteins carrying the Ca-binding EF-hand motif. Note that this S-100 hierarchy contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100 proteins are expressed exclusively in vertebrates, and are implicated in intracellular and extracellular regulatory activities. Intracellularly, S100 proteins act as Ca-signaling or Ca-buffering proteins. The most unusual characteristic of certain S100 proteins is their occurrence in extracellular space, where they act in a cytokine-like manner through RAGE, the receptor for advanced glycation products. Structural data suggest that many S100 members exist within cells as homo- or heterodimers and even oligomers; oligomerization contributes to their functional diversification. Upon binding calcium, most S100 proteins change conformation to a more open structure exposing a hydrophobic cleft. This hydrophobic surface represents the interaction site of S100 proteins with their target proteins. There is experimental evidence showing that many S100 proteins have multiple binding partners with diverse mode of interaction with different targets. In addition to S100 proteins (such as S100A1,-3,-4,-6,-7,-10,-11,and -13), this group includes the ''fused'' gene family, a group of calcium binding S100-related proteins. The ''fused'' gene family includes multifunctional epidermal differentiation proteins - profilaggrin, trichohyalin, repetin, hornerin, and cornulin; functionally these proteins are associated with keratin intermediate filaments and partially crosslinked to the cell envelope. These ''fused'' gene proteins contain N-terminal sequence with two Ca-binding EF-hands motif, which may be associated with calcium signaling in epidermal cells and autoprocessing in a calcium-dependent manner. In contrast to S100 proteins, "fused" gene family proteins contain an extraordinary high number of almost perfect peptide repeats with regular array of polar and charged residues similar to many known cell envelope proteins.
• Changed! cd S-100 85aa 7e-15 in modified transcript

FLRT3

• refseq_FLRT3.F1 refseq_FLRT3.R1 191 385
• NCBIGene 36.3 23767
• Single exon skipping, size difference: 194
• Exclusion in 5'UTR
• Reference transcript: NM_198391

• cd LRR_RI 271aa 1e-04 in ref transcript
  • Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1).
• TIGR PCC 78aa 2e-08 in ref transcript
  • Note: this model is restricted to the amino half because a full-length model is incompatible with the HMM software package.
• smart LRRNT 31aa 0.005 in ref transcript
  • Leucine rich repeat N-terminal domain.
• COG COG4886 241aa 9e-07 in ref transcript
  • Leucine-rich repeat (LRR) protein [Function unknown].

FMNL3

• refseq_FMNL3.F1 refseq_FMNL3.R1 127 280
• NCBIGene 36.3 91010
• Single exon skipping, size difference: 153
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_175736

• pfam FH2 366aa 1e-77 in ref transcript
  • Formin Homology 2 Domain.
• pfam Drf_FH3 202aa 8e-42 in ref transcript
  • Diaphanous FH3 Domain. This region is found in the Formin-like and and diaphanous proteins.
• Changed! pfam Drf_GBD 116aa 6e-26 in ref transcript
  • Diaphanous GTPase-binding Domain. This domain is bound to by GTP-attached Rho proteins, leading to activation of the Drf protein.
• Changed! pfam Drf_GBD 49aa 1e-12 in ref transcript
• Changed! pfam Drf_GBD 183aa 7e-44 in modified transcript

FMO3

• refseq_FMO3.F2 refseq_FMO3.R2 96 113
• NCBIGene 36.3 2328
• Alternative 5-prime, size difference: 17
• Exclusion in 5'UTR
• Reference transcript: NM_001002294

• pfam FMO-like 531aa 0.0 in ref transcript
  • Flavin-binding monooxygenase-like. This family includes FMO proteins and cyclohexanone monooxygenase.
• COG TrkA 340aa 4e-34 in ref transcript
  • Predicted flavoprotein involved in K+ transport [Inorganic ion transport and metabolism].

FOLH1

• refseq_FOLH1.F1 refseq_FOLH1.R1 249 342
• NCBIGene 36.3 2346
• Single exon skipping, size difference: 93
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_004476

• cd PA_GCPII_like 227aa 9e-72 in ref transcript
  • PA_GCPII_like: Protease-associated domain containing protein, glutamate carboxypeptidase II (GCPII)-like. This group contains various PA domain-containing proteins similar to GCPII including, GCPIII (NAALADase2) and NAALADase L. These proteins belong to the peptidase M28 family. GCPII is also known N-acetylated-alpha-linked acidic dipeptidase (NAALDase1), folate hydrolase or prostate-specific membrane antigen (PSMA). GCPII is found in various human tissues including prostate, small intestine, and the central nervous system. In the brain, GCPII is known as NAALDase1, it functions as a NAALDase hydrolyzing the neuropeptide N-acetyl-L-aspartyl-L-glutamate (alpha-NAAG), to release free glutamate. In the small intestine, GCPII releases the terminal glutamate from poly-gamma-glutamated folates. GCPII (PSMA) is a useful cancer marker; its expression is markedly increased in prostate cancer and in tumor-associated neovasculature. GCPIII hydrolyzes alpha-NAAG with a lower efficiency than does GCPII; NAALADase L is not able to hydrolyze alpha-NAAG. The GCPII PA domain (referred to as the apical domain) participates in substrate binding and may act as a protein-protein interaction domain.
• Changed! pfam TFR_dimer 138aa 8e-48 in ref transcript
  • Transferrin receptor-like dimerisation domain. This domain is involved in dimerisation of the transferrin receptor as shown in its crystal structure.
• pfam PA 93aa 5e-15 in ref transcript
  • PA domain. The PA (Protease associated) domain is found as an insert domain in diverse proteases. The PA domain is also found in a plant vacuolar sorting receptor and members of the RZF family. It has been suggested that this domain forms a lid-like structure that covers the active site in active proteases, and is involved in protein recognition in vacuolar sorting receptors.
• pfam Peptidase_M28 85aa 8e-13 in ref transcript
  • Peptidase family M28.
• Changed! COG Iap 219aa 2e-09 in ref transcript
  • Predicted aminopeptidases [General function prediction only].
• Changed! pfam TFR_dimer 107aa 8e-26 in modified transcript
• Changed! COG Iap 238aa 2e-09 in modified transcript

FOLR1

• refseq_FOLR1.F1 refseq_FOLR1.R1 157 223
• NCBIGene 36.3 2348
• Single exon skipping, size difference: 66
• Exclusion in 5'UTR
• Reference transcript: NM_016724

• pfam Folate_rec 185aa 4e-78 in ref transcript
  • Folate receptor family. This family includes the folate receptor which binds to folate and reduced folic acid derivatives and mediates delivery of 5-methyltetrahydrofolate to the interior of cells. These proteins are attached to the membrane by a GPI-anchor. The proteins contain 16 conserved cysteines that form eight disulphide bridges.

FOXI1

• refseq_FOXI1.F1 refseq_FOXI1.R1 100 385
• NCBIGene 36.3 2299
• Alternative 3-prime, size difference: 285
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_012188

• Changed! cd FH 78aa 2e-36 in ref transcript
  • Forkhead (FH), also known as a "winged helix". FH is named for the Drosophila fork head protein, a transcription factor which promotes terminal rather than segmental development. This family of transcription factor domains, which bind to B-DNA as monomers, are also found in the Hepatocyte nuclear factor (HNF) proteins, which provide tissue-specific gene regulation. The structure contains 2 flexible loops or "wings" in the C-terminal region, hence the term winged helix.
• Changed! smart FH 89aa 7e-43 in ref transcript
  • FORKHEAD. FORKHEAD, also known as a "winged helix".
• Changed! COG COG5025 92aa 2e-15 in ref transcript
  • Transcription factor of the Forkhead/HNF3 family [Transcription].
• Changed! cd FH 69aa 4e-30 in modified transcript
• Changed! smart FH 69aa 3e-31 in modified transcript
• Changed! COG COG5025 121aa 1e-12 in modified transcript

FOXM1

• refseq_FOXM1.F2 refseq_FOXM1.R2 100 145
• NCBIGene 36.3 2305
• Single exon skipping, size difference: 45
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_202002

• cd FH 76aa 2e-28 in ref transcript
  • Forkhead (FH), also known as a "winged helix". FH is named for the Drosophila fork head protein, a transcription factor which promotes terminal rather than segmental development. This family of transcription factor domains, which bind to B-DNA as monomers, are also found in the Hepatocyte nuclear factor (HNF) proteins, which provide tissue-specific gene regulation. The structure contains 2 flexible loops or "wings" in the C-terminal region, hence the term winged helix.
• smart FH 81aa 2e-30 in ref transcript
  • FORKHEAD. FORKHEAD, also known as a "winged helix".
• COG COG5025 78aa 9e-10 in ref transcript
  • Transcription factor of the Forkhead/HNF3 family [Transcription].

FOXM1

• refseq_FOXM1.F3 refseq_FOXM1.R3 284 398
• NCBIGene 36.3 2305
• Single exon skipping, size difference: 114
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_202002

• cd FH 76aa 2e-28 in ref transcript
  • Forkhead (FH), also known as a "winged helix". FH is named for the Drosophila fork head protein, a transcription factor which promotes terminal rather than segmental development. This family of transcription factor domains, which bind to B-DNA as monomers, are also found in the Hepatocyte nuclear factor (HNF) proteins, which provide tissue-specific gene regulation. The structure contains 2 flexible loops or "wings" in the C-terminal region, hence the term winged helix.
• smart FH 81aa 2e-30 in ref transcript
  • FORKHEAD. FORKHEAD, also known as a "winged helix".
• COG COG5025 78aa 9e-10 in ref transcript
  • Transcription factor of the Forkhead/HNF3 family [Transcription].

FRMPD2

• refseq_FRMPD2.F1 refseq_FRMPD2.R1 169 235
• NCBIGene 36.3 143162
• Single exon skipping, size difference: 66
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001018071

• cd PDZ_signaling 82aa 1e-12 in ref transcript
  • PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of PDZ domains an N-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in proteases.
• cd FERM_C 93aa 9e-11 in ref transcript
  • The FERM_C domain is the third structural domain within the FERM domain. The FERM domain is found in the cytoskeletal-associated proteins such as ezrin, moesin, radixin, 4.1R, and merlin. These proteins provide a link between the membrane and cytoskeleton and are involved in signal transduction pathways. The FERM_C domain is also found in protein tyrosine phosphatases (PTPs) , the tryosine kinases FAKand JAK, in addition to other proteins involved in signaling. This domain is structuraly similar to the PH and PTB domains and consequently is capable of binding to both peptides and phospholipids at different sites.
• cd PDZ_signaling 87aa 8e-10 in ref transcript
• cd PDZ_signaling 85aa 2e-08 in ref transcript
• Changed! smart KIND 173aa 6e-39 in ref transcript
  • kinase non-catalytic C-lobe domain. It is an interaction domain identified as being similar to the C-terminal protein kinase catalytic fold (C lobe). Its presence at the N terminus of signalling proteins and the absence of the active-site residues in the catalytic and activation loops suggest that it folds independently and is likely to be non-catalytic. The occurrence of KIND only in metazoa implies that it has evolved from the catalytic protein kinase domain into an interaction domain possibly by keeping the substrate-binding features.
• smart B41 205aa 2e-32 in ref transcript
  • Band 4.1 homologues. Also known as ezrin/radixin/moesin (ERM) protein domains. Present in myosins, ezrin, radixin, moesin, protein tyrosine phosphatases. Plasma membrane-binding domain. These proteins play structural and regulatory roles in the assembly and stabilization of specialized plasmamembrane domains. Some PDZ domain containing proteins bind one or more of this family. Now includes JAKs.
• pfam FERM_C 88aa 2e-25 in ref transcript
  • FERM C-terminal PH-like domain.
• smart PDZ 88aa 4e-16 in ref transcript
  • Domain present in PSD-95, Dlg, and ZO-1/2. Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities.
• smart PDZ 90aa 3e-13 in ref transcript
• TIGR degP_htrA_DO 191aa 2e-06 in ref transcript
  • This family consists of a set proteins various designated DegP, heat shock protein HtrA, and protease DO. The ortholog in Pseudomonas aeruginosa is designated MucD and is found in an operon that controls mucoid phenotype. This family also includes the DegQ (HhoA) paralog in E. coli which can rescue a DegP mutant, but not the smaller DegS paralog, which cannot. Members of this family are located in the periplasm and have separable functions as both protease and chaperone. Members have a trypsin domain and two copies of a PDZ domain. This protein protects bacteria from thermal and other stresses and may be important for the survival of bacterial pathogens.// The chaperone function is dominant at low temperatures, whereas the proteolytic activity is turned on at elevated temperatures.
• smart PDZ 86aa 6e-05 in ref transcript
• COG Prc 62aa 3e-06 in ref transcript
  • Periplasmic protease [Cell envelope biogenesis, outer membrane].
• COG Prc 68aa 2e-05 in ref transcript
• Changed! smart KIND 151aa 6e-28 in modified transcript

FSHB

• refseq_FSHB.F1 refseq_FSHB.R1 144 174
• NCBIGene 36.3 2488
• Alternative 5-prime, size difference: 30
• Exclusion in 5'UTR
• Reference transcript: NM_000510

• cd GHB 102aa 5e-34 in ref transcript
  • Glycoprotein hormone beta chain homologues. Gonadotropins; reproductive hormones consisting of two glycosylated chains (alpha and beta) of similar topology with Cysteine-knot motifs.
• smart GHB 107aa 2e-39 in ref transcript
  • Glycoprotein hormone beta chain homologues. Also called gonadotropins. Glycoprotein hormones consist of two glycosylated chains (alpha and beta) of similar topology.

FST

• refseq_FST.F1 refseq_FST.R1 134 398
• NCBIGene 36.3 10468
• Alternative 3-prime, size difference: 264
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_013409

• cd FSL_SPARC 56aa 2e-05 in ref transcript
  • Follistatin-like SPARC (secreted protein, acidic, and rich in cysteines) domain; SPARC/BM-40/osteonectin is a multifunctional glycoprotein which modulates cellular interaction with the extracellular matrix by its binding to structural matrix proteins such as collagen and vitronectin. The protein it composed of an N-terminal acidic region, a follistatin (FS) domain and an EF-hand calcium binding domain. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a small hydrophobic core of alpha/beta structure (Kazal domain) and has five disulfide bonds and a conserved N-glycosylation site. The FSL_SPARC domain is a member of the superfamily of kazal-like proteinase inhibitors and follistatin-like proteins.
• cd KAZAL_FS 33aa 5e-04 in ref transcript
  • Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD.
• cd KAZAL_FS 40aa 7e-04 in ref transcript
• Changed! cd FSL_SPARC 60aa 0.009 in ref transcript
• smart KAZAL 48aa 7e-07 in ref transcript
  • Kazal type serine protease inhibitors. Kazal type serine protease inhibitors and follistatin-like domains.
• smart KAZAL 47aa 4e-06 in ref transcript
• smart KAZAL 48aa 8e-06 in ref transcript
• pfam PRKCSH 55aa 3e-05 in ref transcript
  • Glucosidase II beta subunit-like protein. The sequences found in this family are similar to a region found in the beta-subunit of glucosidase II, which is also known as protein kinase C substrate 80K-H (PRKCSH). The enzyme catalyses the sequential removal of two alpha-1,3-linked glucose residues in the second step of N-linked oligosaccharide processing. The beta subunit is required for the solubility and stability of the heterodimeric enzyme, and is involved in retaining the enzyme within the endoplasmic reticulum. Mutations in the gene coding for PRKCSH have been found to be involved in the development of autosomal dominant polycystic liver disease (ADPLD), but the precise role the protein has in the pathogenesis of this disease is unknown. This family also includes an ER sensor for misfolded glycoproteins and is therefore likely to be a generic sugar binding domain.
• pfam FOLN 22aa 0.004 in ref transcript
  • Follistatin/Osteonectin-like EGF domain. Members of this family are predominantly found in osteonectin and follistatin and adopt an EGF-like structure.

AKTIP

• refseq_FTS.F2 refseq_FTS.R2 142 171
• NCBIGene 36.3 64400
• Alternative 5-prime, size difference: 29
• Exclusion in 5'UTR
• Reference transcript: NM_001012398

• cd UBCc 135aa 4e-11 in ref transcript
  • Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin protein ligase enzymes, E3. This pathway regulates many fundamental cellular processes. There are also other E2s which form thiol-ester linkages without the use of E3s as well as several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) which lack the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways which were omitted from the scope of this CD.
• smart UBCc 142aa 2e-24 in ref transcript
  • Ubiquitin-conjugating enzyme E2, catalytic domain homologues. Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. This pathway functions in regulating many fundamental processes required for cell viability.TSG101 is one of several UBC homologues that lacks this active site cysteine.
• COG COG5078 140aa 1e-12 in ref transcript
  • Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones].

FTSJ1

• refseq_FTSJ1.F2 refseq_FTSJ1.R2 254 360
• NCBIGene 36.3 24140
• Single exon skipping, size difference: 106
• Inclusion in 5'UTR
• Reference transcript: NM_012280

• pfam FtsJ 179aa 2e-58 in ref transcript
  • FtsJ-like methyltransferase. This family consists of FtsJ from various bacterial and archaeal sources FtsJ is a methyltransferase, but actually has no effect on cell division. FtsJ's substrate is the 23S rRNA. The 1.5 A crystal structure of FtsJ in complex with its cofactor S-adenosylmethionine revealed that FtsJ has a methyltransferase fold. This family also includes the N terminus of flaviviral NS5 protein. It has been hypothesised that the N-terminal domain of NS5 is a methyltransferase involved in viral RNA capping.
• COG FtsJ 200aa 1e-56 in ref transcript
  • 23S rRNA methylase [Translation, ribosomal structure and biogenesis].

FUS

• refseq_FUS.F2 refseq_FUS.R2 155 190
• NCBIGene 36.2 2521
• Single exon skipping, size difference: 35
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_004960

• Changed! cd RRM 83aa 2e-11 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• Changed! smart RRM_2 82aa 3e-11 in ref transcript
  • RNA recognition motif.
• Changed! pfam zf-RanBP 24aa 0.007 in ref transcript
  • Zn-finger in Ran binding protein and others.
• Changed! COG COG0724 107aa 1e-06 in ref transcript
  • RNA-binding proteins (RRM domain) [General function prediction only].

FUT8

• refseq_FUT8.F1 refseq_FUT8.R1 264 366
• NCBIGene 36.3 2530
• Single exon skipping, size difference: 102
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_178155

• cd SH3 53aa 5e-05 in ref transcript
  • Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
• smart SH3 54aa 1e-06 in ref transcript
  • Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.

FUT8

• refseq_FUT8.F3 refseq_FUT8.R3 186 284
• NCBIGene 36.3 2530
• Single exon skipping, size difference: 98
• Exclusion in 5'UTR
• Reference transcript: NM_178155

• cd SH3 53aa 5e-05 in ref transcript
  • Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
• smart SH3 54aa 1e-06 in ref transcript
  • Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.

FXR1

• refseq_FXR1.F1 refseq_FXR1.R1 103 447
• NCBIGene 36.3 8087
• Single exon skipping, size difference: 344
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_005087

• Changed! cd KH-I 67aa 1e-05 in ref transcript
  • K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
• Changed! pfam Agenet 60aa 1e-07 in ref transcript
  • Agenet domain. This domain is related to the TUDOR domain pfam00567. The function of the agenet domain is unknown. This family currently only matches one of the two Agenet domains in the FMR proteins.
• Changed! pfam KH_1 59aa 9e-06 in ref transcript
  • KH domain. KH motifs can bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.
• Changed! TIGR polynuc_phos 89aa 0.002 in ref transcript
  • Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
• Changed! PRK PRK11824 59aa 7e-04 in ref transcript
  • polynucleotide phosphorylase/polyadenylase; Provisional.
• Changed! COG Pnp 156aa 0.002 in ref transcript
  • Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis].

FXR1

• refseq_FXR1.F3 refseq_FXR1.R3 270 362
• NCBIGene 36.3 8087
• Single exon skipping, size difference: 92
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_005087

• cd KH-I 67aa 1e-05 in ref transcript
  • K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
• pfam Agenet 60aa 1e-07 in ref transcript
  • Agenet domain. This domain is related to the TUDOR domain pfam00567. The function of the agenet domain is unknown. This family currently only matches one of the two Agenet domains in the FMR proteins.
• pfam KH_1 59aa 9e-06 in ref transcript
  • KH domain. KH motifs can bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.
• Changed! TIGR polynuc_phos 89aa 0.002 in ref transcript
  • Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
• PRK PRK11824 59aa 7e-04 in ref transcript
  • polynucleotide phosphorylase/polyadenylase; Provisional.
• COG Pnp 156aa 0.002 in ref transcript
  • Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis].
• Changed! TIGR nusA_arch 87aa 0.001 in modified transcript
  • This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.

FXYD3

• refseq_FXYD3.F1 refseq_FXYD3.R1 102 186
• NCBIGene 36.3 5349
• Single exon skipping, size difference: 84
• Exclusion in 5'UTR
• Reference transcript: NM_021910

• pfam ATP1G1_PLM_MAT8 74aa 2e-15 in ref transcript
  • ATP1G1/PLM/MAT8 family.

FYB

• refseq_FYB.F1 refseq_FYB.R1 93 231
• NCBIGene 36.3 2533
• Single exon skipping, size difference: 138
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001465

• cd SH3 54aa 0.003 in ref transcript
  • Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
• smart SH3 58aa 5e-05 in ref transcript
  • Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.

FYTTD1

• refseq_FYTTD1.F1 refseq_FYTTD1.R1 149 322
• NCBIGene 36.3 84248
• Single exon skipping, size difference: 173
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_032288

• Changed! pfam FYTT 316aa 1e-143 in ref transcript
  • Forty-two-three protein. This family consists of several mammalian proteins of around 320 residues in length called 40-2-3 proteins. The function of this family is unknown.
• Changed! pfam FYTT 76aa 2e-29 in modified transcript

G3BP1

• refseq_G3BP.F2 refseq_G3BP.R2 131 162
• NCBIGene 36.3 10146
• Alternative 3-prime, size difference: 31
• Inclusion in 5'UTR
• Reference transcript: NM_198395

• cd NTF2 129aa 8e-32 in ref transcript
  • Nuclear transport factor 2 (NTF2) domain plays an important role in the trafficking of macromolecules, ions and small molecules between the cytoplasm and nucleus. This bi-directional transport of macromolecules across the nuclear envelope requires many soluble factors that includes GDP-binding protein Ran (RanGDP). RanGDP is required for both import and export of proteins and poly(A) RNA. RanGDP also has been implicated in cell cycle control, specifically in mitotic spindle assembly. In interphase cells, RanGDP is predominately nuclear and thought to be GTP bound, but it is also present in the cytoplasm, probably in the GDP-bound state. NTF2 mediates the nuclear import of RanGDP. NTF2 binds to both RanGDP and FxFG repeat-containing nucleoporins.
• cd RRM 70aa 9e-11 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• pfam NTF2 123aa 1e-24 in ref transcript
  • Nuclear transport factor 2 (NTF2) domain. This family includes the NTF2-like Delta-5-3-ketosteroid isomerase proteins.
• pfam RRM_1 56aa 1e-10 in ref transcript
  • RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain). The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have a N terminus rrm which is included in the seed. There is a second region towards the C terminus that has some features of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.
• COG COG0724 105aa 2e-05 in ref transcript
  • RNA-binding proteins (RRM domain) [General function prediction only].

GAB1

• refseq_GAB1.F2 refseq_GAB1.R2 275 365
• NCBIGene 36.3 2549
• Single exon skipping, size difference: 90
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_207123

• cd PH_Gab 108aa 2e-52 in ref transcript
  • Gab (Grb2-associated binder) pleckstrin homology (PH) domain. The Gab subfamily includes several Gab proteins, Drosophila DOS and C. elegans SOC-1. They are scaffolding adaptor proteins, which possess N-terminal PH domains and a C-terminus with proline-rich regions and multiple phosphorylation sites. Following activation of growth factor receptors, Gab proteins are tyrosine phosphorylated and activate PI3K, which generates 3-phosphoinositide lipids. By binding to these lipids via the PH domain, Gab proteins remain in proximity to the receptor, leading to further signaling. While not all Gab proteins depend on the PH domain for recruitment, it is required for Gab activity. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
• pfam PH 110aa 8e-17 in ref transcript
  • PH domain. PH stands for pleckstrin homology.

GABBR1

• refseq_GABBR1.F1 refseq_GABBR1.R1 129 315
• NCBIGene 36.3 2550
• Single exon skipping, size difference: 186
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001470

• cd PBP1_GABAb_receptor 393aa 1e-118 in ref transcript
  • Ligand-binding domain of GABAb receptors, which are metabotropic transmembrane receptors for gamma-aminobutyric acid (GABA). GABA is the major inhibitory neurotransmitter in the mammalian CNS and, like glutamate and other transmitters, acts via both ligand gated ion channels (GABAa receptors) and G-protein coupled receptors (GABAb). GABAa receptors are members of the ionotropic receptor superfamily which includes alpha-adrenergic and glycine receptors. The GABAb receptor is a member of a receptor superfamily which includes the mGlu receptors. The GABAb receptor is coupled to G alpha_i proteins, and activation causes a decrease in calcium, an increase in potassium membrane conductance, and inhibition of cAMP formation. The response is thus inhibitory and leads to hyperpolarization and decreased neurotransmitter release, for example.
• Changed! cd CCP 53aa 1e-05 in ref transcript
  • Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR); The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function.
• pfam ANF_receptor 357aa 5e-63 in ref transcript
  • Receptor family ligand binding region. This family includes extracellular ligand binding domains of a wide range of receptors. This family also includes the bacterial amino acid binding proteins of known structure.
• pfam 7tm_3 259aa 5e-38 in ref transcript
  • 7 transmembrane sweet-taste receptor of 3 GCPR. This is a domain of seven transmembrane regions that forms the C-terminus of some subclass 3 G-coupled-protein receptors. It is often associated with a downstream cysteine-rich linker domain, NCD3G pfam07562, which is the human sweet-taste receptor, and the N-terminal domain, ANF_receptor pfam01094. The seven TM regions assemble in such a way as to produce a docking pocket into which such molecules as cyclamate and lactisole have been found to bind and consequently confer the taste of sweetness.
• Changed! smart CCP 52aa 7e-06 in ref transcript
  • Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR). The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. A missense mutation in seventh CCP domain causes deficiency of the b subunit of factor XIII.
• COG LivK 386aa 5e-27 in ref transcript
  • ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism].

GABBR1

• refseq_GABBR1.F3 refseq_GABBR1.R3 144 295
• NCBIGene 36.3 2550
• Single exon skipping, size difference: 151
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_001470

• cd PBP1_GABAb_receptor 393aa 1e-118 in ref transcript
  • Ligand-binding domain of GABAb receptors, which are metabotropic transmembrane receptors for gamma-aminobutyric acid (GABA). GABA is the major inhibitory neurotransmitter in the mammalian CNS and, like glutamate and other transmitters, acts via both ligand gated ion channels (GABAa receptors) and G-protein coupled receptors (GABAb). GABAa receptors are members of the ionotropic receptor superfamily which includes alpha-adrenergic and glycine receptors. The GABAb receptor is a member of a receptor superfamily which includes the mGlu receptors. The GABAb receptor is coupled to G alpha_i proteins, and activation causes a decrease in calcium, an increase in potassium membrane conductance, and inhibition of cAMP formation. The response is thus inhibitory and leads to hyperpolarization and decreased neurotransmitter release, for example.
• cd CCP 53aa 1e-05 in ref transcript
  • Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR); The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function.
• pfam ANF_receptor 357aa 5e-63 in ref transcript
  • Receptor family ligand binding region. This family includes extracellular ligand binding domains of a wide range of receptors. This family also includes the bacterial amino acid binding proteins of known structure.
• Changed! pfam 7tm_3 259aa 5e-38 in ref transcript
  • 7 transmembrane sweet-taste receptor of 3 GCPR. This is a domain of seven transmembrane regions that forms the C-terminus of some subclass 3 G-coupled-protein receptors. It is often associated with a downstream cysteine-rich linker domain, NCD3G pfam07562, which is the human sweet-taste receptor, and the N-terminal domain, ANF_receptor pfam01094. The seven TM regions assemble in such a way as to produce a docking pocket into which such molecules as cyclamate and lactisole have been found to bind and consequently confer the taste of sweetness.
• smart CCP 52aa 7e-06 in ref transcript
  • Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR). The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. A missense mutation in seventh CCP domain causes deficiency of the b subunit of factor XIII.
• COG LivK 386aa 5e-27 in ref transcript
  • ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism].

GABPB2

• refseq_GABPB2.F1 refseq_GABPB2.R1 135 159
• NCBIGene 36.3 2553
• Single exon skipping, size difference: 24
• Inclusion in 5'UTR
• Reference transcript: NM_005254

• cd ANK 123aa 4e-29 in ref transcript
  • ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats.
• pfam Ank 30aa 1e-07 in ref transcript
  • Ankyrin repeat. There's no clear separation between noise and signal on the HMM search Ankyrin repeats generally consist of a beta, alpha, alpha, beta order of secondary structures. The repeats associate to form a higher order structure.
• TIGR trp 156aa 1e-06 in ref transcript
  • after chronic exposure to capsaicin. (McCleskey and Gold, 1999).
• COG Arp 132aa 5e-14 in ref transcript
  • FOG: Ankyrin repeat [General function prediction only].

GABPB2

• refseq_GABPB2.F3 refseq_GABPB2.R3 199 235
• NCBIGene 36.3 2553
• Alternative 5-prime, size difference: 36
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_005254

• cd ANK 123aa 4e-29 in ref transcript
  • ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats.
• pfam Ank 30aa 1e-07 in ref transcript
  • Ankyrin repeat. There's no clear separation between noise and signal on the HMM search Ankyrin repeats generally consist of a beta, alpha, alpha, beta order of secondary structures. The repeats associate to form a higher order structure.
• TIGR trp 156aa 1e-06 in ref transcript
  • after chronic exposure to capsaicin. (McCleskey and Gold, 1999).
• COG Arp 132aa 5e-14 in ref transcript
  • FOG: Ankyrin repeat [General function prediction only].

GABRB2

• refseq_GABRB2.F1 refseq_GABRB2.R1 285 399
• NCBIGene 36.3 2561
• Single exon skipping, size difference: 114
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_021911

• Changed! TIGR LIC 502aa 1e-129 in ref transcript
  • selective while glycine receptors are anion selective).
• Changed! TIGR LIC 464aa 1e-131 in modified transcript

GABRG2

• refseq_GABRG2.F1 refseq_GABRG2.R1 101 125
• NCBIGene 36.3 2566
• Single exon skipping, size difference: 24
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_198904

• Changed! TIGR LIC 404aa 2e-73 in ref transcript
  • selective while glycine receptors are anion selective).
• Changed! TIGR LIC 396aa 7e-74 in modified transcript

GABRG2

• refseq_GABRG2.F2 refseq_GABRG2.R2 127 189
• NCBIGene 36.3 2566
• Alternative 3-prime, size difference: 62
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_198904

• Changed! TIGR LIC 404aa 2e-73 in ref transcript
  • selective while glycine receptors are anion selective).
• Changed! pfam Neur_chan_LBD 41aa 2e-05 in modified transcript
  • Neurotransmitter-gated ion-channel ligand binding domain. This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.

GANAB

• refseq_GANAB.F1 refseq_GANAB.R1 169 235
• NCBIGene 36.3 23193
• Single exon skipping, size difference: 66
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_198335

• cd GH31_GANC_GANAB_alpha 339aa 0.0 in ref transcript
  • This family includes the closely related glycosyl hydrolase family 31 (GH31) isozymes, neutral alpha-glucosidase C (GANC) and the alpha subunit of heterodimeric neutral alpha-glucosidase AB (GANAB). Initially distinguished on the basis of differences in electrophoretic mobility in starch gel, GANC and GANAB have been shown to have other differences, including those of substrate specificity. GANC and GANAB are key enzymes in glycogen metabolism that hydrolyze terminal, non-reducing 1,4-linked alpha-D-glucose residues from glycogen in the endoplasmic reticulum. The GANC/GANAB family includes the alpha-glucosidase II (ModA) from Dictyostelium discoideum as well as the alpha-glucosidase II (GLS2, or ROT2 - Reversal of TOR2 lethality protein 2) from Saccharomyces cerevisiae.
• pfam Glyco_hydro_31 446aa 1e-171 in ref transcript
  • Glycosyl hydrolases family 31. Glycosyl hydrolases are key enzymes of carbohydrate metabolism. Family 31 comprises of enzymes that are, or similar to, alpha- galactosidases.
• COG COG1501 634aa 1e-147 in ref transcript
  • Alpha-glucosidases, family 31 of glycosyl hydrolases [Carbohydrate transport and metabolism].

GARNL1

• refseq_GARNL1.F1 refseq_GARNL1.R1 121 152
• NCBIGene 36.3 253959
• Single exon skipping, size difference: 31
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_194301

• pfam Rap_GAP 180aa 2e-19 in ref transcript
  • Rap/ran-GAP.

GCDH

• refseq_GCDH.F1 refseq_GCDH.R1 160 392
• NCBIGene 36.3 2639
• Alternative 3-prime, size difference: 232
• Exclusion of the stop codon
• Reference transcript: NM_000159

• Changed! cd GCD 387aa 0.0 in ref transcript
  • Glutaryl-CoA dehydrogenase (GCD). GCD is an acyl-CoA dehydrogenase, which catalyzes the oxidative decarboxylation of glutaryl-CoA to crotonyl-CoA and carbon dioxide in the catabolism of lysine, hydroxylysine, and tryptophan. It uses electron transfer flavoprotein (ETF) as an electron acceptor. GCD is a homotetramer. GCD deficiency leads to a severe neurological disorder in humans.
• pfam Acyl-CoA_dh_N 112aa 4e-32 in ref transcript
  • Acyl-CoA dehydrogenase, N-terminal domain. The N-terminal domain of Acyl-CoA dehydrogenase is an all-alpha domain.
• Changed! TIGR cyc_hxne_CoA_dh 367aa 1e-25 in ref transcript
  • Cyclohex-1-ene-1carboxyl-CoA is an intermediate in the anaerobic degradation of benzoyl-CoA derived from varioius aromatic compounds, in Rhodopseudomonas palustris but not Thauera aromatica. The aliphatic compound cyclohexanecarboxylate, can be converted to the same intermediate in two steps. The first step is its ligation to coenzyme A. The second is the action of this enzyme, cyclohexanecarboxyl-CoA dehydrogenase.
• Changed! COG CaiA 375aa 2e-70 in ref transcript
  • Acyl-CoA dehydrogenases [Lipid metabolism].
• Changed! cd GCD 367aa 1e-180 in modified transcript
• Changed! TIGR cyc_hxne_CoA_dh 300aa 1e-25 in modified transcript
• Changed! COG CaiA 355aa 1e-65 in modified transcript

GCET2

• refseq_GCET2.F2 refseq_GCET2.R2 318 485
• NCBIGene 36.3 257144
• Alternative 3-prime, size difference: 167
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_152785

GCH1

• refseq_GCH1.F1 refseq_GCH1.R1 101 375
• NCBIGene 36.3 2643
• Alternative 3-prime, size difference: 274
• Exclusion of the stop codon
• Reference transcript: NM_000161

• Changed! cd GTP_cyclohydro1 168aa 7e-83 in ref transcript
  • GTP cyclohydrolase I (GTP-CH-I) catalyzes the conversion of GTP into dihydroneopterin triphosphate. The enzyme product is the precursor of tetrahydrofolate in eubacteria, fungi, and plants and of the folate analogs in methanogenic bacteria. In vertebrates and insects it is the biosynthtic precursor of tetrahydrobiopterin (BH4) which is involved in the formation of catacholamines, nitric oxide, and the stimulation of T lymphocytes. The biosynthetic reaction of BH4 is controlled by a regulatory protein GFRP which mediates feedback inhibition of GTP-CH-I by BH4. This inhibition is reversed by phenylalanine. The decameric GTP-CH-I forms a complex with two pentameric GFRP in the presence of phenylalanine or a combination of GTP and BH4, respectively.
• Changed! TIGR folE 168aa 1e-73 in ref transcript
  • GTP cyclohydrolase I (EC 3.5.4.16) catalyzes the biosynthesis of formic acid and dihydroneopterin triphosphate from GTP. This reaction is the first step in the biosynthesis of tetrahydrofolate in prokaryotes, of tetrahydrobiopterin in vertebrates, and of pteridine-containing pigments in insects.
• Changed! PRK folE 168aa 4e-81 in ref transcript
  • GTP cyclohydrolase I; Provisional.
• Changed! cd GTP_cyclohydro1 127aa 9e-62 in modified transcript
• Changed! TIGR folE 127aa 2e-53 in modified transcript
• Changed! PRK folE 127aa 3e-59 in modified transcript
• Changed! PRK PRK01297 54aa 0.010 in modified transcript
  • ATP-dependent RNA helicase RhlB; Provisional.

GEM

• refseq_GEM.F2 refseq_GEM.R2 110 225
• NCBIGene 36.3 2669
• Alternative 5-prime, size difference: 115
• Exclusion in 5'UTR
• Reference transcript: NM_005261

• cd RGK 221aa 1e-99 in ref transcript
  • RGK subfamily. The RGK (Rem, Rem2, Rad, Gem/Kir) subfamily of Ras GTPases are expressed in a tissue-specific manner and are dynamically regulated by transcriptional and posttranscriptional mechanisms in response to environmental cues. RGK proteins bind to the beta subunit of L-type calcium channels, causing functional down-regulation of these voltage-dependent calcium channels, and either termination of calcium-dependent secretion or modulation of electrical conduction and contractile function. Inhibition of L-type calcium channels by Rem2 may provide a mechanism for modulating calcium-triggered exocytosis in hormone-secreting cells, and has been proposed to influence the secretion of insulin in pancreatic beta cells. RGK proteins also interact with and inhibit the Rho/Rho kinase pathway to modulate remodeling of the cytoskeleton. Two characteristics of RGK proteins cited in the literature are N-terminal and C-terminal extensions beyond the GTPase domain typical of Ras superfamily members. The N-terminal extension is not conserved among family members; the C-terminal extension is reported to be conserved among the family and lack the CaaX prenylation motif typical of membrane-associated Ras proteins. However, a putative CaaX motif has been identified in the alignment of the C-terminal residues of this CD.
• smart RAS 165aa 2e-34 in ref transcript
  • Ras subfamily of RAS small GTPases. Similar in fold and function to the bacterial EF-Tu GTPase. p21Ras couples receptor Tyr kinases and G protein receptors to protein kinase cascades.
• COG COG1100 191aa 1e-13 in ref transcript
  • GTPase SAR1 and related small G proteins [General function prediction only].

GEMIN7

• refseq_GEMIN7.F2 refseq_GEMIN7.R2 272 395
• NCBIGene 36.3 79760
• Single exon skipping, size difference: 123
• Exclusion in 5'UTR
• Reference transcript: NM_024707

GFM2

• refseq_GFM2.F1 refseq_GFM2.R1 168 309
• NCBIGene 36.3 84340
• Single exon skipping, size difference: 141
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_032380

• cd EF-G 281aa 1e-125 in ref transcript
  • Elongation factor G (EF-G) subfamily. Translocation is mediated by EF-G (also called translocase). The structure of EF-G closely resembles that of the complex between EF-Tu and tRNA. This is an example of molecular mimicry; a protein domain evolved so that it mimics the shape of a tRNA molecule. EF-G in the GTP form binds to the ribosome, primarily through the interaction of its EF-Tu-like domain with the 50S subunit. The binding of EF-G to the ribosome in this manner stimulates the GTPase activity of EF-G. On GTP hydrolysis, EF-G undergoes a conformational change that forces its arm deeper into the A site on the 30S subunit. To accommodate this domain, the peptidyl-tRNA in the A site moves to the P site, carrying the mRNA and the deacylated tRNA with it. The ribosome may be prepared for these rearrangements by the initial binding of EF-G as well. The dissociation of EF-G leaves the ribosome ready to accept the next aminoacyl-tRNA into the A site. This group contains both eukaryotic and bacterial members.
• cd mtEFG2_like_IV 121aa 1e-44 in ref transcript
  • mtEF-G2 domain IV. This subfamily is a part the of mitochondrial transcriptional elongation factor, mtEF-G2. Mitochondrial translation is crucial for maintaining mitochondrial function and mutations in this system lead to a breakdown in the respiratory chain-oxidative phosphorylation system and to impaired maintenance of mitochondrial DNA. In complex with GTP, EF-G promotes the translocation step of translation. During translocation the peptidyl-tRNA is moved from the A site to the P site of the small subunit of ribosome and the mRNA is shifted one codon relative to the ribosome.
• Changed! cd mtEFG2_II_like 82aa 3e-35 in ref transcript
  • mtEFG2_C: C-terminus of mitochondrial Elongation factor G2 (mtEFG2)-like proteins found in eukaryotes. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. Eukaryotic EF-2 operates in the cytosolic protein synthesis machinery of eukaryotes, EF-Gs in protein synthesis in bacteria. Eukaryotic mtEFG1 proteins show significant homology to bacterial EF-Gs. No clear phenotype has been found for mutants in the yeast homologue of mtEFG2, MEF2. There are two forms of mtEFG present in mammals (designated mtEFG1s and mtEFG2s) mtEFG1s are not present in this group.
• cd EFG_mtEFG_C 77aa 1e-21 in ref transcript
  • EFG_mtEFG_C: domains similar to the C-terminal domain of the bacterial translational elongation factor (EF) EF-G. Included in this group is the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2) proteins. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. During the process of peptide synthesis and tRNA site changes, the ribosome is moved along the mRNA a distance equal to one codon with the addition of each amino acid. In bacteria this translocation step is catalyzed by EF-G_GTP, which is hydrolyzed to provide the required energy. Thus, this action releases the uncharged tRNA from the P site and transfers the newly formed peptidyl-tRNA from the A site to the P site. Eukaryotic mtEFG1 proteins show significant homology to bacterial EF-Gs. Mutants in yeast mtEFG1 have impaired mitochondrial protein synthesis, respiratory defects and a tendency to lose mitochondrial DNA. No clear phenotype has been found for mutants in the yeast homologue of mtEFG2, MEF2.
• Changed! TIGR EF-G 695aa 1e-157 in ref transcript
  • After peptide bond formation, this elongation factor of bacteria and organelles catalyzes the translocation of the tRNA-mRNA complex, with its attached nascent polypeptide chain, from the A-site to the P-site of the ribosome. Every completed bacterial genome has at least one copy, but some species have additional EF-G-like proteins. The closest homolog to canonical (e.g. E. coli) EF-G in the spirochetes clusters as if it is derived from mitochondrial forms, while a more distant second copy is also present. Synechocystis PCC6803 has a few proteins more closely related to EF-G than to any other characterized protein. Two of these resemble E. coli EF-G more closely than does the best match from the spirochetes; it may be that both function as authentic EF-G.
• Changed! PRK PRK12739 712aa 0.0 in ref transcript
  • elongation factor G; Reviewed.
• Changed! cd mtEFG2_II_like 41aa 1e-13 in modified transcript
• Changed! TIGR EF-G 289aa 4e-89 in modified transcript
• Changed! TIGR EF-G 353aa 6e-55 in modified transcript
• Changed! COG FusA 663aa 1e-132 in modified transcript
  • Translation elongation factors (GTPases) [Translation, ribosomal structure and biogenesis].

GFRA4

• refseq_GFRA4.F2 refseq_GFRA4.R2 288 378
• NCBIGene 36.3 64096
• Intron retention, size difference: 79
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_145762

• Changed! pfam GDNF 80aa 0.001 in ref transcript
  • GDNF/GAS1 domain. This cysteine rich domain is found in multiple copies in GNDF and GAS1 proteins. GDNF and neurturin (NTN) receptors are potent survival factors for sympathetic, sensory and central nervous system neurons. GDNF and neurturin promote neuronal survival by signaling through similar multicomponent receptors that consist of a common receptor tyrosine kinase and a member of a GPI-linked family of receptors that determines ligand specificity.
• Changed! pfam GDNF 60aa 7e-04 in modified transcript

GGA1

• refseq_GGA1.F1 refseq_GGA1.R1 100 361
• NCBIGene 36.3 26088
• Multiple exon skipping, size difference: 261
• Exclusion in the protein (no frameshift), Exclusion in the protein (no frameshift)
• Reference transcript: NM_013365

• cd VHS_GGA 139aa 3e-64 in ref transcript
  • VHS domain family, GGA subfamily; GGA (Golgi-localized, Gamma-ear-containing, Arf-binding) comprise a subfamily of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins. The VHS domain has a superhelical structure similar to the structure of the ARM (Armadillo) repeats and is present at the N-termini of proteins. GGA proteins have a multidomain structure consisting of an N-terminal VHS domain linked by a short proline-rich linker to a GAT (GGA and TOM) domain, which is followed by a long flexible linker to the C-terminal appendage, GAE (gamma-adaptin ear) domain. The VHS domain of GGA proteins binds to the acidic-cluster dileucine (DxxLL) motif found on the cytoplasmic tails of cargo proteins trafficked between the trans-Golgi network and the endosomal system.
• pfam VHS 135aa 1e-38 in ref transcript
  • VHS domain. Domain present in VPS-27, Hrs and STAM.
• Changed! pfam GAT 97aa 6e-27 in ref transcript
  • GAT domain. The GAT domain is responsible for binding of GGA proteins to several members of the ARF family including ARF1 and ARF3. The GAT domain stabilises membrane bound ARF1 in its GTP bound state, by interfering with GAP proteins.
• pfam Alpha_adaptinC2 124aa 7e-24 in ref transcript
  • Adaptin C-terminal domain. Alpha adaptin is a heterotetramer which regulates clathrin-bud formation. The carboxyl-terminal appendage of the alpha subunit regulates translocation of endocytic accessory proteins to the bud site. This ig-fold domain is found in alpha, beta and gamma adaptins.
• Changed! pfam GAT 73aa 2e-16 in modified transcript

GGA3

• refseq_GGA3.F1 refseq_GGA3.R1 127 226
• NCBIGene 36.3 23163
• Single exon skipping, size difference: 99
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_138619

• Changed! cd VHS_GGA 139aa 9e-69 in ref transcript
  • VHS domain family, GGA subfamily; GGA (Golgi-localized, Gamma-ear-containing, Arf-binding) comprise a subfamily of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins. The VHS domain has a superhelical structure similar to the structure of the ARM (Armadillo) repeats and is present at the N-termini of proteins. GGA proteins have a multidomain structure consisting of an N-terminal VHS domain linked by a short proline-rich linker to a GAT (GGA and TOM) domain, which is followed by a long flexible linker to the C-terminal appendage, GAE (gamma-adaptin ear) domain. The VHS domain of GGA proteins binds to the acidic-cluster dileucine (DxxLL) motif found on the cytoplasmic tails of cargo proteins trafficked between the trans-Golgi network and the endosomal system.
• Changed! pfam VHS 135aa 3e-48 in ref transcript
  • VHS domain. Domain present in VPS-27, Hrs and STAM.
• pfam GAT 95aa 4e-30 in ref transcript
  • GAT domain. The GAT domain is responsible for binding of GGA proteins to several members of the ARF family including ARF1 and ARF3. The GAT domain stabilises membrane bound ARF1 in its GTP bound state, by interfering with GAP proteins.
• pfam Alpha_adaptinC2 124aa 3e-26 in ref transcript
  • Adaptin C-terminal domain. Alpha adaptin is a heterotetramer which regulates clathrin-bud formation. The carboxyl-terminal appendage of the alpha subunit regulates translocation of endocytic accessory proteins to the bud site. This ig-fold domain is found in alpha, beta and gamma adaptins.
• Changed! cd VHS_GGA 106aa 4e-43 in modified transcript
• Changed! smart VHS 132aa 5e-29 in modified transcript
  • Domain present in VPS-27, Hrs and STAM. Unpublished observations. Domain of unknown function.

GGPS1

• refseq_GGPS1.F1 refseq_GGPS1.R1 235 328
• NCBIGene 36.3 9453
• Single exon skipping, size difference: 93
• Exclusion of the protein initiation site
• Reference transcript: NM_004837

• Changed! cd Trans_IPPS_HT 212aa 4e-52 in ref transcript
  • Trans-Isoprenyl Diphosphate Synthases (Trans_IPPS), head-to-tail (HT) (1'-4) condensation reactions. This CD includes all-trans (E)-isoprenyl diphosphate synthases which synthesis various chain length (C10, C15, C20, C25, C30, C35, C40, C45, and C50) linear isoprenyl diphosphates from precursors, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). They catalyze the successive 1'-4 condensation of the 5-carbon IPP to allylic substrates geranyl-, farnesyl-, or geranylgeranyl-diphosphate. Isoprenoid chain elongation reactions proceed via electrophilic alkylations in which a new carbon-carbon single bond is generated through interaction between a highly reactive electron-deficient allylic carbocation and an electron-rich carbon-carbon double bond. The catalytic site consists of a large central cavity formed by mostly antiparallel alpha helices with two aspartate-rich regions (DDXX(XX)D) located on opposite walls. These residues mediate binding of prenyl phosphates via bridging Mg2+ ions, inducing proposed conformational changes that close the active site to solvent, protecting and stabilizing reactive carbocation intermediates. Farnesyl diphosphate synthases produce the precursors of steroids, cholesterol, sesquiterpenes, farnsylated proteins, heme, and vitamin K12; and geranylgeranyl diphosphate and longer chain synthases produce the precursors of carotenoids, retinoids, diterpenes, geranylgeranylated chlorophylls, ubiquinone, and archaeal ether linked lipids. Isoprenyl diphosphate synthases are widely distributed among archaea, bacteria, and eukareya.
• Changed! pfam polyprenyl_synt 251aa 4e-43 in ref transcript
  • Polyprenyl synthetase.
• Changed! COG IspA 277aa 1e-38 in ref transcript
  • Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism].
• Changed! cd Trans_IPPS_HT 167aa 2e-43 in modified transcript
• Changed! pfam polyprenyl_synt 208aa 5e-36 in modified transcript
• Changed! COG IspA 233aa 8e-34 in modified transcript

GGT1

• refseq_GGT1.F1 refseq_GGT1.R1 364 472
• NCBIGene 36.3 2678
• Alternative 3-prime, size difference: 108
• Inclusion in 5'UTR
• Reference transcript: NM_001032364

• pfam G_glu_transpept 508aa 1e-174 in ref transcript
  • Gamma-glutamyltranspeptidase.
• COG Ggt 543aa 1e-124 in ref transcript
  • Gamma-glutamyltransferase [Amino acid transport and metabolism].

GH2

• refseq_GH2.F1 refseq_GH2.R1 207 252
• NCBIGene 36.3 2689
• Alternative 3-prime, size difference: 45
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_022557

• Changed! pfam Hormone_1 131aa 3e-26 in ref transcript
  • Somatotropin hormone family.
• Changed! pfam Hormone_1 116aa 8e-23 in modified transcript

GIMAP6

• refseq_GIMAP6.F1 refseq_GIMAP6.R1 100 324
• NCBIGene 36.3 474344
• Alternative 3-prime, size difference: 224
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_024711

• Changed! cd AIG1 196aa 1e-78 in ref transcript
  • AIG1 (avrRpt2-induced gene 1). This represents Arabidoposis protein AIG1 that appears to be involved in plant resistance to bacteria. The Arabidopsis disease resistance gene RPS2 is involved in recognition of bacterial pathogens carrying the avirulence gene avrRpt2. AIG1 exhibits RPS2- and avrRpt1-dependent induction early after infection with Pseudomonas syringae carrying avrRpt2. This subfamily also includes IAN-4 protein, which has GTP-binding activity and shares sequence homology with a novel family of putative GTP-binding proteins: the immuno-associated nucleotide (IAN) family. The evolutionary conservation of the IAN family provides a unique example of a plant pathogen response gene conserved in animals. The IAN/IMAP subfamily has been proposed to regulate apoptosis in vertebrates and angiosperm plants, particularly in relation to cancer, diabetes, and infections. The human IAN genes were renamed GIMAP (GTPase of the immunity associated proteins).
• Changed! pfam AIG1 209aa 4e-73 in ref transcript
  • AIG1 family. Arabidopsis protein AIG1 appears to be involved in plant resistance to bacteria.
• Changed! PRK rbgA 87aa 3e-04 in ref transcript
  • ribosomal biogenesis GTPase; Reviewed.

GIPC1

• refseq_GIPC1.F1 refseq_GIPC1.R1 100 418
• NCBIGene 36.3 10755
• Single exon skipping, size difference: 318
• Exclusion of the protein initiation site
• Reference transcript: NM_202468

• cd PDZ_signaling 79aa 8e-08 in ref transcript
  • PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of PDZ domains an N-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in proteases.
• smart PDZ 82aa 5e-09 in ref transcript
  • Domain present in PSD-95, Dlg, and ZO-1/2. Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities.

GIT2

• refseq_GIT2.F1 refseq_GIT2.R1 249 339
• NCBIGene 36.3 9815
• Single exon skipping, size difference: 90
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_057169

• cd ANK 112aa 1e-11 in ref transcript
  • ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats.
• smart ArfGap 119aa 4e-39 in ref transcript
  • Putative GTP-ase activating proteins for the small GTPase, ARF. Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs.
• pfam GIT_SHD 31aa 1e-07 in ref transcript
  • Spa2 homology domain (SHD) of GIT. GIT proteins are signaling integrators with GTPase-activating function which may be involved in the organisation of the cytoskeletal matrix assembled at active zones (CAZ). The function of the CAZ might be to define sites of neurotransmitter release. Mutations in the Spa2 homology domain (SHD) domain of GIT1 described here interfere with the association of GIT1 with Piccolo, beta-PIX, and focal adhesion kinase.
• pfam GIT_SHD 22aa 7e-04 in ref transcript
• COG COG5347 115aa 2e-15 in ref transcript
  • GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion].
• PTZ PTZ00322 102aa 2e-06 in ref transcript
  • 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase; Provisional.

GIT2

• refseq_GIT2.F3 refseq_GIT2.R2 101 485
• NCBIGene 36.3 9815
• Exon skipping and alternative 3-prime or 5-prime, size difference: 384
• Exclusion in the protein (no frameshift), Exclusion in the protein (no frameshift), Exclusion in the protein (no frameshift)
• Reference transcript: NM_057169

• cd ANK 112aa 1e-11 in ref transcript
  • ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats.
• smart ArfGap 119aa 4e-39 in ref transcript
  • Putative GTP-ase activating proteins for the small GTPase, ARF. Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs.
• pfam GIT_SHD 31aa 1e-07 in ref transcript
  • Spa2 homology domain (SHD) of GIT. GIT proteins are signaling integrators with GTPase-activating function which may be involved in the organisation of the cytoskeletal matrix assembled at active zones (CAZ). The function of the CAZ might be to define sites of neurotransmitter release. Mutations in the Spa2 homology domain (SHD) domain of GIT1 described here interfere with the association of GIT1 with Piccolo, beta-PIX, and focal adhesion kinase.
• pfam GIT_SHD 22aa 7e-04 in ref transcript
• COG COG5347 115aa 2e-15 in ref transcript
  • GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion].
• PTZ PTZ00322 102aa 2e-06 in ref transcript
  • 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase; Provisional.

GIT2

• refseq_GIT2.F4 refseq_GIT2.R3 180 330
• NCBIGene 36.3 9815
• Single exon skipping, size difference: 150
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_057169

• cd ANK 112aa 1e-11 in ref transcript
  • ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats.
• smart ArfGap 119aa 4e-39 in ref transcript
  • Putative GTP-ase activating proteins for the small GTPase, ARF. Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs.
• pfam GIT_SHD 31aa 1e-07 in ref transcript
  • Spa2 homology domain (SHD) of GIT. GIT proteins are signaling integrators with GTPase-activating function which may be involved in the organisation of the cytoskeletal matrix assembled at active zones (CAZ). The function of the CAZ might be to define sites of neurotransmitter release. Mutations in the Spa2 homology domain (SHD) domain of GIT1 described here interfere with the association of GIT1 with Piccolo, beta-PIX, and focal adhesion kinase.
• pfam GIT_SHD 22aa 7e-04 in ref transcript
• COG COG5347 115aa 2e-15 in ref transcript
  • GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion].
• PTZ PTZ00322 102aa 2e-06 in ref transcript
  • 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase; Provisional.

GIYD2

• refseq_GIYD1.F1 refseq_GIYD1.R1 99 441
• NCBIGene 36.3 79008
• Single exon skipping, size difference: 342
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_024044

• Changed! pfam GIY-YIG 77aa 3e-10 in ref transcript
  • GIY-YIG catalytic domain. This domain called GIY-YIG is found in the amino terminal region of excinuclease abc subunit c (uvrC), bacteriophage T4 endonucleases segA, segB, segC, segD and segE; it is also found in putative endonucleases encoded by group I introns of fungi and phage. The structure of I-TevI a GIY-YIG endonuclease, reveals a novel alpha/beta-fold with a central three-stranded antiparallel beta-sheet flanked by three helices. The most conserved and putative catalytic residues are located on a shallow, concave surface and include a metal coordination site.
• Changed! PRK PRK00329 69aa 1e-05 in ref transcript
  • GIY-YIG nuclease superfamily protein; Validated.
• Changed! pfam GIY-YIG 62aa 2e-07 in modified transcript
• Changed! PRK PRK00329 67aa 3e-05 in modified transcript

GK

• refseq_GK.F1 refseq_GK.R1 102 120
• NCBIGene 36.3 2710
• Single exon skipping, size difference: 18
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_203391

• Changed! TIGR glycerol_kin 509aa 0.0 in ref transcript
  • This model describes glycerol kinase, a member of the FGGY family of carbohydrate kinases.
• Changed! PRK glpK 508aa 0.0 in ref transcript
  • glycerol kinase; Provisional.
• Changed! TIGR glycerol_kin 503aa 0.0 in modified transcript
• Changed! PRK glpK 502aa 0.0 in modified transcript

GLT8D1

• refseq_GLT8D1.F1 refseq_GLT8D1.R1 176 405
• NCBIGene 36.3 55830
• Single exon skipping, size difference: 229
• Exclusion in 5'UTR
• Reference transcript: NM_001010983

• cd GT8_like_1 286aa 2e-89 in ref transcript
  • GT8_like_1 represents a subfamily of GT8 with unknown function. A subfamily of glycosyltransferase family 8 with unknown function: Glycosyltransferase family 8 comprises enzymes with a number of known activities; lipopolysaccharide galactosyltransferase lipopolysaccharide glucosyltransferase 1, glycogenin glucosyltransferase and inositol 1-alpha-galactosyltransferase. It is classified as a retaining glycosyltransferase, based on the relative anomeric stereochemistry of the substrate and product in the reaction catalyzed.
• pfam Glyco_transf_8 274aa 2e-45 in ref transcript
  • Glycosyl transferase family 8. This family includes enzymes that transfer sugar residues to donor molecules. Members of this family are involved in lipopolysaccharide biosynthesis and glycogen synthesis. This family includes Lipopolysaccharide galactosyltransferase, lipopolysaccharide glucosyltransferase 1, and glycogenin glucosyltransferase.
• COG RfaJ 286aa 3e-15 in ref transcript
  • Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane].

GLUL

• refseq_GLUL.F1 refseq_GLUL.R1 100 456
• NCBIGene 36.3 2752
• Single exon skipping, size difference: 356
• Exclusion in 5'UTR
• Reference transcript: NM_002065

• pfam Gln-synt_C 252aa 1e-69 in ref transcript
  • Glutamine synthetase, catalytic domain.
• pfam Gln-synt_N 81aa 2e-26 in ref transcript
  • Glutamine synthetase, beta-Grasp domain.
• COG GlnA 349aa 3e-61 in ref transcript
  • Glutamine synthetase [Amino acid transport and metabolism].

GMEB1

• refseq_GMEB1.F1 refseq_GMEB1.R1 141 171
• NCBIGene 36.3 10691
• Alternative 3-prime, size difference: 30
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_006582

• pfam SAND 81aa 2e-30 in ref transcript
  • SAND domain. The DNA binding activity of two proteins has been mapped to the SAND domain. The conserved KDWK motif is necessary for DNA binding, and it appears to be important for dimerisation.

GMPPA

• refseq_GMPPA.F1 refseq_GMPPA.R1 106 417
• NCBIGene 36.3 29926
• Alternative 5-prime and 3-prime, size difference: 311
• Inclusion in 5'UTR, Exclusion in 5'UTR
• Reference transcript: NM_205847

• cd M1P_guanylylT_A_like_N 258aa 1e-136 in ref transcript
  • N-terminal domain of M1P_guanylyl_A_ like proteins are likely to be a isoform of GDP-mannose pyrophosphorylase. N-terminal domain of the M1P-guanylyltransferase A-isoform like proteins: The proteins of this family are likely to be a isoform of GDP-mannose pyrophosphorylase. Their sequences are highly conserved with mannose-1-phosphate guanyltransferase, but generally about 40-60 bases longer. GDP-mannose pyrophosphorylase (GTP: alpha-d-mannose-1-phosphate guanyltransferase) catalyzes the formation of GDP-d-mannose from GTP and alpha-d-mannose-1-Phosphate. It contains an N-terminal catalytic domain that resembles a dinucleotide-binding Rossmann fold and a C-terminal LbH fold domain. GDP-d-mannose is the activated form of mannose for formation of cell wall lipoarabinomannan and various mannose-containing glycolipids and polysaccharides. The function of GDP-mannose pyrophosphorylase is essential for cell wall integrity, morphogenesis and viability. Repression of GDP-mannose pyrophosphorylase in yeast leads to phenotypes including cell lysis, defective cell wall, and failure of polarized growth and cell separation.
• cd LbH_M1P_guanylylT_C 67aa 1e-19 in ref transcript
  • Mannose-1-phosphate guanylyltransferase, C-terminal Left-handed parallel beta helix (LbH) domain: Mannose-1-phosphate guanylyltransferase is also known as GDP-mannose pyrophosphorylase. It catalyzes the synthesis of GDP-mannose from GTP and mannose-1-phosphate, and is involved in the maintenance of cell wall integrity and glycosylation. Similar to ADP-glucose pyrophosphorylase, it contains an N-terminal catalytic domain that resembles a dinucleotide-binding Rossmann fold and a C-terminal LbH fold domain, presumably with 4 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes showing acyltransferase activity.
• pfam NTP_transferase 189aa 2e-25 in ref transcript
  • Nucleotidyl transferase. This family includes a wide range of enzymes which transfer nucleotides onto phosphosugars.
• TIGR lipid_A_lpxA 53aa 3e-07 in ref transcript
  • This model describes LpxA, an enzyme for the biosynthesis of lipid A, a component oflipopolysaccharide (LPS) in the outer membrane outer leaflet of most Gram-negative bacteria. Some differences are found between lipid A of different species, but this protein represents the first step (from UDP-N-acetyl-D-glucosamine) and appears to be conserved in function. Proteins from this family contain many copies of the bacterial transferase hexapeptide repeat (pfam00132).
• COG GCD1 349aa 1e-52 in ref transcript
  • Nucleoside-diphosphate-sugar pyrophosphorylase involved in lipopolysaccharide biosynthesis/translation initiation factor 2B, gamma/epsilon subunits (eIF-2Bgamma/eIF-2Bepsilon) [Cell envelope biogenesis, outer membrane / Translation, ribosomal structure and biogenesis].

GMPR2

• refseq_GMPR2.F1 refseq_GMPR2.R1 193 252
• NCBIGene 36.3 51292
• Alternative 5-prime, size difference: 59
• Exclusion in 5'UTR
• Reference transcript: NM_001002000

• cd IMPDH 327aa 5e-98 in ref transcript
  • IMPDH: The catalytic domain of the inosine monophosphate dehydrogenase. IMPDH catalyzes the NAD-dependent oxidation of inosine 5'-monophosphate (IMP) to xanthosine 5' monophosphate (XMP). It is a rate-limiting step in the de novo synthesis of the guanine nucleotides. There is often a CBS domain inserted in the middle of this domain, which is proposed to play a regulatory role. IMPDH is a key enzyme in the regulation of cell proliferation and differentiation. It has been identified as an attractive target for developing chemotherapeutic agents.
• TIGR GMP_reduct_1 341aa 1e-179 in ref transcript
  • A deep split separates two families of GMP reductase. This family includes both eukaryotic and some proteobacterial sequences, while the other family contains other bacterial sequences.
• PRK PRK05096 342aa 0.0 in ref transcript
  • guanosine 5'-monophosphate oxidoreductase; Provisional.

GNAS

• refseq_GNAS.F1 refseq_GNAS.R1 238 280
• NCBIGene 36.3 2778
• Mutually exclusive exon skipping, size difference: 42
• Inclusion in the protein (no stop codon or frameshift), Exclusion in the protein (no frameshift)
• Reference transcript: NM_000516

• Changed! cd G-alpha 350aa 1e-138 in ref transcript
  • G protein alpha subunit. The alpha subunit of G proteins contains the guanine nucleotide binding site. The heterotrimeric GNP-binding proteins are signal transducers that communicate signals from many hormones, neurotransmitters, chemokines, and autocrine and paracrine factors. Extracellular signals are received by receptors, which activate the G proteins, which in turn route the signals to several distinct intracellular signaling pathways. The alpha subunit of G proteins is a weak GTPase. In the resting state, heterotrimeric G proteins are associated at the cytosolic face of the plasma membrane and the alpha subunit binds to GDP. Upon activation by a receptor GDP is replaced with GTP, and the G-alpha/GTP complex dissociates from the beta and gamma subunits. This results in activation of downstream signaling pathways, such as cAMP synthesis by adenylyl cyclase, which is terminated when GTP is hydrolized and the heterotrimers reconstitute.
• Changed! pfam G-alpha 372aa 1e-143 in ref transcript
  • G-protein alpha subunit. G proteins couple receptors of extracellular signals to intracellular signaling pathways. The G protein alpha subunit binds guanyl nucleotide and is a weak GTPase.
• PTZ PTZ00133 80aa 1e-04 in ref transcript
  • ADP-ribosylation factor; Provisional.
• Changed! cd G-alpha 336aa 1e-139 in modified transcript
• Changed! pfam G-alpha 358aa 1e-143 in modified transcript

GNLY

• refseq_GNLY.F1 refseq_GNLY.R1 112 356
• NCBIGene 36.3 10578
• Single exon skipping, size difference: 244
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_006433

• Changed! smart SapB 71aa 4e-08 in ref transcript
  • Saposin (B) Domains. Present in multiple copies in prosaposin and in pulmonary surfactant-associated protein B. In plant aspartic proteinases, a saposin domain is circularly permuted. This causes the prediction algorithm to predict two such domains, where only one is truly present.

GNRHR

• refseq_GNRHR.F1 refseq_GNRHR.R1 229 357
• NCBIGene 36.3 2798
• Alternative 3-prime, size difference: 128
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_000406

• Changed! pfam 7tm_1 218aa 2e-22 in ref transcript
  • 7 transmembrane receptor (rhodopsin family). This family contains, amongst other G-protein-coupled receptors (GCPRs), members of the opsin family, which have been considered to be typical members of the rhodopsin superfamily. They share several motifs, mainly the seven transmembrane helices, GCPRs of the rhodopsin superfamily. All opsins bind a chromophore, such as 11-cis-retinal. The function of most opsins other than the photoisomerases is split into two steps: light absorption and G-protein activation. Photoisomerases, on the other hand, are not coupled to G-proteins - they are thought to generate and supply the chromophore that is used by visual opsins.
• Changed! pfam 7tm_1 70aa 3e-09 in modified transcript

GOPC

• refseq_GOPC.F1 refseq_GOPC.R1 136 160
• NCBIGene 36.3 57120
• Single exon skipping, size difference: 24
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_020399

• cd PDZ_signaling 83aa 2e-17 in ref transcript
  • PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of PDZ domains an N-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in proteases.
• smart PDZ 84aa 8e-16 in ref transcript
  • Domain present in PSD-95, Dlg, and ZO-1/2. Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities.
• COG COG3975 207aa 0.001 in ref transcript
  • Predicted protease with the C-terminal PDZ domain [General function prediction only].
• Changed! PRK PRK09039 178aa 0.006 in ref transcript
  • hypothetical protein; Validated.
• Changed! PRK PRK09039 170aa 2e-04 in modified transcript

GPATCH4

• refseq_GPATC4.F2 refseq_GPATC4.R2 118 192
• NCBIGene 36.3 54865
• Alternative 3-prime, size difference: 74
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_015590

• Changed! pfam G-patch 44aa 7e-06 in ref transcript
  • G-patch domain. This domain is found in a number of RNA binding proteins, and is also found in proteins that contain RNA binding domains. This suggests that this domain may have an RNA binding function. This domain has seven highly conserved glycines.

GPHN

• refseq_GPHN.F2 refseq_GPHN.R2 296 395
• NCBIGene 36.3 10243
• Single exon skipping, size difference: 99
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_020806

• cd MoeA 407aa 1e-118 in ref transcript
  • MoeA family. Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF), an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and eukaryotes. MoCF contains a tricyclic pyranopterin, termed molybdopterin (MPT). MoeA, together with MoaB, is responsible for the metal incorporation into MPT, the third step in MoCF biosynthesis. The plant homolog Cnx1 is a MoeA-MogA fusion protein. The mammalian homolog gephyrin is a MogA-MoeA fusion protein, that plays a critical role in postsynaptic anchoring of inhibitory glycine receptors and major GABAa receptor subtypes.
• cd MogA_MoaB 155aa 5e-51 in ref transcript
  • MogA_MoaB family. Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF) an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea, and eukaryotes. MoCF contains a tricyclic pyranopterin, termed molybdopterin (MPT). MogA, together with MoeA, is responsible for the metal incorporation into MPT, the third step in MoCF biosynthesis. The plant homolog Cnx1 is a MoeA-MogA fusion protein. The mammalian homolog gephyrin is a MogA-MoeA fusion protein, that plays a critical role in postsynaptic anchoring of inhibitory glycine receptors and major GABAa receptor subtypes. In contrast, MoaB shows high similarity to MogA, but little is known about its physiological role. All well studied members of this family form highly stable trimers.
• pfam MoeA_N 167aa 2e-51 in ref transcript
  • MoeA N-terminal region (domain I and II). This family contains two structural domains. One of these contains the conserved DGXA motif. This region is found in proteins involved in biosynthesis of molybdopterin cofactor however the exact molecular function of this region is uncertain.
• TIGR molyb_syn 146aa 1e-33 in ref transcript
  • The Drosophila protein cinnamon, the Arabidopsis protein cnx1, and rat protein gephyrin each have one domain like MoeA and one like MoaB and Mog. These domains are, however, distantly related to each other, as captured by this HMM. Gephyrin is unusual in that it seems to be a tubulin-binding neuroprotein involved in the clustering of both blycine receptors and GABA receptors, rather than a protein of molybdenum cofactor biosynthesis.
• TIGR molyb_syn 143aa 1e-30 in ref transcript
• pfam MoeA_C 77aa 1e-13 in ref transcript
  • MoeA C-terminal region (domain IV). This domain is found in proteins involved in biosynthesis of molybdopterin cofactor however the exact molecular function of this domain is uncertain. The structure of this domain is known and forms an incomplete beta barrel.
• COG MoeA 410aa 1e-92 in ref transcript
  • Molybdopterin biosynthesis enzyme [Coenzyme metabolism].
• PRK moaC 158aa 2e-37 in ref transcript
  • bifunctional molybdenum cofactor biosynthesis protein C/molybdopterin-binding protein; Provisional.

GPM6A

• refseq_GPM6A.F2 refseq_GPM6A.R2 333 392
• NCBIGene 36.3 2823
• Single exon skipping, size difference: 59
• Exclusion of the protein initiation site
• Reference transcript: NM_005277

• Changed! pfam Myelin_PLP 242aa 3e-89 in ref transcript
  • Myelin proteolipid protein (PLP or lipophilin).
• Changed! pfam Myelin_PLP 242aa 2e-87 in modified transcript

GPM6B

• refseq_GPM6B.F1 refseq_GPM6B.R1 220 340
• NCBIGene 36.3 2824
• Single exon skipping, size difference: 120
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001001995

• Changed! pfam Myelin_PLP 245aa 1e-127 in ref transcript
  • Myelin proteolipid protein (PLP or lipophilin).
• Changed! pfam Myelin_PLP 245aa 1e-123 in modified transcript

GPNMB

• refseq_GPNMB.F1 refseq_GPNMB.R1 181 217
• NCBIGene 36.3 10457
• Alternative 3-prime, size difference: 36
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001005340

• cd PKD 64aa 2e-05 in ref transcript
  • polycystic kidney disease I (PKD) domain; similar to other cell-surface modules, with an IG-like fold; domain probably functions as a ligand binding site in protein-protein or protein-carbohydrate interactions; a single instance of the repeat is presented here. The domain is also found in microbial collagenases and chitinases.
• smart PKD 58aa 6e-06 in ref transcript
  • Repeats in polycystic kidney disease 1 (PKD1) and other proteins. Polycystic kidney disease 1 protein contains 14 repeats, present elsewhere such as in microbial collagenases.
• TIGR PCC 114aa 0.004 in ref transcript
  • Note: this model is restricted to the amino half because a full-length model is incompatible with the HMM software package.

GPR108

• refseq_GPR108.F1 refseq_GPR108.R1 257 399
• NCBIGene 36.2 56927
• Alternative 3-prime, size difference: 142
• Inclusion in the protein causing a new stop codon
• Reference transcript: XM_933929

• pfam Lung_7-TM_R 289aa 5e-85 in ref transcript
  • Lung seven transmembrane receptor. This family represents a conserved region with eukaryotic lung seven transmembrane receptors and related proteins.

GPR126

• refseq_GPR126.F2 refseq_GPR126.R2 148 232
• NCBIGene 36.3 57211
• Single exon skipping, size difference: 84
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_198569

• cd CUB 104aa 8e-25 in ref transcript
  • CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.
• cd PTX 185aa 1e-07 in ref transcript
  • Pentraxins are plasma proteins characterized by their pentameric discoid assembly and their Ca2+ dependent ligand binding, such as Serum amyloid P component (SAP) and C-reactive Protein (CRP), which are cytokine-inducible acute-phase proteins implicated in innate immunity. CRP binds to ligands containing phosphocholine, SAP binds to amyloid fibrils, DNA, chromatin, fibronectin, C4-binding proteins and glycosaminoglycans. "Long" pentraxins have N-terminal extensions to the common pentraxin domain; one group, the neuronal pentraxins, may be involved in synapse formation and remodeling, and they may also be able to form heteromultimers.
• pfam 7tm_2 259aa 9e-32 in ref transcript
  • 7 transmembrane receptor (Secretin family). This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling.
• smart CUB 97aa 9e-26 in ref transcript
  • Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. This domain is found mostly among developmentally-regulated proteins. Spermadhesins contain only this domain.
• pfam GPS 49aa 3e-10 in ref transcript
  • Latrophilin/CL-1-like GPS domain. Domain present in latrophilin/CL-1, sea urchin REJ and polycystin.
• smart PTX 185aa 3e-08 in ref transcript
  • Pentraxin / C-reactive protein / pentaxin family. This family form a doscoid pentameric structure. Human serum amyloid P demonstrates calcium-mediated ligand-binding.

GPR126

• refseq_GPR126.F3 refseq_GPR126.R3 169 215
• NCBIGene 36.3 57211
• Single exon skipping, size difference: 46
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_198569

• cd CUB 104aa 8e-25 in ref transcript
  • CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.
• cd PTX 185aa 1e-07 in ref transcript
  • Pentraxins are plasma proteins characterized by their pentameric discoid assembly and their Ca2+ dependent ligand binding, such as Serum amyloid P component (SAP) and C-reactive Protein (CRP), which are cytokine-inducible acute-phase proteins implicated in innate immunity. CRP binds to ligands containing phosphocholine, SAP binds to amyloid fibrils, DNA, chromatin, fibronectin, C4-binding proteins and glycosaminoglycans. "Long" pentraxins have N-terminal extensions to the common pentraxin domain; one group, the neuronal pentraxins, may be involved in synapse formation and remodeling, and they may also be able to form heteromultimers.
• pfam 7tm_2 259aa 9e-32 in ref transcript
  • 7 transmembrane receptor (Secretin family). This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling.
• smart CUB 97aa 9e-26 in ref transcript
  • Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. This domain is found mostly among developmentally-regulated proteins. Spermadhesins contain only this domain.
• pfam GPS 49aa 3e-10 in ref transcript
  • Latrophilin/CL-1-like GPS domain. Domain present in latrophilin/CL-1, sea urchin REJ and polycystin.
• smart PTX 185aa 3e-08 in ref transcript
  • Pentraxin / C-reactive protein / pentaxin family. This family form a doscoid pentameric structure. Human serum amyloid P demonstrates calcium-mediated ligand-binding.

GPR155

• refseq_GPR155.F2 refseq_GPR155.R2 223 372
• NCBIGene 36.3 151556
• Single exon skipping, size difference: 149
• Exclusion in 5'UTR
• Reference transcript: NM_001033045

• cd DEP_GPR155 83aa 4e-41 in ref transcript
  • DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in GPR155-like proteins. GRP155-like proteins, also known as PGR22, contain an N-terminal permease domain, a central transmembrane region and a C-terminal DEP domain. They are orphan receptors of the class B G protein-coupled receptors. Their function is unknown.
• TIGR 2a69 329aa 2e-17 in ref transcript
• smart DEP 68aa 6e-10 in ref transcript
  • Domain found in Dishevelled, Egl-10, and Pleckstrin. Domain of unknown function present in signalling proteins that contain PH, rasGEF, rhoGEF, rhoGAP, RGS, PDZ domains. DEP domain in Drosophila dishevelled is essential to rescue planar polarity defects and induce JNK signalling (Cell 94, 109-118).
• COG COG0679 329aa 4e-19 in ref transcript
  • Predicted permeases [General function prediction only].

GPER

• refseq_GPR30.F2 refseq_GPR30.R2 276 400
• NCBIGene 36.3 2852
• Single exon skipping, size difference: 124
• Exclusion in 5'UTR
• Reference transcript: NM_001039966

• pfam 7tm_1 243aa 1e-34 in ref transcript
  • 7 transmembrane receptor (rhodopsin family). This family contains, amongst other G-protein-coupled receptors (GCPRs), members of the opsin family, which have been considered to be typical members of the rhodopsin superfamily. They share several motifs, mainly the seven transmembrane helices, GCPRs of the rhodopsin superfamily. All opsins bind a chromophore, such as 11-cis-retinal. The function of most opsins other than the photoisomerases is split into two steps: light absorption and G-protein activation. Photoisomerases, on the other hand, are not coupled to G-proteins - they are thought to generate and supply the chromophore that is used by visual opsins.

GPR56

• refseq_GPR56.F1 refseq_GPR56.R1 275 397
• NCBIGene 36.3 9289
• Single exon skipping, size difference: 122
• Exclusion in 5'UTR
• Reference transcript: NM_201524

• pfam 7tm_2 250aa 3e-25 in ref transcript
  • 7 transmembrane receptor (Secretin family). This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling.
• pfam GPS 47aa 3e-09 in ref transcript
  • Latrophilin/CL-1-like GPS domain. Domain present in latrophilin/CL-1, sea urchin REJ and polycystin.

GPR56

• refseq_GPR56.F3 refseq_GPR56.R3 100 118
• NCBIGene 36.3 9289
• Alternative 3-prime, size difference: 18
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_005682

• Changed! pfam 7tm_2 256aa 1e-24 in ref transcript
  • 7 transmembrane receptor (Secretin family). This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling.
• pfam GPS 47aa 3e-09 in ref transcript
  • Latrophilin/CL-1-like GPS domain. Domain present in latrophilin/CL-1, sea urchin REJ and polycystin.
• Changed! pfam 7tm_2 250aa 3e-25 in modified transcript

GPRASP2

• refseq_GPRASP2.F1 refseq_GPRASP2.R1 128 216
• NCBIGene 36.3 114928
• Single exon skipping, size difference: 88
• Exclusion in 5'UTR
• Reference transcript: NM_001004051

• pfam DUF634 245aa 1e-53 in ref transcript
  • Protein of unknown function (DUF634). Mammalian protein of unknown function.
• PRK PRK12323 129aa 0.008 in ref transcript
  • DNA polymerase III subunits gamma and tau; Provisional.

GPX4

• refseq_GPX4.F2 refseq_GPX4.R2 102 124
• NCBIGene 36.3 2879
• Alternative 3-prime, size difference: 22
• Inclusion in 3'UTR
• Reference transcript: NM_001039848

• cd GSH_Peroxidase 33aa 2e-08 in ref transcript
  • Glutathione (GSH) peroxidase family; tetrameric selenoenzymes that catalyze the reduction of a variety of hydroperoxides including lipid peroxidases, using GSH as a specific electron donor substrate. GSH peroxidase contains one selenocysteine residue per subunit, which is involved in catalysis. Different isoenzymes are known in mammals,which are involved in protection against reactive oxygen species, redox regulation of many metabolic processes, peroxinitrite scavenging, and modulation of inflammatory processes.
• pfam GSHPx 32aa 1e-10 in ref transcript
  • Glutathione peroxidase.
• COG BtuE 33aa 2e-05 in ref transcript
  • Glutathione peroxidase [Posttranslational modification, protein turnover, chaperones].

GPX5

• refseq_GPX5.F2 refseq_GPX5.R2 128 246
• NCBIGene 36.3 2880
• Single exon skipping, size difference: 118
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_001509

• Changed! cd GSH_Peroxidase 173aa 5e-45 in ref transcript
  • Glutathione (GSH) peroxidase family; tetrameric selenoenzymes that catalyze the reduction of a variety of hydroperoxides including lipid peroxidases, using GSH as a specific electron donor substrate. GSH peroxidase contains one selenocysteine residue per subunit, which is involved in catalysis. Different isoenzymes are known in mammals,which are involved in protection against reactive oxygen species, redox regulation of many metabolic processes, peroxinitrite scavenging, and modulation of inflammatory processes.
• Changed! pfam GSHPx 114aa 4e-42 in ref transcript
  • Glutathione peroxidase.
• Changed! COG BtuE 179aa 2e-33 in ref transcript
  • Glutathione peroxidase [Posttranslational modification, protein turnover, chaperones].
• Changed! cd GSH_Peroxidase 52aa 9e-09 in modified transcript
• Changed! pfam GSHPx 51aa 4e-11 in modified transcript
• Changed! COG BtuE 52aa 2e-07 in modified transcript

GRB10

• refseq_GRB10.F1 refseq_GRB10.R1 142 280
• NCBIGene 36.3 2887
• Single exon skipping, size difference: 138
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_005311

• cd GRB7_RA 83aa 2e-32 in ref transcript
  • Grb7_RA The RA (RAS-associated like) domain of Grb7. Grb7 is an adaptor molecule that mediates signal transduction from multiple cell surface receptors to various downstream signaling pathways. Grb7 and its related family members Grb10 and Grb14 share a conserved domain architecture that includes an amino-terminal proline-rich region, a central segment termed the GM region (for Grb and Mig) which includes the RA, PIR, and PH domains, and a carboxyl-terminal SH2 domain. Grb7/10/14 family proteins are phosphorylated on serine/threonine as well as tyrosine residues and are mainly localized to the cytoplasm.
• Changed! cd PH_Apbb1ip 113aa 8e-20 in ref transcript
  • Apbb1ip (Amyloid beta (A4) Precursor protein-Binding, family B, member 1 Interacting Protein) pleckstrin homology (PH) domain. Apbb1ip consists of a Ras-associated domain and a PH domain. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
• cd SH2 97aa 9e-18 in ref transcript
  • Src homology 2 domains; Signal transduction, involved in recognition of phosphorylated tyrosine (pTyr). SH2 domains typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites.
• smart SH2 90aa 2e-21 in ref transcript
  • Src homology 2 domains. Src homology 2 domains bind phosphotyrosine-containing polypeptides via 2 surface pockets. Specificity is provided via interaction with residues that are distinct from the phosphotyrosine. Only a single occurrence of a SH2 domain has been found in S. cerevisiae.
• pfam BPS 48aa 5e-19 in ref transcript
  • BPS (Between PH and SH2). The BPS (Between PH and SH2) domain, comprised of 2 beta strands and a C-terminal helix, is an approximately 45 residue region found in the adaptor proteins Grb7/10/14 that mediates inhibition of the tyrosine kinase domain of the insulin receptor by binding of the N-terminal portion of the BPS domain to the substrate peptide groove of the kinase, acting as a pseudosubstrate inhibitor.
• smart RA 84aa 1e-13 in ref transcript
  • Ras association (RalGDS/AF-6) domain. RasGTP effectors (in cases of AF6, canoe and RalGDS); putative RasGTP effectors in other cases. Kalhammer et al. have shown that not all RA domains bind RasGTP. Predicted structure similar to that determined, and that of the RasGTP-binding domain of Raf kinase. Predicted RA domains in PLC210 and nore1 found to bind RasGTP. Included outliers (Grb7, Grb14, adenylyl cyclases etc.).
• Changed! smart PH 109aa 6e-09 in ref transcript
  • Pleckstrin homology domain. Domain commonly found in eukaryotic signalling proteins. The domain family possesses multiple functions including the abilities to bind inositol phosphates, and various proteins. PH domains have been found to possess inserted domains (such as in PLC gamma, syntrophins) and to be inserted within other domains. Mutations in Brutons tyrosine kinase (Btk) within its PH domain cause X-linked agammaglobulinaemia (XLA) in patients. Point mutations cluster into the positively charged end of the molecule around the predicted binding site for phosphatidylinositol lipids.
• Changed! cd PH_Apbb1ip 74aa 8e-08 in modified transcript

GRB2

• refseq_GRB2.F2 refseq_GRB2.R2 240 363
• NCBIGene 36.3 2885
• Single exon skipping, size difference: 123
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_002086

• Changed! cd SH2 91aa 2e-21 in ref transcript
  • Src homology 2 domains; Signal transduction, involved in recognition of phosphorylated tyrosine (pTyr). SH2 domains typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites.
• cd SH3 53aa 1e-13 in ref transcript
  • Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
• cd SH3 52aa 3e-11 in ref transcript
• Changed! pfam SH2 76aa 9e-27 in ref transcript
  • SH2 domain.
• smart SH3 57aa 4e-16 in ref transcript
  • Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.
• pfam SH3_1 56aa 1e-13 in ref transcript
  • SH3 domain. SH3 (Src homology 3) domains are often indicative of a protein involved in signal transduction related to cytoskeletal organisation. First described in the Src cytoplasmic tyrosine kinase. The structure is a partly opened beta barrel.
• Changed! cd SH2 49aa 6e-04 in modified transcript
• Changed! pfam SH2 35aa 1e-05 in modified transcript

GRHL1

• refseq_GRHL1.F1 refseq_GRHL1.R1 211 288
• NCBIGene 36.3 29841
• Single exon skipping, size difference: 77
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_014552

• Changed! pfam CP2 229aa 1e-108 in ref transcript
  • CP2 transcription factor. This family represents a conserved region in the CP2 transcription factor family.

GRHL3

• refseq_GRHL3.F1 refseq_GRHL3.R1 107 294
• NCBIGene 36.3 57822
• Single exon skipping, size difference: 187
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_021180

• Changed! pfam CP2 227aa 2e-96 in ref transcript
  • CP2 transcription factor. This family represents a conserved region in the CP2 transcription factor family.

GRIK1

• refseq_GRIK1.F1 refseq_GRIK1.R1 140 185
• NCBIGene 36.3 2897
• Single exon skipping, size difference: 45
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000830

• Changed! cd PBP1_iGluR_Kainate_GluR5_7 396aa 0.0 in ref transcript
  • N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR5-7 subunits of Kainate receptor. While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. There are five types of kainate receptors, GluR5, GluR6, GluR7, KA1, and KA2, which are structurally similar to AMPA and NMDA subunits of ionotropic glutamate receptors. KA1 and KA2 subunits can only form functional receptors with one of the GluR5-7 subunits. Moreover, GluR5-7 can also form functional homomeric receptor channels activated by kainate and glutamate when expressed in heterologous systems. Kainate receptors are involved in excitatory neurotransmission by activating postsynaptic receptors and in inhibitory neurotransmission by modulating release of the inhibitory neurotransmitter GABA through a presynaptic mechanism. Kainate receptors are closely related to AMAP receptors. In contrast of AMPA receptors, kainate receptors play only a minor role in signaling at synapses and their function is not well defined.
• cd PBPb 117aa 1e-10 in ref transcript
  • Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD.
• pfam Lig_chan 282aa 1e-105 in ref transcript
  • Ligand-gated ion channel. This family includes the four transmembrane regions of the ionotropic glutamate receptors and NMDA receptors.
• pfam ANF_receptor 341aa 8e-51 in ref transcript
  • Receptor family ligand binding region. This family includes extracellular ligand binding domains of a wide range of receptors. This family also includes the bacterial amino acid binding proteins of known structure.
• pfam Lig_chan-Glu_bd 65aa 9e-27 in ref transcript
  • Ligated ion channel L-glutamate- and glycine-binding site. This region, sometimes called the S1 domain, is the luminal domain just upstream of the first, M1, transmembrane region of transmembrane ion-channel proteins, and it binds L-glutamate and glycine. It is found in association with Lig_chan, pfam00060.
• COG HisJ 91aa 2e-05 in ref transcript
  • ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms].
• Changed! COG LivK 300aa 3e-04 in ref transcript
  • ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism].
• Changed! cd PBP1_iGluR_Kainate_GluR5_7 381aa 0.0 in modified transcript
• Changed! COG LivK 307aa 1e-04 in modified transcript

GRIK2

• refseq_GRIK2.F1 refseq_GRIK2.R1 315 402
• NCBIGene 36.3 2898
• Single exon skipping, size difference: 87
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_021956

• cd PBP1_iGluR_Kainate_GluR5_7 381aa 0.0 in ref transcript
  • N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR5-7 subunits of Kainate receptor. While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. There are five types of kainate receptors, GluR5, GluR6, GluR7, KA1, and KA2, which are structurally similar to AMPA and NMDA subunits of ionotropic glutamate receptors. KA1 and KA2 subunits can only form functional receptors with one of the GluR5-7 subunits. Moreover, GluR5-7 can also form functional homomeric receptor channels activated by kainate and glutamate when expressed in heterologous systems. Kainate receptors are involved in excitatory neurotransmission by activating postsynaptic receptors and in inhibitory neurotransmission by modulating release of the inhibitory neurotransmitter GABA through a presynaptic mechanism. Kainate receptors are closely related to AMAP receptors. In contrast of AMPA receptors, kainate receptors play only a minor role in signaling at synapses and their function is not well defined.
• cd PBPb 118aa 8e-11 in ref transcript
  • Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD.
• pfam Lig_chan 282aa 1e-106 in ref transcript
  • Ligand-gated ion channel. This family includes the four transmembrane regions of the ionotropic glutamate receptors and NMDA receptors.
• pfam ANF_receptor 344aa 2e-55 in ref transcript
  • Receptor family ligand binding region. This family includes extracellular ligand binding domains of a wide range of receptors. This family also includes the bacterial amino acid binding proteins of known structure.
• pfam Lig_chan-Glu_bd 66aa 1e-26 in ref transcript
  • Ligated ion channel L-glutamate- and glycine-binding site. This region, sometimes called the S1 domain, is the luminal domain just upstream of the first, M1, transmembrane region of transmembrane ion-channel proteins, and it binds L-glutamate and glycine. It is found in association with Lig_chan, pfam00060.
• COG LivK 235aa 9e-08 in ref transcript
  • ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism].
• COG HisJ 121aa 4e-05 in ref transcript
  • ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms].

GRIN1

• refseq_GRIN1.F2 refseq_GRIN1.R2 190 301
• NCBIGene 36.3 2902
• Single exon skipping, size difference: 111
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_007327

• cd PBP1_iGluR_NMDA_NR1 376aa 0.0 in ref transcript
  • N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NR1, an essential channel-forming subunit of the NMDA receptor. The ionotropic N-methyl-d-asparate (NMDA) subtype of glutamate receptor serves critical functions in neuronal development, functioning, and degeneration in the mammalian central nervous system. The functional NMDA receptor is a heterotetramer ccomposed of two NR1 and two NR2 (A, B, C, and D) or of NR3 (A and B) subunits. The receptor controls a cation channel that is highly permeable to monovalent ions and calcium and exhibits voltage-dependent inhibition by magnesium. Dual agonists, glutamate and glycine, are required for efficient activation of the NMDA receptor. When co-expressed with NR1, the NR3 subunits form receptors that are activated by glycine alone and therefore can be classified as excitatory glycine receptors. NR1/NR3 receptors are calcium-impermeable and unaffected by ligands acting at the NR2 glutamate-binding site.
• cd PBPb 96aa 2e-09 in ref transcript
  • Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD.
• cd PBPb 111aa 6e-04 in ref transcript
• pfam Lig_chan 276aa 7e-79 in ref transcript
  • Ligand-gated ion channel. This family includes the four transmembrane regions of the ionotropic glutamate receptors and NMDA receptors.
• pfam ANF_receptor 316aa 5e-28 in ref transcript
  • Receptor family ligand binding region. This family includes extracellular ligand binding domains of a wide range of receptors. This family also includes the bacterial amino acid binding proteins of known structure.
• pfam Lig_chan-Glu_bd 58aa 6e-16 in ref transcript
  • Ligated ion channel L-glutamate- and glycine-binding site. This region, sometimes called the S1 domain, is the luminal domain just upstream of the first, M1, transmembrane region of transmembrane ion-channel proteins, and it binds L-glutamate and glycine. It is found in association with Lig_chan, pfam00060.
• pfam CaM_bdg_C0 29aa 9e-08 in ref transcript
  • Calmodulin-binding domain C0 of NMDA receptor NR1 subunit. This is a very short highly conserved domain that is C-terminal to the cytosolic transmembrane region IV of the NMDA-receptor 1. It has been shown to bind Calmodulin-Calcium with high affinity. The ionotropic N-methyl-D-aspartate receptor (NMDAR) is a major source of calcium flux into neurons in the brain and plays a critical role in learning, memory, neural development, and synaptic plasticity. Calmodulin (CaM) regulates NMDARs by binding tightly to the C0 and C1 regions of their NR1 subunit. The conserved tryptophan is considered to be the anchor residue.
• COG LivK 320aa 1e-10 in ref transcript
  • ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism].
• COG HisJ 89aa 1e-05 in ref transcript
  • ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms].
• COG HisJ 82aa 0.002 in ref transcript

GRINA

• refseq_GRINA.F2 refseq_GRINA.R2 164 276
• NCBIGene 36.3 2907
• Alternative 5-prime, size difference: 112
• Exclusion in 5'UTR
• Reference transcript: NM_000837

• cd BI-1-like 162aa 6e-40 in ref transcript
  • BAX inhibitor (BI)-1 like protein family. Mammalian members of this family of small transmembrane proteins have been shown to have an antiapoptotic effect either by stimulating the antiapoptotic function of Bcl-2, a well characterized oncogene, or inhibiting the proapoptotic effect of Bax, another member of the Bcl-2 family. Their broad tissue distribution and high degree of conservation suggests an important regulatory role. In plants, BI-1 like proteins play a role in pathogen resistance. A prokaryotic member, E.coli YccA, has been shown to interact with ATP-dependent protease FtsH, which degrades abnormal membrane proteins as part of a quality control mechanism to keep the integrity of biological membranes.
• pfam UPF0005 167aa 8e-28 in ref transcript
  • Uncharacterised protein family UPF0005. The Pfam entry finds members not in the Prosite definition.
• COG COG0670 114aa 2e-10 in ref transcript
  • Integral membrane protein, interacts with FtsH [General function prediction only].

GRINL1A

• refseq_GRINL1A.F1 refseq_GRINL1A.R1 198 384
• NCBIGene 36.3 81488
• Alternative 5-prime, size difference: 186
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_015532

GRIP1

• refseq_GRIP1.F1 refseq_GRIP1.R1 180 225
• NCBIGene 36.2 23426
• Single exon skipping, size difference: 45
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: XM_001133924

• cd PDZ_signaling 84aa 2e-14 in ref transcript
  • PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of PDZ domains an N-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in proteases.
• cd PDZ_signaling 82aa 1e-13 in ref transcript
• cd PDZ_signaling 85aa 8e-12 in ref transcript
• cd PDZ_signaling 81aa 2e-11 in ref transcript
• cd PDZ_signaling 71aa 1e-10 in ref transcript
• cd PDZ_signaling 84aa 3e-10 in ref transcript
• cd PDZ_signaling 81aa 2e-09 in ref transcript
• smart PDZ 89aa 2e-16 in ref transcript
  • Domain present in PSD-95, Dlg, and ZO-1/2. Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities.
• smart PDZ 82aa 6e-15 in ref transcript
• smart PDZ 86aa 2e-11 in ref transcript
• smart PDZ 87aa 3e-11 in ref transcript
• smart PDZ 77aa 5e-10 in ref transcript
• smart PDZ 85aa 5e-10 in ref transcript
• smart PDZ 71aa 8e-09 in ref transcript
• COG Prc 78aa 7e-05 in ref transcript
  • Periplasmic protease [Cell envelope biogenesis, outer membrane].
• COG Prc 127aa 1e-04 in ref transcript

GRIP1

• refseq_GRIP1.F3 refseq_GRIP1.R3 179 332
• NCBIGene 36.2 23426
• Exon skipping and alternative 3-prime or 5-prime, size difference: 153
• Inclusion in the protein (no stop codon or frameshift), Exclusion in the protein (no frameshift)
• Reference transcript: XM_001133924

• cd PDZ_signaling 84aa 2e-14 in ref transcript
  • PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of PDZ domains an N-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in proteases.
• cd PDZ_signaling 82aa 1e-13 in ref transcript
• cd PDZ_signaling 85aa 8e-12 in ref transcript
• cd PDZ_signaling 81aa 2e-11 in ref transcript
• cd PDZ_signaling 71aa 1e-10 in ref transcript
• cd PDZ_signaling 84aa 3e-10 in ref transcript
• cd PDZ_signaling 81aa 2e-09 in ref transcript
• smart PDZ 89aa 2e-16 in ref transcript
  • Domain present in PSD-95, Dlg, and ZO-1/2. Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities.
• smart PDZ 82aa 6e-15 in ref transcript
• smart PDZ 86aa 2e-11 in ref transcript
• smart PDZ 87aa 3e-11 in ref transcript
• smart PDZ 77aa 5e-10 in ref transcript
• smart PDZ 85aa 5e-10 in ref transcript
• smart PDZ 71aa 8e-09 in ref transcript
• COG Prc 78aa 7e-05 in ref transcript
  • Periplasmic protease [Cell envelope biogenesis, outer membrane].
• COG Prc 127aa 1e-04 in ref transcript

GRIPAP1

• refseq_GRIPAP1.F1 refseq_GRIPAP1.R1 125 284
• NCBIGene 36.3 56850
• Exon skipping and alternative 3-prime or 5-prime, size difference: 159
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_020137

GRIPAP1

• refseq_GRIPAP1.F3 refseq_GRIPAP1.R3 102 180
• NCBIGene 36.3 56850
• Single exon skipping, size difference: 78
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_020137

GRK4

• refseq_GRK4.F1 refseq_GRK4.R1 234 372
• NCBIGene 36.3 2868
• Single exon skipping, size difference: 138
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_182982

• cd STKc_GRK4 285aa 1e-144 in ref transcript
  • STKc_GRK4: Serine/Threonine Kinases (STKs), G protein-coupled Receptor Kinase (GRK) subfamily, GRK4 isoform, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The GRK subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. GRKs phosphorylate and regulate G protein-coupled receptors (GPCRs), the largest superfamily of cell surface receptors which regulate some part of nearly all physiological functions. Phosphorylated GPCRs bind to arrestins, which prevents further G protein signaling despite the presence of activating ligand. There are seven types of GRKs, named GRK1 to GRK7. GRK4 has a limited tissue distribution. It is mainly found in the testis, but is also present in the cerebellum and kidney. It is expressed as multiple splice variants with different domain architectures. It is post-translationally palmitoylated and localized in the membrane. GRK4 polymorphisms are associated with hypertension and salt sensitivity, as they cause hyperphosphorylation, desensitization, and internalization of the dopamine 1 (D1) receptor while increasing the expression of the angiotensin II type 1 receptor. GRK4 plays a crucial role in the D1 receptor regulation of sodium excretion and blood pressure.
• smart S_TKc 253aa 6e-60 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• smart RGS 120aa 2e-20 in ref transcript
  • Regulator of G protein signalling domain. RGS family members are GTPase-activating proteins for heterotrimeric G-protein alpha-subunits.
• PTZ PTZ00263 273aa 4e-40 in ref transcript
  • protein kinase A catalytic subunit; Provisional.

GRK4

• refseq_GRK4.F3 refseq_GRK4.R3 276 372
• NCBIGene 36.3 2868
• Single exon skipping, size difference: 96
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_182982

• cd STKc_GRK4 285aa 1e-144 in ref transcript
  • STKc_GRK4: Serine/Threonine Kinases (STKs), G protein-coupled Receptor Kinase (GRK) subfamily, GRK4 isoform, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The GRK subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. GRKs phosphorylate and regulate G protein-coupled receptors (GPCRs), the largest superfamily of cell surface receptors which regulate some part of nearly all physiological functions. Phosphorylated GPCRs bind to arrestins, which prevents further G protein signaling despite the presence of activating ligand. There are seven types of GRKs, named GRK1 to GRK7. GRK4 has a limited tissue distribution. It is mainly found in the testis, but is also present in the cerebellum and kidney. It is expressed as multiple splice variants with different domain architectures. It is post-translationally palmitoylated and localized in the membrane. GRK4 polymorphisms are associated with hypertension and salt sensitivity, as they cause hyperphosphorylation, desensitization, and internalization of the dopamine 1 (D1) receptor while increasing the expression of the angiotensin II type 1 receptor. GRK4 plays a crucial role in the D1 receptor regulation of sodium excretion and blood pressure.
• smart S_TKc 253aa 6e-60 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• smart RGS 120aa 2e-20 in ref transcript
  • Regulator of G protein signalling domain. RGS family members are GTPase-activating proteins for heterotrimeric G-protein alpha-subunits.
• PTZ PTZ00263 273aa 4e-40 in ref transcript
  • protein kinase A catalytic subunit; Provisional.

GRM7

• refseq_GRM7.F2 refseq_GRM7.R2 256 348
• NCBIGene 36.3 2917
• Single exon skipping, size difference: 92
• Exclusion of the stop codon
• Reference transcript: NM_181874

• cd PBP1_mGluR_groupIII 465aa 0.0 in ref transcript
  • Ligand-binding domain of the group III metabotropic glutamate receptor, a family which contains mGlu4R, mGluR6R, mGluR7, and mGluR8; all of which inhibit adenylyl cyclase. The metabotropic glutamate receptor is a member of the family C of G-protein-coupled receptors that transduce extracellular signals into G-protein activation and ultimately into intracellular responses. The mGluRs are classified into three groups which comprise eight subtypes.
• pfam 7tm_3 262aa 3e-96 in ref transcript
  • 7 transmembrane sweet-taste receptor of 3 GCPR. This is a domain of seven transmembrane regions that forms the C-terminus of some subclass 3 G-coupled-protein receptors. It is often associated with a downstream cysteine-rich linker domain, NCD3G pfam07562, which is the human sweet-taste receptor, and the N-terminal domain, ANF_receptor pfam01094. The seven TM regions assemble in such a way as to produce a docking pocket into which such molecules as cyclamate and lactisole have been found to bind and consequently confer the taste of sweetness.
• pfam ANF_receptor 408aa 2e-67 in ref transcript
  • Receptor family ligand binding region. This family includes extracellular ligand binding domains of a wide range of receptors. This family also includes the bacterial amino acid binding proteins of known structure.
• pfam NCD3G 52aa 1e-17 in ref transcript
  • Nine Cysteines Domain of family 3 GPCR. This conserved sequence contains several highly-conserved Cys residues that are predicted to form disulphide bridges. It is predicted to lie outside the cell membrane, tethered to the pfam00003 in several receptor proteins.
• COG LivK 310aa 9e-12 in ref transcript
  • ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism].

GRP

• refseq_GRP.F1 refseq_GRP.R1 99 120
• NCBIGene 36.3 2922
• Alternative 3-prime, size difference: 21
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_002091

GSG1

• refseq_GSG1.F2 refseq_GSG1.R2 184 308
• NCBIGene 36.3 83445
• Alternative 5-prime, size difference: 124
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_153823

• Changed! pfam GSG-1 117aa 6e-47 in ref transcript
  • GSG1-like protein. This family contains sequences bearing similarity to a region of GSG1, a protein specifically expressed in testicular germ cells. It is possible that overexpression of the human homolog may be involved in tumourigenesis of human testicular germ cell tumours. The region in question has four highly-conserved cysteine residues.
• Changed! pfam GSG-1 118aa 3e-46 in modified transcript

GSTZ1

• refseq_GSTZ1.F2 refseq_GSTZ1.R2 148 274
• NCBIGene 36.3 2954
• Single exon skipping, size difference: 126
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_145870

• Changed! cd GST_C_Zeta 115aa 2e-42 in ref transcript
  • GST_C family, Class Zeta subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins, and products of oxidative stress. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Class Zeta GSTs, also known as maleylacetoacetate (MAA) isomerases, catalyze the isomerization of MAA to fumarylacetoacetate, the penultimate step in tyrosine/phenylalanine catabolism, using GSH as a cofactor. They show little GSH-conjugating activity towards traditional GST substrates, but display modest GSH peroxidase activity. They are also implicated in the detoxification of the carcinogen dichloroacetic acid by catalyzing its dechlorination to glyoxylic acid.
• Changed! cd GST_N_Zeta 75aa 1e-31 in ref transcript
  • GST_N family, Class Zeta subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. The GST fold contains an N-terminal TRX-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. Class Zeta GSTs, also known as maleylacetoacetate (MAA) isomerases, catalyze the isomerization of MAA to fumarylacetoacetate, the penultimate step in tyrosine/phenylalanine catabolism, using GSH as a cofactor. They show little GSH-conjugating activity towards traditional GST substrates but display modest GSH peroxidase activity. They are also implicated in the detoxification of the carcinogen dichloroacetic acid by catalyzing its dechlorination to glyoxylic acid.
• Changed! TIGR maiA 205aa 4e-96 in ref transcript
  • Maleylacetoacetate isomerase is an enzyme of tyrosine and phenylalanine catabolism. It requires glutathione and belongs by homology to the zeta family of glutathione S-transferases. The enzyme (EC 5.2.1.2) is described as active also on maleylpyruvate, and the example from a Ralstonia sp. catabolic plasmid is described as a maleylpyruvate isomerase involved in gentisate catabolism.
• Changed! COG Gst 195aa 8e-32 in ref transcript
  • Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones].
• Changed! cd GST_C_Zeta 93aa 2e-33 in modified transcript
• Changed! cd GST_N_Zeta 67aa 5e-27 in modified transcript
• Changed! TIGR maiA 163aa 2e-69 in modified transcript
• Changed! COG Gst 153aa 2e-17 in modified transcript

GTDC1

• refseq_GTDC1.F1 refseq_GTDC1.R1 152 407
• NCBIGene 36.3 79712
• Multiple exon skipping, size difference: 255
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_001006636

• Changed! cd GT1_cap1E_like 90aa 1e-04 in ref transcript
  • This family is most closely related to the GT1 family of glycosyltransferases. cap1E in Streptococcus pneumoniae is required for the synthesis of type 1 capsular polysaccharides.
• Changed! pfam Glycos_transf_1 110aa 0.001 in ref transcript
  • Glycosyl transferases group 1. Mutations in this domain of subunit A of phosphatidylinositol N-acetylglucosaminyltransferase lead to disease (Paroxysmal Nocturnal haemoglobinuria). Members of this family transfer activated sugars to a variety of substrates, including glycogen, Fructose-6-phosphate and lipopolysaccharides. Members of this family transfer UDP, ADP, GDP or CMP linked sugars. The eukaryotic glycogen synthases may be distant members of this family.
• Changed! COG RfaG 175aa 1e-07 in ref transcript
  • Glycosyltransferase [Cell envelope biogenesis, outer membrane].

GTF2I

• refseq_GTF2I.F2 refseq_GTF2I.R2 111 174
• NCBIGene 36.3 2969
• Single exon skipping, size difference: 63
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_032999

• pfam GTF2I 73aa 6e-31 in ref transcript
  • GTF2I-like repeat. This region of sequence similarity is found up to six times in a variety of proteins including GTF2I. It has been suggested that this may be a DNA binding domain.
• pfam GTF2I 73aa 1e-30 in ref transcript
• pfam GTF2I 73aa 4e-30 in ref transcript
• pfam GTF2I 73aa 1e-29 in ref transcript
• pfam GTF2I 73aa 3e-26 in ref transcript
• pfam GTF2I 73aa 3e-26 in ref transcript

GTF2IRD1

• refseq_GTF2IRD1.F2 refseq_GTF2IRD1.R2 138 183
• NCBIGene 36.3 9569
• Alternative 3-prime, size difference: 45
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_016328

• pfam GTF2I 73aa 2e-29 in ref transcript
  • GTF2I-like repeat. This region of sequence similarity is found up to six times in a variety of proteins including GTF2I. It has been suggested that this may be a DNA binding domain.
• pfam GTF2I 73aa 3e-29 in ref transcript
• pfam GTF2I 73aa 3e-29 in ref transcript
• pfam GTF2I 73aa 5e-28 in ref transcript
• pfam GTF2I 73aa 2e-25 in ref transcript

GTF3C2

• refseq_GTF3C2.F2 refseq_GTF3C2.R2 195 271
• NCBIGene 36.3 2976
• Single exon skipping, size difference: 76
• Exclusion in 5'UTR
• Reference transcript: NM_001521

• cd WD40 90aa 1e-05 in ref transcript
  • WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.
• smart WD40 38aa 0.002 in ref transcript
  • WD40 repeats. Note that these repeats are permuted with respect to the structural repeats (blades) of the beta propeller domain.

GTPBP8

• refseq_GTPBP8.F1 refseq_GTPBP8.R1 117 248
• NCBIGene 36.2 29083
• Single exon skipping, size difference: 131
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_014170

• Changed! cd YihA_EngB 169aa 1e-50 in ref transcript
  • The YihA (EngB) subfamily. This subfamily of GTPases is typified by the E. coli YihA, an essential protein involved in cell division control. YihA and its orthologs are small proteins that typically contain less than 200 amino acid residues and consists of the GTPase domain only (some of the eukaryotic homologs contain an N-terminal extension of about 120 residues that might be involved in organellar targeting). Homologs of yihA are found in most Gram-positive and Gram-negative pathogenic bacteria, with the exception of Mycobacterium tuberculosis. The broad-spectrum nature of YihA and its essentiality for cell viability in bacteria make it an attractive antibacterial target.
• Changed! TIGR GTPase_YsxC 176aa 2e-47 in ref transcript
  • Members of this protein family are a GTPase associated with ribosome biogenesis, typified by YsxC from Bacillus subutilis. The family is widely but not universally distributed among bacteria. Members commonly are called EngB based on homology to EngA, one of several other GTPases of ribosome biogenesis. Cutoffs as set find essentially all bacterial members, but also identify large numbers of eukaryotic (probably organellar) sequences. This protein is found in about 80 percent of bacterial genomes.
• Changed! PRK engB 188aa 6e-50 in ref transcript
  • GTPase EngB; Reviewed.
• Changed! cd YihA_EngB 34aa 1e-09 in modified transcript
• Changed! TIGR GTPase_YsxC 51aa 7e-13 in modified transcript
• Changed! PRK engB 52aa 6e-14 in modified transcript

GTPBP8

• refseq_GTPBP8.F3 refseq_GTPBP8.R3 129 228
• NCBIGene 36.3 29083
• Single exon skipping, size difference: 99
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_014170

• Changed! cd YihA_EngB 169aa 1e-50 in ref transcript
  • The YihA (EngB) subfamily. This subfamily of GTPases is typified by the E. coli YihA, an essential protein involved in cell division control. YihA and its orthologs are small proteins that typically contain less than 200 amino acid residues and consists of the GTPase domain only (some of the eukaryotic homologs contain an N-terminal extension of about 120 residues that might be involved in organellar targeting). Homologs of yihA are found in most Gram-positive and Gram-negative pathogenic bacteria, with the exception of Mycobacterium tuberculosis. The broad-spectrum nature of YihA and its essentiality for cell viability in bacteria make it an attractive antibacterial target.
• Changed! TIGR GTPase_YsxC 176aa 2e-47 in ref transcript
  • Members of this protein family are a GTPase associated with ribosome biogenesis, typified by YsxC from Bacillus subutilis. The family is widely but not universally distributed among bacteria. Members commonly are called EngB based on homology to EngA, one of several other GTPases of ribosome biogenesis. Cutoffs as set find essentially all bacterial members, but also identify large numbers of eukaryotic (probably organellar) sequences. This protein is found in about 80 percent of bacterial genomes.
• Changed! PRK engB 188aa 6e-50 in ref transcript
  • GTPase EngB; Reviewed.
• Changed! cd YihA_EngB 135aa 4e-35 in modified transcript
• Changed! TIGR GTPase_YsxC 125aa 2e-28 in modified transcript
• Changed! PRK engB 155aa 1e-30 in modified transcript

GUSBL2

• refseq_GUSBL2.F1 refseq_GUSBL2.R1 163 316
• NCBIGene 36.2 375513
• Single exon skipping, size difference: 153
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_206910

GYPC

• refseq_GYPC.F1 refseq_GYPC.R1 125 182
• NCBIGene 36.3 2995
• Single exon skipping, size difference: 57
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_002101

• smart 4.1m 19aa 6e-04 in ref transcript
  • putative band 4.1 homologues' binding motif.

Gcom1

• refseq_Gcom1.F1 refseq_Gcom1.R1 113 206
• NCBIGene 36.2 145781
• Single exon skipping, size difference: 93
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001018090

• Changed! TIGR SMC_prok_B 250aa 2e-08 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• Changed! COG Smc 266aa 4e-05 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].
• Changed! TIGR SMC_prok_B 235aa 2e-05 in modified transcript
• Changed! COG Smc 206aa 4e-04 in modified transcript

Gcom1

• refseq_Gcom1.F3 refseq_Gcom1.R3 138 222
• NCBIGene 36.3 145781
• Single exon skipping, size difference: 84
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001018090

• Changed! TIGR SMC_prok_B 250aa 2e-08 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• Changed! COG Smc 266aa 4e-05 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].
• Changed! TIGR SMC_prok_B 294aa 2e-09 in modified transcript
• Changed! COG Smc 285aa 3e-06 in modified transcript

H2AFV

• refseq_H2AFV.F1 refseq_H2AFV.R1 226 304
• NCBIGene 36.3 94239
• Single exon skipping, size difference: 78
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_012412

• Changed! cd H2A 105aa 1e-37 in ref transcript
  • Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins.
• Changed! smart H2A 106aa 2e-43 in ref transcript
  • Histone 2A.
• Changed! PTZ PTZ00017 110aa 1e-46 in ref transcript
  • histone H2A; Provisional.
• Changed! cd H2A 95aa 1e-33 in modified transcript
• Changed! smart H2A 97aa 9e-39 in modified transcript
• Changed! PTZ PTZ00017 101aa 1e-42 in modified transcript

H2AFV

• refseq_H2AFV.F3 refseq_H2AFV.R3 121 251
• NCBIGene 36.3 94239
• Single exon skipping, size difference: 130
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_012412

• Changed! cd H2A 105aa 1e-37 in ref transcript
  • Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins.
• Changed! smart H2A 106aa 2e-43 in ref transcript
  • Histone 2A.
• Changed! PTZ PTZ00017 110aa 1e-46 in ref transcript
  • histone H2A; Provisional.
• Changed! cd H2A 49aa 8e-14 in modified transcript
• Changed! smart H2A 48aa 1e-17 in modified transcript
• Changed! PTZ PTZ00017 48aa 8e-17 in modified transcript

H2AFV

• refseq_H2AFV.F5 refseq_H2AFV.R5 134 248
• NCBIGene 36.3 94239
• Single exon skipping, size difference: 114
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_012412

• Changed! cd H2A 105aa 1e-37 in ref transcript
  • Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins.
• Changed! smart H2A 106aa 2e-43 in ref transcript
  • Histone 2A.
• Changed! PTZ PTZ00017 110aa 1e-46 in ref transcript
  • histone H2A; Provisional.
• Changed! cd H2A 58aa 5e-18 in modified transcript
• Changed! smart H2A 60aa 2e-19 in modified transcript
• Changed! PTZ PTZ00017 64aa 2e-24 in modified transcript

HSD17B10

• refseq_HADH2.F1 refseq_HADH2.R1 135 162
• NCBIGene 36.3 3028
• Alternative 5-prime, size difference: 27
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_004493

• Changed! TIGR 3oxo_ACP_reduc 210aa 2e-32 in ref transcript
  • This model represents 3-oxoacyl-[ACP] reductase, also called 3-ketoacyl-acyl carrier protein reductase, an enzyme of fatty acid biosynthesis.
• Changed! PRK fabG 254aa 2e-43 in ref transcript
  • 3-ketoacyl-(acyl-carrier-protein) reductase; Validated.
• Changed! TIGR 3oxo_ACP_reduc 201aa 2e-26 in modified transcript
• Changed! PRK fabG 245aa 4e-37 in modified transcript

HAGH

• refseq_HAGH.F2 refseq_HAGH.R2 292 388
• NCBIGene 36.3 3029
• Single exon skipping, size difference: 96
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_005326

• Changed! TIGR GSH_gloB 250aa 5e-70 in ref transcript
  • Members of this protein family are hydroxyacylglutathione hydrolase, a detoxification enzyme known as glyoxalase II. It follows lactoylglutathione lyase, or glyoxalase I, and acts to remove the toxic metabolite methylglyoxal and related compounds. This protein belongs to the broader metallo-beta-lactamase family (pfam00753).
• Changed! PRK PRK10241 255aa 9e-33 in ref transcript
  • hydroxyacylglutathione hydrolase; Provisional.

HAO2

• refseq_HAO2.F1 refseq_HAO2.R1 162 382
• NCBIGene 36.3 51179
• Single exon skipping, size difference: 220
• Exclusion of the protein initiation site
• Reference transcript: NM_001005783

• cd alpha_hydroxyacid_oxid_FMN 336aa 1e-120 in ref transcript
  • Family of homologous FMN-dependent alpha-hydroxyacid oxidizing enzymes. This family occurs in both prokaryotes and eukaryotes. Members of this family include flavocytochrome b2 (FCB2), glycolate oxidase (GOX), lactate monooxygenase (LMO), mandelate dehydrogenase (MDH), and long chain hydroxyacid oxidase (LCHAO). In green plants, glycolate oxidase is one of the key enzymes in photorespiration where it oxidizes glycolate to glyoxylate. LMO catalyzes the oxidation of L-lactate to acetate and carbon dioxide. MDH oxidizes (S)-mandelate to phenylglyoxalate. It is an enzyme in the mandelate pathway that occurs in several strains of Pseudomonas which converts (R)-mandelate to benzoate.
• pfam FMN_dh 336aa 1e-129 in ref transcript
  • FMN-dependent dehydrogenase.
• COG LldD 344aa 1e-81 in ref transcript
  • L-lactate dehydrogenase (FMN-dependent) and related alpha-hydroxy acid dehydrogenases [Energy production and conversion].

HAP1

• refseq_HAP1.F1 refseq_HAP1.R1 187 343
• NCBIGene 36.3 9001
• Single exon skipping, size difference: 156
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_003949

• Changed! pfam HAP1_N 354aa 1e-71 in ref transcript
  • HAP1 N-terminal conserved region. This family represents an N-terminal conserved region found in several huntingtin-associated protein 1 (HAP1) homologues. HAP1 binds to huntingtin in a polyglutamine repeat-length-dependent manner. However, its possible role in the pathogenesis of Huntington's disease is unclear. This family also includes a similar N-terminal conserved region from hypothetical protein products of ALS2CR3 genes found in the human juvenile amyotrophic lateral sclerosis critical region 2q33-2q34.
• Changed! COG Smc 148aa 4e-07 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].
• Changed! pfam HAP1_N 320aa 2e-65 in modified transcript
• Changed! COG Smc 133aa 4e-05 in modified transcript

HAT1

• refseq_HAT1.F2 refseq_HAT1.R2 315 391
• NCBIGene 36.3 8520
• Single exon skipping, size difference: 76
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_003642

• Changed! pfam Hat1_N 161aa 4e-50 in ref transcript
  • Histone acetyl transferase HAT1 N-terminus. This domain is the N-terminal half of the structure of histone acetyl transferase HAT1. It is often found in association with the C-terminal part of the GNAT Acetyltransf_1 (pfam00583) domain. It seems to be motifs C and D of the structure. Histone acetyltransferases (HATs) catalyse the transfer of an acetyl group from acetyl-CoA to the lysine E-amino groups on the N-terminal tails of histones. HATs are involved in transcription since histones tend to be hyper-acetylated in actively transcribed regions of chromatin, whereas in transcriptionally silent regions histones are hypo-acetylated.

HAX1

• refseq_HAX1.F1 refseq_HAX1.R1 232 376
• NCBIGene 36.3 10456
• Alternative 3-prime, size difference: 144
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_006118

HCFC1R1

• refseq_HCFC1R1.F1 refseq_HCFC1R1.R1 139 196
• NCBIGene 36.3 54985
• Single exon skipping, size difference: 57
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_017885

HDAC7A

• refseq_HDAC7A.F2 refseq_HDAC7A.R2 117 237
• NCBIGene 36.3 51564
• Single exon skipping, size difference: 111
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001098415

• pfam Hist_deacetyl 330aa 3e-82 in ref transcript
  • Histone deacetylase domain. Histones can be reversibly acetylated on several lysine residues. Regulation of transcription is caused in part by this mechanism. Histone deacetylases catalyse the removal of the acetyl group. Histone deacetylases are related to other proteins.
• COG AcuC 309aa 3e-57 in ref transcript
  • Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism].

N6AMT1

• refseq_HEMK2.F1 refseq_HEMK2.R1 121 205
• NCBIGene 36.3 29104
• Single exon skipping, size difference: 84
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_013240

• Changed! cd AdoMet_MTases 126aa 3e-04 in ref transcript
  • S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.).
• Changed! TIGR hemK_rel_arch 189aa 1e-23 in ref transcript
  • The gene hemK from E. coli was found to contribute to heme biosynthesis and originally suggested to be protoporphyrinogen oxidase. Functional analysis of the nearest homolog in Saccharomyces cerevisiae, YNL063w, finds it is not protoporphyrinogen oxidase and sequence analysis suggests that HemK homologs have S-adenosyl-methionine-dependent methyltransferase activity. Homologs are found, usually in a single copy, in nearly all completed genomes, but varying somewhat in apparent domain architecture. This model represents an archaeal and eukaryotic protein family that lacks an N-terminal domain found in HemK and its eubacterial homologs. It is found in a single copy in the first six completed archaeal and eukaryotic genomes.
• Changed! COG HemK 171aa 1e-23 in ref transcript
  • Methylase of polypeptide chain release factors [Translation, ribosomal structure and biogenesis].
• Changed! TIGR hemK_rel_arch 161aa 5e-15 in modified transcript
• Changed! COG HemK 143aa 4e-14 in modified transcript

HERC4

• refseq_HERC4.F2 refseq_HERC4.R2 182 342
• NCBIGene 36.2 26091
• Single exon skipping, size difference: 160
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_022079

• Changed! cd HECTc 347aa 1e-108 in ref transcript
  • HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ubiquitin molecules to the end of growing ubiquitin chains.
• Changed! pfam HECT 298aa 5e-93 in ref transcript
  • HECT-domain (ubiquitin-transferase). The name HECT comes from Homologous to the E6-AP Carboxyl Terminus.
• Changed! pfam RCC1 50aa 2e-07 in ref transcript
  • Regulator of chromosome condensation (RCC1).
• Changed! pfam RCC1 48aa 1e-05 in ref transcript
• Changed! pfam RCC1 48aa 0.004 in ref transcript
• Changed! pfam RCC1 50aa 0.006 in ref transcript
• Changed! COG HUL4 398aa 6e-78 in ref transcript
  • Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones].
• Changed! COG ATS1 251aa 3e-35 in ref transcript
  • Alpha-tubulin suppressor and related RCC1 domain-containing proteins [Cell division and chromosome partitioning / Cytoskeleton].
• Changed! COG ATS1 69aa 1e-09 in modified transcript

HERC4

• refseq_HERC4.F3 refseq_HERC4.R3 123 147
• NCBIGene 36.3 26091
• Single exon skipping, size difference: 24
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_022079

• cd HECTc 347aa 1e-108 in ref transcript
  • HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ubiquitin molecules to the end of growing ubiquitin chains.
• pfam HECT 298aa 5e-93 in ref transcript
  • HECT-domain (ubiquitin-transferase). The name HECT comes from Homologous to the E6-AP Carboxyl Terminus.
• pfam RCC1 50aa 2e-07 in ref transcript
  • Regulator of chromosome condensation (RCC1).
• pfam RCC1 48aa 1e-05 in ref transcript
• pfam RCC1 48aa 0.004 in ref transcript
• pfam RCC1 50aa 0.006 in ref transcript
• COG HUL4 398aa 6e-78 in ref transcript
  • Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones].
• COG ATS1 251aa 3e-35 in ref transcript
  • Alpha-tubulin suppressor and related RCC1 domain-containing proteins [Cell division and chromosome partitioning / Cytoskeleton].

HERC4

• refseq_HERC4.F4 refseq_HERC4.R4 204 296
• NCBIGene 36.2 26091
• Single exon skipping, size difference: 92
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_022079

• Changed! cd HECTc 347aa 1e-108 in ref transcript
  • HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ubiquitin molecules to the end of growing ubiquitin chains.
• Changed! pfam HECT 298aa 5e-93 in ref transcript
  • HECT-domain (ubiquitin-transferase). The name HECT comes from Homologous to the E6-AP Carboxyl Terminus.
• pfam RCC1 50aa 2e-07 in ref transcript
  • Regulator of chromosome condensation (RCC1).
• pfam RCC1 48aa 1e-05 in ref transcript
• Changed! pfam RCC1 48aa 0.004 in ref transcript
• Changed! pfam RCC1 50aa 0.006 in ref transcript
• Changed! COG HUL4 398aa 6e-78 in ref transcript
  • Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones].
• Changed! COG ATS1 251aa 3e-35 in ref transcript
  • Alpha-tubulin suppressor and related RCC1 domain-containing proteins [Cell division and chromosome partitioning / Cytoskeleton].
• Changed! COG ATS1 204aa 2e-30 in modified transcript

HERC6

• refseq_HERC6.F1 refseq_HERC6.R1 215 297
• NCBIGene 36.2 55008
• Single exon skipping, size difference: 82
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_017912

• Changed! cd HECTc 343aa 1e-101 in ref transcript
  • HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ubiquitin molecules to the end of growing ubiquitin chains.
• Changed! pfam HECT 288aa 2e-65 in ref transcript
  • HECT-domain (ubiquitin-transferase). The name HECT comes from Homologous to the E6-AP Carboxyl Terminus.
• pfam RCC1 51aa 4e-05 in ref transcript
  • Regulator of chromosome condensation (RCC1).
• pfam RCC1 48aa 6e-04 in ref transcript
• Changed! COG HUL4 608aa 1e-58 in ref transcript
  • Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones].
• COG ATS1 241aa 1e-23 in ref transcript
  • Alpha-tubulin suppressor and related RCC1 domain-containing proteins [Cell division and chromosome partitioning / Cytoskeleton].

HERC6

• refseq_HERC6.F2 refseq_HERC6.R1 282 390
• NCBIGene 36.2 55008
• Single exon skipping, size difference: 108
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_017912

• cd HECTc 343aa 1e-101 in ref transcript
  • HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ubiquitin molecules to the end of growing ubiquitin chains.
• pfam HECT 288aa 2e-65 in ref transcript
  • HECT-domain (ubiquitin-transferase). The name HECT comes from Homologous to the E6-AP Carboxyl Terminus.
• pfam RCC1 51aa 4e-05 in ref transcript
  • Regulator of chromosome condensation (RCC1).
• pfam RCC1 48aa 6e-04 in ref transcript
• Changed! COG HUL4 608aa 1e-58 in ref transcript
  • Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones].
• COG ATS1 241aa 1e-23 in ref transcript
  • Alpha-tubulin suppressor and related RCC1 domain-containing proteins [Cell division and chromosome partitioning / Cytoskeleton].
• Changed! COG HUL4 572aa 1e-62 in modified transcript

HERC6

• refseq_HERC6.F4 refseq_HERC6.R3 209 364
• NCBIGene 36.2 55008
• Single exon skipping, size difference: 155
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_017912

• Changed! cd HECTc 343aa 1e-101 in ref transcript
  • HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ubiquitin molecules to the end of growing ubiquitin chains.
• Changed! pfam HECT 288aa 2e-65 in ref transcript
  • HECT-domain (ubiquitin-transferase). The name HECT comes from Homologous to the E6-AP Carboxyl Terminus.
• pfam RCC1 51aa 4e-05 in ref transcript
  • Regulator of chromosome condensation (RCC1).
• pfam RCC1 48aa 6e-04 in ref transcript
• Changed! COG HUL4 608aa 1e-58 in ref transcript
  • Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones].
• COG ATS1 241aa 1e-23 in ref transcript
  • Alpha-tubulin suppressor and related RCC1 domain-containing proteins [Cell division and chromosome partitioning / Cytoskeleton].

HERC6

• refseq_HERC6.F5 refseq_HERC6.R4 224 346
• NCBIGene 36.2 55008
• Single exon skipping, size difference: 122
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_017912

• Changed! cd HECTc 343aa 1e-101 in ref transcript
  • HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ubiquitin molecules to the end of growing ubiquitin chains.
• Changed! pfam HECT 288aa 2e-65 in ref transcript
  • HECT-domain (ubiquitin-transferase). The name HECT comes from Homologous to the E6-AP Carboxyl Terminus.
• pfam RCC1 51aa 4e-05 in ref transcript
  • Regulator of chromosome condensation (RCC1).
• pfam RCC1 48aa 6e-04 in ref transcript
• Changed! COG HUL4 608aa 1e-58 in ref transcript
  • Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones].
• COG ATS1 241aa 1e-23 in ref transcript
  • Alpha-tubulin suppressor and related RCC1 domain-containing proteins [Cell division and chromosome partitioning / Cytoskeleton].

HFE

• refseq_HFE.F1 refseq_HFE.R1 284 353
• NCBIGene 36.3 3077
• Alternative 3-prime, size difference: 69
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000410

• cd IGc 76aa 2e-12 in ref transcript
  • Immunoglobulin domain constant region subfamily; members of the IGc subfamily are components of immunoglobulins, T-cell receptors, CD1 cell surface glycoproteins, secretory glycoproteins A/C, and Major Histocompatibility Complex (MHC) class I/II molecules. In immunoglobulins, each chain is composed of one variable domain (IGv) and one or more constant domains (IGc); these names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. T-cell receptors form heterodimers, pairing two chains (alpha/beta or gamma/delta), each with a IGv and IGc domain. MHCs form heterodimers pairing two chains (alpha/beta or delta/epsilon), each with a MHC and IGc domain. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• Changed! pfam MHC_I 176aa 3e-31 in ref transcript
  • Class I Histocompatibility antigen, domains alpha 1 and 2.
• pfam C1-set 72aa 2e-15 in ref transcript
  • Immunoglobulin C1-set domain.
• Changed! pfam MHC_I 157aa 6e-27 in modified transcript

HFE

• refseq_HFE.F3 refseq_HFE.R3 202 244
• NCBIGene 36.3 3077
• Alternative 3-prime, size difference: 42
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000410

• Changed! cd IGc 76aa 2e-12 in ref transcript
  • Immunoglobulin domain constant region subfamily; members of the IGc subfamily are components of immunoglobulins, T-cell receptors, CD1 cell surface glycoproteins, secretory glycoproteins A/C, and Major Histocompatibility Complex (MHC) class I/II molecules. In immunoglobulins, each chain is composed of one variable domain (IGv) and one or more constant domains (IGc); these names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. T-cell receptors form heterodimers, pairing two chains (alpha/beta or gamma/delta), each with a IGv and IGc domain. MHCs form heterodimers pairing two chains (alpha/beta or delta/epsilon), each with a MHC and IGc domain. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• pfam MHC_I 176aa 3e-31 in ref transcript
  • Class I Histocompatibility antigen, domains alpha 1 and 2.
• Changed! pfam C1-set 72aa 2e-15 in ref transcript
  • Immunoglobulin C1-set domain.
• Changed! cd IGc 92aa 3e-13 in modified transcript
• Changed! pfam C1-set 73aa 6e-16 in modified transcript

HFE

• refseq_HFE.F5 refseq_HFE.R3 130 406
• NCBIGene 36.3 3077
• Single exon skipping, size difference: 276
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000410

• cd IGc 76aa 2e-12 in ref transcript
  • Immunoglobulin domain constant region subfamily; members of the IGc subfamily are components of immunoglobulins, T-cell receptors, CD1 cell surface glycoproteins, secretory glycoproteins A/C, and Major Histocompatibility Complex (MHC) class I/II molecules. In immunoglobulins, each chain is composed of one variable domain (IGv) and one or more constant domains (IGc); these names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. T-cell receptors form heterodimers, pairing two chains (alpha/beta or gamma/delta), each with a IGv and IGc domain. MHCs form heterodimers pairing two chains (alpha/beta or delta/epsilon), each with a MHC and IGc domain. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• Changed! pfam MHC_I 176aa 3e-31 in ref transcript
  • Class I Histocompatibility antigen, domains alpha 1 and 2.
• pfam C1-set 72aa 2e-15 in ref transcript
  • Immunoglobulin C1-set domain.
• Changed! pfam MHC_I 87aa 4e-08 in modified transcript

HFE2

• refseq_HFE2.F2 refseq_HFE2.R2 103 289
• NCBIGene 36.3 148738
• Single exon skipping, size difference: 186
• Exclusion of the protein initiation site
• Reference transcript: NM_213653

• pfam RGM_C 197aa 4e-81 in ref transcript
  • Repulsive guidance molecule (RGM) C-terminus. This family consists of several mammalian and one bird sequence from Gallus gallus (Chicken). This family represents the C-terminal region of several sequences but in others it represents the full protein. All of the mammalian proteins are hypothetical and have no known function but the member from chicken is annotated as being a repulsive guidance molecule (RGM). RGM is a GPI-linked axon guidance molecule of the retinotectal system. RGM is repulsive for a subset of axons, those from the temporal half of the retina. Temporal retinal axons invade the anterior optic tectum in a superficial layer, and encounter RGM expressed in a gradient with increasing concentration along the anterior-posterior axis. Temporal axons are able to receive posterior-dependent information by sensing gradients or concentrations of guidance cues. Thus, RGM is likely to provide positional information for temporal axons invading the optic tectum in the stratum opticum.
• Changed! pfam RGM_N 195aa 3e-57 in ref transcript
  • Repulsive guidance molecule (RGM) N-terminus. This family consists of the N-terminal region of several mammalian and one bird sequence from Gallus gallus (Chicken). All of the mammalian proteins are hypothetical and have no known function but the member from chicken is annotated as being a repulsive guidance molecule (RGM). RGM is a GPI-linked axon guidance molecule of the retinotectal system. RGM is repulsive for a subset of axons, those from the temporal half of the retina. Temporal retinal axons invade the anterior optic tectum in a superficial layer, and encounter RGM expressed in a gradient with increasing concentration along the anterior-posterior axis. Temporal axons are able to receive posterior-dependent information by sensing gradients or concentrations of guidance cues. Thus, RGM is likely to provide positional information for temporal axons invading the optic tectum in the stratum opticum.
• Changed! pfam RGM_N 114aa 7e-40 in modified transcript

HGD

• refseq_HGD.F2 refseq_HGD.R2 143 366
• NCBIGene 36.2 3081
• Alternative 5-prime and 3-prime, size difference: 223
• Exclusion in the protein (no frameshift), Exclusion in the protein causing a frameshift
• Reference transcript: XM_001125869

• Changed! TIGR hmgA 432aa 0.0 in ref transcript
  • Missing in human disease alkaptonuria.
• Changed! PRK PRK05341 439aa 0.0 in ref transcript
  • homogentisate 1,2-dioxygenase; Provisional.
• Changed! TIGR hmgA 301aa 1e-170 in modified transcript
• Changed! PRK PRK05341 303aa 1e-132 in modified transcript

HHLA3

• refseq_HHLA3.F2 refseq_HHLA3.R2 262 314
• NCBIGene 36.3 11147
• Single exon skipping, size difference: 52
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_001031693

HIBCH

• refseq_HIBCH.F1 refseq_HIBCH.R1 191 225
• NCBIGene 36.3 26275
• Single exon skipping, size difference: 34
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_014362

• cd crotonase-like 185aa 2e-39 in ref transcript
  • Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase. Many of these play important roles in fatty acid metabolism. In addition to a conserved structural core and the formation of trimers (or dimers of trimers), a common feature in this superfamily is the stabilization of an enolate anion intermediate derived from an acyl-CoA substrate. This is accomplished by two conserved backbone NH groups in active sites that form an oxyanion hole.
• pfam ECH 170aa 4e-15 in ref transcript
  • Enoyl-CoA hydratase/isomerase family. This family contains a diverse set of enzymes including: Enoyl-CoA hydratase. Napthoate synthase. Carnitate racemase. 3-hydoxybutyryl-CoA dehydratase. Dodecanoyl-CoA delta-isomerase.
• Changed! PRK PRK05617 355aa 1e-116 in ref transcript
  • enoyl-CoA hydratase; Provisional.
• Changed! PRK PRK05617 306aa 9e-93 in modified transcript

NFU1

• refseq_HIRIP5.F2 refseq_HIRIP5.R2 307 443
• NCBIGene 36.3 27247
• Single exon skipping, size difference: 136
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_015700

• Changed! pfam Nfu_N 88aa 3e-38 in ref transcript
  • Scaffold protein Nfu/NifU N terminal. This domain is found at the N terminus of NifU and NifU related proteins, and in the human Nfu protein. Both of these proteins are thought to be involved in the the assembly of iron-sulphur clusters.
• Changed! pfam NifU 69aa 7e-20 in ref transcript
  • NifU-like domain. This is an alignment of the carboxy-terminal domain. This is the only common region between the NifU protein from nitrogen-fixing bacteria and rhodobacterial species. The biochemical function of NifU is unknown.
• Changed! COG COG0694 85aa 4e-22 in ref transcript
  • Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones].

NFU1

• refseq_HIRIP5.F3 refseq_HIRIP5.R3 184 274
• NCBIGene 36.3 27247
• Alternative 5-prime, size difference: 90
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_001002755

• Changed! pfam Nfu_N 88aa 2e-38 in ref transcript
  • Scaffold protein Nfu/NifU N terminal. This domain is found at the N terminus of NifU and NifU related proteins, and in the human Nfu protein. Both of these proteins are thought to be involved in the the assembly of iron-sulphur clusters.
• Changed! pfam NifU 69aa 7e-20 in ref transcript
  • NifU-like domain. This is an alignment of the carboxy-terminal domain. This is the only common region between the NifU protein from nitrogen-fixing bacteria and rhodobacterial species. The biochemical function of NifU is unknown.
• Changed! COG COG0694 85aa 4e-22 in ref transcript
  • Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones].

HISPPD2A

• refseq_HISPPD2A.F1 refseq_HISPPD2A.R1 98 500
• NCBIGene 36.3 9677
• Exon skipping and alternative 3-prime or 5-prime, size difference: 402
• Exclusion in the protein causing a frameshift, Exclusion in the protein (no frameshift), Exclusion in the protein causing a frameshift
• Reference transcript: NM_014659

• cd HP_HAP_like 80aa 4e-16 in ref transcript
  • Histidine phosphatase domain found in histidine acid phosphatases and phytases; contains a His residue which is phosphorylated during the reaction. Catalytic domain of HAP (histidine acid phosphatases) and phytases (myo-inositol hexakisphosphate phosphohydrolases). The conserved catalytic core of this domain contains a His residue which is phosphorylated in the reaction. Functions in this subgroup include roles in metabolism, signaling, or regulation, for example Escherichia coli glucose-1-phosphatase functions to scavenge glucose from glucose-1-phosphate and the signaling molecules inositol 1,3,4,5,6-pentakisphosphate (InsP5) and inositol hexakisphosphate (InsP6) are in vivo substrates for eukaryotic multiple inositol polyphosphate phosphatase 1 (Minpp1). Phytases scavenge phosphate from extracellular sources and are added to animal feed while prostatic acid phosphatase (PAP) has been used for many years as a serum marker for prostate cancer. Recently PAP has been shown in mouse models to suppress pain by functioning as an ecto-5prime-nucleotidase. In vivo it dephosphorylates extracellular adenosine monophosphate (AMP) generating adenosine,and leading to the activation of A1-adenosine receptors in dorsal spinal cord.
• cd HP_HAP_like 139aa 8e-09 in ref transcript
• pfam Acid_phosphat_A 407aa 5e-37 in ref transcript
  • Histidine acid phosphatase.
• pfam Acid_phosphat_A 47aa 3e-07 in ref transcript

HISPPD2A

• refseq_HISPPD2A.F4 refseq_HISPPD2A.R4 113 392
• NCBIGene 36.3 9677
• Exon skipping and alternative 3-prime or 5-prime, size difference: 279
• Exclusion in the protein causing a frameshift, Exclusion in the protein (no frameshift), Exclusion in the protein causing a frameshift
• Reference transcript: NM_014659

• cd HP_HAP_like 80aa 4e-16 in ref transcript
  • Histidine phosphatase domain found in histidine acid phosphatases and phytases; contains a His residue which is phosphorylated during the reaction. Catalytic domain of HAP (histidine acid phosphatases) and phytases (myo-inositol hexakisphosphate phosphohydrolases). The conserved catalytic core of this domain contains a His residue which is phosphorylated in the reaction. Functions in this subgroup include roles in metabolism, signaling, or regulation, for example Escherichia coli glucose-1-phosphatase functions to scavenge glucose from glucose-1-phosphate and the signaling molecules inositol 1,3,4,5,6-pentakisphosphate (InsP5) and inositol hexakisphosphate (InsP6) are in vivo substrates for eukaryotic multiple inositol polyphosphate phosphatase 1 (Minpp1). Phytases scavenge phosphate from extracellular sources and are added to animal feed while prostatic acid phosphatase (PAP) has been used for many years as a serum marker for prostate cancer. Recently PAP has been shown in mouse models to suppress pain by functioning as an ecto-5prime-nucleotidase. In vivo it dephosphorylates extracellular adenosine monophosphate (AMP) generating adenosine,and leading to the activation of A1-adenosine receptors in dorsal spinal cord.
• Changed! cd HP_HAP_like 139aa 8e-09 in ref transcript
• Changed! pfam Acid_phosphat_A 407aa 5e-37 in ref transcript
  • Histidine acid phosphatase.
• pfam Acid_phosphat_A 47aa 3e-07 in ref transcript
• Changed! cd HP_HAP_like 108aa 8e-05 in modified transcript
• Changed! pfam Acid_phosphat_A 372aa 2e-32 in modified transcript

HISPPD2A

• refseq_HISPPD2A.F5 refseq_HISPPD2A.R5 130 193
• NCBIGene 36.3 9677
• Single exon skipping, size difference: 63
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_014659

• cd HP_HAP_like 80aa 4e-16 in ref transcript
  • Histidine phosphatase domain found in histidine acid phosphatases and phytases; contains a His residue which is phosphorylated during the reaction. Catalytic domain of HAP (histidine acid phosphatases) and phytases (myo-inositol hexakisphosphate phosphohydrolases). The conserved catalytic core of this domain contains a His residue which is phosphorylated in the reaction. Functions in this subgroup include roles in metabolism, signaling, or regulation, for example Escherichia coli glucose-1-phosphatase functions to scavenge glucose from glucose-1-phosphate and the signaling molecules inositol 1,3,4,5,6-pentakisphosphate (InsP5) and inositol hexakisphosphate (InsP6) are in vivo substrates for eukaryotic multiple inositol polyphosphate phosphatase 1 (Minpp1). Phytases scavenge phosphate from extracellular sources and are added to animal feed while prostatic acid phosphatase (PAP) has been used for many years as a serum marker for prostate cancer. Recently PAP has been shown in mouse models to suppress pain by functioning as an ecto-5prime-nucleotidase. In vivo it dephosphorylates extracellular adenosine monophosphate (AMP) generating adenosine,and leading to the activation of A1-adenosine receptors in dorsal spinal cord.
• cd HP_HAP_like 139aa 8e-09 in ref transcript
• pfam Acid_phosphat_A 407aa 5e-37 in ref transcript
  • Histidine acid phosphatase.
• pfam Acid_phosphat_A 47aa 3e-07 in ref transcript

HISPPD2A

• refseq_HISPPD2A.F7 refseq_HISPPD2A.R7 111 135
• NCBIGene 36.3 9677
• Alternative 5-prime, size difference: 24
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_014659

• cd HP_HAP_like 80aa 4e-16 in ref transcript
  • Histidine phosphatase domain found in histidine acid phosphatases and phytases; contains a His residue which is phosphorylated during the reaction. Catalytic domain of HAP (histidine acid phosphatases) and phytases (myo-inositol hexakisphosphate phosphohydrolases). The conserved catalytic core of this domain contains a His residue which is phosphorylated in the reaction. Functions in this subgroup include roles in metabolism, signaling, or regulation, for example Escherichia coli glucose-1-phosphatase functions to scavenge glucose from glucose-1-phosphate and the signaling molecules inositol 1,3,4,5,6-pentakisphosphate (InsP5) and inositol hexakisphosphate (InsP6) are in vivo substrates for eukaryotic multiple inositol polyphosphate phosphatase 1 (Minpp1). Phytases scavenge phosphate from extracellular sources and are added to animal feed while prostatic acid phosphatase (PAP) has been used for many years as a serum marker for prostate cancer. Recently PAP has been shown in mouse models to suppress pain by functioning as an ecto-5prime-nucleotidase. In vivo it dephosphorylates extracellular adenosine monophosphate (AMP) generating adenosine,and leading to the activation of A1-adenosine receptors in dorsal spinal cord.
• Changed! cd HP_HAP_like 139aa 8e-09 in ref transcript
• Changed! pfam Acid_phosphat_A 407aa 5e-37 in ref transcript
  • Histidine acid phosphatase.
• pfam Acid_phosphat_A 47aa 3e-07 in ref transcript
• Changed! cd HP_HAP_like 102aa 5e-07 in modified transcript
• Changed! pfam Acid_phosphat_A 399aa 6e-38 in modified transcript

HK1

• refseq_HK1.F2 refseq_HK1.R2 102 156
• NCBIGene 36.3 3098
• Alternative 5-prime, size difference: 54
• Exclusion in 5'UTR
• Reference transcript: NM_033498

• pfam Hexokinase_2 237aa 1e-113 in ref transcript
  • Hexokinase. Hexokinase (EC:2.7.1.1) contains two structurally similar domains represented by this family and pfam00349. Some members of the family have two copies of each of these domains.
• pfam Hexokinase_2 238aa 1e-108 in ref transcript
• pfam Hexokinase_1 206aa 6e-94 in ref transcript
  • Hexokinase. Hexokinase (EC:2.7.1.1) contains two structurally similar domains represented by this family and pfam03727. Some members of the family have two copies of each of these domains.
• pfam Hexokinase_1 201aa 8e-90 in ref transcript
• COG COG5026 443aa 5e-84 in ref transcript
  • Hexokinase [Carbohydrate transport and metabolism].
• COG COG5026 442aa 1e-74 in ref transcript

HK1

• refseq_HK1.F3 refseq_HK1.R3 113 206
• NCBIGene 36.3 3098
• Single exon skipping, size difference: 93
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_033497

• Changed! pfam Hexokinase_2 237aa 1e-113 in ref transcript
  • Hexokinase. Hexokinase (EC:2.7.1.1) contains two structurally similar domains represented by this family and pfam00349. Some members of the family have two copies of each of these domains.
• Changed! pfam Hexokinase_2 238aa 1e-108 in ref transcript
• Changed! pfam Hexokinase_1 206aa 6e-94 in ref transcript
  • Hexokinase. Hexokinase (EC:2.7.1.1) contains two structurally similar domains represented by this family and pfam03727. Some members of the family have two copies of each of these domains.
• Changed! pfam Hexokinase_1 201aa 8e-90 in ref transcript
• Changed! COG COG5026 443aa 5e-84 in ref transcript
  • Hexokinase [Carbohydrate transport and metabolism].
• Changed! COG COG5026 442aa 1e-74 in ref transcript

HM13

• refseq_HM13.F2 refseq_HM13.R2 162 218
• NCBIGene 36.3 81502
• Alternative 5-prime, size difference: 56
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_178581

• pfam Peptidase_A22B 286aa 1e-89 in ref transcript
  • Signal peptide peptidase. The members of this family are membrane proteins. In some proteins this region is found associated with pfam02225. This family corresponds with Merops subfamily A22B, the type example of which is signal peptide peptidase. There is a sequence-similarity relationship with pfam01080.
• COG COG3389 176aa 3e-05 in ref transcript
  • Uncharacterized protein conserved in archaea [Function unknown].

HMG2L1

• refseq_HMG2L1.F1 refseq_HMG2L1.R1 248 363
• NCBIGene 36.3 10042
• Single exon skipping, size difference: 115
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_001003681

• Changed! cd HMG-box 60aa 5e-11 in ref transcript
  • High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4; and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions.
• Changed! pfam HMG_box 61aa 5e-11 in ref transcript
  • HMG (high mobility group) box.
• Changed! COG NHP6B 72aa 9e-04 in ref transcript
  • Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics].

HMG2L1

• refseq_HMG2L1.F3 refseq_HMG2L1.R3 100 199
• NCBIGene 36.3 10042
• Single exon skipping, size difference: 99
• Exclusion of the protein initiation site
• Reference transcript: NM_001003681

• cd HMG-box 60aa 5e-11 in ref transcript
  • High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4; and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions.
• Changed! pfam HMG_box 61aa 5e-11 in ref transcript
  • HMG (high mobility group) box.
• COG NHP6B 72aa 9e-04 in ref transcript
  • Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics].

HMGN3

• refseq_HMGN3.F1 refseq_HMGN3.R1 111 152
• NCBIGene 36.3 9324
• Alternative 5-prime, size difference: 41
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_004242

HN1

• refseq_HN1.F2 refseq_HN1.R2 139 234
• NCBIGene 36.3 51155
• Single exon skipping, size difference: 95
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_001002032

HNRNPA2B1

• refseq_HNRPA2B1.F2 refseq_HNRPA2B1.R2 180 216
• NCBIGene 36.3 3181
• Single exon skipping, size difference: 36
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_031243

• Changed! cd RRM 73aa 3e-13 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• cd RRM 74aa 8e-11 in ref transcript
• Changed! TIGR SF-CC1 140aa 9e-15 in ref transcript
  • A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed.
• Changed! COG COG0724 155aa 3e-10 in ref transcript
  • RNA-binding proteins (RRM domain) [General function prediction only].
• Changed! cd RRM 74aa 3e-13 in modified transcript
• Changed! TIGR SF-CC1 150aa 2e-15 in modified transcript
• Changed! COG COG0724 164aa 1e-09 in modified transcript

HNRPAB

• refseq_HNRPAB.F2 refseq_HNRPAB.R2 129 270
• NCBIGene 36.3 3182
• Single exon skipping, size difference: 141
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_031266

• cd RRM 70aa 6e-14 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• cd RRM 48aa 4e-10 in ref transcript
• TIGR SF-CC1 137aa 2e-18 in ref transcript
  • A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed.
• pfam CBFNT 71aa 6e-06 in ref transcript
  • CBFNT (NUC161) domain. This N terminal domain is found in proteins of CARG-binding factor A-like proteins.
• COG COG0724 142aa 6e-08 in ref transcript
  • RNA-binding proteins (RRM domain) [General function prediction only].

HNRPD

• refseq_HNRPD.F2 refseq_HNRPD.R2 160 217
• NCBIGene 36.3 3184
• Single exon skipping, size difference: 57
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_031370

• cd RRM 79aa 2e-14 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• cd RRM 74aa 9e-14 in ref transcript
• Changed! TIGR PABP-1234 143aa 2e-19 in ref transcript
  • There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, and of unknown tissue range.
• Changed! COG COG0724 179aa 2e-07 in ref transcript
  • RNA-binding proteins (RRM domain) [General function prediction only].
• Changed! TIGR PABP-1234 155aa 2e-20 in modified transcript
• Changed! COG COG0724 162aa 5e-07 in modified transcript

HNRPD

• refseq_HNRPD.F3 refseq_HNRPD.R3 189 336
• NCBIGene 36.3 3184
• Single exon skipping, size difference: 147
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_031370

• cd RRM 79aa 2e-14 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• cd RRM 74aa 9e-14 in ref transcript
• TIGR PABP-1234 143aa 2e-19 in ref transcript
  • There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, and of unknown tissue range.
• COG COG0724 179aa 2e-07 in ref transcript
  • RNA-binding proteins (RRM domain) [General function prediction only].

HNRPDL

• refseq_HNRPDL.F1 refseq_HNRPDL.R1 133 238
• NCBIGene 36.3 9987
• Single exon skipping, size difference: 105
• Exclusion in 3'UTR
• Reference transcript: NR_003249

• cd RRM 74aa 1e-14 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• cd RRM 70aa 1e-14 in ref transcript
• TIGR SF-CC1 149aa 1e-18 in ref transcript
  • A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed.
• COG COG0724 170aa 3e-08 in ref transcript
  • RNA-binding proteins (RRM domain) [General function prediction only].

HNRPH3

• refseq_HNRPH3.F1 refseq_HNRPH3.R1 120 165
• NCBIGene 36.3 3189
• Alternative 5-prime, size difference: 45
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_012207

• cd RRM 74aa 5e-08 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• cd RRM 71aa 1e-07 in ref transcript
• smart RRM_2 69aa 4e-08 in ref transcript
  • RNA recognition motif.
• smart RRM_2 72aa 5e-08 in ref transcript

HNRPK

• refseq_HNRPK.F1 refseq_HNRPK.R1 283 343
• NCBIGene 36.3 3190
• Alternative 3-prime, size difference: 60
• Exclusion of the stop codon
• Reference transcript: NM_002140

• cd PCBP_like_KH 62aa 1e-11 in ref transcript
  • K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
• cd PCBP_like_KH 65aa 1e-07 in ref transcript
• pfam ROKNT 43aa 3e-12 in ref transcript
  • ROKNT (NUC014) domain. This presumed domain is found at the N-terminus of RNP K-like proteins that also contains KH domains pfam00013.
• pfam KH_1 61aa 7e-10 in ref transcript
  • KH domain. KH motifs can bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.
• PRK PRK11824 52aa 0.001 in ref transcript
  • polynucleotide phosphorylase/polyadenylase; Provisional.

HNRNPU

• refseq_HNRPU.F2 refseq_HNRPU.R2 134 191
• NCBIGene 36.3 3192
• Alternative 5-prime, size difference: 57
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_031844

• pfam SPRY 117aa 6e-23 in ref transcript
  • SPRY domain. SPRY Domain is named from SPla and the RYanodine Receptor. Domain of unknown function. Distant homologues are domains in butyrophilin/marenostrin/pyrin homologues.
• TIGR PNK-3'Pase 111aa 0.003 in ref transcript
  • Note that the EC number for the kinase function is: 2.7.1.78.
• COG COG4639 151aa 0.005 in ref transcript
  • Predicted kinase [General function prediction only].

HNRPUL1

• refseq_HNRPUL1.F2 refseq_HNRPUL1.R2 231 387
• NCBIGene 36.2 11100
• Alternative 3-prime, size difference: 156
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_007040

• pfam SPRY 133aa 2e-25 in ref transcript
  • SPRY domain. SPRY Domain is named from SPla and the RYanodine Receptor. Domain of unknown function. Distant homologues are domains in butyrophilin/marenostrin/pyrin homologues.
• TIGR selen_PSTK 146aa 0.005 in ref transcript
  • Members of this protein are L-seryl-tRNA(Sec) kinase. This enzyme is part of a two-step pathway in Eukaryota and Archaea for performing selenocysteine biosynthesis by changing serine misacylated on selenocysteine-tRNA to selenocysteine. This enzyme performs the first step, phosphorylation of the OH group of the serine side chain. This family represents archaeal proteins with this activity.
• COG COG4639 131aa 0.009 in ref transcript
  • Predicted kinase [General function prediction only].

HOMER2

• refseq_HOMER2.F1 refseq_HOMER2.R1 131 164
• NCBIGene 36.3 9455
• Alternative 3-prime, size difference: 33
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_199330

• cd Homer 111aa 6e-54 in ref transcript
  • Homer type EVH1 domain. Homer is a synaptic scaffolding protein, involved in neuronal signaling. It contains an EVH1 domain, which binds to both neurotransmitter receptors, such as the metabotropic glutamate receptor (mGluR) and to other scaffolding proteins via PPXXF motifs, in order to target them to the synaptic junction. It has a PH-like fold, despite having minimal sequence similarity to PH or PTB domains.
• pfam WH1 104aa 6e-32 in ref transcript
  • WH1 domain. WASp Homology domain 1 (WH1) domain. WASP is the protein that is defective in Wiskott-Aldrich syndrome (WAS). The majority of point mutations occur within the amino- terminal WH1 domain. The metabotropic glutamate receptors mGluR1alpha and mGluR5 bind a protein called homer, which is a WH1 domain homologue. A subset of WH1 domains has been termed a "EVH1" domain and appear to bind a polyproline motif.
• TIGR SMC_prok_A 190aa 8e-05 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent.
• Changed! COG Smc 188aa 0.008 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].
• Changed! COG SbcC 237aa 0.001 in modified transcript
  • ATPase involved in DNA repair [DNA replication, recombination, and repair].

HOMER2

• refseq_HOMER2.F4 refseq_HOMER2.R4 281 446
• NCBIGene 36.3 9455
• Alternative 5-prime and 3-prime, size difference: 165
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_199330

• cd Homer 111aa 6e-54 in ref transcript
  • Homer type EVH1 domain. Homer is a synaptic scaffolding protein, involved in neuronal signaling. It contains an EVH1 domain, which binds to both neurotransmitter receptors, such as the metabotropic glutamate receptor (mGluR) and to other scaffolding proteins via PPXXF motifs, in order to target them to the synaptic junction. It has a PH-like fold, despite having minimal sequence similarity to PH or PTB domains.
• pfam WH1 104aa 6e-32 in ref transcript
  • WH1 domain. WASp Homology domain 1 (WH1) domain. WASP is the protein that is defective in Wiskott-Aldrich syndrome (WAS). The majority of point mutations occur within the amino- terminal WH1 domain. The metabotropic glutamate receptors mGluR1alpha and mGluR5 bind a protein called homer, which is a WH1 domain homologue. A subset of WH1 domains has been termed a "EVH1" domain and appear to bind a polyproline motif.
• Changed! TIGR SMC_prok_A 190aa 8e-05 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent.
• Changed! COG Smc 188aa 0.008 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].

HOPX

• refseq_HOP.F1 refseq_HOP.R1 237 362
• NCBIGene 36.3 84525
• Single exon skipping, size difference: 125
• Exclusion of the protein initiation site
• Reference transcript: NM_032495

• cd homeodomain 53aa 1e-06 in ref transcript
  • Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
• pfam Homeobox 52aa 4e-05 in ref transcript
  • Homeobox domain.

HPCAL1

• refseq_HPCAL1.F1 refseq_HPCAL1.R1 178 351
• NCBIGene 36.3 3241
• Single exon skipping, size difference: 173
• Exclusion in 5'UTR
• Reference transcript: NM_134421

• cd EFh 62aa 3e-11 in ref transcript
  • EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers.
• cd EFh 75aa 2e-10 in ref transcript
• cd EFh 61aa 0.008 in ref transcript
• smart EFh 29aa 8e-04 in ref transcript
  • EF-hand, calcium binding motif. EF-hands are calcium-binding motifs that occur at least in pairs. Links between disease states and genes encoding EF-hands, particularly the S100 subclass, are emerging. Each motif consists of a 12 residue loop flanked on either side by a 12 residue alpha-helix. EF-hands undergo a conformational change unpon binding calcium ions.
• COG FRQ1 167aa 8e-27 in ref transcript
  • Ca2+-binding protein (EF-Hand superfamily) [Signal transduction mechanisms / Cytoskeleton / Cell division and chromosome partitioning / General function prediction only].

HPS1

• refseq_HPS1.F1 refseq_HPS1.R1 106 149
• NCBIGene 36.2 3257
• Alternative 5-prime, size difference: 43
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_000195

HPS1

• refseq_HPS1.F2 refseq_HPS1.R2 149 292
• NCBIGene 36.2 3257
• Single exon skipping, size difference: 143
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_000195

HPS1

• refseq_HPS1.F4 refseq_HPS1.R4 140 239
• NCBIGene 36.2 3257
• Single exon skipping, size difference: 99
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000195

HPS4

• refseq_HPS4.F2 refseq_HPS4.R2 144 198
• NCBIGene 36.2 89781
• Single exon skipping, size difference: 54
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_022081

HPS5

• refseq_HPS5.F2 refseq_HPS5.R2 222 379
• NCBIGene 36.3 11234
• Single exon skipping, size difference: 157
• Exclusion of the protein initiation site
• Reference transcript: NM_181507

HR

• refseq_HR.F1 refseq_HR.R1 243 408
• NCBIGene 36.3 55806
• Single exon skipping, size difference: 165
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_005144

• Changed! pfam JmjC 41aa 4e-06 in ref transcript
  • JmjC domain. The JmjC domain belongs to the Cupin superfamily. JmjC-domain proteins may be protein hydroxylases that catalyse a novel histone modification.

HSD11B1L

• refseq_HSD11B1L.F1 refseq_HSD11B1L.R1 189 252
• NCBIGene 36.3 374875
• Exon skipping and alternative 3-prime or 5-prime, size difference: 63
• Inclusion in the protein (no stop codon or frameshift), Exclusion of the protein initiation site
• Reference transcript: NM_198533

• Changed! pfam adh_short 165aa 4e-13 in ref transcript
  • short chain dehydrogenase. This family contains a wide variety of dehydrogenases.
• Changed! PRK PRK06181 234aa 7e-28 in ref transcript
  • short chain dehydrogenase; Provisional.
• Changed! pfam adh_short 109aa 9e-04 in modified transcript
• Changed! PRK PRK06181 177aa 6e-14 in modified transcript

HSD11B1L

• refseq_HSD11B1L.F3 refseq_HSD11B1L.R3 134 246
• NCBIGene 36.3 374875
• Single exon skipping, size difference: 112
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_198533

• Changed! pfam adh_short 165aa 4e-13 in ref transcript
  • short chain dehydrogenase. This family contains a wide variety of dehydrogenases.
• Changed! PRK PRK06181 234aa 7e-28 in ref transcript
  • short chain dehydrogenase; Provisional.
• Changed! PRK PRK05866 44aa 5e-07 in modified transcript
  • short chain dehydrogenase; Provisional.

HSD11B1L

• refseq_HSD11B1L.F6 refseq_HSD11B1L.R6 223 386
• NCBIGene 36.3 374875
• Alternative 3-prime, size difference: 163
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_198533

• pfam adh_short 165aa 4e-13 in ref transcript
  • short chain dehydrogenase. This family contains a wide variety of dehydrogenases.
• Changed! PRK PRK06181 234aa 7e-28 in ref transcript
  • short chain dehydrogenase; Provisional.
• Changed! PRK PRK06181 216aa 9e-26 in modified transcript

HTATIP

• refseq_HTATIP.F1 refseq_HTATIP.R1 105 261
• NCBIGene 36.3 10524
• Single exon skipping, size difference: 156
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_182710

• cd CHROMO 53aa 0.003 in ref transcript
  • Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence implicates the chromo domain in the binding activity of these proteins to methylated histone tails and maybe RNA. May occur as single instance, in a tandem arrangement or followd by a related "chromo shadow" domain.
• pfam MOZ_SAS 193aa 1e-95 in ref transcript
  • MOZ/SAS family. This region of these proteins has been suggested to be homologous to acetyltransferases.
• smart CHROMO 52aa 2e-04 in ref transcript
  • Chromatin organization modifier domain.
• Changed! COG SAS2 275aa 6e-96 in ref transcript
  • Histone acetyltransferase (MYST family) [Chromatin structure and dynamics].
• Changed! COG SAS2 72aa 2e-07 in ref transcript
• Changed! COG SAS2 443aa 1e-102 in modified transcript

HTR4

• refseq_HTR4.F1 refseq_HTR4.R1 235 355
• NCBIGene 36.3 3360
• Single exon skipping, size difference: 120
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001040173

• pfam 7tm_1 271aa 5e-51 in ref transcript
  • 7 transmembrane receptor (rhodopsin family). This family contains, amongst other G-protein-coupled receptors (GCPRs), members of the opsin family, which have been considered to be typical members of the rhodopsin superfamily. They share several motifs, mainly the seven transmembrane helices, GCPRs of the rhodopsin superfamily. All opsins bind a chromophore, such as 11-cis-retinal. The function of most opsins other than the photoisomerases is split into two steps: light absorption and G-protein activation. Photoisomerases, on the other hand, are not coupled to G-proteins - they are thought to generate and supply the chromophore that is used by visual opsins.

HTR4

• refseq_HTR4.F3 refseq_HTR4.R3 223 265
• NCBIGene 36.3 3360
• Single exon skipping, size difference: 42
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_001040173

• Changed! pfam 7tm_1 271aa 5e-51 in ref transcript
  • 7 transmembrane receptor (rhodopsin family). This family contains, amongst other G-protein-coupled receptors (GCPRs), members of the opsin family, which have been considered to be typical members of the rhodopsin superfamily. They share several motifs, mainly the seven transmembrane helices, GCPRs of the rhodopsin superfamily. All opsins bind a chromophore, such as 11-cis-retinal. The function of most opsins other than the photoisomerases is split into two steps: light absorption and G-protein activation. Photoisomerases, on the other hand, are not coupled to G-proteins - they are thought to generate and supply the chromophore that is used by visual opsins.
• Changed! pfam 7tm_1 285aa 3e-50 in modified transcript

HTR4

• refseq_HTR4.F5 refseq_HTR4.R6 247 323
• NCBIGene 36.3 3360
• Single exon skipping, size difference: 76
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_001040169

• pfam 7tm_1 271aa 6e-50 in ref transcript
  • 7 transmembrane receptor (rhodopsin family). This family contains, amongst other G-protein-coupled receptors (GCPRs), members of the opsin family, which have been considered to be typical members of the rhodopsin superfamily. They share several motifs, mainly the seven transmembrane helices, GCPRs of the rhodopsin superfamily. All opsins bind a chromophore, such as 11-cis-retinal. The function of most opsins other than the photoisomerases is split into two steps: light absorption and G-protein activation. Photoisomerases, on the other hand, are not coupled to G-proteins - they are thought to generate and supply the chromophore that is used by visual opsins.

HTRA2

• refseq_HTRA2.F1 refseq_HTRA2.R1 209 305
• NCBIGene 36.3 27429
• Single exon skipping, size difference: 96
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_013247

• Changed! cd PDZ_serine_protease 93aa 1e-12 in ref transcript
  • PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of protease-associated PDZ domains a C-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins.
• Changed! TIGR degP_htrA_DO 304aa 6e-63 in ref transcript
  • This family consists of a set proteins various designated DegP, heat shock protein HtrA, and protease DO. The ortholog in Pseudomonas aeruginosa is designated MucD and is found in an operon that controls mucoid phenotype. This family also includes the DegQ (HhoA) paralog in E. coli which can rescue a DegP mutant, but not the smaller DegS paralog, which cannot. Members of this family are located in the periplasm and have separable functions as both protease and chaperone. Members have a trypsin domain and two copies of a PDZ domain. This protein protects bacteria from thermal and other stresses and may be important for the survival of bacterial pathogens.// The chaperone function is dominant at low temperatures, whereas the proteolytic activity is turned on at elevated temperatures.
• Changed! COG DegQ 312aa 4e-46 in ref transcript
  • Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones].
• Changed! cd PDZ_metalloprotease 51aa 1e-05 in modified transcript
  • PDZ domain of bacterial and plant zinc metalloprotases, presumably membrane-associated or integral membrane proteases, which may be involved in signalling and regulatory mechanisms. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of protease-associated PDZ domains a C-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins.
• Changed! TIGR degP_htrA_DO 272aa 5e-53 in modified transcript
• Changed! COG DegQ 280aa 2e-40 in modified transcript

HTRA2

• refseq_HTRA2.F3 refseq_HTRA2.R3 110 305
• NCBIGene 36.3 27429
• Single exon skipping, size difference: 195
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_013247

• cd PDZ_serine_protease 93aa 1e-12 in ref transcript
  • PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of protease-associated PDZ domains a C-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins.
• Changed! TIGR degP_htrA_DO 304aa 6e-63 in ref transcript
  • This family consists of a set proteins various designated DegP, heat shock protein HtrA, and protease DO. The ortholog in Pseudomonas aeruginosa is designated MucD and is found in an operon that controls mucoid phenotype. This family also includes the DegQ (HhoA) paralog in E. coli which can rescue a DegP mutant, but not the smaller DegS paralog, which cannot. Members of this family are located in the periplasm and have separable functions as both protease and chaperone. Members have a trypsin domain and two copies of a PDZ domain. This protein protects bacteria from thermal and other stresses and may be important for the survival of bacterial pathogens.// The chaperone function is dominant at low temperatures, whereas the proteolytic activity is turned on at elevated temperatures.
• Changed! COG DegQ 312aa 4e-46 in ref transcript
  • Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones].
• Changed! TIGR degP_htrA_DO 239aa 5e-30 in modified transcript
• Changed! COG DegQ 157aa 9e-18 in modified transcript
• Changed! PRK PRK10898 81aa 1e-04 in modified transcript
  • serine endoprotease; Provisional.

HYAL1

• refseq_HYAL1.F1 refseq_HYAL1.R1 101 191
• NCBIGene 36.3 3373
• Single exon skipping, size difference: 90
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_153281

• Changed! pfam Glyco_hydro_56 335aa 1e-146 in ref transcript
  • Hyaluronidase.
• Changed! pfam Glyco_hydro_56 305aa 1e-127 in modified transcript

ICAM4

• refseq_ICAM4.F2 refseq_ICAM4.R2 237 314
• NCBIGene 36.3 3386
• Alternative 3-prime, size difference: 77
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_001039132

• Changed! pfam ICAM_N 87aa 2e-11 in ref transcript
  • Intercellular adhesion molecule (ICAM), N-terminal domain. ICAMs normally functions to promote intercellular adhesion and signalling. However, The N-terminal domain of the receptor binds to the rhinovirus 'canyon' surrounding the icosahedral 5-fold axes, during the viral attachment process. This family is a family that is part of the Ig superfamily and is therefore related to the family ig (pfam00047).
• Changed! pfam ICAM_N 89aa 3e-12 in modified transcript

ICK

• refseq_ICK.F2 refseq_ICK.R2 239 350
• NCBIGene 36.3 22858
• Single exon skipping, size difference: 111
• Exclusion in 5'UTR
• Reference transcript: NM_016513

• cd S_TKc 282aa 3e-74 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• pfam Pkinase 281aa 1e-79 in ref transcript
  • Protein kinase domain.
• PTZ PTZ00024 275aa 2e-43 in ref transcript
  • cyclin-dependent protein kinase; Provisional.

IDH3B

• refseq_IDH3B.F2 refseq_IDH3B.R2 101 416
• NCBIGene 36.3 3420
• Alternative 3-prime, size difference: 315
• Exclusion of the stop codon
• Reference transcript: NM_006899

• Changed! TIGR mito_nad_idh 334aa 1e-133 in ref transcript
  • The NADP-dependent IDH of Thermus aquaticus thermophilus strain HB8 resembles these NAD-dependent IDH, except for the residues involved in cofactor specificity, much more closely than it resembles other prokaryotic NADP-dependent IDH, including that of Thermus aquaticus strain YT1.
• Changed! COG LeuB 336aa 1e-81 in ref transcript
  • Isocitrate/isopropylmalate dehydrogenase [Amino acid transport and metabolism].
• Changed! TIGR mito_nad_idh 334aa 1e-133 in modified transcript
• Changed! COG LeuB 334aa 1e-82 in modified transcript

IFIT1

• refseq_IFIT1.F2 refseq_IFIT1.R2 201 310
• NCBIGene 36.2 3434
• Single exon skipping, size difference: 109
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_001001887

• Changed! cd TPR 85aa 8e-05 in ref transcript
  • Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here.
• Changed! cd TPR 91aa 0.001 in ref transcript
• Changed! TIGR PEP_TPR_lipo 412aa 1e-08 in ref transcript
  • This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of tetratricopeptide repeats (TPR) suggests protein-protein interaction, possibly for the regulation of PEP-CTERM protein expression, since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator.
• Changed! COG PilF 144aa 0.002 in ref transcript
  • Tfp pilus assembly protein PilF [Cell motility and secretion / Intracellular trafficking and secretion].

IFNAR2

• refseq_IFNAR2.F1 refseq_IFNAR2.R1 186 232
• NCBIGene 36.3 3455
• Alternative 3-prime, size difference: 46
• Inclusion in 5'UTR
• Reference transcript: NM_207585

• pfam Interfer-bind 101aa 1e-48 in ref transcript
  • Interferon-alpha/beta receptor, fibronectin type III. Members of this family adopt a secondary structure consisting of seven beta-strands arranged in an immunoglobulin-like beta-sandwich, in a Greek-key topology. They are required for binding to interferon-alpha.

IFT122

• refseq_IFT122.F2 refseq_IFT122.R2 218 395
• NCBIGene 36.3 55764
• Single exon skipping, size difference: 177
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_052985

• Changed! cd WD40 230aa 2e-14 in ref transcript
  • WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.
• Changed! cd WD40 259aa 6e-08 in ref transcript
• smart WD40 39aa 2e-06 in ref transcript
  • WD40 repeats. Note that these repeats are permuted with respect to the structural repeats (blades) of the beta propeller domain.
• TIGR PEP_TPR_lipo 209aa 0.002 in ref transcript
  • This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of tetratricopeptide repeats (TPR) suggests protein-protein interaction, possibly for the regulation of PEP-CTERM protein expression, since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator.
• Changed! COG COG2319 229aa 6e-08 in ref transcript
  • FOG: WD40 repeat [General function prediction only].
• Changed! COG COG2319 269aa 3e-04 in ref transcript
• Changed! cd WD40 293aa 3e-16 in modified transcript
• Changed! COG COG2319 329aa 4e-13 in modified transcript

IFT122

• refseq_IFT122.F3 refseq_IFT122.R3 119 272
• NCBIGene 36.3 55764
• Single exon skipping, size difference: 153
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_052985

• Changed! cd WD40 230aa 2e-14 in ref transcript
  • WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.
• Changed! cd WD40 259aa 6e-08 in ref transcript
• smart WD40 39aa 2e-06 in ref transcript
  • WD40 repeats. Note that these repeats are permuted with respect to the structural repeats (blades) of the beta propeller domain.
• TIGR PEP_TPR_lipo 209aa 0.002 in ref transcript
  • This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of tetratricopeptide repeats (TPR) suggests protein-protein interaction, possibly for the regulation of PEP-CTERM protein expression, since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator.
• Changed! COG COG2319 229aa 6e-08 in ref transcript
  • FOG: WD40 repeat [General function prediction only].
• Changed! COG COG2319 269aa 3e-04 in ref transcript
• Changed! cd WD40 176aa 1e-16 in modified transcript
• Changed! cd WD40 302aa 9e-14 in modified transcript
• Changed! COG COG2319 345aa 1e-11 in modified transcript

IFT88

• refseq_IFT88.F1 refseq_IFT88.R1 115 344
• NCBIGene 36.3 8100
• Multiple exon skipping, size difference: 229
• Exclusion in 5'UTR, Exclusion of the protein initiation site
• Reference transcript: NM_175605

• cd TPR 99aa 6e-12 in ref transcript
  • Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here.
• cd TPR 100aa 9e-08 in ref transcript
• cd TPR 95aa 4e-07 in ref transcript
• cd TPR 98aa 8e-06 in ref transcript
• cd TPR 93aa 3e-05 in ref transcript
• TIGR PEP_TPR_lipo 270aa 1e-14 in ref transcript
  • This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of tetratricopeptide repeats (TPR) suggests protein-protein interaction, possibly for the regulation of PEP-CTERM protein expression, since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator.
• TIGR PEP_TPR_lipo 135aa 0.005 in ref transcript
• Changed! COG NrfG 259aa 3e-05 in ref transcript
  • FOG: TPR repeat [General function prediction only].
• Changed! COG PilF 213aa 4e-05 in modified transcript
  • Tfp pilus assembly protein PilF [Cell motility and secretion / Intracellular trafficking and secretion].
• Changed! COG COG4235 125aa 8e-04 in modified transcript
  • Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones].

IGF2BP2

• refseq_IGF2BP2.F1 refseq_IGF2BP2.R1 224 353
• NCBIGene 36.3 10644
• Single exon skipping, size difference: 129
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_006548

• cd PCBP_like_KH 64aa 1e-09 in ref transcript
  • K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
• cd RRM 70aa 8e-09 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• cd KH-I 64aa 2e-08 in ref transcript
  • K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
• cd KH-I 66aa 3e-08 in ref transcript
• cd RRM 72aa 6e-07 in ref transcript
• cd KH-I 63aa 5e-06 in ref transcript
• smart KH 74aa 2e-08 in ref transcript
  • K homology RNA-binding domain.
• smart KH 68aa 3e-08 in ref transcript
• pfam KH_1 64aa 1e-07 in ref transcript
  • KH domain. KH motifs can bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.
• pfam KH_1 63aa 4e-07 in ref transcript
• smart RRM 66aa 5e-07 in ref transcript
  • RNA recognition motif.
• TIGR PABP-1234 107aa 2e-06 in ref transcript
  • There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, and of unknown tissue range.
• TIGR arCOG04150 132aa 2e-04 in ref transcript
  • This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.
• PRK PRK13763 140aa 8e-05 in ref transcript
  • putative RNA-processing protein; Provisional.
• COG COG0724 76aa 1e-04 in ref transcript
  • RNA-binding proteins (RRM domain) [General function prediction only].
• PRK PRK12705 123aa 9e-04 in ref transcript
  • hypothetical protein; Provisional.
• Changed! cd PCBP_like_KH 56aa 8e-06 in modified transcript

IGLL1

• refseq_IGLL1.F2 refseq_IGLL1.R2 225 341
• NCBIGene 36.3 3543
• Single exon skipping, size difference: 116
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_020070

• Changed! cd IGc 95aa 5e-22 in ref transcript
  • Immunoglobulin domain constant region subfamily; members of the IGc subfamily are components of immunoglobulins, T-cell receptors, CD1 cell surface glycoproteins, secretory glycoproteins A/C, and Major Histocompatibility Complex (MHC) class I/II molecules. In immunoglobulins, each chain is composed of one variable domain (IGv) and one or more constant domains (IGc); these names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. T-cell receptors form heterodimers, pairing two chains (alpha/beta or gamma/delta), each with a IGv and IGc domain. MHCs form heterodimers pairing two chains (alpha/beta or delta/epsilon), each with a MHC and IGc domain. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• Changed! smart IGc1 75aa 2e-21 in ref transcript
  • Immunoglobulin C-Type.

IGSF3

• refseq_IGSF3.F2 refseq_IGSF3.R2 334 394
• NCBIGene 36.3 3321
• Single exon skipping, size difference: 60
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001542

• cd IGv 94aa 8e-04 in ref transcript
  • Immunoglobulin domain variable region (v) subfamily; members of the IGv subfamily are components of immunoglobulins and T-cell receptors. In immunoglobulins, each chain is composed of one variable domain (IGv) and one or more constant domains (IGc); these names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. Within the variable domain, there are regions of even more variability called the hypervariable or complementarity-determining regions (CDRs) which are responsible for antigen binding. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• cd IGv 86aa 8e-04 in ref transcript
• pfam V-set 105aa 8e-08 in ref transcript
  • Immunoglobulin V-set domain. This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.
• pfam V-set 102aa 4e-05 in ref transcript
• pfam V-set 102aa 8e-05 in ref transcript
• pfam V-set 111aa 8e-05 in ref transcript

IHPK2

• refseq_IHPK2.F1 refseq_IHPK2.R1 268 399
• NCBIGene 36.2 51447
• Single exon skipping, size difference: 131
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_001005910

IKIP

• refseq_IKIP.F1 refseq_IKIP.R1 253 371
• NCBIGene 36.3 121457
• Single exon skipping, size difference: 118
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_201612

• Changed! TIGR SMC_prok_B 198aa 3e-06 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• Changed! COG Smc 267aa 2e-04 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].

IL17RC

• refseq_IL17RC.F2 refseq_IL17RC.R2 138 183
• NCBIGene 36.3 84818
• Single exon skipping, size difference: 45
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_153461

• pfam SEFIR 145aa 1e-33 in ref transcript
  • SEFIR domain. This family comprises IL17 receptors (IL17Rs) and SEF proteins. The latter are feedback inhibitors of FGF signalling and are also thought to be receptors. Due to its similarity to the TIR domain (pfam01582), the SEFIR region is thought to be involved in homotypic interactions with other SEFIR/TIR-domain-containing proteins. Thus, SEFs and IL17Rs may be involved in TOLL/IL1R-like signalling pathways.

IL17RC

• refseq_IL17RC.F3 refseq_IL17RC.R3 170 383
• NCBIGene 36.3 84818
• Alternative 5-prime, size difference: 213
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_153461

• pfam SEFIR 145aa 1e-33 in ref transcript
  • SEFIR domain. This family comprises IL17 receptors (IL17Rs) and SEF proteins. The latter are feedback inhibitors of FGF signalling and are also thought to be receptors. Due to its similarity to the TIR domain (pfam01582), the SEFIR region is thought to be involved in homotypic interactions with other SEFIR/TIR-domain-containing proteins. Thus, SEFs and IL17Rs may be involved in TOLL/IL1R-like signalling pathways.

IL17RE

• refseq_IL17RE.F2 refseq_IL17RE.R2 211 284
• NCBIGene 36.2 132014
• Alternative 3-prime, size difference: 73
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_144640

IL18BP

• refseq_IL18BP.F1 refseq_IL18BP.R1 144 256
• NCBIGene 36.3 10068
• Single exon skipping, size difference: 112
• Exclusion in 5'UTR
• Reference transcript: NM_001039659

• pfam Pox_vIL-18BP 100aa 2e-04 in ref transcript
  • Orthopoxvirus interleukin 18 binding protein. Interleukin-18 (IL-18) is a proinflammatory cytokine that plays a key role in the activation of natural killer and T helper 1 cell responses principally by inducing interferon-gamma (IFN-gamma). Several poxvirus genes encode proteins with sequence similarity to IL-18BPs. It has been shown that vaccinia, ectromelia and cowpox viruses secrete from infected cells a soluble IL-18BP (vIL-18BP) that may modulate the host antiviral response. The expression of vIL-18BPs by distinct poxvirus genera that cause local or general viral dissemination, or persistent or acute infections in the host, emphasises the importance of IL-18 in response to viral infections.

IL1F7

• refseq_IL1F7.F1 refseq_IL1F7.R1 116 236
• NCBIGene 36.3 27178
• Single exon skipping, size difference: 120
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_014439

• Changed! cd IL1 146aa 3e-11 in ref transcript
  • Interleukin-1 homologes; Cytokines with various biological functions. Interleukin 1 alpha and beta are also known as hematopoietin and catabolin. This family also contains interleukin-1 receptor antagonists (inhibitors).
• Changed! smart IL1 146aa 8e-12 in ref transcript
  • Interleukin-1 homologues. Cytokines with various biological functions. Interluekin 1 alpha and beta are also known as hematopoietin and catabolin.
• Changed! cd IL1 97aa 3e-11 in modified transcript
• Changed! smart IL1 97aa 4e-11 in modified transcript

IL1F7

• refseq_IL1F7.F3 refseq_IL1F7.R3 195 258
• NCBIGene 36.3 27178
• Single exon skipping, size difference: 63
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_014439

• cd IL1 146aa 3e-11 in ref transcript
  • Interleukin-1 homologes; Cytokines with various biological functions. Interleukin 1 alpha and beta are also known as hematopoietin and catabolin. This family also contains interleukin-1 receptor antagonists (inhibitors).
• smart IL1 146aa 8e-12 in ref transcript
  • Interleukin-1 homologues. Cytokines with various biological functions. Interluekin 1 alpha and beta are also known as hematopoietin and catabolin.

IL22RA2

• refseq_IL22RA2.F1 refseq_IL22RA2.R1 154 324
• NCBIGene 36.3 116379
• Single exon skipping, size difference: 170
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_052962

• Changed! pfam IL10Ra-bind 236aa 6e-15 in ref transcript
  • Interleukin-10 receptor alpha chain. IL10Ra-bind is the cell-membrane bound receptor for interleukin-10, a pleiotropic cytokine produced by subsets of activated T cells, B cells, and macrophages, with a broad spectrum of immunoregulation and anti-inflammatory effects. The activity of IL-10 is mediated through its binding with IL10Ra-bind.
• Changed! pfam IL10Ra-bind 128aa 4e-12 in modified transcript

IL22RA2

• refseq_IL22RA2.F2 refseq_IL22RA2.R2 256 352
• NCBIGene 36.3 116379
• Single exon skipping, size difference: 96
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_052962

• Changed! pfam IL10Ra-bind 236aa 6e-15 in ref transcript
  • Interleukin-10 receptor alpha chain. IL10Ra-bind is the cell-membrane bound receptor for interleukin-10, a pleiotropic cytokine produced by subsets of activated T cells, B cells, and macrophages, with a broad spectrum of immunoregulation and anti-inflammatory effects. The activity of IL-10 is mediated through its binding with IL10Ra-bind.
• Changed! pfam IL10Ra-bind 204aa 8e-20 in modified transcript

IL24

• refseq_IL24.F1 refseq_IL24.R1 109 451
• NCBIGene 36.3 11009
• Multiple exon skipping, size difference: 342
• Exclusion of the protein initiation site, Exclusion in the protein causing a frameshift
• Reference transcript: NM_006850

IL28RA

• refseq_IL28RA.F1 refseq_IL28RA.R1 255 386
• NCBIGene 36.3 163702
• Single exon skipping, size difference: 131
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_170743

IL28RA

• refseq_IL28RA.F4 refseq_IL28RA.R3 138 225
• NCBIGene 36.3 163702
• Alternative 3-prime, size difference: 87
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_170743

IL32

• refseq_IL32.F1 refseq_IL32.R1 110 137
• NCBIGene 36.3 9235
• Single exon skipping, size difference: 27
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_004221

IL32

• refseq_IL32.F3 refseq_IL32.R3 100 160
• NCBIGene 36.3 9235
• Single exon skipping, size difference: 60
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_004221

IL4

• refseq_IL4.F2 refseq_IL4.R2 232 280
• NCBIGene 36.3 3565
• Single exon skipping, size difference: 48
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000589

• Changed! pfam IL4 148aa 4e-53 in ref transcript
  • Interleukin 4.
• Changed! pfam IL4 132aa 2e-43 in modified transcript

IL5RA

• refseq_IL5RA.F2 refseq_IL5RA.R2 140 209
• NCBIGene 36.3 3568
• Single exon skipping, size difference: 69
• Exclusion in 5'UTR
• Reference transcript: NM_000564

• pfam Haemat_rec_S_F2 30aa 3e-08 in ref transcript
  • Haematopoeitin receptor binding domain short. This domain is a common signature for a number of receptors for lymphokines, haematopoietic growth factors and growth hormone-related molecules.

IL6R

• refseq_IL6R.F2 refseq_IL6R.R2 277 371
• NCBIGene 36.3 3570
• Single exon skipping, size difference: 94
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_000565

• cd FN3 93aa 3e-05 in ref transcript
  • Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.
• pfam IL6Ra-bind 102aa 1e-45 in ref transcript
  • Interleukin-6 receptor alpha chain, binding. Members of this family adopt a structure consisting of an immunoglobulin-like beta-sandwich, with seven strands in two beta-sheets, in a Greek-key topology. They are required for binding to the cytokine Interleukin-6.
• smart IGc2 59aa 4e-10 in ref transcript
  • Immunoglobulin C-2 Type.
• smart FN3 86aa 1e-05 in ref transcript
  • Fibronectin type 3 domain. One of three types of internal repeat within the plasma protein, fibronectin. The tenth fibronectin type III repeat contains a RGD cell recognition sequence in a flexible loop between 2 strands. Type III modules are present in both extracellular and intracellular proteins.

IL6ST

• refseq_IL6ST.F1 refseq_IL6ST.R1 313 396
• NCBIGene 36.3 3572
• Single exon skipping, size difference: 83
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_002184

• cd FN3 100aa 8e-12 in ref transcript
  • Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.
• Changed! cd FN3 92aa 8e-06 in ref transcript
• pfam Lep_receptor_Ig 91aa 1e-30 in ref transcript
  • Ig-like C2-type domain. This domain is a ligand-binding immunoglobulin-like domain. The two cysteine residues form a disulphide bridge.
• Changed! smart FN3 81aa 3e-09 in ref transcript
  • Fibronectin type 3 domain. One of three types of internal repeat within the plasma protein, fibronectin. The tenth fibronectin type III repeat contains a RGD cell recognition sequence in a flexible loop between 2 strands. Type III modules are present in both extracellular and intracellular proteins.
• pfam fn3 90aa 1e-08 in ref transcript
  • Fibronectin type III domain.

IMPDH1

• refseq_IMPDH1.F1 refseq_IMPDH1.R1 159 267
• NCBIGene 36.3 3614
• Multiple exon skipping, size difference: 108
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_000883

• cd IMPDH 242aa 1e-95 in ref transcript
  • IMPDH: The catalytic domain of the inosine monophosphate dehydrogenase. IMPDH catalyzes the NAD-dependent oxidation of inosine 5'-monophosphate (IMP) to xanthosine 5' monophosphate (XMP). It is a rate-limiting step in the de novo synthesis of the guanine nucleotides. There is often a CBS domain inserted in the middle of this domain, which is proposed to play a regulatory role. IMPDH is a key enzyme in the regulation of cell proliferation and differentiation. It has been identified as an attractive target for developing chemotherapeutic agents.
• cd CBS_pair_IMPDH_2 116aa 4e-45 in ref transcript
  • This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the inosine 5' monophosphate dehydrogenase (IMPDH) protein. IMPDH is an essential enzyme that catalyzes the first step unique to GTP synthesis, playing a key role in the regulation of cell proliferation and differentiation. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain in IMPDH have been associated with retinitis pigmentosa.
• cd IMPDH 81aa 3e-30 in ref transcript
• pfam IMPDH 477aa 0.0 in ref transcript
  • IMP dehydrogenase / GMP reductase domain. This family is involved in biosynthesis of guanosine nucleotide. Members of this family contain a TIM barrel structure. In the inosine monophosphate dehydrogenases 2 CBS domains pfam00571 are inserted in the TIM barrel. This family is a member of the common phosphate binding site TIM barrel family.
• PTZ PTZ00314 501aa 0.0 in ref transcript
  • inosine-5'-monophosphate dehydrogenase; Provisional.

INSIG1

• refseq_INSIG1.F1 refseq_INSIG1.R1 104 396
• NCBIGene 36.3 3638
• Multiple exon skipping, size difference: 292
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_198336

• Changed! pfam INSIG 184aa 3e-78 in ref transcript
  • Insulin-induced protein (INSIG). This family contains a number of eukaryotic Insulin-induced proteins (INSIG-1 and INSIG-2) approximately 200 residues long. INSIG-1 and INSIG-2 are found in the endoplasmic reticulum and bind the sterol-sensing domain of SREBP cleavage-activating protein (SCAP), preventing it from escorting SREBPs to the Golgi. Their combined action permits feedback regulation of cholesterol synthesis over a wide range of sterol concentrations.
• Changed! pfam INSIG 56aa 5e-14 in modified transcript

INSIG1

• refseq_INSIG1.F4 refseq_INSIG1.R4 202 273
• NCBIGene 36.3 3638
• Single exon skipping, size difference: 71
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_198336

• pfam INSIG 184aa 3e-78 in ref transcript
  • Insulin-induced protein (INSIG). This family contains a number of eukaryotic Insulin-induced proteins (INSIG-1 and INSIG-2) approximately 200 residues long. INSIG-1 and INSIG-2 are found in the endoplasmic reticulum and bind the sterol-sensing domain of SREBP cleavage-activating protein (SCAP), preventing it from escorting SREBPs to the Golgi. Their combined action permits feedback regulation of cholesterol synthesis over a wide range of sterol concentrations.

IQCH

• refseq_IQCH.F1 refseq_IQCH.R1 177 239
• NCBIGene 36.3 64799
• Single exon skipping, size difference: 62
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_001031715

IQCH

• refseq_IQCH.F3 refseq_IQCH.R3 223 329
• NCBIGene 36.3 64799
• Single exon skipping, size difference: 106
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_001031715

IQCH

• refseq_IQCH.F5 refseq_IQCH.R5 104 438
• NCBIGene 36.3 64799
• Multiple exon skipping, size difference: 334
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_001031715

IQWD1

• refseq_IQWD1.F2 refseq_IQWD1.R2 281 341
• NCBIGene 36.3 55827
• Single exon skipping, size difference: 60
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_018442

• cd WD40 244aa 4e-19 in ref transcript
  • WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.
• cd WD40 78aa 7e-05 in ref transcript
• smart WD40 36aa 0.002 in ref transcript
  • WD40 repeats. Note that these repeats are permuted with respect to the structural repeats (blades) of the beta propeller domain.
• COG COG2319 274aa 4e-09 in ref transcript
  • FOG: WD40 repeat [General function prediction only].

IRF7

• refseq_IRF7.F1 refseq_IRF7.R1 114 201
• NCBIGene 36.3 3665
• Single exon skipping, size difference: 87
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_004031

• cd IRF 114aa 2e-25 in ref transcript
  • Interferon Regulatory Factor (IRF); also known as tryptophan pentad repeat. The family of IRF transcription factors is important in the regulation of interferons in response to infection by virus and in the regulation of interferon-inducible genes. The IRF family is characterized by a unique 'tryptophan cluster' DNA-binding region. Viral IRFs bind to cellular IRFs; block type I and II interferons and host IRF-mediated transcriptional activation.
• pfam IRF-3 181aa 5e-50 in ref transcript
  • Interferon-regulatory factor 3. This is the interferon-regulatory factor 3 chain of the hetero-dimeric structure which also contains the shorter chain CREB-binding protein. These two subunits make up the DRAF1 (double-stranded RNA-activated factor 1). Viral dsRNA produced during viral transcription or replication leads to the activation of DRAF1. The DNA-binding specificity of DRAF1 correlates with transcriptional induction of ISG (interferon-alpha,beta-stimulated gene). IRF-3 preexists in the cytoplasm of uninfected cells and translocates to the nucleus following viral infection. Translocation of IRF-3 is accompanied by an increase in serine and threonine phosphorylation, and association with the CREB coactivator occurs only after infection.
• smart IRF 114aa 2e-29 in ref transcript
  • interferon regulatory factor. interferon regulatory factor, also known as trytophan pentad repeat.

ITGA3

• refseq_ITGA3.F1 refseq_ITGA3.R1 174 316
• NCBIGene 36.3 3675
• Single exon skipping, size difference: 142
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_005501

• pfam Integrin_alpha2 455aa 7e-78 in ref transcript
  • Integrin alpha. This domain is found in integrin alpha and integrin alpha precursors to the C terminus of a number of pfam01839 repeats and to the N-terminus of the pfam00357 cytoplasmic region.
• smart Int_alpha 53aa 4e-11 in ref transcript
  • Integrin alpha (beta-propellor repeats). Integrins are cell adhesion molecules that mediate cell-extracellular matrix and cell-cell interactions. They contain both alpha and beta subunits. Alpha integrins are proposed to contain a domain containing a 7-fold repeat that adopts a beta-propellor fold. Some of these domains contain an inserted von Willebrand factor type-A domain. Some repeats contain putative calcium-binding sites. The 7-fold repeat domain is homologous to a similar domain in phosphatidylinositol-glycan-specific phospholipase D.
• smart Int_alpha 49aa 1e-08 in ref transcript
• smart Int_alpha 61aa 1e-05 in ref transcript

ITGB1BP1

• refseq_ITGB1BP1.F2 refseq_ITGB1BP1.R2 251 401
• NCBIGene 36.3 9270
• Single exon skipping, size difference: 150
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_004763

• Changed! cd PTB 130aa 0.003 in ref transcript
  • Phosphotyrosine-binding (PTB) domain; PTB domains have a PH-like fold and are found in various eukaryotic signaling molecules. They were initially identified based upon their ability to recognize phosphorylated tyrosine residues. In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. The PTB domain of SHC binds to a NPXpY sequence. More recent studies have found that some types of PTB domains such as the neuronal protein X11 and in the cell-fate determinant protein Numb can bind to peptides which are not tyrosine phosphorylated; whereas, other PTB domains can bind motifs lacking tyrosine residues altogether.
• Changed! pfam ICAP-1_inte_bdg 171aa 2e-81 in ref transcript
  • Beta-1 integrin binding protein. ICAP-1 is a serine/threonine-rich protein that binds to the cytoplasmic domains of beta-1 integrins in a highly specific manner, binding to a NPXY sequence motif on the beta-1 integrin. The cytoplasmic domains of integrins are essential for cell adhesion, and the fact that phosphorylation of ICAP-1 by interaction with the cell-matrix implies an important role of ICAP-1 during integrin-dependent cell adhesion. Overexpression of ICAP-1 strongly reduces the integrin-mediated cell spreading on extracellular matrix and inhibits both Cdc42 and Rac1. In addition, ICAP-1 induces release of Cdc42 from cellular membranes and prevents the dissociation of GDP from this GTPase. An additional function of ICAP-1 is to promote differentiation of osteoprogenitors by supporting their condensation through modulating the integrin high affinity state,.
• Changed! pfam ICAP-1_inte_bdg 121aa 1e-51 in modified transcript

ITGB1BP3

• refseq_ITGB1BP3.F1 refseq_ITGB1BP3.R1 222 354
• NCBIGene 36.2 27231
• Alternative 5-prime and 3-prime, size difference: 132
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_170678

• Changed! cd NRK1 161aa 9e-69 in ref transcript
  • Nicotinamide riboside kinase (NRK) is an enzyme involved in the metabolism of nicotinamide adenine dinucleotide (NAD+). This enzyme catalyzes the phosphorylation of nicotinamide riboside (NR) to form nicotinamide mononucleotide (NMN). It defines the NR salvage pathway of NAD+ biosynthesis in addition to the pathways through nicotinic acid mononucleotide (NaMN). This enzyme can also phosphorylate the anticancer drug tiazofurin, which is an analog of nicotinamide riboside.
• Changed! COG Udk 153aa 3e-15 in ref transcript
  • Uridine kinase [Nucleotide transport and metabolism].
• Changed! cd NRK1 177aa 7e-48 in modified transcript
• Changed! TIGR udk 45aa 0.009 in modified transcript
  • Model contains a number of longer eukaryotic proteins and starts bringing in phosphoribulokinase hits at scores of 160 and below.
• Changed! COG Udk 141aa 6e-10 in modified transcript

ITGB4

• refseq_ITGB4.F1 refseq_ITGB4.R1 203 362
• NCBIGene 36.3 3691
• Single exon skipping, size difference: 159
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_000213

• cd FN3 91aa 2e-13 in ref transcript
  • Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.
• cd FN3 94aa 1e-11 in ref transcript
• cd FN3 94aa 6e-10 in ref transcript
• cd FN3 88aa 6e-09 in ref transcript
• pfam Integrin_beta 417aa 1e-180 in ref transcript
  • Integrin, beta chain. Integrins have been found in animals and their homologues have also been found in cyanobacteria, probably due to horizontal gene transfer. The sequences repeats have been trimmed due to an overlap with EGF.
• pfam Integrin_B_tail 86aa 7e-21 in ref transcript
  • Integrin beta tail domain. This is the beta tail domain of the Integrin protein. Integrins are receptors which are involved in cell-cell and cell-extracellular matrix interactions.
• pfam fn3 84aa 5e-17 in ref transcript
  • Fibronectin type III domain.
• pfam fn3 87aa 8e-16 in ref transcript
• smart Calx_beta 64aa 2e-15 in ref transcript
  • Domains in Na-Ca exchangers and integrin-beta4. Domain in Na-Ca exchangers and integrin subunit beta4 (and some cyanobacterial proteins).
• pfam fn3 82aa 5e-12 in ref transcript
• pfam fn3 90aa 1e-10 in ref transcript

ITGB4

• refseq_ITGB4.F3 refseq_ITGB4.R3 131 341
• NCBIGene 36.3 3691
• Single exon skipping, size difference: 210
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000213

• cd FN3 91aa 2e-13 in ref transcript
  • Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.
• cd FN3 94aa 1e-11 in ref transcript
• cd FN3 94aa 6e-10 in ref transcript
• cd FN3 88aa 6e-09 in ref transcript
• pfam Integrin_beta 417aa 1e-180 in ref transcript
  • Integrin, beta chain. Integrins have been found in animals and their homologues have also been found in cyanobacteria, probably due to horizontal gene transfer. The sequences repeats have been trimmed due to an overlap with EGF.
• pfam Integrin_B_tail 86aa 7e-21 in ref transcript
  • Integrin beta tail domain. This is the beta tail domain of the Integrin protein. Integrins are receptors which are involved in cell-cell and cell-extracellular matrix interactions.
• pfam fn3 84aa 5e-17 in ref transcript
  • Fibronectin type III domain.
• pfam fn3 87aa 8e-16 in ref transcript
• smart Calx_beta 64aa 2e-15 in ref transcript
  • Domains in Na-Ca exchangers and integrin-beta4. Domain in Na-Ca exchangers and integrin subunit beta4 (and some cyanobacterial proteins).
• pfam fn3 82aa 5e-12 in ref transcript
• pfam fn3 90aa 1e-10 in ref transcript

EIF6

• refseq_ITGB4BP.F1 refseq_ITGB4BP.R1 215 391
• NCBIGene 36.3 3692
• Single exon skipping, size difference: 176
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_002212

• Changed! cd IF6 222aa 1e-90 in ref transcript
  • Ribosome anti-association factor IF6 binds the large ribosomal subunit and prevents the two subunits from associating during translation initiation. IF6 comprises a family of translation factors that includes both eukaryotic (eIF6) and archeal (aIF6) members. All members of this family have a conserved pentameric fold referred to as a beta/alpha propeller. The eukaryotic IF6 members have a moderately conserved C-terminal extension which is not required for ribosomal binding, and may have an alternative function.
• Changed! smart eIF6 201aa 9e-90 in ref transcript
  • translation initiation factor 6.
• Changed! PTZ PTZ00136 244aa 1e-118 in ref transcript
  • eukaryotic translation initiation factor 6; Provisional.
• Changed! cd IF6 67aa 1e-20 in modified transcript
• Changed! smart eIF6 65aa 2e-22 in modified transcript
• Changed! PTZ PTZ00136 68aa 6e-27 in modified transcript

ITM2C

• refseq_ITM2C.F1 refseq_ITM2C.R1 248 359
• NCBIGene 36.3 81618
• Single exon skipping, size difference: 111
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_030926

• Changed! pfam BRICHOS 93aa 6e-28 in ref transcript
  • BRICHOS domain. The BRICHOS domain is about 100 amino acids long. It is found in a variety of proteins implicated in dementia, respiratory distress and cancer. Its exact function is unknown; roles that have been proposed for it include (a) in targeting of the protein to the secretory pathway, (b) intramolecular chaperone-like function, and (c) assisting the specialised intracellular protease processing system.
• Changed! pfam BRICHOS 56aa 5e-08 in modified transcript

ITM2C

• refseq_ITM2C.F3 refseq_ITM2C.R3 149 290
• NCBIGene 36.3 81618
• Single exon skipping, size difference: 141
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_030926

• pfam BRICHOS 93aa 6e-28 in ref transcript
  • BRICHOS domain. The BRICHOS domain is about 100 amino acids long. It is found in a variety of proteins implicated in dementia, respiratory distress and cancer. Its exact function is unknown; roles that have been proposed for it include (a) in targeting of the protein to the secretory pathway, (b) intramolecular chaperone-like function, and (c) assisting the specialised intracellular protease processing system.

ITPA

• refseq_ITPA.F1 refseq_ITPA.R1 146 197
• NCBIGene 36.3 3704
• Alternative 5-prime, size difference: 51
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_033453

• Changed! cd HAM1 179aa 1e-56 in ref transcript
  • NTPase/HAM1. This family consists of the HAM1 protein and pyrophosphate-releasing xanthosine/ inosine triphosphatase. HAM1 protects the cell against mutagenesis by the base analog 6-N-hydroxylaminopurine (HAP) in E. Coli and S. cerevisiae. A Ham1-related protein from Methanococcus jannaschii is a novel NTPase that has been shown to hydrolyze nonstandard nucleotides such as XTP to XMP and ITP to IMP, but not the standard nucleotides, in the presence of Mg or Mn ions. The enzyme exists as a homodimer. The HAM1 protein may be acting as an NTPase by hydrolyzing the HAP triphosphate.
• Changed! pfam Ham1p_like 179aa 2e-39 in ref transcript
  • Ham1 family. This family consists of the HAM1 protein and hypothetical archaeal bacterial and Caenorhabditis elegans proteins. HAM1 controls 6-N-hydroxylaminopurine (HAP) sensitivity and mutagenesis in Saccharomyces cerevisiae HAM1. The HAM1 protein protects the cell from HAP, either on the level of deoxynucleoside triphosphate or the DNA level by a yet unidentified set of reactions.
• Changed! COG COG0127 187aa 1e-42 in ref transcript
  • Xanthosine triphosphate pyrophosphatase [Nucleotide transport and metabolism].
• Changed! cd HAM1 166aa 2e-50 in modified transcript
• Changed! pfam Ham1p_like 165aa 8e-35 in modified transcript
• Changed! COG COG0127 170aa 3e-37 in modified transcript

IVNS1ABP

• refseq_IVNS1ABP.F2 refseq_IVNS1ABP.R2 110 251
• NCBIGene 36.2 10625
• Single exon skipping, size difference: 141
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_006469

• pfam BTB 105aa 2e-22 in ref transcript
  • BTB/POZ domain. The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN.
• Changed! smart BACK 87aa 2e-13 in ref transcript
  • BTB And C-terminal Kelch. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues.
• Changed! smart Kelch 46aa 3e-11 in ref transcript
  • Kelch domain.
• Changed! smart Kelch 47aa 5e-11 in ref transcript
• Changed! pfam Kelch_1 41aa 4e-10 in ref transcript
  • Kelch motif. The kelch motif was initially discovered in Kelch. In this protein there are six copies of the motif. It has been shown that the Drosophila ring canal kelch protein is related to Galactose Oxidase for which a structure has been solved. The kelch motif forms a beta sheet. Several of these sheets associate to form a beta propeller structure as found in pfam00064, pfam00400 and pfam00415.
• Changed! smart Kelch 47aa 1e-09 in ref transcript
• Changed! pfam Kelch_1 47aa 8e-08 in ref transcript
• Changed! smart Kelch 48aa 2e-07 in ref transcript
• Changed! TIGR muta_rot_YjhT 179aa 9e-06 in ref transcript
  • Members of this protein family contain multiple copies of the beta-propeller-forming Kelch repeat. All are full-length homologs to YjhT of Escherichia coli, which has been identified as a mutarotase for sialic acid. This protein improves bacterial ability to obtain host sialic acid, and thus serves as a virulence factor. Some bacteria carry what appears to be a cyclically permuted homolog of this protein.
• Changed! COG COG3055 81aa 6e-05 in ref transcript
  • Uncharacterized protein conserved in bacteria [Function unknown].
• Changed! COG COG3055 171aa 0.001 in ref transcript
• Changed! smart BACK 87aa 1e-11 in modified transcript

JAG2

• refseq_JAG2.F2 refseq_JAG2.R2 100 214
• NCBIGene 36.3 3714
• Single exon skipping, size difference: 114
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_002226

• cd EGF_CA 39aa 5e-04 in ref transcript
  • Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements.
• cd EGF_CA 37aa 0.002 in ref transcript
• cd EGF_CA 37aa 0.003 in ref transcript
• Changed! cd EGF_CA 36aa 0.005 in ref transcript
• pfam MNNL 81aa 2e-22 in ref transcript
  • N terminus of Notch ligand. This entry represents a region of conserved sequence at the N terminus of several Notch ligand proteins.
• pfam DSL 63aa 4e-21 in ref transcript
  • Delta serrate ligand.
• smart VWC_out 72aa 1e-12 in ref transcript
  • von Willebrand factor (vWF) type C domain.
• smart EGF_CA 39aa 4e-04 in ref transcript
  • Calcium-binding EGF-like domain.
• smart EGF_CA 37aa 6e-04 in ref transcript
• Changed! smart EGF_CA 36aa 0.002 in ref transcript
• smart EGF_CA 37aa 0.004 in ref transcript
• Changed! cd EGF_CA 36aa 0.002 in modified transcript
• Changed! smart EGF_CA 36aa 6e-04 in modified transcript

KLHDC9

• refseq_KARCA1.F1 refseq_KARCA1.R1 100 119
• NCBIGene 36.3 126823
• Alternative 3-prime, size difference: 19
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_152366

CCBL2

• refseq_KAT3.F2 refseq_KAT3.R2 164 264
• NCBIGene 36.3 56267
• Single exon skipping, size difference: 100
• Exclusion of the protein initiation site
• Reference transcript: NM_001008661

• cd AAT_like 383aa 6e-78 in ref transcript
  • Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. The major groups in this CD corresponds to Aspartate aminotransferase a, b and c, Tyrosine, Alanine, Aromatic-amino-acid, Glutamine phenylpyruvate, 1-Aminocyclopropane-1-carboxylate synthase, Histidinol-phosphate, gene products of malY and cobC, Valine-pyruvate aminotransferase and Rhizopine catabolism regulatory protein.
• pfam Aminotran_1_2 368aa 3e-44 in ref transcript
  • Aminotransferase class I and II.
• PRK PRK08912 391aa 2e-97 in ref transcript
  • hypothetical protein; Provisional.

KBTBD3

• refseq_KBTBD3.F2 refseq_KBTBD3.R2 125 326
• NCBIGene 36.3 143879
• Single exon skipping, size difference: 201
• Exclusion in 5'UTR
• Reference transcript: NM_198439

• pfam BACK 102aa 1e-25 in ref transcript
  • BTB And C-terminal Kelch. This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation).
• pfam BTB 108aa 3e-17 in ref transcript
  • BTB/POZ domain. The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN.
• pfam Kelch_1 50aa 3e-04 in ref transcript
  • Kelch motif. The kelch motif was initially discovered in Kelch. In this protein there are six copies of the motif. It has been shown that the Drosophila ring canal kelch protein is related to Galactose Oxidase for which a structure has been solved. The kelch motif forms a beta sheet. Several of these sheets associate to form a beta propeller structure as found in pfam00064, pfam00400 and pfam00415.
• pfam Kelch_1 44aa 0.002 in ref transcript

KBTBD4

• refseq_KBTBD4.F1 refseq_KBTBD4.R1 274 383
• NCBIGene 36.3 55709
• Alternative 5-prime and 3-prime, size difference: 109
• Exclusion in 5'UTR, Exclusion in 5'UTR
• Reference transcript: NM_016506

• pfam BTB 104aa 3e-22 in ref transcript
  • BTB/POZ domain. The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN.
• smart BACK 83aa 6e-12 in ref transcript
  • BTB And C-terminal Kelch. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues.

KCNAB2

• refseq_KCNAB2.F2 refseq_KCNAB2.R2 100 142
• NCBIGene 36.3 8514
• Single exon skipping, size difference: 42
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_003636

• Changed! cd Aldo_ket_red 316aa 8e-76 in ref transcript
  • Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial applications. Members have very distinct functions and include the prokaryotic 2,5-diketo-D-gluconic acid reductases and beta-keto ester reductases, the eukaryotic aldose reductases, aldehyde reductases, hydroxysteroid dehydrogenases, steroid 5beta-reductases, potassium channel beta-subunits and aflatoxin aldehyde reductases, among others.
• Changed! TIGR Kv_beta 317aa 1e-179 in ref transcript
  • Plant beta subunits and their closely related bacterial homologs (in Deinococcus radiudurans, Xylella fastidiosa, etc.) appear more closely related to each other than to animal forms. However, the bacterial species lack convincing counterparts the Kv alpha subunit and the Kv beta homolog may serve as an enzyme. Cutoffs are set for this model such that yeast and plant forms and bacterial close homologs score between trusted and noise cutoffs.
• Changed! COG Tas 321aa 2e-67 in ref transcript
  • Predicted oxidoreductases (related to aryl-alcohol dehydrogenases) [Energy production and conversion].
• Changed! cd Aldo_ket_red 316aa 1e-75 in modified transcript
• Changed! TIGR Kv_beta 317aa 1e-179 in modified transcript
• Changed! COG Tas 323aa 8e-68 in modified transcript

KCNC2

• refseq_KCNC2.F2 refseq_KCNC2.R2 125 290
• NCBIGene 36.3 3747
• Single exon skipping, size difference: 165
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_139136

• pfam K_tetra 51aa 6e-19 in ref transcript
  • K+ channel tetramerisation domain. The N-terminal, cytoplasmic tetramerisation domain (T1) of voltage-gated K+ channels encodes molecular determinants for subfamily-specific assembly of alpha-subunits into functional tetrameric channels. It is distantly related to the BTB/POZ domain pfam00651.
• pfam Ion_trans 189aa 2e-16 in ref transcript
  • Ion transport protein. This family contains Sodium, Potassium, Calcium ion channels. This family is 6 transmembrane helices in which the last two helices flank a loop which determines ion selectivity. In some sub-families (e.g. Na channels) the domain is repeated four times, whereas in others (e.g. K channels) the protein forms as a tetramer in the membrane. A bacterial structure of the protein is known for the last two helices but is not the Pfam family due to it lacking the first four helices.
• smart BTB 143aa 5e-07 in ref transcript
  • Broad-Complex, Tramtrack and Bric a brac. Domain in Broad-Complex, Tramtrack and Bric a brac. Also known as POZ (poxvirus and zinc finger) domain. Known to be a protein-protein interaction motif found at the N-termini of several C2H2-type transcription factors as well as Shaw-type potassium channels. Known structure reveals a tightly intertwined dimer formed via interactions between N-terminal strand and helix structures. However in a subset of BTB/POZ domains, these two secondary structures appear to be missing. Be aware SMART predicts BTB/POZ domains without the beta1- and alpha1-secondary structures.
• PRK PRK10537 25aa 0.001 in ref transcript
  • voltage-gated potassium channel; Provisional.

KCND3

• refseq_KCND3.F1 refseq_KCND3.R1 204 261
• NCBIGene 36.3 3752
• Single exon skipping, size difference: 57
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_004980

• pfam K_tetra 90aa 5e-33 in ref transcript
  • K+ channel tetramerisation domain. The N-terminal, cytoplasmic tetramerisation domain (T1) of voltage-gated K+ channels encodes molecular determinants for subfamily-specific assembly of alpha-subunits into functional tetrameric channels. It is distantly related to the BTB/POZ domain pfam00651.
• pfam Ion_trans 162aa 6e-27 in ref transcript
  • Ion transport protein. This family contains Sodium, Potassium, Calcium ion channels. This family is 6 transmembrane helices in which the last two helices flank a loop which determines ion selectivity. In some sub-families (e.g. Na channels) the domain is repeated four times, whereas in others (e.g. K channels) the protein forms as a tetramer in the membrane. A bacterial structure of the protein is known for the last two helices but is not the Pfam family due to it lacking the first four helices.
• PRK PRK10537 87aa 6e-09 in ref transcript
  • voltage-gated potassium channel; Provisional.

KCNG3

• refseq_KCNG3.F1 refseq_KCNG3.R1 134 167
• NCBIGene 36.3 170850
• Alternative 5-prime, size difference: 33
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_133329

• pfam Ion_trans 186aa 2e-25 in ref transcript
  • Ion transport protein. This family contains Sodium, Potassium, Calcium ion channels. This family is 6 transmembrane helices in which the last two helices flank a loop which determines ion selectivity. In some sub-families (e.g. Na channels) the domain is repeated four times, whereas in others (e.g. K channels) the protein forms as a tetramer in the membrane. A bacterial structure of the protein is known for the last two helices but is not the Pfam family due to it lacking the first four helices.
• pfam K_tetra 101aa 4e-19 in ref transcript
  • K+ channel tetramerisation domain. The N-terminal, cytoplasmic tetramerisation domain (T1) of voltage-gated K+ channels encodes molecular determinants for subfamily-specific assembly of alpha-subunits into functional tetrameric channels. It is distantly related to the BTB/POZ domain pfam00651.
• PRK PRK10537 51aa 5e-06 in ref transcript
  • voltage-gated potassium channel; Provisional.

KCNH1

• refseq_KCNH1.F1 refseq_KCNH1.R1 290 371
• NCBIGene 36.3 3756
• Alternative 5-prime, size difference: 81
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_172362

• cd CAP_ED 110aa 5e-17 in ref transcript
  • effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels. Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels.
• cd PAS 95aa 8e-07 in ref transcript
  • PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.
• smart cNMP 115aa 1e-15 in ref transcript
  • Cyclic nucleotide-monophosphate binding domain. Catabolite gene activator protein (CAP) is a prokaryotic homologue of eukaryotic cNMP-binding domains, present in ion channels, and cNMP-dependent kinases.
• Changed! pfam Ion_trans_2 60aa 3e-09 in ref transcript
  • Ion channel. This family includes the two membrane helix type ion channels found in bacteria.
• Changed! pfam Ion_trans 120aa 4e-07 in ref transcript
  • Ion transport protein. This family contains Sodium, Potassium, Calcium ion channels. This family is 6 transmembrane helices in which the last two helices flank a loop which determines ion selectivity. In some sub-families (e.g. Na channels) the domain is repeated four times, whereas in others (e.g. K channels) the protein forms as a tetramer in the membrane. A bacterial structure of the protein is known for the last two helices but is not the Pfam family due to it lacking the first four helices.
• smart PAC 42aa 9e-06 in ref transcript
  • Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain). PAC motif occurs C-terminal to a subset of all known PAS motifs. It is proposed to contribute to the PAS domain fold.
• TIGR sensory_box 123aa 2e-05 in ref transcript
  • The PAS domain was previously described. This sensory box, or S-box domain occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include heme in the oxygen sensor FixL, FAD in the redox potential sensor NifL, and a 4-hydroxycinnamyl chromophore in photoactive yellow protein. Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator.
• PRK PRK13558 100aa 7e-13 in ref transcript
  • bacterio-opsin activator; Provisional.
• COG Crp 121aa 5e-09 in ref transcript
  • cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms].
• PRK PRK10537 49aa 0.001 in ref transcript
  • voltage-gated potassium channel; Provisional.
• Changed! pfam Ion_trans 185aa 4e-10 in modified transcript

KCNH5

• refseq_KCNH5.F1 refseq_KCNH5.R1 205 402
• NCBIGene 36.3 27133
• Single exon skipping, size difference: 197
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_139318

• Changed! cd CAP_ED 110aa 2e-16 in ref transcript
  • effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels. Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels.
• cd PAS 95aa 9e-06 in ref transcript
  • PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.
• Changed! smart cNMP 100aa 4e-13 in ref transcript
  • Cyclic nucleotide-monophosphate binding domain. Catabolite gene activator protein (CAP) is a prokaryotic homologue of eukaryotic cNMP-binding domains, present in ion channels, and cNMP-dependent kinases.
• Changed! pfam Ion_trans_2 75aa 7e-10 in ref transcript
  • Ion channel. This family includes the two membrane helix type ion channels found in bacteria.
• pfam Ion_trans 184aa 7e-07 in ref transcript
  • Ion transport protein. This family contains Sodium, Potassium, Calcium ion channels. This family is 6 transmembrane helices in which the last two helices flank a loop which determines ion selectivity. In some sub-families (e.g. Na channels) the domain is repeated four times, whereas in others (e.g. K channels) the protein forms as a tetramer in the membrane. A bacterial structure of the protein is known for the last two helices but is not the Pfam family due to it lacking the first four helices.
• pfam PAS 92aa 1e-05 in ref transcript
  • PAS fold. The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs. The PAS fold appears in archaea, eubacteria and eukarya.
• PRK PRK13558 100aa 4e-12 in ref transcript
  • bacterio-opsin activator; Provisional.
• Changed! COG Crp 215aa 2e-08 in ref transcript
  • cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms].
• PRK PRK10537 52aa 1e-04 in ref transcript
  • voltage-gated potassium channel; Provisional.
• Changed! cd CAP_ED 52aa 2e-06 in modified transcript
• Changed! pfam Ion_trans_2 77aa 3e-08 in modified transcript
• Changed! smart cNMP 57aa 3e-07 in modified transcript

KCNH6

• refseq_KCNH6.F1 refseq_KCNH6.R1 189 297
• NCBIGene 36.3 81033
• Single exon skipping, size difference: 108
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_030779

• cd CAP_ED 111aa 4e-17 in ref transcript
  • effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels. Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels.
• cd PAS 92aa 2e-06 in ref transcript
  • PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.
• smart cNMP 100aa 2e-16 in ref transcript
  • Cyclic nucleotide-monophosphate binding domain. Catabolite gene activator protein (CAP) is a prokaryotic homologue of eukaryotic cNMP-binding domains, present in ion channels, and cNMP-dependent kinases.
• pfam Ion_trans 177aa 2e-10 in ref transcript
  • Ion transport protein. This family contains Sodium, Potassium, Calcium ion channels. This family is 6 transmembrane helices in which the last two helices flank a loop which determines ion selectivity. In some sub-families (e.g. Na channels) the domain is repeated four times, whereas in others (e.g. K channels) the protein forms as a tetramer in the membrane. A bacterial structure of the protein is known for the last two helices but is not the Pfam family due to it lacking the first four helices.
• pfam PAS 92aa 5e-07 in ref transcript
  • PAS fold. The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs. The PAS fold appears in archaea, eubacteria and eukarya.
• PRK PRK13559 95aa 5e-14 in ref transcript
  • hypothetical protein; Provisional.
• COG Crp 121aa 2e-09 in ref transcript
  • cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms].
• PRK PRK10537 73aa 1e-04 in ref transcript
  • voltage-gated potassium channel; Provisional.

KCNH7

• refseq_KCNH7.F2 refseq_KCNH7.R2 119 140
• NCBIGene 36.3 90134
• Single exon skipping, size difference: 21
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_033272

• cd CAP_ED 111aa 1e-17 in ref transcript
  • effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels. Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels.
• cd PAS 90aa 3e-07 in ref transcript
  • PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.
• smart cNMP 115aa 3e-18 in ref transcript
  • Cyclic nucleotide-monophosphate binding domain. Catabolite gene activator protein (CAP) is a prokaryotic homologue of eukaryotic cNMP-binding domains, present in ion channels, and cNMP-dependent kinases.
• pfam Ion_trans 177aa 2e-11 in ref transcript
  • Ion transport protein. This family contains Sodium, Potassium, Calcium ion channels. This family is 6 transmembrane helices in which the last two helices flank a loop which determines ion selectivity. In some sub-families (e.g. Na channels) the domain is repeated four times, whereas in others (e.g. K channels) the protein forms as a tetramer in the membrane. A bacterial structure of the protein is known for the last two helices but is not the Pfam family due to it lacking the first four helices.
• pfam PAS 89aa 7e-05 in ref transcript
  • PAS fold. The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs. The PAS fold appears in archaea, eubacteria and eukarya.
• PRK PRK13557 80aa 8e-11 in ref transcript
  • histidine kinase; Provisional.
• COG Crp 144aa 1e-09 in ref transcript
  • cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms].
• PRK PRK10537 80aa 8e-05 in ref transcript
  • voltage-gated potassium channel; Provisional.

KCNIP1

• refseq_KCNIP1.F2 refseq_KCNIP1.R2 172 205
• NCBIGene 36.3 30820
• Single exon skipping, size difference: 33
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001034837

• cd EFh 72aa 3e-08 in ref transcript
  • EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers.
• cd EFh 63aa 6e-06 in ref transcript
• smart EFh 29aa 0.002 in ref transcript
  • EF-hand, calcium binding motif. EF-hands are calcium-binding motifs that occur at least in pairs. Links between disease states and genes encoding EF-hands, particularly the S100 subclass, are emerging. Each motif consists of a 12 residue loop flanked on either side by a 12 residue alpha-helix. EF-hands undergo a conformational change unpon binding calcium ions.
• COG FRQ1 167aa 5e-19 in ref transcript
  • Ca2+-binding protein (EF-Hand superfamily) [Signal transduction mechanisms / Cytoskeleton / Cell division and chromosome partitioning / General function prediction only].

KCNIP2

• refseq_KCNIP2.F1 refseq_KCNIP2.R1 121 229
• NCBIGene 36.3 30819
• Single exon skipping, size difference: 108
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_014591

• Changed! cd EFh 63aa 6e-08 in ref transcript
  • EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers.
• Changed! cd EFh 72aa 1e-07 in ref transcript
• Changed! smart EH 87aa 7e-04 in ref transcript
  • Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
• Changed! COG FRQ1 167aa 3e-18 in ref transcript
  • Ca2+-binding protein (EF-Hand superfamily) [Signal transduction mechanisms / Cytoskeleton / Cell division and chromosome partitioning / General function prediction only].
• Changed! cd EFh 72aa 1e-06 in modified transcript
• Changed! COG FRQ1 104aa 2e-08 in modified transcript

KCNJ1

• refseq_KCNJ1.F1 refseq_KCNJ1.R1 229 399
• NCBIGene 36.3 3758
• Single exon skipping, size difference: 170
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_153765

• Changed! pfam IRK 338aa 1e-153 in ref transcript
  • Inward rectifier potassium channel.

KCNJ1

• refseq_KCNJ1.F2 refseq_KCNJ1.R2 258 391
• NCBIGene 36.3 3758
• Single exon skipping, size difference: 133
• Exclusion in 5'UTR
• Reference transcript: NM_153767

• pfam IRK 338aa 1e-153 in ref transcript
  • Inward rectifier potassium channel.

KCNQ1

• refseq_KCNQ1.F1 refseq_KCNQ1.R1 122 214
• NCBIGene 36.2 3784
• Single exon skipping, size difference: 92
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_000218

• Changed! pfam KCNQ_channel 163aa 5e-62 in ref transcript
  • KCNQ voltage-gated potassium channel. This family matches to the C-terminal tail of KCNQ type potassium channels.
• Changed! pfam Ion_trans 190aa 4e-18 in ref transcript
  • Ion transport protein. This family contains Sodium, Potassium, Calcium ion channels. This family is 6 transmembrane helices in which the last two helices flank a loop which determines ion selectivity. In some sub-families (e.g. Na channels) the domain is repeated four times, whereas in others (e.g. K channels) the protein forms as a tetramer in the membrane. A bacterial structure of the protein is known for the last two helices but is not the Pfam family due to it lacking the first four helices.

KCNQ2

• refseq_KCNQ2.F1 refseq_KCNQ2.R1 153 183
• NCBIGene 36.3 3785
• Single exon skipping, size difference: 30
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_172107

• pfam KCNQ_channel 201aa 2e-70 in ref transcript
  • KCNQ voltage-gated potassium channel. This family matches to the C-terminal tail of KCNQ type potassium channels.
• pfam Ion_trans 185aa 8e-25 in ref transcript
  • Ion transport protein. This family contains Sodium, Potassium, Calcium ion channels. This family is 6 transmembrane helices in which the last two helices flank a loop which determines ion selectivity. In some sub-families (e.g. Na channels) the domain is repeated four times, whereas in others (e.g. K channels) the protein forms as a tetramer in the membrane. A bacterial structure of the protein is known for the last two helices but is not the Pfam family due to it lacking the first four helices.
• PRK PRK10537 40aa 0.004 in ref transcript
  • voltage-gated potassium channel; Provisional.

KCNQ4

• refseq_KCNQ4.F1 refseq_KCNQ4.R1 105 267
• NCBIGene 36.3 9132
• Single exon skipping, size difference: 162
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_004700

• pfam KCNQ_channel 197aa 5e-72 in ref transcript
  • KCNQ voltage-gated potassium channel. This family matches to the C-terminal tail of KCNQ type potassium channels.
• pfam Ion_trans 185aa 1e-18 in ref transcript
  • Ion transport protein. This family contains Sodium, Potassium, Calcium ion channels. This family is 6 transmembrane helices in which the last two helices flank a loop which determines ion selectivity. In some sub-families (e.g. Na channels) the domain is repeated four times, whereas in others (e.g. K channels) the protein forms as a tetramer in the membrane. A bacterial structure of the protein is known for the last two helices but is not the Pfam family due to it lacking the first four helices.
• PRK PRK10537 69aa 0.002 in ref transcript
  • voltage-gated potassium channel; Provisional.

KCNRG

• refseq_KCNRG.F2 refseq_KCNRG.R2 267 365
• NCBIGene 36.3 283518
• Single exon skipping, size difference: 98
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_173605

• pfam K_tetra 89aa 4e-12 in ref transcript
  • K+ channel tetramerisation domain. The N-terminal, cytoplasmic tetramerisation domain (T1) of voltage-gated K+ channels encodes molecular determinants for subfamily-specific assembly of alpha-subunits into functional tetrameric channels. It is distantly related to the BTB/POZ domain pfam00651.

KIAA0101

• refseq_KIAA0101.F1 refseq_KIAA0101.R1 129 292
• NCBIGene 36.3 9768
• Single exon skipping, size difference: 163
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_014736

KIAA0841

• refseq_KIAA0841.F2 refseq_KIAA0841.R2 137 198
• NCBIGene 36.2 23354
• Alternative 3-prime, size difference: 61
• Exclusion of the protein initiation site
• Reference transcript: XM_932194

KIAA0859

• refseq_KIAA0859.F2 refseq_KIAA0859.R2 101 426
• NCBIGene 36.3 51603
• Alternative 5-prime, size difference: 325
• Exclusion of the protein initiation site
• Reference transcript: NM_015935

• Changed! cd AdoMet_MTases 109aa 8e-08 in ref transcript
  • S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.).
• Changed! pfam Methyltransf_11 106aa 6e-09 in ref transcript
  • Methyltransferase domain. Members of this family are SAM dependent methyltransferases.
• pfam Spermine_synth 94aa 3e-06 in ref transcript
  • Spermine/spermidine synthase. Spermine and spermidine are polyamines. This family includes spermidine synthase that catalyses the fifth (last) step in the biosynthesis of spermidine from arginine, and spermine synthase.
• COG SpeE 169aa 1e-11 in ref transcript
  • Spermidine synthase [Amino acid transport and metabolism].
• Changed! PRK PRK08317 221aa 5e-09 in ref transcript
  • hypothetical protein; Provisional.
• Changed! PRK PRK08317 64aa 7e-04 in modified transcript

KIAA1462

• refseq_KIAA1462.F2 refseq_KIAA1462.R2 147 187
• NCBIGene 36.2 57608
• Single exon skipping, size difference: 40
• Inclusion in the protein causing a new stop codon
• Reference transcript: XM_929312

FNIP1

• refseq_KIAA1961.F1 refseq_KIAA1961.R1 149 233
• NCBIGene 36.3 96459
• Single exon skipping, size difference: 84
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_133372

KIF23

• refseq_KIF23.F1 refseq_KIF23.R1 104 416
• NCBIGene 36.3 9493
• Single exon skipping, size difference: 312
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_138555

• cd KISc_KIF23_like 219aa 1e-102 in ref transcript
  • Kinesin motor domain, KIF23-like subgroup. Members of this group may play a role in mitosis. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-coil domain close to a second tubulin dimer, about 80 Angstroms along the microtubule. Meanwhile, ATP hydrolysis takes place, and when the second head domain binds to the microtubule, the first domain again replaces ADP with ATP, triggering a conformational change that pulls the first domain forward.
• cd KISc_KIF23_like 123aa 9e-50 in ref transcript
• pfam Kinesin 228aa 1e-74 in ref transcript
  • Kinesin motor domain.
• smart KISc 126aa 3e-30 in ref transcript
  • Kinesin motor, catalytic domain. ATPase. Microtubule-dependent molecular motors that play important roles in intracellular transport of organelles and in cell division.
• pfam SMC_N 168aa 4e-04 in ref transcript
  • RecF/RecN/SMC N terminal domain. This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.
• COG KIP1 236aa 2e-36 in ref transcript
  • Kinesin-like protein [Cytoskeleton].
• COG KIP1 75aa 1e-11 in ref transcript
• COG Smc 184aa 2e-04 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].

KIF25

• refseq_KIF25.F1 refseq_KIF25.R1 145 301
• NCBIGene 36.3 3834
• Single exon skipping, size difference: 156
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_030615

• Changed! cd KISc_C_terminal 336aa 5e-63 in ref transcript
  • Kinesin motor domain, KIFC2/KIFC3/ncd-like carboxy-terminal kinesins. Ncd is a spindle motor protein necessary for chromosome segregation in meiosis. KIFC2/KIFC3-like kinesins have been implicated in motility of the Golgi apparatus as well as dentritic and axonal transport in neurons. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In this subgroup the motor domain is found at the C-terminus (C-type). C-type kinesins are (-) end-directed motors, i.e. they transport cargo towards the (-) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-coil domain close to a second tubulin dimer, about 80 Angstroms along the microtubule. Meanwhile, ATP hydrolysis takes place, and when the second head domain binds to the microtubule, the first domain again replaces ADP with ATP, triggering a conformational change that pulls the first domain forward.
• Changed! pfam Kinesin 333aa 1e-65 in ref transcript
  • Kinesin motor domain.
• Changed! COG KIP1 333aa 6e-38 in ref transcript
  • Kinesin-like protein [Cytoskeleton].
• Changed! cd KISc_C_terminal 284aa 7e-43 in modified transcript
• Changed! smart KISc 287aa 5e-46 in modified transcript
  • Kinesin motor, catalytic domain. ATPase. Microtubule-dependent molecular motors that play important roles in intracellular transport of organelles and in cell division.
• Changed! COG KIP1 281aa 9e-28 in modified transcript

KIF9

• refseq_KIF9.F1 refseq_KIF9.R1 201 396
• NCBIGene 36.3 64147
• Single exon skipping, size difference: 195
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_182902

• cd KISc_KIF9_like 333aa 1e-144 in ref transcript
  • Kinesin motor domain, KIF9-like subgroup; might play a role in cell shape remodeling. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-coil domain close to a second tubulin dimer, about 80 Angstroms along the microtubule. Meanwhile, ATP hydrolysis takes place, and when the second head domain binds to the microtubule, the first domain again replaces ADP with ATP, triggering a conformational change that pulls the first domain forward.
• pfam Kinesin 329aa 1e-107 in ref transcript
  • Kinesin motor domain.
• COG KIP1 300aa 2e-54 in ref transcript
  • Kinesin-like protein [Cytoskeleton].

KIRREL2

• refseq_KIRREL2.F1 refseq_KIRREL2.R1 202 352
• NCBIGene 36.3 84063
• Single exon skipping, size difference: 150
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_199180

• cd IGcam 82aa 8e-10 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• cd IGcam 79aa 2e-05 in ref transcript
• Changed! cd IGcam 95aa 0.001 in ref transcript
• cd IGcam 73aa 0.002 in ref transcript
• pfam I-set 80aa 9e-12 in ref transcript
  • Immunoglobulin I-set domain.
• pfam C2-set_2 90aa 3e-07 in ref transcript
  • CD80-like C2-set immunoglobulin domain. These domains belong to the immunoglobulin superfamily.
• Changed! pfam I-set 83aa 7e-07 in ref transcript
• pfam I-set 74aa 3e-04 in ref transcript
• Changed! smart IG_like 44aa 0.005 in modified transcript
  • Immunoglobulin like. IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.

KL

• refseq_KL.F2 refseq_KL.R2 209 255
• NCBIGene 36.2 9365
• Alternative 5-prime and 3-prime, size difference: 46
• Inclusion in the protein causing a new stop codon, Exclusion in the protein causing a frameshift
• Reference transcript: NM_004795

• pfam Glyco_hydro_1 449aa 1e-115 in ref transcript
  • Glycosyl hydrolase family 1.
• Changed! pfam Glyco_hydro_1 372aa 6e-78 in ref transcript
• COG BglB 446aa 4e-79 in ref transcript
  • Beta-glucosidase/6-phospho-beta-glucosidase/beta- galactosidase [Carbohydrate transport and metabolism].
• Changed! COG BglB 371aa 5e-49 in ref transcript

KLHL5

• refseq_KLHL5.F1 refseq_KLHL5.R1 144 327
• NCBIGene 36.3 51088
• Single exon skipping, size difference: 183
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_015990

• pfam BACK 100aa 4e-35 in ref transcript
  • BTB And C-terminal Kelch. This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation).
• Changed! pfam BTB 108aa 2e-26 in ref transcript
  • BTB/POZ domain. The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN.
• pfam Kelch_1 46aa 1e-12 in ref transcript
  • Kelch motif. The kelch motif was initially discovered in Kelch. In this protein there are six copies of the motif. It has been shown that the Drosophila ring canal kelch protein is related to Galactose Oxidase for which a structure has been solved. The kelch motif forms a beta sheet. Several of these sheets associate to form a beta propeller structure as found in pfam00064, pfam00400 and pfam00415.
• smart Kelch 47aa 3e-12 in ref transcript
  • Kelch domain.
• pfam Kelch_1 44aa 2e-10 in ref transcript
• smart Kelch 45aa 9e-10 in ref transcript
• smart Kelch 46aa 1e-08 in ref transcript
• pfam Kelch_1 52aa 2e-07 in ref transcript
• TIGR mutarot_permut 200aa 6e-06 in ref transcript
  • Members of this protein family show essentially full-length homology, cyclically permuted, to YjhT from Escherichia coli. YjhT was shown to act as a mutarotase for sialic acid, and by this ability to be able to act as a virulence factor. Members of the YjhT family (TIGR03547) and this cyclically-permuted family have multiple repeats of the beta-propeller-forming Kelch repeat.
• TIGR muta_rot_YjhT 119aa 5e-05 in ref transcript
  • Members of this protein family contain multiple copies of the beta-propeller-forming Kelch repeat. All are full-length homologs to YjhT of Escherichia coli, which has been identified as a mutarotase for sialic acid. This protein improves bacterial ability to obtain host sialic acid, and thus serves as a virulence factor. Some bacteria carry what appears to be a cyclically permuted homolog of this protein.
• Changed! pfam BTB 74aa 8e-13 in modified transcript

KLHL7

• refseq_KLHL7.F1 refseq_KLHL7.R1 240 371
• NCBIGene 36.3 55975
• Single exon skipping, size difference: 131
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_001031710

• Changed! pfam BACK 103aa 2e-32 in ref transcript
  • BTB And C-terminal Kelch. This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation).
• Changed! pfam BTB 107aa 5e-29 in ref transcript
  • BTB/POZ domain. The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN.
• Changed! pfam Kelch_1 46aa 6e-09 in ref transcript
  • Kelch motif. The kelch motif was initially discovered in Kelch. In this protein there are six copies of the motif. It has been shown that the Drosophila ring canal kelch protein is related to Galactose Oxidase for which a structure has been solved. The kelch motif forms a beta sheet. Several of these sheets associate to form a beta propeller structure as found in pfam00064, pfam00400 and pfam00415.
• Changed! pfam Kelch_1 48aa 7e-08 in ref transcript
• Changed! smart Kelch 48aa 2e-05 in ref transcript
  • Kelch domain.
• Changed! TIGR muta_rot_YjhT 65aa 0.002 in ref transcript
  • Members of this protein family contain multiple copies of the beta-propeller-forming Kelch repeat. All are full-length homologs to YjhT of Escherichia coli, which has been identified as a mutarotase for sialic acid. This protein improves bacterial ability to obtain host sialic acid, and thus serves as a virulence factor. Some bacteria carry what appears to be a cyclically permuted homolog of this protein.

KLK12

• refseq_KLK12.F1 refseq_KLK12.R1 131 391
• NCBIGene 36.3 43849
• Single exon skipping, size difference: 260
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_019598

• Changed! cd Tryp_SPc 215aa 8e-50 in ref transcript
  • Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
• Changed! smart Tryp_SPc 216aa 9e-56 in ref transcript
  • Trypsin-like serine protease. Many of these are synthesised as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. A few, however, are active as single chain molecules, and others are inactive due to substitutions of the catalytic triad residues.
• Changed! COG COG5640 236aa 2e-15 in ref transcript
  • Secreted trypsin-like serine protease [Posttranslational modification, protein turnover, chaperones].
• Changed! cd Tryp_SPc 50aa 9e-11 in modified transcript
• Changed! smart Tryp_SPc 43aa 2e-12 in modified transcript
• Changed! COG COG5640 63aa 9e-06 in modified transcript

KLK3

• refseq_KLK3.F2 refseq_KLK3.R2 247 376
• NCBIGene 36.3 354
• Alternative 3-prime, size difference: 129
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001648

• Changed! cd Tryp_SPc 232aa 3e-64 in ref transcript
  • Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
• Changed! smart Tryp_SPc 230aa 5e-71 in ref transcript
  • Trypsin-like serine protease. Many of these are synthesised as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. A few, however, are active as single chain molecules, and others are inactive due to substitutions of the catalytic triad residues.
• Changed! COG COG5640 250aa 1e-21 in ref transcript
  • Secreted trypsin-like serine protease [Posttranslational modification, protein turnover, chaperones].
• Changed! cd Tryp_SPc 189aa 1e-52 in modified transcript
• Changed! smart Tryp_SPc 187aa 2e-60 in modified transcript
• Changed! COG COG5640 207aa 8e-19 in modified transcript

KLRC1

• refseq_KLRC1.F1 refseq_KLRC1.R1 215 269
• NCBIGene 36.3 3821
• Single exon skipping, size difference: 54
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_213658

• cd CLECT_NK_receptors_like 113aa 4e-26 in ref transcript
  • CLECT_NK_receptors_like: C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs), including proteins similar to oxidized low density lipoprotein (OxLDL) receptor (LOX-1), CD94, CD69, NKG2-A and -D, osteoclast inhibitory lectin (OCIL), dendritic cell-associated C-type lectin-1 (dectin-1), human myeloid inhibitory C-type lectin-like receptor (MICL), mast cell-associated functional antigen (MAFA), killer cell lectin-like receptors: subfamily F, member 1 (KLRF1) and subfamily B, member 1 (KLRB1), and lys49 receptors. CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. NKRs are variously associated with activation or inhibition of natural killer (NK) cells. Activating NKRs stimulate cytolysis by NK cells of virally infected or transformed cells; inhibitory NKRs block cytolysis upon recognition of markers of healthy self cells. Most Lys49 receptors are inhibitory; some are stimulatory. OCIL inhibits NK cell function via binding to the receptor NKRP1D. Murine OCIL in addition to inhibiting NK cell function inhibits osteoclast differentiation. MAFA clusters with the type I Fc epsilon receptor (FcepsilonRI) and inhibits the mast cells secretory response to FcepsilonRI stimulus. CD72 is a negative regulator of B cell receptor signaling. NKG2D is an activating receptor for stress-induced antigens; human NKG2D ligands include the stress induced MHC-I homologs, MICA, MICB, and ULBP family of glycoproteins Several NKRs have a carbohydrate-binding capacity which is not mediated through calcium ions (e.g. OCIL binds a range of high molecular weight sulfated glycosaminoglycans including dextran sulfate, fucoidan, and gamma-carrageenan sugars). Dectin-1 binds fungal beta-glucans and in involved in the innate immune responses to fungal pathogens. MAFA binds saccharides having terminal alpha-D mannose residues in a calcium-dependent manner. LOX-1 is the major receptor for OxLDL in endothelial cells and thought to play a role in the pathology of atherosclerosis. Some NKRs exist as homodimers (e.g.Lys49, NKG2D, CD69, LOX-1) and some as heterodimers (e.g. CD94/NKG2A). Dectin-1 can function as a monomer in vitro.
• smart CLECT 112aa 4e-17 in ref transcript
  • C-type lectin (CTL) or carbohydrate-recognition domain (CRD). Many of these domains function as calcium-dependent carbohydrate binding modules.

KLRD1

• refseq_KLRD1.F1 refseq_KLRD1.R1 135 228
• NCBIGene 36.3 3824
• Single exon skipping, size difference: 93
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_002262

• cd CLECT_NK_receptors_like 116aa 3e-26 in ref transcript
  • CLECT_NK_receptors_like: C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs), including proteins similar to oxidized low density lipoprotein (OxLDL) receptor (LOX-1), CD94, CD69, NKG2-A and -D, osteoclast inhibitory lectin (OCIL), dendritic cell-associated C-type lectin-1 (dectin-1), human myeloid inhibitory C-type lectin-like receptor (MICL), mast cell-associated functional antigen (MAFA), killer cell lectin-like receptors: subfamily F, member 1 (KLRF1) and subfamily B, member 1 (KLRB1), and lys49 receptors. CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. NKRs are variously associated with activation or inhibition of natural killer (NK) cells. Activating NKRs stimulate cytolysis by NK cells of virally infected or transformed cells; inhibitory NKRs block cytolysis upon recognition of markers of healthy self cells. Most Lys49 receptors are inhibitory; some are stimulatory. OCIL inhibits NK cell function via binding to the receptor NKRP1D. Murine OCIL in addition to inhibiting NK cell function inhibits osteoclast differentiation. MAFA clusters with the type I Fc epsilon receptor (FcepsilonRI) and inhibits the mast cells secretory response to FcepsilonRI stimulus. CD72 is a negative regulator of B cell receptor signaling. NKG2D is an activating receptor for stress-induced antigens; human NKG2D ligands include the stress induced MHC-I homologs, MICA, MICB, and ULBP family of glycoproteins Several NKRs have a carbohydrate-binding capacity which is not mediated through calcium ions (e.g. OCIL binds a range of high molecular weight sulfated glycosaminoglycans including dextran sulfate, fucoidan, and gamma-carrageenan sugars). Dectin-1 binds fungal beta-glucans and in involved in the innate immune responses to fungal pathogens. MAFA binds saccharides having terminal alpha-D mannose residues in a calcium-dependent manner. LOX-1 is the major receptor for OxLDL in endothelial cells and thought to play a role in the pathology of atherosclerosis. Some NKRs exist as homodimers (e.g.Lys49, NKG2D, CD69, LOX-1) and some as heterodimers (e.g. CD94/NKG2A). Dectin-1 can function as a monomer in vitro.
• smart CLECT 115aa 9e-21 in ref transcript
  • C-type lectin (CTL) or carbohydrate-recognition domain (CRD). Many of these domains function as calcium-dependent carbohydrate binding modules.

KREMEN1

• refseq_KREMEN1.F2 refseq_KREMEN1.R2 186 237
• NCBIGene 36.3 83999
• Alternative 5-prime, size difference: 51
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001039570

• cd KR 84aa 9e-18 in ref transcript
  • Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides.
• cd CUB 107aa 1e-15 in ref transcript
  • CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.
• pfam WSC 81aa 3e-19 in ref transcript
  • WSC domain. This domain may be involved in carbohydrate binding.
• smart KR 84aa 3e-18 in ref transcript
  • Kringle domain. Named after a Danish pastry. Found in several serine proteases and in ROR-like receptors. Can occur in up to 38 copies (in apolipoprotein(a)). Plasminogen-like kringles possess affinity for free lysine and lysine- containing peptides.
• pfam CUB 105aa 1e-14 in ref transcript
  • CUB domain.

KREMEN2

• refseq_KREMEN2.F1 refseq_KREMEN2.R1 266 345
• NCBIGene 36.3 79412
• Single exon skipping, size difference: 79
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_172229

• cd CUB 106aa 2e-15 in ref transcript
  • CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.
• cd KR 86aa 2e-15 in ref transcript
  • Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides.
• pfam WSC 82aa 7e-17 in ref transcript
  • WSC domain. This domain may be involved in carbohydrate binding.
• smart KR 86aa 3e-16 in ref transcript
  • Kringle domain. Named after a Danish pastry. Found in several serine proteases and in ROR-like receptors. Can occur in up to 38 copies (in apolipoprotein(a)). Plasminogen-like kringles possess affinity for free lysine and lysine- containing peptides.
• pfam CUB 105aa 9e-14 in ref transcript
  • CUB domain.

KRIT1

• refseq_KRIT1.F2 refseq_KRIT1.R2 153 301
• NCBIGene 36.3 889
• Single exon skipping, size difference: 148
• Exclusion in 5'UTR
• Reference transcript: NM_194456

• cd ANK 121aa 1e-14 in ref transcript
  • ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats.
• smart B41 220aa 1e-32 in ref transcript
  • Band 4.1 homologues. Also known as ezrin/radixin/moesin (ERM) protein domains. Present in myosins, ezrin, radixin, moesin, protein tyrosine phosphatases. Plasma membrane-binding domain. These proteins play structural and regulatory roles in the assembly and stabilization of specialized plasmamembrane domains. Some PDZ domain containing proteins bind one or more of this family. Now includes JAKs.
• COG Arp 127aa 3e-06 in ref transcript
  • FOG: Ankyrin repeat [General function prediction only].

KRIT1

• refseq_KRIT1.F4 refseq_KRIT1.R4 231 306
• NCBIGene 36.3 889
• Alternative 5-prime and 3-prime, size difference: 75
• Exclusion in 5'UTR, Exclusion in 5'UTR
• Reference transcript: NM_194456

• cd ANK 121aa 1e-14 in ref transcript
  • ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats.
• smart B41 220aa 1e-32 in ref transcript
  • Band 4.1 homologues. Also known as ezrin/radixin/moesin (ERM) protein domains. Present in myosins, ezrin, radixin, moesin, protein tyrosine phosphatases. Plasma membrane-binding domain. These proteins play structural and regulatory roles in the assembly and stabilization of specialized plasmamembrane domains. Some PDZ domain containing proteins bind one or more of this family. Now includes JAKs.
• COG Arp 127aa 3e-06 in ref transcript
  • FOG: Ankyrin repeat [General function prediction only].

KRIT1

• refseq_KRIT1.F5 refseq_KRIT1.R5 103 466
• NCBIGene 36.3 889
• Alternative 5-prime, size difference: 363
• Exclusion in 5'UTR
• Reference transcript: NM_004912

• cd ANK 121aa 1e-14 in ref transcript
  • ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats.
• smart B41 220aa 1e-32 in ref transcript
  • Band 4.1 homologues. Also known as ezrin/radixin/moesin (ERM) protein domains. Present in myosins, ezrin, radixin, moesin, protein tyrosine phosphatases. Plasma membrane-binding domain. These proteins play structural and regulatory roles in the assembly and stabilization of specialized plasmamembrane domains. Some PDZ domain containing proteins bind one or more of this family. Now includes JAKs.
• COG Arp 127aa 3e-06 in ref transcript
  • FOG: Ankyrin repeat [General function prediction only].

KRIT1

• refseq_KRIT1.F8 refseq_KRIT1.R8 135 279
• NCBIGene 36.3 889
• Single exon skipping, size difference: 144
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_194456

• Changed! cd ANK 121aa 1e-14 in ref transcript
  • ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats.
• smart B41 220aa 1e-32 in ref transcript
  • Band 4.1 homologues. Also known as ezrin/radixin/moesin (ERM) protein domains. Present in myosins, ezrin, radixin, moesin, protein tyrosine phosphatases. Plasma membrane-binding domain. These proteins play structural and regulatory roles in the assembly and stabilization of specialized plasmamembrane domains. Some PDZ domain containing proteins bind one or more of this family. Now includes JAKs.
• Changed! COG Arp 127aa 3e-06 in ref transcript
  • FOG: Ankyrin repeat [General function prediction only].
• Changed! cd ANK 85aa 1e-06 in modified transcript
• Changed! PTZ PTZ00322 74aa 2e-04 in modified transcript
  • 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase; Provisional.

KRT13

• refseq_KRT13.F2 refseq_KRT13.R2 136 162
• NCBIGene 36.3 3860
• Single exon skipping, size difference: 26
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_153490

• pfam Filament 313aa 1e-109 in ref transcript
  • Intermediate filament protein.

L3MBTL

• refseq_L3MBTL.F1 refseq_L3MBTL.R1 241 400
• NCBIGene 36.2 26013
• Intron retention, size difference: 118
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_015478

• smart MBT 97aa 8e-37 in ref transcript
  • Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2. Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2. These proteins are involved in transcriptional regulation.
• smart MBT 93aa 2e-36 in ref transcript
• smart MBT 98aa 1e-35 in ref transcript
• pfam zf-C2HC 29aa 4e-10 in ref transcript
  • Zinc finger, C2HC type. This is a DNA binding zinc finger domain.

L3MBTL2

• refseq_L3MBTL2.F2 refseq_L3MBTL2.R2 176 281
• NCBIGene 36.2 83746
• Single exon skipping, size difference: 105
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_031488

• smart MBT 94aa 6e-38 in ref transcript
  • Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2. Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2. These proteins are involved in transcriptional regulation.
• smart MBT 97aa 3e-28 in ref transcript
• smart MBT 101aa 6e-19 in ref transcript
• smart MBT 93aa 2e-17 in ref transcript

L3MBTL3

• refseq_L3MBTL3.F2 refseq_L3MBTL3.R2 204 279
• NCBIGene 36.3 84456
• Single exon skipping, size difference: 75
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_032438

• cd SAM 64aa 4e-08 in ref transcript
  • Sterile alpha motif.; Widespread domain in signalling and nuclear proteins. In EPH-related tyrosine kinases, appears to mediate cell-cell initiated signal transduction via the binding of SH2-containing proteins to a conserved tyrosine that is phosphorylated. In many cases mediates homodimerization.
• smart MBT 97aa 1e-33 in ref transcript
  • Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2. Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2. These proteins are involved in transcriptional regulation.
• smart MBT 93aa 2e-33 in ref transcript
• smart MBT 95aa 7e-30 in ref transcript
• pfam SAM_1 63aa 5e-11 in ref transcript
  • SAM domain (Sterile alpha motif). It has been suggested that SAM is an evolutionarily conserved protein binding domain that is involved in the regulation of numerous developmental processes in diverse eukaryotes. The SAM domain can potentially function as a protein interaction module through its ability to homo- and heterooligomerise with other SAM domains.

LAIR1

• refseq_LAIR1.F1 refseq_LAIR1.R1 265 316
• NCBIGene 36.3 3903
• Single exon skipping, size difference: 51
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_002287

LAIR2

• refseq_LAIR2.F2 refseq_LAIR2.R2 280 331
• NCBIGene 36.3 3904
• Single exon skipping, size difference: 51
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_002288

LARGE

• refseq_LARGE.F1 refseq_LARGE.R1 174 237
• NCBIGene 36.3 9215
• Single exon skipping, size difference: 63
• Exclusion in 5'UTR
• Reference transcript: NM_004737

• cd GT8_LARGE_C 280aa 1e-165 in ref transcript
  • LARGE catalytic domain has closest homology to GT8 glycosyltransferase involved in lipooligosaccharide synthesis. The catalytic domain of LARGE is a putative glycosyltransferase. Mutations of LARGE in mouse and human cause dystroglycanopathies, a disease associated with hypoglycosylation of the membrane protein alpha-dystroglycan (alpha-DG) and consequent loss of extracellular ligand binding. LARGE needs to both physically interact with alpha-dystroglycan and function as a glycosyltransferase in order to stimulate alpha-dystroglycan hyperglycosylation. LARGE localizes to the Golgi apparatus and contains three conserved DxD motifs. While two of the motifs are indispensible for glycosylation function, one is important for localization of th eenzyme. LARGE was originally named because it covers approximately large trunck of genomic DNA, more than 600bp long. The predicted protein structure contains an N-terminal cytoplasmic domain, a transmembrane region, a coiled-coil motif, and two putative catalytic domains. This catalytic domain has closest homology to GT8 glycosyltransferase involved in lipooligosaccharide synthesis.
• pfam Glyco_transf_8 245aa 3e-17 in ref transcript
  • Glycosyl transferase family 8. This family includes enzymes that transfer sugar residues to donor molecules. Members of this family are involved in lipopolysaccharide biosynthesis and glycogen synthesis. This family includes Lipopolysaccharide galactosyltransferase, lipopolysaccharide glucosyltransferase 1, and glycogenin glucosyltransferase.
• COG RfaJ 251aa 2e-10 in ref transcript
  • Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane].

LARP4

• refseq_LARP4.F2 refseq_LARP4.R2 161 374
• NCBIGene 36.3 113251
• Single exon skipping, size difference: 213
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_199188

• cd RRM 67aa 0.004 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• smart LA 79aa 5e-29 in ref transcript
  • Domain in the RNA-binding Lupus La protein; unknown function.

LASS2

• refseq_LASS2.F2 refseq_LASS2.R2 224 264
• NCBIGene 36.3 29956
• Alternative 3-prime, size difference: 40
• Inclusion in 5'UTR
• Reference transcript: NM_022075

• cd homeodomain 58aa 0.001 in ref transcript
  • Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
• smart TLC 202aa 1e-42 in ref transcript
  • TRAM, LAG1 and CLN8 homology domains. Protein domain with at least 5 transmembrane alpha-helices. Lag1p and Lac1p are essential for acyl-CoA-dependent ceramide synthesis, TRAM is a subunit of the translocon and the CLN8 gene is mutated in Northern epilepsy syndrome. The family may possess multiple functions such as lipid trafficking, metabolism, or sensing. Trh homologues possess additional homeobox domains.
• COG LAG1 220aa 3e-22 in ref transcript
  • Protein transporter of the TRAM (translocating chain-associating membrane) superfamily, longevity assurance factor [Intracellular trafficking and secretion].

LAT2

• refseq_LAT2.F1 refseq_LAT2.R1 117 187
• NCBIGene 36.3 7462
• Alternative 5-prime, size difference: 70
• Exclusion in 5'UTR
• Reference transcript: NM_032464

LCMT1

• refseq_LCMT1.F1 refseq_LCMT1.R1 116 281
• NCBIGene 36.3 51451
• Multiple exon skipping, size difference: 165
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_016309

• Changed! pfam LCM 299aa 1e-127 in ref transcript
  • Leucine carboxyl methyltransferase. Family of leucine carboxyl methyltransferases EC:2.1.1.-. This family may need divides a the full alignment contains a significantly shorter mouse sequence.
• Changed! COG COG3315 195aa 6e-14 in ref transcript
  • O-Methyltransferase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism].
• Changed! pfam LCM 244aa 1e-101 in modified transcript
• Changed! COG COG3315 140aa 7e-09 in modified transcript

LDHC

• refseq_LDHC.F1 refseq_LDHC.R1 121 175
• NCBIGene 36.3 3948
• Alternative 5-prime, size difference: 54
• Exclusion in 5'UTR
• Reference transcript: NM_002301

• cd LDH_1 312aa 1e-145 in ref transcript
  • A subgroup of L-lactate dehydrogenases. L-lactate dehydrogenases (LDH) are tetrameric enzymes catalyzing the last step of glycolysis in which pyruvate is converted to L-lactate. This subgroup is composed of eukaryotic LDHs. Vertebrate LDHs are non-allosteric. This is in contrast to some bacterial LDHs that are activated by an allosteric effector such as fructose-1,6-bisphosphate. LDHs are part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)-binding domains of alcohol dehydrogenases, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate dehydrogenases, formate/glycerate dehydrogenases, siroheme synthases, 6-phosphogluconate dehydrogenases, aminoacid dehydrogenases, repressor rex, and NAD-binding potassium channel domains, among others.
• TIGR L-LDH-NAD 301aa 1e-110 in ref transcript
  • This model represents the NAD-dependent L-lactate dehydrogenases from bacteria and eukaryotes. This enzyme function as as the final step in anaerobic glycolysis. Although lactate dehydrogenases have in some cases been mistaken for malate dehydrogenases due to the similarity of these two substrates and the apparent ease with which evolution can toggle these activities, critical residues have been identified which can discriminate between the two activities. At the time of the creation of this model no hits above the trusted cutoff contained critical residues typical of malate dehydrogenases.
• PRK ldh 309aa 8e-87 in ref transcript
  • L-lactate dehydrogenase; Reviewed.

LDHD

• refseq_LDHD.F1 refseq_LDHD.R1 225 294
• NCBIGene 36.3 197257
• Alternative 3-prime, size difference: 69
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_153486

• Changed! TIGR glcD 437aa 2e-84 in ref transcript
  • This protein, the glycolate oxidase GlcD subunit, is similar in sequence to that of several D-lactate dehydrogenases, including that of E. coli. The glycolate oxidase has been found to have some D-lactate dehydrogenase activity.
• Changed! COG GlcD 474aa 2e-80 in ref transcript
  • FAD/FMN-containing dehydrogenases [Energy production and conversion].
• Changed! TIGR glcD 414aa 3e-86 in modified transcript
• Changed! COG GlcD 451aa 5e-83 in modified transcript

LETMD1

• refseq_LETMD1.F1 refseq_LETMD1.R1 104 220
• NCBIGene 36.2 25875
• Single exon skipping, size difference: 116
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_015416

• Changed! pfam LETM1 255aa 4e-32 in ref transcript
  • LETM1-like protein. Members of this family are inner mitochondrial membrane proteins which play a role in potassium and hydrogen ion exchange. Deletion of LETM1 is thought to be involved in the development of Wolf-Hirschhorn syndrome in humans.

LETMD1

• refseq_LETMD1.F4 refseq_LETMD1.R4 166 273
• NCBIGene 36.3 25875
• Alternative 5-prime, size difference: 107
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_015416

• Changed! pfam LETM1 255aa 4e-32 in ref transcript
  • LETM1-like protein. Members of this family are inner mitochondrial membrane proteins which play a role in potassium and hydrogen ion exchange. Deletion of LETM1 is thought to be involved in the development of Wolf-Hirschhorn syndrome in humans.

LGALS14

• refseq_LGALS14.F1 refseq_LGALS14.R1 102 407
• NCBIGene 36.3 56891
• Single exon skipping, size difference: 305
• Exclusion of the protein initiation site
• Reference transcript: NM_203471

• Changed! cd GLECT 130aa 4e-28 in ref transcript
  • Galectin/galactose-binding lectin. This domain exclusively binds beta-galactosides, such as lactose, and does not require metal ions for activity. GLECT domains occur as homodimers or tandemly repeated domains. They are developmentally regulated and may be involved in differentiation, cell-cell interaction and cellular regulation.
• Changed! pfam Gal-bind_lectin 129aa 8e-31 in ref transcript
  • Galactoside-binding lectin. This family contains galactoside binding lectins. The family also includes enzymes such as human eosinophil lysophospholipase (EC:3.1.1.5).
• Changed! cd GLECT 131aa 1e-28 in modified transcript
• Changed! pfam Gal-bind_lectin 131aa 3e-31 in modified transcript

LGALS8

• refseq_LGALS8.F2 refseq_LGALS8.R2 206 332
• NCBIGene 36.3 3964
• Single exon skipping, size difference: 126
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_201545

• cd GLECT 132aa 5e-34 in ref transcript
  • Galectin/galactose-binding lectin. This domain exclusively binds beta-galactosides, such as lactose, and does not require metal ions for activity. GLECT domains occur as homodimers or tandemly repeated domains. They are developmentally regulated and may be involved in differentiation, cell-cell interaction and cellular regulation.
• cd GLECT 129aa 2e-32 in ref transcript
• pfam Gal-bind_lectin 132aa 7e-39 in ref transcript
  • Galactoside-binding lectin. This family contains galactoside binding lectins. The family also includes enzymes such as human eosinophil lysophospholipase (EC:3.1.1.5).
• pfam Gal-bind_lectin 129aa 4e-37 in ref transcript

LGMN

• refseq_LGMN.F2 refseq_LGMN.R2 171 289
• NCBIGene 36.3 5641
• Single exon skipping, size difference: 118
• Exclusion in 5'UTR
• Reference transcript: NM_001008530

• pfam Peptidase_C13 257aa 1e-125 in ref transcript
  • Peptidase C13 family. Members of this family are asparaginyl peptidases. The blood fluke parasite Schistosoma mansoni has at least five Clan CA cysteine peptidases in its digestive tract including cathepsins B (2 isoforms), C, F and L. All have been recombinantly expressed as active enzymes, albeit in various stages of activation. In addition, a Clan CD peptidase, termed asparaginyl endopeptidase or 'legumain' has been identified. This has formerly been characterised as a 'haemoglobinase', but this term is probably incorrect. Two cDNAs have been described for Schistosoma mansoni legumain; one encodes an active enzyme whereas the active site cysteine residue encoded by the second cDNA is substituted by an asparagine residue. Both forms have been recombinantly expressed.
• COG GPI8 194aa 2e-26 in ref transcript
  • Glycosylphosphatidylinositol transamidase (GPIT), subunit GPI8 [Posttranslational modification, protein turnover, chaperones].

LGR6

• refseq_LGR6.F1 refseq_LGR6.R1 100 388
• NCBIGene 36.3 59352
• Multiple exon skipping, size difference: 288
• Exclusion in the protein (no frameshift), Exclusion in the protein (no frameshift)
• Reference transcript: NM_001017403

• Changed! cd LRR_RI 262aa 6e-08 in ref transcript
  • Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1).
• Changed! cd LRR_RI 143aa 1e-06 in ref transcript
• Changed! COG COG4886 215aa 1e-17 in ref transcript
  • Leucine-rich repeat (LRR) protein [Function unknown].
• Changed! COG COG4886 253aa 2e-14 in ref transcript
• Changed! cd LRR_RI 226aa 9e-09 in modified transcript
• Changed! COG COG4886 241aa 9e-16 in modified transcript

LHX6

• refseq_LHX6.F2 refseq_LHX6.R2 287 391
• NCBIGene 36.3 26468
• Single exon skipping, size difference: 104
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_014368

• cd homeodomain 58aa 6e-14 in ref transcript
  • Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
• pfam Homeobox 57aa 1e-17 in ref transcript
  • Homeobox domain.
• pfam LIM 58aa 1e-09 in ref transcript
  • LIM domain. This family represents two copies of the LIM structural domain.
• pfam LIM 55aa 8e-09 in ref transcript
• COG COG5576 91aa 3e-10 in ref transcript
  • Homeodomain-containing transcription factor [Transcription].

LIAS

• refseq_LIAS.F2 refseq_LIAS.R2 213 325
• NCBIGene 36.3 11019
• Single exon skipping, size difference: 112
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_006859

• Changed! cd Radical_SAM 197aa 7e-07 in ref transcript
  • Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster. Mechanistically, they share the transfer of a single electron from the iron-sulfur cluster to SAM, which leads to its reductive cleavage to methionine and a 5'-deoxyadenosyl radical, which, in turn, abstracts a hydrogen from the appropriately positioned carbon atom. Depending on the enzyme, SAM is consumed during this process or it is restored and reused. Radical SAM enzymes catalyze steps in metabolism, DNA repair, the biosynthesis of vitamins and coenzymes, and the biosynthesis of many antibiotics. Examples are biotin synthase (BioB), lipoyl synthase (LipA), pyruvate formate-lyase (PFL), coproporphyrinogen oxidase (HemN), lysine 2,3-aminomutase (LAM), anaerobic ribonucleotide reductase (ARR), and MoaA, an enzyme of the biosynthesis of molybdopterin.
• Changed! TIGR lipA 302aa 1e-104 in ref transcript
  • The family shows strong sequence conservation.
• Changed! PRK PRK05481 293aa 1e-126 in ref transcript
  • lipoyl synthase; Provisional.
• Changed! cd Radical_SAM 177aa 6e-07 in modified transcript
• Changed! TIGR lipA 255aa 7e-86 in modified transcript
• Changed! PRK PRK05481 248aa 1e-105 in modified transcript

LILRA5

• refseq_LILRA5.F2 refseq_LILRA5.R2 167 203
• NCBIGene 36.3 353514
• Single exon skipping, size difference: 36
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_021250

LLGL2

• refseq_LLGL2.F1 refseq_LLGL2.R1 101 144
• NCBIGene 36.3 3993
• Single exon skipping, size difference: 43
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_001031803

• cd WD40 233aa 6e-05 in ref transcript
  • WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.
• pfam LLGL 105aa 6e-39 in ref transcript
  • LLGL2. This domain is found in lethal giant larvae homolog 2 (LLGL2) proteins and syntaxin-binding proteins like tomosyn. It has been identified in eukaryotes and tends to be found together with WD repeats (pfam00400).
• COG COG2319 227aa 3e-05 in ref transcript
  • FOG: WD40 repeat [General function prediction only].

LMNA

• refseq_LMNA.F1 refseq_LMNA.R1 218 308
• NCBIGene 36.3 4000
• Single exon skipping, size difference: 90
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_170707

• pfam Filament 349aa 3e-52 in ref transcript
  • Intermediate filament protein.
• Changed! pfam IF_tail 111aa 1e-47 in ref transcript
  • Intermediate filament tail domain. The Prosite motif does not correspond to this Pfam entry.
• COG Smc 290aa 4e-05 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].
• Changed! pfam IF_tail 102aa 3e-44 in modified transcript

LMX1A

• refseq_LMX1A.F1 refseq_LMX1A.R1 109 242
• NCBIGene 36.3 4009
• Single exon skipping, size difference: 133
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_177398

• cd homeodomain 57aa 4e-13 in ref transcript
  • Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
• pfam Homeobox 57aa 6e-17 in ref transcript
  • Homeobox domain.
• pfam LIM 56aa 1e-12 in ref transcript
  • LIM domain. This family represents two copies of the LIM structural domain.
• pfam LIM 59aa 2e-10 in ref transcript
• COG COG5576 77aa 1e-08 in ref transcript
  • Homeodomain-containing transcription factor [Transcription].

LOC144983

• refseq_LOC144983.F1 refseq_LOC144983.R1 248 389
• NCBIGene 36.3 144983
• Single exon skipping, size difference: 141
• Exclusion in 5'UTR
• Reference transcript: NM_001011724

• cd RRM 74aa 2e-15 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• cd RRM 73aa 2e-13 in ref transcript
• smart RRM 70aa 6e-16 in ref transcript
  • RNA recognition motif.
• TIGR SF-CC1 142aa 5e-15 in ref transcript
  • A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed.
• COG COG0724 171aa 1e-10 in ref transcript
  • RNA-binding proteins (RRM domain) [General function prediction only].

LOC150223

• refseq_LOC150223.F1 refseq_LOC150223.R1 100 159
• NCBIGene 36.2 150223
• Alternative 5-prime, size difference: 59
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_001017964

• Changed! pfam YdjC 283aa 8e-60 in ref transcript
  • YdjC-like protein. Family of YdjC-like proteins. This region is possibly involved in the the cleavage of cellobiose-phosphate.
• Changed! PRK PRK02134 294aa 3e-34 in ref transcript
  • hypothetical protein; Provisional.
• Changed! pfam YdjC 105aa 6e-27 in modified transcript
• Changed! PRK PRK02134 104aa 8e-15 in modified transcript

LOC150383

• refseq_LOC150383.F1 refseq_LOC150383.R1 140 263
• NCBIGene 36.2 150383
• Single exon skipping, size difference: 123
• Exclusion in 5'UTR
• Reference transcript: NM_001008917

LOC219854

• refseq_LOC219854.F2 refseq_LOC219854.R2 103 162
• NCBIGene 36.2 219854
• Single exon skipping, size difference: 59
• Exclusion in 5'UTR
• Reference transcript: XM_933911

LOC219854

• refseq_LOC219854.F4 refseq_LOC219854.R4 114 162
• NCBIGene 36.2 219854
• Alternative 5-prime, size difference: 48
• Exclusion in 5'UTR
• Reference transcript: XM_933911

LOC219854

• refseq_LOC219854.F6 refseq_LOC219854.R6 214 292
• NCBIGene 36.2 219854
• Single exon skipping, size difference: 78
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: XM_933894

LOC255411

• refseq_LOC255411.F2 refseq_LOC255411.R2 218 303
• NCBIGene 36.3 255411
• Single exon skipping, size difference: 85
• Inclusion in the protein causing a new stop codon
• Reference transcript: XM_170708

C19orf63

• refseq_LOC284361.F1 refseq_LOC284361.R1 241 328
• NCBIGene 36.3 284361
• Single exon skipping, size difference: 87
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_206538

LOC339287

• refseq_LOC339287.F1 refseq_LOC339287.R1 109 157
• NCBIGene 36.2 339287
• Single exon skipping, size difference: 48
• Exclusion in the protein (no frameshift)
• Reference transcript: XM_932097

C16orf84

• refseq_LOC348180.F2 refseq_LOC348180.R2 224 283
• NCBIGene 36.3 348180
• Single exon skipping, size difference: 59
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_001012759

• pfam DUF2392 101aa 5e-37 in ref transcript
  • Protein of unknown function (DUF2392). This is a family of proteins conserved from plants to humans. The function is not known. It carries a characteristic GRG sequence motif.
• COG MesJ 153aa 0.001 in ref transcript
  • Predicted ATPase of the PP-loop superfamily implicated in cell cycle control [Cell division and chromosome partitioning].

LOC348801

• refseq_LOC348801.F1 refseq_LOC348801.R1 220 259
• NCBIGene 36.2 348801
• Alternative 3-prime, size difference: 39
• Exclusion in the protein (no frameshift)
• Reference transcript: XM_931908

LOC352909

• refseq_LOC352909.F1 refseq_LOC352909.R1 112 188
• NCBIGene 36.2 352909
• Alternative 5-prime, size difference: 76
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_178837

LOC374569

• refseq_LOC374569.F1 refseq_LOC374569.R1 101 119
• NCBIGene 36.2 374569
• Alternative 3-prime, size difference: 18
• Exclusion in the protein (no frameshift)
• Reference transcript: XM_370777

• cd Asparaginase 340aa 8e-93 in ref transcript
  • Asparaginase (amidohydrolase): Asparaginases are tetrameric enzymes that catalyze the hydrolysis of asparagine to aspartic acid and ammonia. In bacteria, there are two classes of amidohydrolases, one highly specific for asparagine and localised to the periplasm, and a second (asparaginase- glutaminase) present in the cytosol that hydrolyzises both asparagine and glutamine with similar specificities.
• cd ANK 124aa 2e-17 in ref transcript
  • ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats.
• smart Asparaginase 339aa 1e-82 in ref transcript
  • Asparaginase, which is found in various plant, animal and bacterial cells, catalyses the deamination of asparagine to yield aspartic acid and an ammonium ion, resulting in a depletion of free circulatory asparagine in plasma PUBMED:3026924. The enzyme is effective in the treatment of human malignant lymphomas, which have a diminished capacity to produce asparagine synthetase: in order to survive, such cells absorb asparagine from blood plasma PUBMED:2407723, PUBMED:3379033 - if Asn levels have been depleted by injection of asparaginase, the lymphoma cells die.
• pfam Ank 32aa 3e-06 in ref transcript
  • Ankyrin repeat. There's no clear separation between noise and signal on the HMM search Ankyrin repeats generally consist of a beta, alpha, alpha, beta order of secondary structures. The repeats associate to form a higher order structure.
• TIGR trp 76aa 1e-04 in ref transcript
  • after chronic exposure to capsaicin. (McCleskey and Gold, 1999).
• PRK ansA 353aa 1e-101 in ref transcript
  • cytoplasmic asparaginase I; Provisional.
• PTZ PTZ00322 81aa 7e-10 in ref transcript
  • 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase; Provisional.
• COG Arp 132aa 2e-08 in ref transcript
  • FOG: Ankyrin repeat [General function prediction only].

NHLRC3

• refseq_LOC387921.F1 refseq_LOC387921.R1 129 330
• NCBIGene 36.3 387921
• Single exon skipping, size difference: 201
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001012754

• pfam NHL 28aa 1e-05 in ref transcript
  • NHL repeat. The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in the peptidyl-glycine alpha-amidating monooxygenase (PAM), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. The human tripartite motif-containing protein 32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats.
• Changed! COG COG3391 243aa 1e-05 in ref transcript
  • Uncharacterized conserved protein [Function unknown].
• Changed! COG COG3391 153aa 9e-07 in modified transcript

LOC388276

• refseq_LOC388276.F1 refseq_LOC388276.R1 106 234
• NCBIGene 36.2 388276
• Multiple exon skipping, size difference: 128
• Inclusion in the protein causing a new stop codon, Inclusion in the protein causing a frameshift
• Reference transcript: XM_931511

LOC389073

• refseq_LOC389073.F1 refseq_LOC389073.R1 119 238
• NCBIGene 36.2 389073
• Single exon skipping, size difference: 119
• Exclusion in the protein causing a frameshift
• Reference transcript: XM_371592

LOC441155

• refseq_LOC441155.F1 refseq_LOC441155.R1 108 390
• NCBIGene 36.2 441155
• Alternative 3-prime, size difference: 282
• Inclusion in 5'UTR
• Reference transcript: XM_930997

LOC51149

• refseq_LOC51149.F1 refseq_LOC51149.R1 155 235
• NCBIGene 36.2 51149
• Single exon skipping, size difference: 80
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_016175

LOC643446

• refseq_LOC643446.F1 refseq_LOC643446.R1 149 237
• NCBIGene 36.3 643446
• Alternative 5-prime, size difference: 88
• Exclusion in 5'UTR
• Reference transcript: XM_001130637

• cd RRM 73aa 3e-15 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• smart RRM 70aa 8e-14 in ref transcript
  • RNA recognition motif.
• COG COG0724 76aa 3e-05 in ref transcript
  • RNA-binding proteins (RRM domain) [General function prediction only].

LOC643446

• refseq_LOC643446.F3 refseq_LOC643446.R3 149 337
• NCBIGene 36.3 643446
• Alternative 3-prime, size difference: 188
• Exclusion of the protein initiation site
• Reference transcript: XM_001130681

• cd RRM 73aa 3e-15 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• smart RRM 70aa 8e-14 in ref transcript
  • RNA recognition motif.
• COG COG0724 76aa 3e-05 in ref transcript
  • RNA-binding proteins (RRM domain) [General function prediction only].

LOC643847

• refseq_LOC643847.F1 refseq_LOC643847.R1 101 131
• NCBIGene 36.2 643847
• Alternative 3-prime, size difference: 30
• Exclusion in the protein (no frameshift)
• Reference transcript: XM_001129508

• cd pepsin_A 323aa 1e-173 in ref transcript
  • Pepsin A, aspartic protease produced in gastric mucosa of mammals. Pepsin, a well-known aspartic protease, is produced by the human gastric mucosa in seven different zymogen isoforms, subdivided into two types: pepsinogen A and pepsinogen C. The prosequence of the zymogens are self cleaved under acidic pH. The mature enzymes are called pepsin A and pepsin C, correspondingly. The well researched porcine pepsin is also in this pepsin A family. Pepsins play an integral role in the digestion process of vertebrates. Pepsins are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localized between the two lobes of the molecule. One lobe may be evolved from the other through ancient gene-duplication event. More recently evolved enzymes have similar three-dimensional structures, however their amino acid sequences are more divergent except for the conserved catalytic site motif. Pepsins specifically cleave bonds in peptides which have at least six residues in length with hydrophobic residues in both the P1 and P1' positions. The active site is located at the groove formed by the two lobes, with an extended loop projecting over the cleft to form an 11-residue flap, which encloses substrates and inhibitors in the active site. Specificity is determined by nearest-neighbor hydrophobic residues surrounding the catalytic aspartates, and by three residues in the flap. This family of aspartate proteases is classified by MEROPS as the peptidase family A1 (pepsin A, clan AA).
• pfam Asp 315aa 1e-129 in ref transcript
  • Eukaryotic aspartyl protease. Aspartyl (acid) proteases include pepsins, cathepsins, and renins. Two-domain structure, probably arising from ancestral duplication. This family does not include the retroviral nor retrotransposon proteases (pfam00077), which are much smaller and appear to be homologous to a single domain of the eukaryotic asp proteases.
• Changed! pfam A1_Propeptide 29aa 7e-09 in ref transcript
  • A1 Propeptide. Most eukaryotic endopeptidases (Merops Family A1) are synthesised with signal and propeptides. The animal pepsin-like endopeptidase propeptides form a distinct family of propeptides, which contain a conserved motif approximately 30 residues long. In pepsinogen A, the first 11 residues of the mature pepsin sequence are displaced by residues of the propeptide. The propeptide contains two helices that block the active site cleft, in particular the conserved Asp11 residue, in pepsin, hydrogen bonds to a conserved Arg residues in the propeptide. This hydrogen bond stabilises the propeptide conformation and is probably responsible for triggering the conversion of pepsinogen to pepsin under acidic conditions.
• Changed! PTZ PTZ00165 367aa 2e-63 in ref transcript
  • aspartyl protease; Provisional.
• Changed! PTZ PTZ00165 327aa 2e-63 in modified transcript

LOC645687

• refseq_LOC645687.F1 refseq_LOC645687.R1 150 356
• NCBIGene 36.2 645687
• Alternative 3-prime, size difference: 206
• Exclusion of the stop codon
• Reference transcript: XM_001133543

LOC653423

• refseq_LOC653423.F1 refseq_LOC653423.R1 319 397
• NCBIGene 36.2 653423
• Single exon skipping, size difference: 78
• Exclusion in the protein (no frameshift)
• Reference transcript: XM_933397

• pfam Sperm_Ag_HE2 70aa 2e-28 in ref transcript
  • Sperm antigen HE2. This family consists of several variants of the human and chimpanzee sperm antigen proteins (HE2 and EP2 respectively). The EP2 gene codes for a family of androgen-dependent, epididymis-specific secretory proteins.The EP2 gene uses alternative promoters and differential splicing to produce a family of variant messages. The translated putative protein variants differ significantly from each other. Some of these putative proteins have similarity to beta-defensins, a family of antimicrobial peptides.

LOC653423

• refseq_LOC653423.F2 refseq_LOC653423.R2 148 224
• NCBIGene 36.2 653423
• Single exon skipping, size difference: 76
• Inclusion in the protein causing a frameshift
• Reference transcript: XM_929074

• Changed! pfam Sperm_Ag_HE2 70aa 2e-30 in ref transcript
  • Sperm antigen HE2. This family consists of several variants of the human and chimpanzee sperm antigen proteins (HE2 and EP2 respectively). The EP2 gene codes for a family of androgen-dependent, epididymis-specific secretory proteins.The EP2 gene uses alternative promoters and differential splicing to produce a family of variant messages. The translated putative protein variants differ significantly from each other. Some of these putative proteins have similarity to beta-defensins, a family of antimicrobial peptides.
• Changed! pfam Defensin_beta 36aa 3e-05 in ref transcript
  • Beta defensin. The beta defensins are antimicrobial peptides implicated in the resistance of epithelial surfaces to microbial colonisation.
• Changed! pfam Sperm_Ag_HE2 74aa 8e-30 in modified transcript

LOC653423

• refseq_LOC653423.F4 refseq_LOC653423.R4 263 369
• NCBIGene 36.2 653423
• Multiple exon skipping, size difference: 106
• Inclusion in the protein causing a frameshift, Inclusion in the protein causing a new stop codon
• Reference transcript: XM_933397

• pfam Sperm_Ag_HE2 70aa 2e-28 in ref transcript
  • Sperm antigen HE2. This family consists of several variants of the human and chimpanzee sperm antigen proteins (HE2 and EP2 respectively). The EP2 gene codes for a family of androgen-dependent, epididymis-specific secretory proteins.The EP2 gene uses alternative promoters and differential splicing to produce a family of variant messages. The translated putative protein variants differ significantly from each other. Some of these putative proteins have similarity to beta-defensins, a family of antimicrobial peptides.

LOC653489

• refseq_LOC653489.F1 refseq_LOC653489.R1 102 120
• NCBIGene 36.2 653489
• Alternative 5-prime and 3-prime, size difference: 18
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: XM_934115

• cd RanBD 121aa 2e-35 in ref transcript
  • Ran-binding domain; This domain of approximately 150 residues shares structural similarity to the PH domain, but lacks detectable sequence similarity. Ran is a Ras-like nuclear small GTPase, which regulates receptor-mediated transport between the nucleus and the cytoplasm. RanGTP hydrolysis is stimulated by RanGAP together with the Ran-binding domain containing acessory proteins RanBP1 and RanBP2. These accessory proteins stabilize the active GTP-bound form of Ran . The Ran-binding domain is found in multiple copies in Nuclear pore complex proteins.
• cd RanBD 117aa 1e-34 in ref transcript
• cd TPR 97aa 1e-05 in ref transcript
  • Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here.
• pfam Ran_BP1 122aa 1e-50 in ref transcript
  • RanBP1 domain.
• pfam Ran_BP1 120aa 3e-50 in ref transcript
• pfam GRIP 45aa 3e-09 in ref transcript
  • GRIP domain. The GRIP (golgin-97, RanBP2alpha,Imh1p and p230/golgin-245) domain is found in many large coiled-coil proteins. It has been shown to be sufficient for targeting to the Golgi. The GRIP domain contains a completely conserved tyrosine residue. At least some of these domains have been shown to bind to GTPase Arl1, see structures.
• TIGR type_IV_pilW 152aa 0.008 in ref transcript
  • Members of this family are designated PilF in ref (PMID:8973346) and PilW in ref (PMID:15612916). This outer membrane protein is required both for pilus stability and for pilus function such as adherence to human cells. Members of this family contain copies of the TPR (tetratricopeptide repeat) domain.
• COG YRB1 160aa 2e-31 in ref transcript
  • Ran GTPase-activating protein (Ran-binding protein) [Intracellular trafficking and secretion].
• COG YRB1 160aa 2e-23 in ref transcript

LOC653689

• refseq_LOC653689.F1 refseq_LOC653689.R1 124 166
• NCBIGene 36.2 653689
• Alternative 5-prime, size difference: 42
• Exclusion in the protein (no frameshift)
• Reference transcript: XM_928923

• Changed! cd GST_C_Theta 126aa 4e-39 in ref transcript
  • GST_C family, Class Theta subfamily; composed of eukaryotic class Theta GSTs and bacterial dichloromethane (DCM) dehalogenase. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Mammalian class Theta GSTs show poor GSH conjugating activity towards the standard substrates, CDNB and ethacrynic acid, differentiating them from other mammalian GSTs. GSTT1-1 shows similar cataytic activity as bacterial DCM dehalogenase, catalyzing the GSH-dependent hydrolytic dehalogenation of dihalomethanes. This is an essential process in methylotrophic bacteria to enable them to use chloromethane and DCM as sole carbon and energy sources. The presence of polymorphisms in human GSTT1-1 and its relationship to the onset of diseases including cancer is subject of many studies. Human GSTT2-2 exhibits a highly specific sulfatase activity, catalyzing the cleavage of sulfate ions from aralkyl sufate esters, but not from the aryl or alkyl sulfate esters.
• cd GST_N_Theta 76aa 3e-27 in ref transcript
  • GST_N family, Class Theta subfamily; composed of eukaryotic class Theta GSTs and bacterial dichloromethane (DCM) dehalogenase. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. The GST fold contains an N-terminal TRX-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. Mammalian class Theta GSTs show poor GSH conjugating activity towards the standard substrates, CDNB and ethacrynic acid, differentiating them from other mammalian GSTs. GSTT1-1 shows similar cataytic activity as bacterial DCM dehalogenase, catalyzing the GSH-dependent hydrolytic dehalogenation of dihalomethanes. This is an essential process in methylotrophic bacteria to enable them to use chloromethane and DCM as sole carbon and energy sources. The presence of polymorphisms in human GSTT1-1 and its relationship to the onset of diseases including cancer is subject of many studies. Human GSTT2-2 exhibits a highly specific sulfatase activity, catalyzing the cleavage of sulfate ions from aralkyl sufate esters, but not from aryl or alkyl sulfate esters.
• Changed! TIGR maiA 143aa 2e-11 in ref transcript
  • Maleylacetoacetate isomerase is an enzyme of tyrosine and phenylalanine catabolism. It requires glutathione and belongs by homology to the zeta family of glutathione S-transferases. The enzyme (EC 5.2.1.2) is described as active also on maleylpyruvate, and the example from a Ralstonia sp. catabolic plasmid is described as a maleylpyruvate isomerase involved in gentisate catabolism.
• Changed! COG Gst 208aa 3e-19 in ref transcript
  • Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones].
• Changed! cd GST_C_Theta 112aa 4e-30 in modified transcript
• Changed! TIGR maiA 134aa 7e-10 in modified transcript
• Changed! COG Gst 194aa 2e-16 in modified transcript

LOC653820

• refseq_LOC653820.F1 refseq_LOC653820.R1 278 398
• NCBIGene 36.2 653820
• Alternative 5-prime, size difference: 120
• Exclusion in the protein (no frameshift)
• Reference transcript: XM_930579

LOC727761

• refseq_LOC727761.F2 refseq_LOC727761.R2 139 211
• NCBIGene 36.3 727761
• Alternative 3-prime, size difference: 72
• Exclusion in the protein (no frameshift)
• Reference transcript: XM_001126211

• Changed! cd TMPK 185aa 3e-23 in ref transcript
  • Thymidine monophosphate kinase (TMPK), also known as thymidylate kinase, catalyzes the phosphorylation of thymidine monophosphate (TMP) to thymidine diphosphate (TDP) utilizing ATP as its preferred phophoryl donor. TMPK represents the rate-limiting step in either de novo or salvage biosynthesis of thymidine triphosphate (TTP).
• Changed! pfam Thymidylate_kin 181aa 3e-54 in ref transcript
  • Thymidylate kinase.
• Changed! COG Tmk 188aa 2e-32 in ref transcript
  • Thymidylate kinase [Nucleotide transport and metabolism].
• Changed! cd TMPK 161aa 4e-17 in modified transcript
• Changed! pfam Thymidylate_kin 157aa 7e-41 in modified transcript
• Changed! COG Tmk 164aa 2e-23 in modified transcript

LOC727761

• refseq_LOC727761.F4 refseq_LOC727761.R3 98 227
• NCBIGene 36.3 727761
• Exon skipping and alternative 3-prime or 5-prime, size difference: 129
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: XM_001126211

• Changed! cd TMPK 185aa 3e-23 in ref transcript
  • Thymidine monophosphate kinase (TMPK), also known as thymidylate kinase, catalyzes the phosphorylation of thymidine monophosphate (TMP) to thymidine diphosphate (TDP) utilizing ATP as its preferred phophoryl donor. TMPK represents the rate-limiting step in either de novo or salvage biosynthesis of thymidine triphosphate (TTP).
• Changed! pfam Thymidylate_kin 181aa 3e-54 in ref transcript
  • Thymidylate kinase.
• Changed! COG Tmk 188aa 2e-32 in ref transcript
  • Thymidylate kinase [Nucleotide transport and metabolism].
• Changed! cd TMPK 142aa 2e-11 in modified transcript
• Changed! pfam Thymidylate_kin 138aa 2e-31 in modified transcript
• Changed! COG Tmk 145aa 4e-16 in modified transcript

LOC727778

• refseq_LOC727778.F2 refseq_LOC727778.R2 273 334
• NCBIGene 36.2 727778
• Alternative 5-prime, size difference: 61
• Exclusion in the protein causing a frameshift
• Reference transcript: XM_001125727

• Changed! pfam DUF1242 36aa 3e-05 in ref transcript
  • Protein of unknown function (DUF1242). This family consists of a number of eukaryotic proteins of around 72 residues in length. The function of this family is unknown.

LOC728005

• refseq_LOC728005.F1 refseq_LOC728005.R1 150 315
• NCBIGene 36.2 728005
• Multiple exon skipping, size difference: 165
• Inclusion in 5'UTR, Inclusion in 5'UTR
• Reference transcript: XM_001127140

• cd PH_centaurin 61aa 2e-11 in ref transcript
  • Centaurin Pleckstrin homology (PH) domain. Centaurin beta and gamma consist of a PH domain, an ArfGAP domain and three ankyrin repeats. Centaurain gamma also has an N-terminal Ras homology domain. Centaurin alpha has a different domain architecture and its PH domain is in a different subfamily. Centaurin can bind to phosphatidlyinositol (3,4,5)P3. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
• cd ANK 90aa 3e-11 in ref transcript
  • ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats.
• cd PH_centaurin 32aa 2e-04 in ref transcript
• pfam ArfGap 117aa 6e-34 in ref transcript
  • Putative GTPase activating protein for Arf. Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs.
• smart PH 64aa 8e-08 in ref transcript
  • Pleckstrin homology domain. Domain commonly found in eukaryotic signalling proteins. The domain family possesses multiple functions including the abilities to bind inositol phosphates, and various proteins. PH domains have been found to possess inserted domains (such as in PLC gamma, syntrophins) and to be inserted within other domains. Mutations in Brutons tyrosine kinase (Btk) within its PH domain cause X-linked agammaglobulinaemia (XLA) in patients. Point mutations cluster into the positively charged end of the molecule around the predicted binding site for phosphatidylinositol lipids.
• pfam PH 160aa 1e-06 in ref transcript
  • PH domain. PH stands for pleckstrin homology.
• pfam Ank 32aa 8e-06 in ref transcript
  • Ankyrin repeat. There's no clear separation between noise and signal on the HMM search Ankyrin repeats generally consist of a beta, alpha, alpha, beta order of secondary structures. The repeats associate to form a higher order structure.
• COG COG5347 117aa 4e-23 in ref transcript
  • GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion].
• PTZ PTZ00322 97aa 2e-05 in ref transcript
  • 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase; Provisional.

LOC728229

• refseq_LOC728229.F1 refseq_LOC728229.R1 127 157
• NCBIGene 36.2 728229
• Exon skipping and alternative 3-prime or 5-prime, size difference: 30
• Inclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: XM_001128423

LOC728239

• refseq_LOC728239.F2 refseq_LOC728239.R2 215 263
• NCBIGene 36.2 728239
• Single exon skipping, size difference: 48
• Exclusion in the protein (no frameshift)
• Reference transcript: XM_001127104

• Changed! pfam MAGE 186aa 1e-71 in ref transcript
  • MAGE family. The MAGE (melanoma antigen-encoding gene) family are expressed in a wide variety of tumours but not in normal cells, with the exception of the male germ cells, placenta, and, possibly, cells of the developing embryo. The cellular function of this family is unknown. This family also contains the yeast protein, Nse3. The Nse3 protein is part of the Smc5-6 complex. Nse3 has been demonstrated to be important for meiosis.
• PRK PRK07003 168aa 0.002 in ref transcript
  • DNA polymerase III subunits gamma and tau; Validated.
• Changed! pfam MAGE 170aa 8e-75 in modified transcript

LOC728461

• refseq_LOC728461.F2 refseq_LOC728461.R2 198 249
• NCBIGene 36.2 728461
• Alternative 5-prime, size difference: 51
• Exclusion in the protein (no frameshift)
• Reference transcript: XM_001126956

LOC728635

• refseq_LOC728635.F2 refseq_LOC728635.R2 239 350
• NCBIGene 36.2 728635
• Multiple exon skipping, size difference: 111
• Exclusion in the protein (no frameshift), Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: XM_001131318

• Changed! TIGR 3oxo_ACP_reduc 242aa 1e-45 in ref transcript
  • This model represents 3-oxoacyl-[ACP] reductase, also called 3-ketoacyl-acyl carrier protein reductase, an enzyme of fatty acid biosynthesis.
• Changed! PRK fabG 247aa 5e-53 in ref transcript
  • 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional.
• Changed! TIGR 3oxo_ACP_reduc 205aa 3e-37 in modified transcript
• Changed! PRK fabG 210aa 2e-44 in modified transcript

LOC728742

• refseq_LOC728742.F1 refseq_LOC728742.R1 148 246
• NCBIGene 36.2 728742
• Single exon skipping, size difference: 98
• Inclusion in the protein causing a new stop codon
• Reference transcript: XM_001128742

• Changed! cd CobW_like 165aa 7e-44 in ref transcript
  • The function of this protein family is unkown. The amino acid sequence of YjiA protein in E. coli contains several conserved motifs that characterizes it as a P-loop GTPase. YijA gene is among the genes significantly induced in response to DNA-damage caused by mitomycin. YijA gene is a homologue of the CobW gene which encodes the cobalamin synthesis protein/P47K.
• Changed! TIGR CobW 328aa 9e-39 in ref transcript
  • A broader CobW family is delineated by two PFAM models which identify the N- and C-terminal domains (pfam02492 and pfam07683).
• Changed! COG COG0523 335aa 8e-67 in ref transcript
  • Putative GTPases (G3E family) [General function prediction only].

LOC728835

• refseq_LOC728835.F1 refseq_LOC728835.R1 165 206
• NCBIGene 36.2 728835
• Alternative 3-prime, size difference: 41
• Inclusion in the protein causing a new stop codon
• Reference transcript: XM_001133183

• cd Chemokine_CC 31aa 6e-06 in ref transcript
  • Chemokine_CC: 1 of 4 subgroup designations based on the arrangement of the two N-terminal cysteine residues; includes a number of secreted growth factors and interferons involved in mitogenic, chemotactic, and inflammatory activity; some members (e.g. 2HCC) contain an additional disulfide bond which is thought to compensate for the highly conserved Trp missing in these; chemotatic for monocytes, macrophages, eosinophils, basophils, and T cells, but not neutrophils; exist as monomers and dimers, but are believed to be functional as monomers; found only in vertebrates and a few viruses; a subgroup of CC, identified by an N-terminal DCCL motif (Exodus-1, Exodus-2, and Exodus-3), has been shown to inhibit specific types of human cancer cell growth in a mouse model. See CDs: Chemokine (cd00169) for the general alignment of chemokines, or Chemokine_CXC (cd00273), Chemokine_C (cd00271), and Chemokine_CX3C (cd00274) for the additional chemokine subgroups, and Chemokine_CC_DCCL for the DCCL subgroup of this CD.
• Changed! pfam IL8 41aa 2e-08 in ref transcript
  • Small cytokines (intecrine/chemokine), interleukin-8 like. Includes a number of secreted growth factors and interferons involved in mitogenic, chemotactic, and inflammatory activity. Structure contains two highly conserved disulfide bonds.
• Changed! pfam IL8 40aa 1e-07 in modified transcript

LOC728860

• refseq_LOC728860.F1 refseq_LOC728860.R1 100 128
• NCBIGene 36.2 728860
• Alternative 3-prime, size difference: 28
• Inclusion in the protein causing a frameshift
• Reference transcript: XM_001133267

• Changed! cd ARM 113aa 8e-22 in ref transcript
  • Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model.
• Changed! cd ARM 121aa 7e-21 in ref transcript
• Changed! cd ARM 126aa 1e-18 in ref transcript
• Changed! pfam IBB 95aa 8e-29 in ref transcript
  • Importin beta binding domain. This family consists of the importin alpha (karyopherin alpha), importin beta (karyopherin beta) binding domain. The domain mediates formation of the importin alpha beta complex; required for classical NLS import of proteins into the nucleus, through the nuclear pore complex and across the nuclear envelope. Also in the alignment is the NLS of importin alpha which overlaps with the IBB domain.
• Changed! pfam Arm 41aa 4e-07 in ref transcript
  • Armadillo/beta-catenin-like repeat. Approx. 40 amino acid repeat. Tandem repeats form super-helix of helices that is proposed to mediate interaction of beta-catenin with its ligands. CAUTION: This family does not contain all known armadillo repeats.
• Changed! pfam Arm 40aa 5e-07 in ref transcript
• Changed! smart ARM 41aa 2e-05 in ref transcript
  • Armadillo/beta-catenin-like repeats. Approx. 40 amino acid repeat. Tandem repeats form superhelix of helices that is proposed to mediate interaction of beta-catenin with its ligands. Involved in transducing the Wingless/Wnt signal. In plakoglobin arm repeats bind alpha-catenin and N-cadherin.
• Changed! pfam Arm 39aa 2e-04 in ref transcript
• Changed! pfam Arm 39aa 4e-04 in ref transcript
• Changed! pfam Arm 41aa 9e-04 in ref transcript
• Changed! smart ARM 40aa 0.001 in ref transcript
• Changed! COG SRP1 519aa 1e-137 in ref transcript
  • Karyopherin (importin) alpha [Intracellular trafficking and secretion].

LOC728860

• refseq_LOC728860.F3 refseq_LOC728860.R3 157 187
• NCBIGene 36.2 728860
• Alternative 3-prime, size difference: 30
• Inclusion in 5'UTR
• Reference transcript: XM_001133267

• cd ARM 113aa 8e-22 in ref transcript
  • Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model.
• cd ARM 121aa 7e-21 in ref transcript
• cd ARM 126aa 1e-18 in ref transcript
• pfam IBB 95aa 8e-29 in ref transcript
  • Importin beta binding domain. This family consists of the importin alpha (karyopherin alpha), importin beta (karyopherin beta) binding domain. The domain mediates formation of the importin alpha beta complex; required for classical NLS import of proteins into the nucleus, through the nuclear pore complex and across the nuclear envelope. Also in the alignment is the NLS of importin alpha which overlaps with the IBB domain.
• pfam Arm 41aa 4e-07 in ref transcript
  • Armadillo/beta-catenin-like repeat. Approx. 40 amino acid repeat. Tandem repeats form super-helix of helices that is proposed to mediate interaction of beta-catenin with its ligands. CAUTION: This family does not contain all known armadillo repeats.
• pfam Arm 40aa 5e-07 in ref transcript
• smart ARM 41aa 2e-05 in ref transcript
  • Armadillo/beta-catenin-like repeats. Approx. 40 amino acid repeat. Tandem repeats form superhelix of helices that is proposed to mediate interaction of beta-catenin with its ligands. Involved in transducing the Wingless/Wnt signal. In plakoglobin arm repeats bind alpha-catenin and N-cadherin.
• pfam Arm 39aa 2e-04 in ref transcript
• pfam Arm 39aa 4e-04 in ref transcript
• pfam Arm 41aa 9e-04 in ref transcript
• smart ARM 40aa 0.001 in ref transcript
• COG SRP1 519aa 1e-137 in ref transcript
  • Karyopherin (importin) alpha [Intracellular trafficking and secretion].

ANAPC11

• refseq_LOC728919.F1 refseq_ANAPC11.R1 94 102
• NCBIGene 36.3 51529
• Alternative 5-prime, size difference: 8
• Exclusion in 5'UTR
• Reference transcript: NM_001002248

LOC728919

• refseq_LOC728919.F1 refseq_LOC728919.R1 101 123
• NCBIGene 36.2 728919
• Alternative 5-prime, size difference: 22
• Exclusion in 5'UTR
• Reference transcript: XM_001133292

• COG APC11 88aa 2e-19 in ref transcript
  • Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning].

LOC729059

• refseq_LOC729059.F2 refseq_LOC729059.R2 301 400
• NCBIGene 36.2 729059
• Alternative 3-prime, size difference: 99
• Exclusion in the protein (no frameshift)
• Reference transcript: XM_001133127

LOC729264

• refseq_LOC729264.F1 refseq_LOC729264.R1 156 280
• NCBIGene 36.3 729264
• Alternative 5-prime, size difference: 124
• Exclusion in the protein causing a frameshift
• Reference transcript: XM_001133674

LOC729355

• refseq_LOC729264.F1 refseq_LOC729355.R1 154 278
• NCBIGene 36.2 729355
• Alternative 5-prime, size difference: 124
• Exclusion in the protein causing a frameshift
• Reference transcript: XM_001133681

LOC730258

• refseq_LOC730258.F1 refseq_LOC730258.R1 209 327
• NCBIGene 36.2 730258
• Single exon skipping, size difference: 118
• Exclusion in 5'UTR
• Reference transcript: XM_001134401

LONRF3

• refseq_LONRF3.F2 refseq_LONRF3.R2 257 380
• NCBIGene 36.3 79836
• Single exon skipping, size difference: 123
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001031855

• Changed! cd TPR 96aa 3e-10 in ref transcript
  • Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here.
• cd RING 40aa 4e-06 in ref transcript
  • RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H).
• pfam LON 172aa 4e-19 in ref transcript
  • ATP-dependent protease La (LON) domain.
• TIGR rad18 86aa 1e-09 in ref transcript
  • This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
• Changed! TIGR 3a0801s09 115aa 1e-07 in ref transcript
• TIGR rad18 40aa 7e-06 in ref transcript
• COG COG2802 197aa 1e-15 in ref transcript
  • Uncharacterized protein, similar to the N-terminal domain of Lon protease [General function prediction only].
• COG RAD18 61aa 4e-06 in ref transcript
  • RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms].
• COG RAD18 39aa 2e-04 in ref transcript
• Changed! cd TPR 63aa 2e-05 in modified transcript
• Changed! TIGR 3a0801s09 66aa 0.001 in modified transcript

LRDD

• refseq_LRDD.F1 LRDD.u.r.22 121 154
• NCBIGene 36.3 55367
• Alternative 5-prime, size difference: 33
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_145886

• pfam Death 79aa 3e-09 in ref transcript
  • Death domain.
• pfam Peptidase_S68 34aa 2e-08 in ref transcript
  • Peptidase S68. This family of serine peptidases contains PIDD proteins. PIDD forms a complex with RAIDD and procaspase-2 that is known as the 'PIDDosome'. The PIDDosome forms when DNA damage occurs and either activates NF-kappaB, leading to cell survival, or caspase-2, which leads to apoptosis.
• smart ZU5 63aa 9e-04 in ref transcript
  • Domain present in ZO-1 and Unc5-like netrin receptors. Domain of unknown function.
• COG COG4886 96aa 3e-07 in ref transcript
  • Leucine-rich repeat (LRR) protein [Function unknown].

LRDD

• refseq_LRDD.F4 refseq_LRDD.R4 260 320
• NCBIGene 36.3 55367
• Alternative 3-prime, size difference: 60
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_145886

• Changed! pfam Death 79aa 3e-09 in ref transcript
  • Death domain.
• Changed! pfam Peptidase_S68 34aa 2e-08 in ref transcript
  • Peptidase S68. This family of serine peptidases contains PIDD proteins. PIDD forms a complex with RAIDD and procaspase-2 that is known as the 'PIDDosome'. The PIDDosome forms when DNA damage occurs and either activates NF-kappaB, leading to cell survival, or caspase-2, which leads to apoptosis.
• Changed! smart ZU5 63aa 9e-04 in ref transcript
  • Domain present in ZO-1 and Unc5-like netrin receptors. Domain of unknown function.
• Changed! COG COG4886 96aa 3e-07 in ref transcript
  • Leucine-rich repeat (LRR) protein [Function unknown].

LRDD

• refseq_LRDD.F6 refseq_LRDD.R6 145 196
• NCBIGene 36.3 55367
• Alternative 5-prime, size difference: 51
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_145886

• pfam Death 79aa 3e-09 in ref transcript
  • Death domain.
• pfam Peptidase_S68 34aa 2e-08 in ref transcript
  • Peptidase S68. This family of serine peptidases contains PIDD proteins. PIDD forms a complex with RAIDD and procaspase-2 that is known as the 'PIDDosome'. The PIDDosome forms when DNA damage occurs and either activates NF-kappaB, leading to cell survival, or caspase-2, which leads to apoptosis.
• smart ZU5 63aa 9e-04 in ref transcript
  • Domain present in ZO-1 and Unc5-like netrin receptors. Domain of unknown function.
• COG COG4886 96aa 3e-07 in ref transcript
  • Leucine-rich repeat (LRR) protein [Function unknown].

LRP8

• refseq_LRP8.F2 refseq_LRP8.R2 167 392
• NCBIGene 36.3 7804
• Single exon skipping, size difference: 225
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_004631

• cd LDLa 32aa 7e-06 in ref transcript
  • Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure.
• cd LDLa 35aa 1e-05 in ref transcript
• cd LDLa 36aa 2e-04 in ref transcript
• cd LDLa 37aa 3e-04 in ref transcript
• cd LDLa 27aa 0.002 in ref transcript
• pfam Ldl_recept_b 41aa 2e-11 in ref transcript
  • Low-density lipoprotein receptor repeat class B. This domain is also known as the YWTD motif after the most conserved region of the repeat. The YWTD repeat is found in multiple tandem repeats and has been predicted to form a beta-propeller structure.
• smart LY 43aa 1e-10 in ref transcript
  • Low-density lipoprotein-receptor YWTD domain. Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
• smart LY 43aa 3e-08 in ref transcript
• smart LDLa 33aa 9e-07 in ref transcript
  • Low-density lipoprotein receptor domain class A. Cysteine-rich repeat in the low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. The N-terminal type A repeats in LDL receptor bind the lipoproteins. Other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement. Mutations in the LDL receptor gene cause familial hypercholesterolemia.
• pfam Ldl_recept_b 40aa 1e-06 in ref transcript
• pfam Ldl_recept_a 37aa 4e-06 in ref transcript
  • Low-density lipoprotein receptor domain class A.
• pfam Ldl_recept_a 38aa 8e-06 in ref transcript
• pfam Ldl_recept_a 27aa 3e-05 in ref transcript
• smart EGF_CA 31aa 8e-04 in ref transcript
  • Calcium-binding EGF-like domain.
• smart LY 36aa 0.002 in ref transcript
• smart LDLa 34aa 0.003 in ref transcript
• pfam Ldl_recept_b 44aa 0.005 in ref transcript
• Changed! COG COG3391 189aa 3e-05 in ref transcript
  • Uncharacterized conserved protein [Function unknown].
• Changed! COG COG3391 205aa 1e-05 in modified transcript

LRP8

• refseq_LRP8.F3 refseq_LRP8.R3 100 487
• NCBIGene 36.3 7804
• Single exon skipping, size difference: 387
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_004631

• cd LDLa 32aa 7e-06 in ref transcript
  • Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure.
• cd LDLa 35aa 1e-05 in ref transcript
• Changed! cd LDLa 36aa 2e-04 in ref transcript
• cd LDLa 37aa 3e-04 in ref transcript
• Changed! cd LDLa 27aa 0.002 in ref transcript
• pfam Ldl_recept_b 41aa 2e-11 in ref transcript
  • Low-density lipoprotein receptor repeat class B. This domain is also known as the YWTD motif after the most conserved region of the repeat. The YWTD repeat is found in multiple tandem repeats and has been predicted to form a beta-propeller structure.
• smart LY 43aa 1e-10 in ref transcript
  • Low-density lipoprotein-receptor YWTD domain. Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
• smart LY 43aa 3e-08 in ref transcript
• smart LDLa 33aa 9e-07 in ref transcript
  • Low-density lipoprotein receptor domain class A. Cysteine-rich repeat in the low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. The N-terminal type A repeats in LDL receptor bind the lipoproteins. Other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement. Mutations in the LDL receptor gene cause familial hypercholesterolemia.
• pfam Ldl_recept_b 40aa 1e-06 in ref transcript
• pfam Ldl_recept_a 37aa 4e-06 in ref transcript
  • Low-density lipoprotein receptor domain class A.
• Changed! pfam Ldl_recept_a 38aa 8e-06 in ref transcript
• Changed! pfam Ldl_recept_a 27aa 3e-05 in ref transcript
• smart EGF_CA 31aa 8e-04 in ref transcript
  • Calcium-binding EGF-like domain.
• smart LY 36aa 0.002 in ref transcript
• smart LDLa 34aa 0.003 in ref transcript
• pfam Ldl_recept_b 44aa 0.005 in ref transcript
• COG COG3391 189aa 3e-05 in ref transcript
  • Uncharacterized conserved protein [Function unknown].

LRP8

• refseq_LRP8.F6 refseq_LRP8.R6 136 313
• NCBIGene 36.3 7804
• Single exon skipping, size difference: 177
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_004631

• cd LDLa 32aa 7e-06 in ref transcript
  • Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure.
• cd LDLa 35aa 1e-05 in ref transcript
• cd LDLa 36aa 2e-04 in ref transcript
• cd LDLa 37aa 3e-04 in ref transcript
• cd LDLa 27aa 0.002 in ref transcript
• pfam Ldl_recept_b 41aa 2e-11 in ref transcript
  • Low-density lipoprotein receptor repeat class B. This domain is also known as the YWTD motif after the most conserved region of the repeat. The YWTD repeat is found in multiple tandem repeats and has been predicted to form a beta-propeller structure.
• smart LY 43aa 1e-10 in ref transcript
  • Low-density lipoprotein-receptor YWTD domain. Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
• smart LY 43aa 3e-08 in ref transcript
• smart LDLa 33aa 9e-07 in ref transcript
  • Low-density lipoprotein receptor domain class A. Cysteine-rich repeat in the low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. The N-terminal type A repeats in LDL receptor bind the lipoproteins. Other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement. Mutations in the LDL receptor gene cause familial hypercholesterolemia.
• pfam Ldl_recept_b 40aa 1e-06 in ref transcript
• pfam Ldl_recept_a 37aa 4e-06 in ref transcript
  • Low-density lipoprotein receptor domain class A.
• pfam Ldl_recept_a 38aa 8e-06 in ref transcript
• pfam Ldl_recept_a 27aa 3e-05 in ref transcript
• smart EGF_CA 31aa 8e-04 in ref transcript
  • Calcium-binding EGF-like domain.
• smart LY 36aa 0.002 in ref transcript
• smart LDLa 34aa 0.003 in ref transcript
• pfam Ldl_recept_b 44aa 0.005 in ref transcript
• COG COG3391 189aa 3e-05 in ref transcript
  • Uncharacterized conserved protein [Function unknown].

LRRC17

• refseq_LRRC17.F1 refseq_LRRC17.R1 198 251
• NCBIGene 36.3 10234
• Single exon skipping, size difference: 53
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_001031692

• Changed! cd LRR_RI 93aa 0.008 in ref transcript
  • Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1).
• Changed! COG COG4886 163aa 1e-05 in ref transcript
  • Leucine-rich repeat (LRR) protein [Function unknown].

LRRC20

• refseq_LRRC20.F1 refseq_LRRC20.R1 127 295
• NCBIGene 36.3 55222
• Single exon skipping, size difference: 168
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_207119

• Changed! cd LRR_RI 84aa 0.003 in ref transcript
  • Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1).
• Changed! COG COG4886 126aa 4e-04 in ref transcript
  • Leucine-rich repeat (LRR) protein [Function unknown].

LRRC20

• refseq_LRRC20.F3 refseq_LRRC20.R3 187 337
• NCBIGene 36.3 55222
• Single exon skipping, size difference: 150
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_207119

• Changed! cd LRR_RI 84aa 0.003 in ref transcript
  • Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1).
• Changed! COG COG4886 126aa 4e-04 in ref transcript
  • Leucine-rich repeat (LRR) protein [Function unknown].
• Changed! cd LRR_RI 74aa 0.009 in modified transcript
• Changed! COG COG4886 84aa 0.001 in modified transcript

LRRC23

• refseq_LRRC23.F1 refseq_LRRC23.R1 100 398
• NCBIGene 36.3 10233
• Single exon skipping, size difference: 298
• Exclusion of the stop codon
• Reference transcript: NM_201650

• Changed! COG COG4886 163aa 0.008 in ref transcript
  • Leucine-rich repeat (LRR) protein [Function unknown].
• Changed! COG COG4886 169aa 3e-05 in modified transcript

LRRFIP2

• refseq_LRRFIP2.F1 refseq_LRRFIP2.R1 254 326
• NCBIGene 36.3 9209
• Single exon skipping, size difference: 72
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_006309

• Changed! pfam DUF2051 354aa 1e-54 in ref transcript
  • Double stranded RNA binding protein (DUF2051). This is a novel protein identified as interacting with the leucine-rich repeat domain of human flightless-I, FliI protein.
• COG SbcC 333aa 3e-07 in ref transcript
  • ATPase involved in DNA repair [DNA replication, recombination, and repair].
• Changed! pfam DUF2051 330aa 1e-55 in modified transcript

LRRN2

• refseq_LRRN5.F1 refseq_LRRN5.R1 270 398
• NCBIGene 36.3 10446
• Single exon skipping, size difference: 128
• Exclusion in 5'UTR
• Reference transcript: NM_006338

• cd IGcam 92aa 6e-14 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• cd LRR_RI 174aa 6e-05 in ref transcript
  • Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1).
• cd LRR_RI 236aa 1e-04 in ref transcript
• pfam I-set 85aa 2e-13 in ref transcript
  • Immunoglobulin I-set domain.
• TIGR PCC 79aa 3e-09 in ref transcript
  • Note: this model is restricted to the amino half because a full-length model is incompatible with the HMM software package.
• COG COG4886 241aa 1e-10 in ref transcript
  • Leucine-rich repeat (LRR) protein [Function unknown].

LSR

• refseq_LSR.F2 refseq_LSR.R2 205 262
• NCBIGene 36.3 51599
• Single exon skipping, size difference: 57
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_205834

LST1

• refseq_LST1.F2 refseq_LST1.R2 180 225
• NCBIGene 36.3 7940
• Alternative 3-prime, size difference: 45
• Exclusion of the protein initiation site
• Reference transcript: NM_205839

• Changed! pfam LST1 39aa 3e-08 in modified transcript
  • LST-1 protein. B144/LST1 is a gene encoded in the human major histocompatibility complex that produces multiple forms of alternatively spliced mRNA and encodes peptides fewer than 100 amino acids in length. B144/LST1 is strongly expressed in dendritic cells. Transfection of B144/LST1 into a variety of cells induces morphologic changes including the production of long, thin filopodia.

LTB

• refseq_LTB.F1 refseq_LTB.R1 160 206
• NCBIGene 36.3 4050
• Single exon skipping, size difference: 46
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_002341

• Changed! cd TNF 154aa 1e-27 in ref transcript
  • Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT (lymphotoxin-alpha, TNF-beta), CD40 ligand, Apo2L (TRAIL), Fas ligand, and osteoprotegerin (OPG) ligand. These proteins generally have an intracellular N-terminal domain, a short transmembrane segment, an extracellular stalk, and a globular TNF-like extracellular domain of about 150 residues. They initiate apoptosis by binding to related receptors, some of which have intracellular death domains. They generally form homo- or hetero- trimeric complexes.TNF cytokines bind one elongated receptor molecule along each of three clefts formed by neighboring monomers of the trimer with ligand trimerization a requiste for receptor binding.
• Changed! smart TNF 142aa 3e-29 in ref transcript
  • Tumour necrosis factor family. Family of cytokines that form homotrimeric or heterotrimeric complexes. TNF mediates mature T-cell receptor-induced apoptosis through the p75 TNF receptor.

LTK

• refseq_LTK.F1 refseq_LTK.R1 129 312
• NCBIGene 36.3 4058
• Single exon skipping, size difference: 183
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_002344

• cd PTKc_ALK_LTK 277aa 1e-160 in ref transcript
  • Catalytic Domain of the Protein Tyrosine Kinases, Anaplastic Lymphoma Kinase and Leukocyte Tyrosine Kinase. Protein Tyrosine Kinase (PTK) family; Anaplastic lymphoma kinase (ALK) and Leukocyte tyrosine (tyr) kinase (LTK); catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyr residues in protein substrates. ALK and LTK are orphan receptor tyr kinases (RTKs) whose ligands are not yet well-defined. RTKs contain an extracellular ligand-binding domain, a transmembrane region, and an intracellular tyr kinase domain. They are usually activated through ligand binding, which causes dimerization and autophosphorylation of the intracellular tyr kinase catalytic domain. ALK appears to play an important role in mammalian neural development as well as visceral muscle differentiation in Drosophila. ALK is aberrantly expressed as fusion proteins, due to chromosomal translocations, in about 60% of anaplastic large cell lymphomas (ALCLs). ALK fusion proteins are also found in rare cases of diffuse large B cell lymphomas (DLBCLs). LTK is mainly expressed in B lymphocytes and neuronal tissues. It is important in cell proliferation and survival. Transgenic mice expressing TLK display retarded growth and high mortality rate. In addition, a polymorphism in mouse and human LTK is implicated in the pathogenesis of systemic lupus erythematosus.
• pfam Pkinase_Tyr 268aa 1e-104 in ref transcript
  • Protein tyrosine kinase.
• COG SPS1 269aa 1e-20 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].

LY6G5C

• refseq_LY6G5C.F2 refseq_LY6G5C.R2 123 217
• NCBIGene 36.2 80741
• Alternative 5-prime, size difference: 94
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_025262

LYCAT

• refseq_LYCAT.F2 refseq_LYCAT.R2 208 400
• NCBIGene 36.3 253558
• Exon skipping and alternative 3-prime or 5-prime, size difference: 192
• Exclusion in 5'UTR, Exclusion of the protein initiation site
• Reference transcript: NM_182551

• smart PlsC 122aa 1e-13 in ref transcript
  • Phosphate acyltransferases. Function in phospholipid biosynthesis and have either glycerolphosphate, 1-acylglycerolphosphate, or 2-acylglycerolphosphoethanolamine acyltransferase activities. Tafazzin, the product of the gene mutated in patients with Barth syndrome, is a member of this family.
• COG PlsC 151aa 2e-11 in ref transcript
  • 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism].

LYK5

• refseq_LYK5.F1 refseq_LYK5.R1 103 132
• NCBIGene 36.3 92335
• Single exon skipping, size difference: 29
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_001003787

• Changed! cd STKc_OSR1_SPAK 311aa 2e-57 in ref transcript
  • Serine/threonine kinases (STKs), oxidative stress response kinase (OSR1) and Ste20-related proline alanine-rich kinase (SPAK) subfamily, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The OSR1 and SPAK subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. SPAK is also referred to as STK39 or PASK (proline-alanine-rich STE20-related kinase). OSR1 and SPAK regulate the activity of cation-chloride cotransporters through direct interaction and phosphorylation. They are also implicated in cytoskeletal rearrangement, cell differentiation, transformation and proliferation. OSR1 and SPAK contain a conserved C-terminal (CCT) domain, which recognizes a unique motif ([RK]FX[VI]) present in their activating kinases (WNK1/WNK4) and their substrates.
• Changed! smart S_TKc 296aa 2e-41 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• Changed! COG SPS1 323aa 4e-19 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].

LYST

• refseq_LYST.F1 refseq_LYST.R1 125 285
• NCBIGene 36.2 1130
• Alternative 5-prime, size difference: 160
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_000081

• Changed! cd Beach 291aa 1e-109 in ref transcript
  • BEACH (Beige and Chediak-Higashi) domains, implicated in membrane trafficking, are present in a family of proteins conserved throughout eukaryotes. This group contains human lysosomal trafficking regulator (LYST), LPS-responsive and beige-like anchor (LRBA) and neurobeachin. Disruption of LYST leads to Chediak-Higashi syndrome, characterized by severe immunodeficiency, albinism, poor blood coagulation and neurologic problems. Neurobeachin is a candidate gene linked to autism. LBRA seems to be upregulated in several cancer types. It has been shown that the BEACH domain itself is important for the function of these proteins.
• Changed! cd WD40 302aa 2e-22 in ref transcript
  • WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.
• Changed! pfam Beach 291aa 1e-114 in ref transcript
  • Beige/BEACH domain.
• Changed! COG COG2319 253aa 7e-11 in ref transcript
  • FOG: WD40 repeat [General function prediction only].

M-RIP

• refseq_M-RIP.F1 refseq_M-RIP.R1 114 177
• NCBIGene 36.3 23164
• Single exon skipping, size difference: 63
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_015134

• cd PH_outspread 104aa 5e-48 in ref transcript
  • Outspread Pleckstrin homology (PH) domain. Outspread contains two PH domains and a C-terminal coiled-coil region. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinsases, regulators of G-proteins, endocytotic GTPAses, adaptors, a well as cytoskeletal associated molecules and in lipid associated enzymes.
• cd PH 92aa 1e-09 in ref transcript
  • Pleckstrin homology (PH) domain. PH domains are only found in eukaryotes. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes.
• smart PH 94aa 7e-13 in ref transcript
  • Pleckstrin homology domain. Domain commonly found in eukaryotic signalling proteins. The domain family possesses multiple functions including the abilities to bind inositol phosphates, and various proteins. PH domains have been found to possess inserted domains (such as in PLC gamma, syntrophins) and to be inserted within other domains. Mutations in Brutons tyrosine kinase (Btk) within its PH domain cause X-linked agammaglobulinaemia (XLA) in patients. Point mutations cluster into the positively charged end of the molecule around the predicted binding site for phosphatidylinositol lipids.
• pfam PH 102aa 1e-06 in ref transcript
  • PH domain. PH stands for pleckstrin homology.

MACF1

• refseq_MACF1.F1 refseq_MACF1.R1 102 120
• NCBIGene 36.3 23499
• Single exon skipping, size difference: 18
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_033044

• cd SPEC 210aa 1e-20 in ref transcript
  • Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here.
• cd SPEC 215aa 3e-19 in ref transcript
• cd SPEC 217aa 5e-17 in ref transcript
• cd SPEC 218aa 1e-16 in ref transcript
• cd SPEC 214aa 1e-15 in ref transcript
• cd SPEC 214aa 1e-12 in ref transcript
• cd SPEC 213aa 8e-12 in ref transcript
• cd SPEC 216aa 1e-11 in ref transcript
• cd SPEC 217aa 4e-11 in ref transcript
• cd SPEC 229aa 2e-10 in ref transcript
• cd SPEC 222aa 6e-10 in ref transcript
• cd SPEC 245aa 2e-09 in ref transcript
• cd SPEC 218aa 6e-09 in ref transcript
• cd SPEC 248aa 7e-08 in ref transcript
• cd SPEC 216aa 9e-08 in ref transcript
• cd SPEC 213aa 1e-07 in ref transcript
• cd SPEC 216aa 1e-06 in ref transcript
• cd EFh 63aa 1e-06 in ref transcript
  • EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers.
• cd SPEC 214aa 4e-06 in ref transcript
• cd SPEC 238aa 3e-05 in ref transcript
• cd SPEC 198aa 1e-04 in ref transcript
• cd SPEC 214aa 0.005 in ref transcript
• Changed! smart GAS2 79aa 5e-32 in ref transcript
  • Growth-Arrest-Specific Protein 2 Domain. GROWTH-ARREST-SPECIFIC PROTEIN 2 Domain.
• pfam SMC_N 882aa 4e-13 in ref transcript
  • RecF/RecN/SMC N terminal domain. This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.
• smart SPEC 98aa 8e-11 in ref transcript
  • Spectrin repeats.
• smart SPEC 101aa 2e-10 in ref transcript
• smart SPEC 103aa 8e-10 in ref transcript
• pfam Plectin 42aa 7e-09 in ref transcript
  • Plectin repeat. This family includes repeats from plectin, desmoplakin, envoplakin and bullous pemphigoid antigen.
• pfam Plectin 45aa 9e-08 in ref transcript
• smart SPEC 102aa 1e-07 in ref transcript
• smart SPEC 103aa 2e-07 in ref transcript
• pfam Plectin 45aa 2e-07 in ref transcript
• smart SPEC 102aa 3e-07 in ref transcript
• pfam Plectin 45aa 3e-07 in ref transcript
• TIGR SMC_prok_B 802aa 5e-07 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• pfam Plectin 43aa 2e-06 in ref transcript
• pfam Plectin 45aa 3e-06 in ref transcript
• pfam Plectin 43aa 4e-06 in ref transcript
• pfam Plectin 45aa 6e-06 in ref transcript
• smart SPEC 101aa 7e-06 in ref transcript
• smart SPEC 103aa 8e-06 in ref transcript
• TIGR SMC_prok_B 408aa 3e-05 in ref transcript
• smart SPEC 102aa 6e-05 in ref transcript
• pfam Spectrin 109aa 3e-04 in ref transcript
  • Spectrin repeat. Spectrin repeats are found in several proteins involved in cytoskeletal structure. These include spectrin, alpha-actinin and dystrophin. The sequence repeat used in this family is taken from the structural repeat in reference. The spectrin repeat forms a three helix bundle. The second helix is interrupted by proline in some sequences. The repeats are defined by a characteristic tryptophan (W) residue at position 17 in helix A and a leucine (L) at 2 residues from the carboxyl end of helix C.
• TIGR SMC_prok_B 308aa 4e-04 in ref transcript
• smart SPEC 101aa 0.006 in ref transcript
• smart SPEC 111aa 0.006 in ref transcript
• smart SPEC 119aa 0.009 in ref transcript
• COG Smc 839aa 3e-19 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].
• COG Smc 828aa 7e-09 in ref transcript
• COG FRQ1 56aa 0.001 in ref transcript
  • Ca2+-binding protein (EF-Hand superfamily) [Signal transduction mechanisms / Cytoskeleton / Cell division and chromosome partitioning / General function prediction only].
• PRK mukB 199aa 0.002 in ref transcript
  • cell division protein MukB; Provisional.
• Changed! COG SbcC 571aa 0.010 in ref transcript
  • ATPase involved in DNA repair [DNA replication, recombination, and repair].
• Changed! smart GAS2 73aa 5e-34 in modified transcript

MAD1L1

• refseq_MAD1L1.F2 refseq_MAD1L1.R2 162 202
• NCBIGene 36.3 8379
• Alternative 3-prime, size difference: 40
• Inclusion in 5'UTR
• Reference transcript: NM_001013837

• pfam MAD 705aa 1e-154 in ref transcript
  • Mitotic checkpoint protein. This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.
• COG Smc 213aa 0.006 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].

MADCAM1

• refseq_MADCAM1.F1 refseq_MADCAM1.R1 115 376
• NCBIGene 36.3 8174
• Single exon skipping, size difference: 261
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_130760

• Changed! pfam Adhes-Ig_like 112aa 5e-40 in ref transcript
  • Adhesion molecule, immunoglobulin-like. Members of this family are found in a set of mucosal cellular adhesion proteins and adopt an immunoglobulin-like beta-sandwich structure, with seven strands arranged in two beta-sheets in a Greek-key topology. They are essential for recruitment of lymphocytes to specific tissues.
• Changed! pfam Adhes-Ig_like 110aa 2e-39 in modified transcript

MADD

• refseq_MADD.F10 refseq_MADD.R10 118 178
• NCBIGene 36.3 8567
• Single exon skipping, size difference: 60
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_003682

• pfam DENN 230aa 3e-62 in ref transcript
  • DENN (AEX-3) domain. DENN (after differentially expressed in neoplastic vs normal cells) is a domain which occurs in several proteins involved in Rab- mediated processes or regulation of MAPK signalling pathways.
• pfam uDENN 91aa 2e-20 in ref transcript
  • uDENN domain. This region is always found associated with pfam02141. It is predicted to form an all beta domain.
• pfam dDENN 74aa 2e-11 in ref transcript
  • dDENN domain. This region is always found associated with pfam02141. It is predicted to form a globular domain. This domain is predicted to be completely alpha helical. Although not statistically supported it has been suggested that this domain may be similar to members of the Rho/Rac/Cdc42 GEF family.

MADD

• refseq_MADD.F2 refseq_MADD.R2 181 310
• NCBIGene 36.3 8567
• Alternative 5-prime, size difference: 129
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_003682

• pfam DENN 230aa 3e-62 in ref transcript
  • DENN (AEX-3) domain. DENN (after differentially expressed in neoplastic vs normal cells) is a domain which occurs in several proteins involved in Rab- mediated processes or regulation of MAPK signalling pathways.
• pfam uDENN 91aa 2e-20 in ref transcript
  • uDENN domain. This region is always found associated with pfam02141. It is predicted to form an all beta domain.
• pfam dDENN 74aa 2e-11 in ref transcript
  • dDENN domain. This region is always found associated with pfam02141. It is predicted to form a globular domain. This domain is predicted to be completely alpha helical. Although not statistically supported it has been suggested that this domain may be similar to members of the Rho/Rac/Cdc42 GEF family.

MADD

• refseq_MADD.F3 refseq_MADD.R3 116 186
• NCBIGene 36.3 8567
• Single exon skipping, size difference: 70
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_003682

• pfam DENN 230aa 3e-62 in ref transcript
  • DENN (AEX-3) domain. DENN (after differentially expressed in neoplastic vs normal cells) is a domain which occurs in several proteins involved in Rab- mediated processes or regulation of MAPK signalling pathways.
• pfam uDENN 91aa 2e-20 in ref transcript
  • uDENN domain. This region is always found associated with pfam02141. It is predicted to form an all beta domain.
• pfam dDENN 74aa 2e-11 in ref transcript
  • dDENN domain. This region is always found associated with pfam02141. It is predicted to form a globular domain. This domain is predicted to be completely alpha helical. Although not statistically supported it has been suggested that this domain may be similar to members of the Rho/Rac/Cdc42 GEF family.

MADD

• refseq_MADD.F5 refseq_MADD.R5 152 215
• NCBIGene 36.3 8567
• Single exon skipping, size difference: 63
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_003682

• pfam DENN 230aa 3e-62 in ref transcript
  • DENN (AEX-3) domain. DENN (after differentially expressed in neoplastic vs normal cells) is a domain which occurs in several proteins involved in Rab- mediated processes or regulation of MAPK signalling pathways.
• pfam uDENN 91aa 2e-20 in ref transcript
  • uDENN domain. This region is always found associated with pfam02141. It is predicted to form an all beta domain.
• pfam dDENN 74aa 2e-11 in ref transcript
  • dDENN domain. This region is always found associated with pfam02141. It is predicted to form a globular domain. This domain is predicted to be completely alpha helical. Although not statistically supported it has been suggested that this domain may be similar to members of the Rho/Rac/Cdc42 GEF family.

MADD

• refseq_MADD.F8 refseq_MADD.R8 175 229
• NCBIGene 36.3 8567
• Single exon skipping, size difference: 54
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_003682

• pfam DENN 230aa 3e-62 in ref transcript
  • DENN (AEX-3) domain. DENN (after differentially expressed in neoplastic vs normal cells) is a domain which occurs in several proteins involved in Rab- mediated processes or regulation of MAPK signalling pathways.
• pfam uDENN 91aa 2e-20 in ref transcript
  • uDENN domain. This region is always found associated with pfam02141. It is predicted to form an all beta domain.
• pfam dDENN 74aa 2e-11 in ref transcript
  • dDENN domain. This region is always found associated with pfam02141. It is predicted to form a globular domain. This domain is predicted to be completely alpha helical. Although not statistically supported it has been suggested that this domain may be similar to members of the Rho/Rac/Cdc42 GEF family.
• Changed! pfam HPC2 208aa 0.007 in modified transcript
  • Histone promoter control 2 (HPC2). HPC2 is required for cell-cycle regulation of histone transcription. It regulates transcription of the histone genes during the S-phase of the cell cycle by repressing transcription at other cell cycle stages. HPC2 mutants display synthetic interactions with FACT complex which allows RNA Pol II to elongate through nucleosomes.

MAEA

• refseq_MAEA.F1 refseq_MAEA.R1 117 240
• NCBIGene 36.3 10296
• Single exon skipping, size difference: 123
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001017405

• smart CRA 93aa 6e-13 in ref transcript
  • CT11-RanBPM. protein-protein interaction domain present in crown eukaryotes (plants, animals, fungi).
• Changed! smart CTLH 58aa 1e-10 in ref transcript
  • C-terminal to LisH motif. Alpha-helical motif of unknown function.
• Changed! smart LisH 34aa 2e-04 in ref transcript
  • Lissencephaly type-1-like homology motif. Alpha-helical motif present in Lis1, treacle, Nopp140, some katanin p60 subunits, muskelin, tonneau, LEUNIG and numerous WD40 repeat-containing proteins. It is suggested that LisH motifs contribute to the regulation of microtubule dynamics, either by mediating dimerisation, or else by binding cytoplasmic dynein heavy chain or microtubules directly.
• Changed! smart CTLH 51aa 8e-06 in modified transcript

MAG

• refseq_MAG.F1 refseq_MAG.R1 187 232
• NCBIGene 36.3 4099
• Single exon skipping, size difference: 45
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_002361

• cd IGcam 81aa 2e-07 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• cd IGcam 80aa 1e-04 in ref transcript
• smart IG_like 78aa 3e-09 in ref transcript
  • Immunoglobulin like. IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
• pfam I-set 83aa 5e-06 in ref transcript
  • Immunoglobulin I-set domain.
• pfam C2-set_2 82aa 3e-05 in ref transcript
  • CD80-like C2-set immunoglobulin domain. These domains belong to the immunoglobulin superfamily.

MAGEA10

• refseq_MAGEA10.F1 refseq_MAGEA10.R1 293 384
• NCBIGene 36.3 4109
• Single exon skipping, size difference: 91
• Exclusion in 5'UTR
• Reference transcript: NM_001011543

• pfam MAGE 171aa 6e-79 in ref transcript
  • MAGE family. The MAGE (melanoma antigen-encoding gene) family are expressed in a wide variety of tumours but not in normal cells, with the exception of the male germ cells, placenta, and, possibly, cells of the developing embryo. The cellular function of this family is unknown. This family also contains the yeast protein, Nse3. The Nse3 protein is part of the Smc5-6 complex. Nse3 has been demonstrated to be important for meiosis.

MAGEA2

• refseq_MAGEA2.F1 refseq_MAGEA2.R1 110 192
• NCBIGene 36.3 4101
• Single exon skipping, size difference: 82
• Exclusion in 5'UTR
• Reference transcript: NM_175742

• pfam MAGE 171aa 1e-64 in ref transcript
  • MAGE family. The MAGE (melanoma antigen-encoding gene) family are expressed in a wide variety of tumours but not in normal cells, with the exception of the male germ cells, placenta, and, possibly, cells of the developing embryo. The cellular function of this family is unknown. This family also contains the yeast protein, Nse3. The Nse3 protein is part of the Smc5-6 complex. Nse3 has been demonstrated to be important for meiosis.

MAGEA2

• refseq_MAGEA2.F3 refseq_MAGEA2.R3 148 246
• NCBIGene 36.3 4101
• Single exon skipping, size difference: 98
• Exclusion in 5'UTR
• Reference transcript: NM_175743

• pfam MAGE 171aa 1e-64 in ref transcript
  • MAGE family. The MAGE (melanoma antigen-encoding gene) family are expressed in a wide variety of tumours but not in normal cells, with the exception of the male germ cells, placenta, and, possibly, cells of the developing embryo. The cellular function of this family is unknown. This family also contains the yeast protein, Nse3. The Nse3 protein is part of the Smc5-6 complex. Nse3 has been demonstrated to be important for meiosis.

MAGEB1

• refseq_MAGEB1.F1 refseq_MAGEB1.R1 114 197
• NCBIGene 36.3 4112
• Single exon skipping, size difference: 83
• Exclusion in 5'UTR
• Reference transcript: NM_002363

• pfam MAGE 171aa 4e-78 in ref transcript
  • MAGE family. The MAGE (melanoma antigen-encoding gene) family are expressed in a wide variety of tumours but not in normal cells, with the exception of the male germ cells, placenta, and, possibly, cells of the developing embryo. The cellular function of this family is unknown. This family also contains the yeast protein, Nse3. The Nse3 protein is part of the Smc5-6 complex. Nse3 has been demonstrated to be important for meiosis.

MAGED1

• refseq_MAGED1.F2 refseq_MAGED1.R2 111 279
• NCBIGene 36.3 9500
• Single exon skipping, size difference: 168
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001005333

• pfam MAGE 170aa 1e-70 in ref transcript
  • MAGE family. The MAGE (melanoma antigen-encoding gene) family are expressed in a wide variety of tumours but not in normal cells, with the exception of the male germ cells, placenta, and, possibly, cells of the developing embryo. The cellular function of this family is unknown. This family also contains the yeast protein, Nse3. The Nse3 protein is part of the Smc5-6 complex. Nse3 has been demonstrated to be important for meiosis.

MAGED4B

• refseq_MAGED4.F1 refseq_MAGED4.R1 131 161
• NCBIGene 36.3 81557
• Alternative 3-prime, size difference: 30
• Inclusion in 5'UTR
• Reference transcript: NM_177535

• pfam MAGE 170aa 8e-75 in ref transcript
  • MAGE family. The MAGE (melanoma antigen-encoding gene) family are expressed in a wide variety of tumours but not in normal cells, with the exception of the male germ cells, placenta, and, possibly, cells of the developing embryo. The cellular function of this family is unknown. This family also contains the yeast protein, Nse3. The Nse3 protein is part of the Smc5-6 complex. Nse3 has been demonstrated to be important for meiosis.
• PRK PRK07003 168aa 0.002 in ref transcript
  • DNA polymerase III subunits gamma and tau; Validated.

MAGI1

• refseq_MAGI1.F1 refseq_MAGI1.R1 194 283
• NCBIGene 36.3 9223
• Single exon skipping, size difference: 89
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_001033057

• cd PDZ_signaling 95aa 7e-17 in ref transcript
  • PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of PDZ domains an N-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in proteases.
• cd PDZ_signaling 78aa 8e-16 in ref transcript
• cd PDZ_signaling 76aa 3e-13 in ref transcript
• cd GMPK 70aa 4e-12 in ref transcript
  • Guanosine monophosphate kinase (GMPK, EC 2.7.4.8), also known as guanylate kinase (GKase), catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to guanosine monophosphate (GMP) to yield adenosine diphosphate (ADP) and guanosine diphosphate (GDP). It plays an essential role in the biosynthesis of guanosine triphosphate (GTP). This enzyme is also important for the activation of some antiviral and anticancer agents, such as acyclovir, ganciclovir, carbovir, and thiopurines.
• cd PDZ_signaling 68aa 1e-10 in ref transcript
• cd PDZ_signaling 80aa 6e-10 in ref transcript
• cd WW 30aa 3e-06 in ref transcript
  • Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
• cd WW 30aa 0.001 in ref transcript
• smart GuKc 183aa 3e-31 in ref transcript
  • Guanylate kinase homologues. Active enzymes catalyze ATP-dependent phosphorylation of GMP to GDP. Structure resembles that of adenylate kinase. So-called membrane-associated guanylate kinase homologues (MAGUKs) do not possess guanylate kinase activities; instead at least some possess protein-binding functions.
• smart PDZ 83aa 1e-18 in ref transcript
  • Domain present in PSD-95, Dlg, and ZO-1/2. Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities.
• smart PDZ 99aa 3e-17 in ref transcript
• smart PDZ 87aa 3e-14 in ref transcript
• smart PDZ 87aa 4e-14 in ref transcript
• smart PDZ 84aa 8e-14 in ref transcript
• TIGR degP_htrA_DO 235aa 6e-11 in ref transcript
  • This family consists of a set proteins various designated DegP, heat shock protein HtrA, and protease DO. The ortholog in Pseudomonas aeruginosa is designated MucD and is found in an operon that controls mucoid phenotype. This family also includes the DegQ (HhoA) paralog in E. coli which can rescue a DegP mutant, but not the smaller DegS paralog, which cannot. Members of this family are located in the periplasm and have separable functions as both protease and chaperone. Members have a trypsin domain and two copies of a PDZ domain. This protein protects bacteria from thermal and other stresses and may be important for the survival of bacterial pathogens.// The chaperone function is dominant at low temperatures, whereas the proteolytic activity is turned on at elevated temperatures.
• pfam WW 30aa 3e-07 in ref transcript
  • WW domain. The WW domain is a protein module with two highly conserved tryptophans that binds proline-rich peptide motifs in vitro.
• pfam WW 30aa 1e-05 in ref transcript
• COG Gmk 62aa 5e-14 in ref transcript
  • Guanylate kinase [Nucleotide transport and metabolism].
• COG Prc 76aa 8e-07 in ref transcript
  • Periplasmic protease [Cell envelope biogenesis, outer membrane].
• COG Prc 77aa 8e-05 in ref transcript
• COG Prc 70aa 3e-04 in ref transcript

MAGI1

• refseq_MAGI1.F3 refseq_MAGI1.R3 257 341
• NCBIGene 36.3 9223
• Single exon skipping, size difference: 84
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_001033057

• cd PDZ_signaling 95aa 7e-17 in ref transcript
  • PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of PDZ domains an N-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in proteases.
• cd PDZ_signaling 78aa 8e-16 in ref transcript
• cd PDZ_signaling 76aa 3e-13 in ref transcript
• cd GMPK 70aa 4e-12 in ref transcript
  • Guanosine monophosphate kinase (GMPK, EC 2.7.4.8), also known as guanylate kinase (GKase), catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to guanosine monophosphate (GMP) to yield adenosine diphosphate (ADP) and guanosine diphosphate (GDP). It plays an essential role in the biosynthesis of guanosine triphosphate (GTP). This enzyme is also important for the activation of some antiviral and anticancer agents, such as acyclovir, ganciclovir, carbovir, and thiopurines.
• cd PDZ_signaling 68aa 1e-10 in ref transcript
• cd PDZ_signaling 80aa 6e-10 in ref transcript
• cd WW 30aa 3e-06 in ref transcript
  • Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
• cd WW 30aa 0.001 in ref transcript
• smart GuKc 183aa 3e-31 in ref transcript
  • Guanylate kinase homologues. Active enzymes catalyze ATP-dependent phosphorylation of GMP to GDP. Structure resembles that of adenylate kinase. So-called membrane-associated guanylate kinase homologues (MAGUKs) do not possess guanylate kinase activities; instead at least some possess protein-binding functions.
• smart PDZ 83aa 1e-18 in ref transcript
  • Domain present in PSD-95, Dlg, and ZO-1/2. Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities.
• smart PDZ 99aa 3e-17 in ref transcript
• smart PDZ 87aa 3e-14 in ref transcript
• smart PDZ 87aa 4e-14 in ref transcript
• smart PDZ 84aa 8e-14 in ref transcript
• TIGR degP_htrA_DO 235aa 6e-11 in ref transcript
  • This family consists of a set proteins various designated DegP, heat shock protein HtrA, and protease DO. The ortholog in Pseudomonas aeruginosa is designated MucD and is found in an operon that controls mucoid phenotype. This family also includes the DegQ (HhoA) paralog in E. coli which can rescue a DegP mutant, but not the smaller DegS paralog, which cannot. Members of this family are located in the periplasm and have separable functions as both protease and chaperone. Members have a trypsin domain and two copies of a PDZ domain. This protein protects bacteria from thermal and other stresses and may be important for the survival of bacterial pathogens.// The chaperone function is dominant at low temperatures, whereas the proteolytic activity is turned on at elevated temperatures.
• pfam WW 30aa 3e-07 in ref transcript
  • WW domain. The WW domain is a protein module with two highly conserved tryptophans that binds proline-rich peptide motifs in vitro.
• pfam WW 30aa 1e-05 in ref transcript
• COG Gmk 62aa 5e-14 in ref transcript
  • Guanylate kinase [Nucleotide transport and metabolism].
• COG Prc 76aa 8e-07 in ref transcript
  • Periplasmic protease [Cell envelope biogenesis, outer membrane].
• COG Prc 77aa 8e-05 in ref transcript
• COG Prc 70aa 3e-04 in ref transcript

MAGI3

• refseq_MAGI3.F1 refseq_MAGI3.R1 107 182
• NCBIGene 36.2 260425
• Single exon skipping, size difference: 75
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_020965

• cd PDZ_signaling 79aa 2e-16 in ref transcript
  • PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of PDZ domains an N-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in proteases.
• cd GMPK 101aa 2e-15 in ref transcript
  • Guanosine monophosphate kinase (GMPK, EC 2.7.4.8), also known as guanylate kinase (GKase), catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to guanosine monophosphate (GMP) to yield adenosine diphosphate (ADP) and guanosine diphosphate (GDP). It plays an essential role in the biosynthesis of guanosine triphosphate (GTP). This enzyme is also important for the activation of some antiviral and anticancer agents, such as acyclovir, ganciclovir, carbovir, and thiopurines.
• cd PDZ_signaling 87aa 3e-15 in ref transcript
• cd PDZ_signaling 78aa 4e-11 in ref transcript
• cd PDZ_signaling 65aa 2e-10 in ref transcript
• cd WW 30aa 3e-06 in ref transcript
  • Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
• cd PDZ_signaling 68aa 3e-04 in ref transcript
• cd PDZ_signaling 35aa 0.002 in ref transcript
• smart GuKc 86aa 2e-20 in ref transcript
  • Guanylate kinase homologues. Active enzymes catalyze ATP-dependent phosphorylation of GMP to GDP. Structure resembles that of adenylate kinase. So-called membrane-associated guanylate kinase homologues (MAGUKs) do not possess guanylate kinase activities; instead at least some possess protein-binding functions.
• smart PDZ 81aa 4e-18 in ref transcript
  • Domain present in PSD-95, Dlg, and ZO-1/2. Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities.
• smart PDZ 88aa 9e-15 in ref transcript
• smart PDZ 81aa 3e-13 in ref transcript
• smart PDZ 84aa 5e-13 in ref transcript
• smart PDZ 82aa 1e-07 in ref transcript
• pfam WW 30aa 4e-07 in ref transcript
  • WW domain. The WW domain is a protein module with two highly conserved tryptophans that binds proline-rich peptide motifs in vitro.
• smart PDZ 40aa 0.009 in ref transcript
• PRK gmk 74aa 7e-18 in ref transcript
  • guanylate kinase; Provisional.
• COG Prc 67aa 5e-05 in ref transcript
  • Periplasmic protease [Cell envelope biogenesis, outer membrane].
• COG Prc 55aa 8e-05 in ref transcript
• COG Prc 83aa 0.002 in ref transcript
• Changed! COG HUL4 53aa 0.007 in ref transcript
  • Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones].
• Changed! cd WW 31aa 2e-04 in modified transcript
• Changed! pfam WW 30aa 9e-06 in modified transcript
• Changed! COG HUL4 76aa 2e-04 in modified transcript

MAL

• refseq_MAL.F2 refseq_MAL.R2 191 317
• NCBIGene 36.3 4118
• Single exon skipping, size difference: 126
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_002371

• Changed! pfam MARVEL 115aa 5e-14 in ref transcript
  • Membrane-associating domain. MARVEL domain-containing proteins are often found in lipid-associating proteins - such as Occludin and MAL family proteins. It may be part of the machinery of membrane apposition events, such as transport vesicle biogenesis.
• Changed! pfam MARVEL 75aa 0.002 in modified transcript

MAL

• refseq_MAL.F3 refseq_MAL.R3 111 279
• NCBIGene 36.3 4118
• Single exon skipping, size difference: 168
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_002371

• Changed! pfam MARVEL 115aa 5e-14 in ref transcript
  • Membrane-associating domain. MARVEL domain-containing proteins are often found in lipid-associating proteins - such as Occludin and MAL family proteins. It may be part of the machinery of membrane apposition events, such as transport vesicle biogenesis.
• Changed! pfam MARVEL 65aa 4e-06 in modified transcript

MALT1

• refseq_MALT1.F1 refseq_MALT1.R1 101 134
• NCBIGene 36.3 10892
• Single exon skipping, size difference: 33
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_006785

• cd IGcam 67aa 4e-07 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• cd IGcam 65aa 5e-05 in ref transcript
• pfam Peptidase_C14 218aa 3e-21 in ref transcript
  • Caspase domain.
• smart IG_like 70aa 1e-07 in ref transcript
  • Immunoglobulin like. IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
• smart IG_like 76aa 2e-06 in ref transcript
• COG COG4249 234aa 8e-07 in ref transcript
  • Uncharacterized protein containing caspase domain [General function prediction only].

MANBAL

• refseq_MANBAL.F1 refseq_MANBAL.R1 232 349
• NCBIGene 36.3 63905
• Single exon skipping, size difference: 117
• Exclusion in 5'UTR
• Reference transcript: NM_022077

MANEAL

• refseq_MANEAL.F1 refseq_MANEAL.R1 156 356
• NCBIGene 36.3 149175
• Exon skipping and alternative 3-prime or 5-prime, size difference: 200
• Inclusion in the protein causing a new stop codon, Exclusion in the protein causing a frameshift
• Reference transcript: NM_001031740

MAP2

• refseq_MAP2.F1 refseq_MAP2.R1 119 290
• NCBIGene 36.3 4133
• Single exon skipping, size difference: 171
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_002374

• pfam MAP2_projctn 1129aa 0.0 in ref transcript
  • MAP2/Tau projection domain. This domain is found in the MAP2/Tau family of proteins which includes MAP2, MAP4, Tau, and their homologs. All isoforms contain a conserved C-terminal domain containing tubulin-binding repeats (pfam00418), and a N-terminal projection domain of varying size. This domain has a net negative charge and exerts a long-range repulsive force. This provides a mechanism that can regulate microtubule spacing which might facilitate efficient organelle transport.
• pfam Tubulin-binding 31aa 5e-09 in ref transcript
  • Tau and MAP protein, tubulin-binding repeat. This family includes the vertebrate proteins MAP2, MAP4 and Tau, as well as other animal homologs. MAP4 is present in many tissues but is usually absent from neurons; MAP2 and Tau are mainly neuronal. Members of this family have the ability to bind to and stabilise microtubules. As a result, they are involved in neuronal migration, supporting dendrite elongation, and regulating microtubules during mitotic metaphase. Note that Tau is involved in neurofibrillary tangle formation in Alzheimer's disease and some other dementias. This family features a C-terminal microtubule binding repeat that contains a conserved KXGS motif.
• pfam Tubulin-binding 32aa 1e-06 in ref transcript
• pfam Tubulin-binding 32aa 6e-06 in ref transcript

MAP2

• refseq_MAP2.F3 refseq_MAP2.R3 300 393
• NCBIGene 36.3 4133
• Single exon skipping, size difference: 93
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_002374

• pfam MAP2_projctn 1129aa 0.0 in ref transcript
  • MAP2/Tau projection domain. This domain is found in the MAP2/Tau family of proteins which includes MAP2, MAP4, Tau, and their homologs. All isoforms contain a conserved C-terminal domain containing tubulin-binding repeats (pfam00418), and a N-terminal projection domain of varying size. This domain has a net negative charge and exerts a long-range repulsive force. This provides a mechanism that can regulate microtubule spacing which might facilitate efficient organelle transport.
• pfam Tubulin-binding 31aa 5e-09 in ref transcript
  • Tau and MAP protein, tubulin-binding repeat. This family includes the vertebrate proteins MAP2, MAP4 and Tau, as well as other animal homologs. MAP4 is present in many tissues but is usually absent from neurons; MAP2 and Tau are mainly neuronal. Members of this family have the ability to bind to and stabilise microtubules. As a result, they are involved in neuronal migration, supporting dendrite elongation, and regulating microtubules during mitotic metaphase. Note that Tau is involved in neurofibrillary tangle formation in Alzheimer's disease and some other dementias. This family features a C-terminal microtubule binding repeat that contains a conserved KXGS motif.
• pfam Tubulin-binding 32aa 1e-06 in ref transcript
• pfam Tubulin-binding 32aa 6e-06 in ref transcript
• Changed! pfam Tubulin-binding 31aa 6e-09 in modified transcript

MAP3K3

• refseq_MAP3K3.F2 refseq_MAP3K3.R2 133 226
• NCBIGene 36.3 4215
• Single exon skipping, size difference: 93
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_203351

• cd STKc_MEKK3 266aa 1e-158 in ref transcript
  • Serine/threonine kinases (STKs), MAP/ERK kinase kinase 3 (MEKK3) subfamily, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The MEKK3 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. MEKK3 is a mitogen-activated protein kinase (MAPK) kinase kinase (MAPKKK or MKKK or MAP3K), that phosphorylates and activates the MAPK kinase MEK5 (or MKK5), which in turn phosphorylates and activates extracellular signal-regulated kinase 5 (ERK5). The ERK5 cascade plays roles in promoting cell proliferation, differentiation, neuronal survival, and neuroprotection. MEKK3 plays an essential role in embryonic angiogenesis and early heart development. In addition, MEKK3 is involved in interleukin-1 receptor and Toll-like receptor 4 signaling. It is also a specific regulator of the proinflammatory cytokines IL-6 and GM-CSF in some immune cells. MEKK3 also regulates calcineurin, which plays a critical role in T cell activation, apoptosis, skeletal myocyte differentiation, and cardiac hypertrophy.
• cd PB1_Mekk2_3 79aa 1e-34 in ref transcript
  • The PB1 domain is present in the two mitogen-activated protein kinase kinases MEKK2 and MEKK3 which are two members of the signaling kinase cascade involved in angiogenesis and early cardiovascular development. The PB1 domain of MEKK2 (and/or MEKK3) interacts with the PB1 domain of another member of the kinase cascade Map2k5. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants. The MEKK2 and MEKK3 proteins contain a type II PB1 domain.
• smart S_TKc 250aa 3e-79 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• smart PB1 77aa 6e-12 in ref transcript
  • PB1 domain. Phox and Bem1p domain, present in many eukaryotic cytoplasmic signalling proteins. The domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pairs associate.
• COG SPS1 263aa 4e-30 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].

MAP3K4

• refseq_MAP3K4.F1 refseq_MAP3K4.R1 139 289
• NCBIGene 36.3 4216
• Single exon skipping, size difference: 150
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_005922

• cd STKc_MEKK4 260aa 1e-134 in ref transcript
  • Serine/threonine kinases (STKs), MAP/ERK kinase kinase 4 (MEKK4) subfamily, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The MEKK4 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. MEKK4 is a mitogen-activated protein kinase (MAPK) kinase kinase (MAPKKK or MKKK or MAP3K), that phosphorylates and activates MAPK kinases (MAPKKs or MKKs or MAP2Ks), which in turn phosphorylate and activate MAPKs during signaling cascades that are important in mediating cellular responses to extracellular signals. MEKK4 activates the c-Jun N-terminal kinase (JNK) and p38 MAPK signaling pathways by directly activating their respective MAPKKs, MKK4/MKK7 and MKK3/MKK6. JNK and p38 are collectively known as stress-activated MAPKs, as they are activated in response to a variety of environmental stresses and pro-inflammatory cytokines. MEKK4 also plays roles in the re-polarization of the actin cytoskeleton in response to osmotic stress, in the proper closure of the neural tube, in cardiovascular development, and in immune responses.
• smart S_TKc 248aa 7e-73 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• COG SPS1 267aa 3e-35 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].

MAP3K7

• refseq_MAP3K7.F1 refseq_MAP3K7.R1 207 323
• NCBIGene 36.3 6885
• Single exon skipping, size difference: 116
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_145331

• cd S_TKc 240aa 4e-61 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• smart TyrKc 242aa 3e-61 in ref transcript
  • Tyrosine kinase, catalytic domain. Phosphotransferases. Tyrosine-specific kinase subfamily.
• Changed! pfam Mnd1 83aa 8e-04 in ref transcript
  • Mnd1 family. This family of proteins includes MND1 from Saccharomyces cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.
• COG SPS1 318aa 1e-26 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].

MAP3K7

• refseq_MAP3K7.F3 refseq_MAP3K7.R3 152 233
• NCBIGene 36.3 6885
• Single exon skipping, size difference: 81
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_145331

• cd S_TKc 240aa 4e-61 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• smart TyrKc 242aa 3e-61 in ref transcript
  • Tyrosine kinase, catalytic domain. Phosphotransferases. Tyrosine-specific kinase subfamily.
• pfam Mnd1 83aa 8e-04 in ref transcript
  • Mnd1 family. This family of proteins includes MND1 from Saccharomyces cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.
• COG SPS1 318aa 1e-26 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].

MAP4K4

• refseq_MAP4K4.F1 refseq_MAP4K4.R1 146 377
• NCBIGene 36.3 9448
• Single exon skipping, size difference: 231
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_145686

• cd STKc_MAP4K4_6 282aa 1e-149 in ref transcript
  • Serine/threonine kinases (STKs), mitogen-activated protein kinase (MAPK) kinase kinase kinase 4 (MAPKKKK4 or MAP4K4) and MAPKKKK6 (or MAP4K6) subfamily, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The MAP4K4/MAP4K6 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. Members of this subfamily contain an N-terminal catalytic domain and a C-terminal citron homology (CNH) regulatory domain. MAP4Ks (or MAPKKKKs) are involved in MAPK signaling pathways that are important in mediating cellular responses to extracellular signals by activating a MAPK kinase kinase (MAPKKK or MAP3K or MKKK). Each MAPK cascade is activated either by a small GTP-binding protein or by an adaptor protein, which transmits the signal either directly to a MAP3K to start the triple kinase core cascade or indirectly through a mediator kinase, a MAP4K. MAP4K4 is also called Nck Interacting kinase (NIK). It facilitates the activation of the MAPKs, extracellular signal-regulated kinase (ERK) 1, ERK2, and c-Jun N-terminal kinase (JNK), by phosphorylating and activating MEKK1. MAP4K4 plays a role in tumor necrosis factor (TNF) alpha-induced insulin resistance. MAP4K4 silencing in skeletal muscle cells from type II diabetic patients restores insulin-mediated glucose uptake. MAP4K4, through JNK, also plays a broad role in cell motility, which impacts inflammation, homeostasis, as well as the invasion and spread of cancer. MAP4K4 is found to be highly expressed in most tumor cell lines relative to normal tissue. MAP4K6 (also called MINK for Misshapen/NIKs-related kinase) is activated after Ras induction and mediates activation of p38 MAPK. MAP4K6 plays a role in cell cycle arrest, cytoskeleton organization, cell adhesion, and cell motility.
• smart CNH 299aa 2e-87 in ref transcript
  • Domain found in NIK1-like kinases, mouse citron and yeast ROM1, ROM2. Unpublished observations.
• smart S_TKc 255aa 2e-61 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• COG SPS1 293aa 5e-27 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].
• COG ROM1 286aa 1e-06 in ref transcript
  • RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms].

MAP4K4

• refseq_MAP4K4.F3 refseq_MAP4K4.R3 172 265
• NCBIGene 36.3 9448
• Alternative 3-prime, size difference: 93
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_145686

• cd STKc_MAP4K4_6 282aa 1e-149 in ref transcript
  • Serine/threonine kinases (STKs), mitogen-activated protein kinase (MAPK) kinase kinase kinase 4 (MAPKKKK4 or MAP4K4) and MAPKKKK6 (or MAP4K6) subfamily, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The MAP4K4/MAP4K6 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. Members of this subfamily contain an N-terminal catalytic domain and a C-terminal citron homology (CNH) regulatory domain. MAP4Ks (or MAPKKKKs) are involved in MAPK signaling pathways that are important in mediating cellular responses to extracellular signals by activating a MAPK kinase kinase (MAPKKK or MAP3K or MKKK). Each MAPK cascade is activated either by a small GTP-binding protein or by an adaptor protein, which transmits the signal either directly to a MAP3K to start the triple kinase core cascade or indirectly through a mediator kinase, a MAP4K. MAP4K4 is also called Nck Interacting kinase (NIK). It facilitates the activation of the MAPKs, extracellular signal-regulated kinase (ERK) 1, ERK2, and c-Jun N-terminal kinase (JNK), by phosphorylating and activating MEKK1. MAP4K4 plays a role in tumor necrosis factor (TNF) alpha-induced insulin resistance. MAP4K4 silencing in skeletal muscle cells from type II diabetic patients restores insulin-mediated glucose uptake. MAP4K4, through JNK, also plays a broad role in cell motility, which impacts inflammation, homeostasis, as well as the invasion and spread of cancer. MAP4K4 is found to be highly expressed in most tumor cell lines relative to normal tissue. MAP4K6 (also called MINK for Misshapen/NIKs-related kinase) is activated after Ras induction and mediates activation of p38 MAPK. MAP4K6 plays a role in cell cycle arrest, cytoskeleton organization, cell adhesion, and cell motility.
• smart CNH 299aa 2e-87 in ref transcript
  • Domain found in NIK1-like kinases, mouse citron and yeast ROM1, ROM2. Unpublished observations.
• smart S_TKc 255aa 2e-61 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• COG SPS1 293aa 5e-27 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].
• COG ROM1 286aa 1e-06 in ref transcript
  • RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms].

MAP4K4

• refseq_MAP4K4.F5 refseq_MAP4K4.R5 136 160
• NCBIGene 36.3 9448
• Alternative 5-prime, size difference: 24
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_145686

• cd STKc_MAP4K4_6 282aa 1e-149 in ref transcript
  • Serine/threonine kinases (STKs), mitogen-activated protein kinase (MAPK) kinase kinase kinase 4 (MAPKKKK4 or MAP4K4) and MAPKKKK6 (or MAP4K6) subfamily, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The MAP4K4/MAP4K6 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. Members of this subfamily contain an N-terminal catalytic domain and a C-terminal citron homology (CNH) regulatory domain. MAP4Ks (or MAPKKKKs) are involved in MAPK signaling pathways that are important in mediating cellular responses to extracellular signals by activating a MAPK kinase kinase (MAPKKK or MAP3K or MKKK). Each MAPK cascade is activated either by a small GTP-binding protein or by an adaptor protein, which transmits the signal either directly to a MAP3K to start the triple kinase core cascade or indirectly through a mediator kinase, a MAP4K. MAP4K4 is also called Nck Interacting kinase (NIK). It facilitates the activation of the MAPKs, extracellular signal-regulated kinase (ERK) 1, ERK2, and c-Jun N-terminal kinase (JNK), by phosphorylating and activating MEKK1. MAP4K4 plays a role in tumor necrosis factor (TNF) alpha-induced insulin resistance. MAP4K4 silencing in skeletal muscle cells from type II diabetic patients restores insulin-mediated glucose uptake. MAP4K4, through JNK, also plays a broad role in cell motility, which impacts inflammation, homeostasis, as well as the invasion and spread of cancer. MAP4K4 is found to be highly expressed in most tumor cell lines relative to normal tissue. MAP4K6 (also called MINK for Misshapen/NIKs-related kinase) is activated after Ras induction and mediates activation of p38 MAPK. MAP4K6 plays a role in cell cycle arrest, cytoskeleton organization, cell adhesion, and cell motility.
• Changed! smart CNH 299aa 2e-87 in ref transcript
  • Domain found in NIK1-like kinases, mouse citron and yeast ROM1, ROM2. Unpublished observations.
• smart S_TKc 255aa 2e-61 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• COG SPS1 293aa 5e-27 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].
• Changed! COG ROM1 286aa 1e-06 in ref transcript
  • RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms].
• Changed! smart CNH 307aa 4e-86 in modified transcript
• Changed! COG ROM1 294aa 2e-06 in modified transcript

MAP4K5

• refseq_MAP4K5.F1 refseq_MAP4K5.R1 256 304
• NCBIGene 36.3 11183
• Alternative 5-prime, size difference: 48
• Exclusion in 5'UTR
• Reference transcript: NM_198794

• cd STKc_MAP4K5 267aa 1e-159 in ref transcript
  • Serine/threonine kinases (STKs), mitogen-activated protein kinase (MAPK) kinase kinase kinase 5 (MAPKKKK5 or MAP4K5) subfamily, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The MAP4K5 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. Members of this subfamily contain an N-terminal catalytic domain and a C-terminal citron homology (CNH) regulatory domain, similar to MAP4K4/6. MAP4Ks are involved in some MAPK signaling pathways that are important in mediating cellular responses to extracellular signals by activating a MAPK kinase kinase (MAPKKK or MAP3K or MKKK). Each MAPK cascade is activated either by a small GTP-binding protein or by an adaptor protein, which transmits the signal either directly to a MAP3K to start the triple kinase core cascade or indirectly through a mediator kinase, a MAP4K. MAP4K5, also called germinal center kinase-related enzyme (GCKR), has been shown to activate the MAPK c-Jun N-terminal kinase (JNK). MAP4K5 also facilitates Wnt signaling in B cells, and may therefore be implicated in the control of cell fate, proliferation, and polarity.
• smart CNH 316aa 2e-81 in ref transcript
  • Domain found in NIK1-like kinases, mouse citron and yeast ROM1, ROM2. Unpublished observations.
• smart S_TKc 248aa 3e-66 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• COG SPS1 349aa 3e-33 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].

MAPK10

• refseq_MAPK10.F1 refseq_MAPK10.R1 138 197
• NCBIGene 36.3 5602
• Single exon skipping, size difference: 59
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_138982

• Changed! cd S_TKc 297aa 1e-66 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• Changed! smart S_TKc 284aa 1e-67 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• Changed! PTZ PTZ00024 292aa 1e-34 in ref transcript
  • cyclin-dependent protein kinase; Provisional.
• Changed! cd S_TKc 62aa 1e-10 in modified transcript
• Changed! smart STYKc 61aa 3e-09 in modified transcript
  • Protein kinase; unclassified specificity. Phosphotransferases. The specificity of this class of kinases can not be predicted. Possible dual-specificity Ser/Thr/Tyr kinase.
• Changed! COG SPS1 59aa 0.003 in modified transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].

MAPK7

• refseq_MAPK7.F1 refseq_MAPK7.R1 97 500
• NCBIGene 36.3 5598
• Multiple exon skipping, size difference: 403
• Exclusion of the protein initiation site, Exclusion in the protein causing a frameshift
• Reference transcript: NM_139033

• Changed! cd S_TKc 294aa 2e-74 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• Changed! smart S_TKc 283aa 8e-72 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• Changed! PTZ PTZ00024 293aa 9e-45 in ref transcript
  • cyclin-dependent protein kinase; Provisional.
• Changed! cd S_TKc 205aa 2e-51 in modified transcript
• Changed! smart S_TKc 205aa 2e-53 in modified transcript
• Changed! PTZ PTZ00024 214aa 4e-34 in modified transcript

MAPK7

• refseq_MAPK7.F4 refseq_MAPK7.R4 157 245
• NCBIGene 36.3 5598
• Alternative 5-prime, size difference: 88
• Exclusion in 5'UTR
• Reference transcript: NM_002749

• cd S_TKc 294aa 2e-74 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• smart S_TKc 283aa 8e-72 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• PTZ PTZ00024 293aa 9e-45 in ref transcript
  • cyclin-dependent protein kinase; Provisional.

MAPK8IP3

• refseq_MAPK8IP3.F1 refseq_MAPK8IP3.R1 102 120
• NCBIGene 36.3 23162
• Single exon skipping, size difference: 18
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_015133

• pfam Jnk-SapK_ap_N 158aa 1e-69 in ref transcript
  • JNK_SAPK-associated protein-1. This is the N-terminal 200 residues of a set of proteins conserved from yeasts to humans. Most of the proteins in this entry have an RhoGEF pfam00621 domain at their C-terminal end.
• pfam Trypan_PARP 70aa 2e-04 in ref transcript
  • Procyclic acidic repetitive protein (PARP). This family consists of several Trypanosoma brucei procyclic acidic repetitive protein (PARP) like sequences. The procyclic acidic repetitive protein (parp) genes of Trypanosoma brucei encode a small family of abundant surface proteins whose expression is restricted to the procyclic form of the parasite. They are found at two unlinked loci, parpA and parpB; transcription of both loci is developmentally regulated.
• Changed! TIGR SMC_prok_B 127aa 3e-04 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• COG SbcC 155aa 1e-05 in ref transcript
  • ATPase involved in DNA repair [DNA replication, recombination, and repair].
• Changed! COG Smc 158aa 5e-04 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].
• Changed! TIGR SMC_prok_B 185aa 7e-05 in modified transcript
• Changed! COG Smc 176aa 5e-05 in modified transcript

MAPKAP1

• refseq_MAPKAP1.F1 refseq_MAPKAP1.R1 129 270
• NCBIGene 36.3 79109
• Single exon skipping, size difference: 141
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001006617

• Changed! pfam SIN1 464aa 1e-140 in ref transcript
  • Stress-activated map kinase interacting protein 1 (SIN1). This family consists of several stress-activated map kinase interacting protein 1 (MAPKAP1 OR SIN1) sequences. The fission yeast Sty1/Spc1 mitogen-activated protein (MAP) kinase is a member of the eukaryotic stress-activated MAP kinase (SAPK) family. Sin1 interacts with Sty1/Spc1. Cells lacking Sin1 display many, but not all, of the phenotypes of cells lacking the Sty1/Spc1 MAP kinase including sterility, multiple stress sensitivity and a cell-cycle delay. Sin1 is phosphorylated after stress but this is not Sty1/Spc1-dependent.
• Changed! pfam SIN1 417aa 1e-107 in modified transcript

MAPKAP1

• refseq_MAPKAP1.F3 refseq_MAPKAP1.R3 226 334
• NCBIGene 36.3 79109
• Single exon skipping, size difference: 108
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001006617

• Changed! pfam SIN1 464aa 1e-140 in ref transcript
  • Stress-activated map kinase interacting protein 1 (SIN1). This family consists of several stress-activated map kinase interacting protein 1 (MAPKAP1 OR SIN1) sequences. The fission yeast Sty1/Spc1 mitogen-activated protein (MAP) kinase is a member of the eukaryotic stress-activated MAP kinase (SAPK) family. Sin1 interacts with Sty1/Spc1. Cells lacking Sin1 display many, but not all, of the phenotypes of cells lacking the Sty1/Spc1 MAP kinase including sterility, multiple stress sensitivity and a cell-cycle delay. Sin1 is phosphorylated after stress but this is not Sty1/Spc1-dependent.
• Changed! pfam SIN1 428aa 1e-131 in modified transcript

MAPKAP1

• refseq_MAPKAP1.F5 refseq_MAPKAP1.R5 135 463
• NCBIGene 36.3 79109
• Single exon skipping, size difference: 328
• Exclusion of the protein initiation site
• Reference transcript: NM_001006617

• Changed! pfam SIN1 464aa 1e-140 in ref transcript
  • Stress-activated map kinase interacting protein 1 (SIN1). This family consists of several stress-activated map kinase interacting protein 1 (MAPKAP1 OR SIN1) sequences. The fission yeast Sty1/Spc1 mitogen-activated protein (MAP) kinase is a member of the eukaryotic stress-activated MAP kinase (SAPK) family. Sin1 interacts with Sty1/Spc1. Cells lacking Sin1 display many, but not all, of the phenotypes of cells lacking the Sty1/Spc1 MAP kinase including sterility, multiple stress sensitivity and a cell-cycle delay. Sin1 is phosphorylated after stress but this is not Sty1/Spc1-dependent.
• Changed! pfam SIN1 289aa 4e-87 in modified transcript

MAPT

• refseq_MAPT.F2 refseq_MAPT.R2 128 221
• NCBIGene 36.3 4137
• Single exon skipping, size difference: 93
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_016835

• Changed! pfam Tubulin-binding 31aa 8e-10 in ref transcript
  • Tau and MAP protein, tubulin-binding repeat. This family includes the vertebrate proteins MAP2, MAP4 and Tau, as well as other animal homologs. MAP4 is present in many tissues but is usually absent from neurons; MAP2 and Tau are mainly neuronal. Members of this family have the ability to bind to and stabilise microtubules. As a result, they are involved in neuronal migration, supporting dendrite elongation, and regulating microtubules during mitotic metaphase. Note that Tau is involved in neurofibrillary tangle formation in Alzheimer's disease and some other dementias. This family features a C-terminal microtubule binding repeat that contains a conserved KXGS motif.
• pfam Tubulin-binding 31aa 2e-08 in ref transcript
• pfam Tubulin-binding 32aa 2e-06 in ref transcript
• pfam Tubulin-binding 32aa 3e-06 in ref transcript
• pfam Hid1 123aa 3e-04 in ref transcript
  • High-temperature-induced dauer-formation protein. Hid1 (high-temperature-induced dauer-formation protein 1) represents proteins of approximately 800 residues long and is conserved from fungi to humans. It contains up to seven potential transmembrane domains separated by regions of low complexity. Functionally it might be involved in vesicle secretion or be an inter-cellular signalling protein or be a novel insulin receptor.

MAPT

• refseq_MAPT.F3 refseq_MAPT.R3 181 379
• NCBIGene 36.3 4137
• Single exon skipping, size difference: 198
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_016835

• pfam Tubulin-binding 31aa 8e-10 in ref transcript
  • Tau and MAP protein, tubulin-binding repeat. This family includes the vertebrate proteins MAP2, MAP4 and Tau, as well as other animal homologs. MAP4 is present in many tissues but is usually absent from neurons; MAP2 and Tau are mainly neuronal. Members of this family have the ability to bind to and stabilise microtubules. As a result, they are involved in neuronal migration, supporting dendrite elongation, and regulating microtubules during mitotic metaphase. Note that Tau is involved in neurofibrillary tangle formation in Alzheimer's disease and some other dementias. This family features a C-terminal microtubule binding repeat that contains a conserved KXGS motif.
• pfam Tubulin-binding 31aa 2e-08 in ref transcript
• pfam Tubulin-binding 32aa 2e-06 in ref transcript
• pfam Tubulin-binding 32aa 3e-06 in ref transcript
• pfam Hid1 123aa 3e-04 in ref transcript
  • High-temperature-induced dauer-formation protein. Hid1 (high-temperature-induced dauer-formation protein 1) represents proteins of approximately 800 residues long and is conserved from fungi to humans. It contains up to seven potential transmembrane domains separated by regions of low complexity. Functionally it might be involved in vesicle secretion or be an inter-cellular signalling protein or be a novel insulin receptor.

MAPT

• refseq_MAPT.F5 refseq_MAPT.R5 109 283
• NCBIGene 36.3 4137
• Multiple exon skipping, size difference: 174
• Exclusion in the protein (no frameshift), Exclusion in the protein (no frameshift)
• Reference transcript: NM_016835

• pfam Tubulin-binding 31aa 8e-10 in ref transcript
  • Tau and MAP protein, tubulin-binding repeat. This family includes the vertebrate proteins MAP2, MAP4 and Tau, as well as other animal homologs. MAP4 is present in many tissues but is usually absent from neurons; MAP2 and Tau are mainly neuronal. Members of this family have the ability to bind to and stabilise microtubules. As a result, they are involved in neuronal migration, supporting dendrite elongation, and regulating microtubules during mitotic metaphase. Note that Tau is involved in neurofibrillary tangle formation in Alzheimer's disease and some other dementias. This family features a C-terminal microtubule binding repeat that contains a conserved KXGS motif.
• pfam Tubulin-binding 31aa 2e-08 in ref transcript
• pfam Tubulin-binding 32aa 2e-06 in ref transcript
• pfam Tubulin-binding 32aa 3e-06 in ref transcript
• Changed! pfam Hid1 123aa 3e-04 in ref transcript
  • High-temperature-induced dauer-formation protein. Hid1 (high-temperature-induced dauer-formation protein 1) represents proteins of approximately 800 residues long and is conserved from fungi to humans. It contains up to seven potential transmembrane domains separated by regions of low complexity. Functionally it might be involved in vesicle secretion or be an inter-cellular signalling protein or be a novel insulin receptor.

MARCH2

• refseq_MARCH2.F1 refseq_MARCH2.R1 123 394
• NCBIGene 36.3 51257
• Single exon skipping, size difference: 271
• Exclusion in 5'UTR
• Reference transcript: NM_016496

• smart RINGv 48aa 1e-12 in ref transcript
  • The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins. Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Classical RING domain: C-x (2) -C-x (9-39)-C-x(1-3)-H-x(2-3)-C-x(2)-C-x(4-48) -C-x(2)-C.
• pfam Vpu 52aa 0.002 in ref transcript
  • Vpu protein. The Vpu protein contains an N-terminal transmembrane spanning region and a C-terminal cytoplasmic region. The HIV-1 Vpu protein stimulates virus production by enhancing the release of viral particles from infected cells. The VPU protein binds specifically to CD4.
• COG SSM4 58aa 3e-12 in ref transcript
  • Protein involved in mRNA turnover and stability [RNA processing and modification].

MARCH2

• refseq_MARCH2.F3 refseq_MARCH2.R3 159 369
• NCBIGene 36.3 51257
• Single exon skipping, size difference: 210
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001005415

• smart RINGv 48aa 1e-12 in ref transcript
  • The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins. Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Classical RING domain: C-x (2) -C-x (9-39)-C-x(1-3)-H-x(2-3)-C-x(2)-C-x(4-48) -C-x(2)-C.
• Changed! pfam Vpu 52aa 0.002 in ref transcript
  • Vpu protein. The Vpu protein contains an N-terminal transmembrane spanning region and a C-terminal cytoplasmic region. The HIV-1 Vpu protein stimulates virus production by enhancing the release of viral particles from infected cells. The VPU protein binds specifically to CD4.
• COG SSM4 58aa 3e-12 in ref transcript
  • Protein involved in mRNA turnover and stability [RNA processing and modification].

MARCH8

• refseq_MARCH8.F1 refseq_MARCH8.R1 124 217
• NCBIGene 36.3 220972
• Single exon skipping, size difference: 93
• Exclusion in 5'UTR
• Reference transcript: NM_001002265

• smart RINGv 49aa 1e-15 in ref transcript
  • The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins. Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Classical RING domain: C-x (2) -C-x (9-39)-C-x(1-3)-H-x(2-3)-C-x(2)-C-x(4-48) -C-x(2)-C.
• COG SSM4 60aa 8e-16 in ref transcript
  • Protein involved in mRNA turnover and stability [RNA processing and modification].

MARK2

• refseq_MARK2.F2 refseq_MARK2.R2 106 133
• NCBIGene 36.3 2011
• Single exon skipping, size difference: 27
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001039469

• cd S_TKc 253aa 4e-87 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• cd UBA 38aa 0.001 in ref transcript
  • Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
• smart S_TKc 241aa 8e-89 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• pfam KA1 43aa 7e-14 in ref transcript
  • Kinase associated domain 1.
• smart UBA 37aa 3e-05 in ref transcript
  • Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
• PTZ PTZ00263 250aa 3e-46 in ref transcript
  • protein kinase A catalytic subunit; Provisional.
• COG RER1 45aa 0.002 in ref transcript
  • Golgi protein involved in Golgi-to-ER retrieval [Intracellular trafficking and secretion].

MARK2

• refseq_MARK2.F4 refseq_MARK2.R4 112 274
• NCBIGene 36.3 2011
• Single exon skipping, size difference: 162
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001039469

• cd S_TKc 253aa 4e-87 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• cd UBA 38aa 0.001 in ref transcript
  • Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
• smart S_TKc 241aa 8e-89 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• pfam KA1 43aa 7e-14 in ref transcript
  • Kinase associated domain 1.
• smart UBA 37aa 3e-05 in ref transcript
  • Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
• PTZ PTZ00263 250aa 3e-46 in ref transcript
  • protein kinase A catalytic subunit; Provisional.
• COG RER1 45aa 0.002 in ref transcript
  • Golgi protein involved in Golgi-to-ER retrieval [Intracellular trafficking and secretion].

MATN2

• refseq_MATN2.F1 refseq_MATN2.R1 139 196
• NCBIGene 36.3 4147
• Alternative 3-prime, size difference: 57
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_002380

• cd vWA_Matrilin 223aa 7e-99 in ref transcript
  • VWA_Matrilin: In cartilaginous plate, extracellular matrix molecules mediate cell-matrix and matrix-matrix interactions thereby providing tissue integrity. Some members of the matrilin family are expressed specifically in developing cartilage rudiments. The matrilin family consists of at least four members. All the members of the matrilin family contain VWA domains, EGF-like domains and a heptad repeat coiled-coiled domain at the carboxy terminus which is responsible for the oligomerization of the matrilins. The VWA domains have been shown to be essential for matrilin network formation by interacting with matrix ligands.
• Changed! cd vWA_Matrilin 241aa 5e-92 in ref transcript
• cd vWA_Matrilin 44aa 5e-09 in ref transcript
• cd vWA_Matrilin 44aa 2e-06 in ref transcript
• cd vWA_Matrilin 44aa 2e-06 in ref transcript
• cd vWA_Matrilin 43aa 5e-06 in ref transcript
• cd vWA_Matrilin 52aa 5e-06 in ref transcript
• cd vWA_Matrilin 43aa 7e-06 in ref transcript
• cd vWA_Matrilin 50aa 5e-04 in ref transcript
• pfam VWA 176aa 4e-49 in ref transcript
  • von Willebrand factor type A domain.
• pfam VWA 176aa 2e-48 in ref transcript
• pfam Matrilin_ccoil 44aa 1e-11 in ref transcript
  • Trimeric coiled-coil oligomerisation domain of matrilin. This short domain is a coiled coil structure and has a single cysteine residue at the start which is likely to form a di-sulfide bridge with a corresponding cysteine in an upstream EGF (pfam00008) domain thereby spanning a VWA (pfam00092) domain. All three domains can be associated together as in the cartilage matrix protein matrilin, where this domain is likely to be responsible for oligomerisation.
• smart EGF_CA 39aa 0.008 in ref transcript
  • Calcium-binding EGF-like domain.
• Changed! cd vWA_Matrilin 222aa 6e-89 in modified transcript

MATN4

• refseq_MATN4.F2 refseq_MATN4.R2 256 379
• NCBIGene 36.3 8785
• Single exon skipping, size difference: 123
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_003833

• cd vWA_Matrilin 237aa 3e-88 in ref transcript
  • VWA_Matrilin: In cartilaginous plate, extracellular matrix molecules mediate cell-matrix and matrix-matrix interactions thereby providing tissue integrity. Some members of the matrilin family are expressed specifically in developing cartilage rudiments. The matrilin family consists of at least four members. All the members of the matrilin family contain VWA domains, EGF-like domains and a heptad repeat coiled-coiled domain at the carboxy terminus which is responsible for the oligomerization of the matrilins. The VWA domains have been shown to be essential for matrilin network formation by interacting with matrix ligands.
• Changed! cd vWA_Matrilin 223aa 6e-86 in ref transcript
• Changed! cd vWA_Matrilin 44aa 0.001 in ref transcript
• pfam VWA 176aa 2e-47 in ref transcript
  • von Willebrand factor type A domain.
• pfam VWA 172aa 2e-41 in ref transcript
• pfam Matrilin_ccoil 44aa 2e-08 in ref transcript
  • Trimeric coiled-coil oligomerisation domain of matrilin. This short domain is a coiled coil structure and has a single cysteine residue at the start which is likely to form a di-sulfide bridge with a corresponding cysteine in an upstream EGF (pfam00008) domain thereby spanning a VWA (pfam00092) domain. All three domains can be associated together as in the cartilage matrix protein matrilin, where this domain is likely to be responsible for oligomerisation.
• Changed! smart EGF_CA 39aa 5e-04 in ref transcript
  • Calcium-binding EGF-like domain.
• Changed! cd vWA_Matrilin 223aa 3e-82 in modified transcript
• Changed! smart EGF_CA 40aa 0.006 in modified transcript

MAX

• refseq_MAX.F2 refseq_MAX.R2 125 226
• NCBIGene 36.3 4149
• Single exon skipping, size difference: 101
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_002382

• cd HLH 57aa 6e-07 in ref transcript
  • Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins.
• pfam HLH 52aa 5e-12 in ref transcript
  • Helix-loop-helix DNA-binding domain.

MAX

• refseq_MAX.F3 refseq_MAX.R3 141 168
• NCBIGene 36.3 4149
• Single exon skipping, size difference: 27
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_002382

• Changed! cd HLH 57aa 6e-07 in ref transcript
  • Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins.
• pfam HLH 52aa 5e-12 in ref transcript
  • Helix-loop-helix DNA-binding domain.
• Changed! cd HLH 59aa 4e-07 in modified transcript

MBD1

• refseq_MBD1.F1 refseq_MBD1.R1 123 261
• NCBIGene 36.3 4152
• Single exon skipping, size difference: 138
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_015846

• cd MeCP2_MBD 62aa 1e-15 in ref transcript
  • MeCP2, MBD1, MBD2, MBD3, and MBD4 are members of a protein family that share the methyl-CpG-binding domain (MBD). The MBD, consists of about 70 residues and is defined as the minimal region required for binding to methylated DNA by a methyl-CpG-binding protein which binds specifically to methylated DNA. The MBD can recognize a single symmetrically methylated CpG either as naked DNA or within chromatin. MeCP2, MBD1 and MBD2 (and likely MBD3) form complexes with histone deacetylase and are involved in histone deacetylase-dependent repression of transcription. MBD4 is an endonuclease that forms a complex with the DNA mismatch-repair protein MLH1.
• smart MBD 74aa 7e-20 in ref transcript
  • Methyl-CpG binding domain. Methyl-CpG binding domain, also known as the TAM (TTF-IIP5, ARBP, MeCP1) domain.
• pfam zf-CXXC 47aa 1e-11 in ref transcript
  • CXXC zinc finger domain. This domain contains eight conserved cysteine residues that bind to two zinc ions. The CXXC domain is found in a variety of chromatin-associated proteins. This domain binds to nonmethyl-CpG dinucleotides. The domain is characterised by two CGXCXXC repeats. The RecQ helicase has a single repeat that also binds to zinc, but this has not been included in this family. The DNA binding interface has been identified by NMR.
• pfam zf-CXXC 48aa 8e-08 in ref transcript
• pfam zf-CXXC 46aa 1e-06 in ref transcript

MBD1

• refseq_MBD1.F4 refseq_MBD1.R4 135 204
• NCBIGene 36.3 4152
• Single exon skipping, size difference: 69
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_015846

• cd MeCP2_MBD 62aa 1e-15 in ref transcript
  • MeCP2, MBD1, MBD2, MBD3, and MBD4 are members of a protein family that share the methyl-CpG-binding domain (MBD). The MBD, consists of about 70 residues and is defined as the minimal region required for binding to methylated DNA by a methyl-CpG-binding protein which binds specifically to methylated DNA. The MBD can recognize a single symmetrically methylated CpG either as naked DNA or within chromatin. MeCP2, MBD1 and MBD2 (and likely MBD3) form complexes with histone deacetylase and are involved in histone deacetylase-dependent repression of transcription. MBD4 is an endonuclease that forms a complex with the DNA mismatch-repair protein MLH1.
• smart MBD 74aa 7e-20 in ref transcript
  • Methyl-CpG binding domain. Methyl-CpG binding domain, also known as the TAM (TTF-IIP5, ARBP, MeCP1) domain.
• pfam zf-CXXC 47aa 1e-11 in ref transcript
  • CXXC zinc finger domain. This domain contains eight conserved cysteine residues that bind to two zinc ions. The CXXC domain is found in a variety of chromatin-associated proteins. This domain binds to nonmethyl-CpG dinucleotides. The domain is characterised by two CGXCXXC repeats. The RecQ helicase has a single repeat that also binds to zinc, but this has not been included in this family. The DNA binding interface has been identified by NMR.
• pfam zf-CXXC 48aa 8e-08 in ref transcript
• pfam zf-CXXC 46aa 1e-06 in ref transcript

MBD1

• refseq_MBD1.F5 refseq_MBD1.R5 163 235
• NCBIGene 36.3 4152
• Single exon skipping, size difference: 72
• Exclusion of the stop codon
• Reference transcript: NM_015846

• cd MeCP2_MBD 62aa 1e-15 in ref transcript
  • MeCP2, MBD1, MBD2, MBD3, and MBD4 are members of a protein family that share the methyl-CpG-binding domain (MBD). The MBD, consists of about 70 residues and is defined as the minimal region required for binding to methylated DNA by a methyl-CpG-binding protein which binds specifically to methylated DNA. The MBD can recognize a single symmetrically methylated CpG either as naked DNA or within chromatin. MeCP2, MBD1 and MBD2 (and likely MBD3) form complexes with histone deacetylase and are involved in histone deacetylase-dependent repression of transcription. MBD4 is an endonuclease that forms a complex with the DNA mismatch-repair protein MLH1.
• smart MBD 74aa 7e-20 in ref transcript
  • Methyl-CpG binding domain. Methyl-CpG binding domain, also known as the TAM (TTF-IIP5, ARBP, MeCP1) domain.
• pfam zf-CXXC 47aa 1e-11 in ref transcript
  • CXXC zinc finger domain. This domain contains eight conserved cysteine residues that bind to two zinc ions. The CXXC domain is found in a variety of chromatin-associated proteins. This domain binds to nonmethyl-CpG dinucleotides. The domain is characterised by two CGXCXXC repeats. The RecQ helicase has a single repeat that also binds to zinc, but this has not been included in this family. The DNA binding interface has been identified by NMR.
• pfam zf-CXXC 48aa 8e-08 in ref transcript
• pfam zf-CXXC 46aa 1e-06 in ref transcript

MBD1

• refseq_MBD1.F7 refseq_MBD1.R7 156 303
• NCBIGene 36.3 4152
• Single exon skipping, size difference: 147
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_015846

• cd MeCP2_MBD 62aa 1e-15 in ref transcript
  • MeCP2, MBD1, MBD2, MBD3, and MBD4 are members of a protein family that share the methyl-CpG-binding domain (MBD). The MBD, consists of about 70 residues and is defined as the minimal region required for binding to methylated DNA by a methyl-CpG-binding protein which binds specifically to methylated DNA. The MBD can recognize a single symmetrically methylated CpG either as naked DNA or within chromatin. MeCP2, MBD1 and MBD2 (and likely MBD3) form complexes with histone deacetylase and are involved in histone deacetylase-dependent repression of transcription. MBD4 is an endonuclease that forms a complex with the DNA mismatch-repair protein MLH1.
• smart MBD 74aa 7e-20 in ref transcript
  • Methyl-CpG binding domain. Methyl-CpG binding domain, also known as the TAM (TTF-IIP5, ARBP, MeCP1) domain.
• pfam zf-CXXC 47aa 1e-11 in ref transcript
  • CXXC zinc finger domain. This domain contains eight conserved cysteine residues that bind to two zinc ions. The CXXC domain is found in a variety of chromatin-associated proteins. This domain binds to nonmethyl-CpG dinucleotides. The domain is characterised by two CGXCXXC repeats. The RecQ helicase has a single repeat that also binds to zinc, but this has not been included in this family. The DNA binding interface has been identified by NMR.
• Changed! pfam zf-CXXC 48aa 8e-08 in ref transcript
• Changed! pfam zf-CXXC 46aa 1e-06 in ref transcript
• Changed! pfam zf-CXXC 46aa 9e-08 in modified transcript

MBD1

• refseq_MBD1.F9 refseq_MBD1.R9 144 312
• NCBIGene 36.3 4152
• Single exon skipping, size difference: 168
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_015846

• cd MeCP2_MBD 62aa 1e-15 in ref transcript
  • MeCP2, MBD1, MBD2, MBD3, and MBD4 are members of a protein family that share the methyl-CpG-binding domain (MBD). The MBD, consists of about 70 residues and is defined as the minimal region required for binding to methylated DNA by a methyl-CpG-binding protein which binds specifically to methylated DNA. The MBD can recognize a single symmetrically methylated CpG either as naked DNA or within chromatin. MeCP2, MBD1 and MBD2 (and likely MBD3) form complexes with histone deacetylase and are involved in histone deacetylase-dependent repression of transcription. MBD4 is an endonuclease that forms a complex with the DNA mismatch-repair protein MLH1.
• smart MBD 74aa 7e-20 in ref transcript
  • Methyl-CpG binding domain. Methyl-CpG binding domain, also known as the TAM (TTF-IIP5, ARBP, MeCP1) domain.
• Changed! pfam zf-CXXC 47aa 1e-11 in ref transcript
  • CXXC zinc finger domain. This domain contains eight conserved cysteine residues that bind to two zinc ions. The CXXC domain is found in a variety of chromatin-associated proteins. This domain binds to nonmethyl-CpG dinucleotides. The domain is characterised by two CGXCXXC repeats. The RecQ helicase has a single repeat that also binds to zinc, but this has not been included in this family. The DNA binding interface has been identified by NMR.
• pfam zf-CXXC 48aa 8e-08 in ref transcript
• pfam zf-CXXC 46aa 1e-06 in ref transcript

MBNL1

• refseq_MBNL1.F2 refseq_MBNL1.R2 153 189
• NCBIGene 36.3 4154
• Single exon skipping, size difference: 36
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_207293

• smart ZnF_C3H1 25aa 0.004 in ref transcript
  • zinc finger.

MBNL1

• refseq_MBNL1.F3 refseq_MBNL1.R3 298 352
• NCBIGene 36.3 4154
• Single exon skipping, size difference: 54
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_207293

• smart ZnF_C3H1 25aa 0.004 in ref transcript
  • zinc finger.

MBNL1

• refseq_MBNL1.F5 refseq_MBNL1.R5 108 312
• NCBIGene 36.3 4154
• Single exon skipping, size difference: 204
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_207293

• Changed! smart ZnF_C3H1 25aa 0.004 in ref transcript
  • zinc finger.
• Changed! smart ZnF_C3H1 25aa 0.008 in modified transcript

MBNL1

• refseq_MBNL1.F7 refseq_MBNL1.R7 159 254
• NCBIGene 36.3 4154
• Single exon skipping, size difference: 95
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_021038

• smart ZnF_C3H1 25aa 0.005 in ref transcript
  • zinc finger.

MBNL1

• refseq_MBNL1.F8 refseq_MBNL1.R8 115 179
• NCBIGene 36.3 4154
• Single exon skipping, size difference: 64
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_207293

• smart ZnF_C3H1 25aa 0.004 in ref transcript
  • zinc finger.

MBNL2

• refseq_MBNL2.F1 refseq_MBNL2.R1 205 336
• NCBIGene 36.3 10150
• Multiple exon skipping, size difference: 131
• Exclusion in the protein (no frameshift), Exclusion in the protein causing a frameshift
• Reference transcript: NM_144778

MBNL3

• refseq_MBNL3.F2 refseq_MBNL3.R2 156 230
• NCBIGene 36.3 55796
• Single exon skipping, size difference: 74
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_018388

• smart ZnF_C3H1 27aa 0.005 in ref transcript
  • zinc finger.

MBNL3

• refseq_MBNL3.F4 refseq_MBNL3.R4 269 374
• NCBIGene 36.3 55796
• Alternative 3-prime, size difference: 105
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_018388

• smart ZnF_C3H1 27aa 0.005 in ref transcript
  • zinc finger.

MBP

• refseq_MBP.F2 refseq_MBP.R2 134 212
• NCBIGene 36.3 4155
• Single exon skipping, size difference: 78
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_001025101

• Changed! pfam Myelin_MBP 154aa 1e-59 in ref transcript
  • Myelin basic protein.
• Changed! pfam Myelin_MBP 180aa 7e-56 in modified transcript

MCHR2

• refseq_MCHR2.F1 refseq_MCHR2.R1 219 458
• NCBIGene 36.3 84539
• Alternative 5-prime, size difference: 239
• Exclusion in 5'UTR
• Reference transcript: NM_001040179

• pfam 7tm_1 250aa 7e-24 in ref transcript
  • 7 transmembrane receptor (rhodopsin family). This family contains, amongst other G-protein-coupled receptors (GCPRs), members of the opsin family, which have been considered to be typical members of the rhodopsin superfamily. They share several motifs, mainly the seven transmembrane helices, GCPRs of the rhodopsin superfamily. All opsins bind a chromophore, such as 11-cis-retinal. The function of most opsins other than the photoisomerases is split into two steps: light absorption and G-protein activation. Photoisomerases, on the other hand, are not coupled to G-proteins - they are thought to generate and supply the chromophore that is used by visual opsins.

MCM8

• refseq_MCM8.F2 refseq_MCM8.R2 269 323
• NCBIGene 36.3 84515
• Alternative 5-prime, size difference: 54
• Inclusion in 5'UTR
• Reference transcript: NM_032485

• cd AAA 159aa 1e-04 in ref transcript
  • The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.
• smart MCM 543aa 1e-121 in ref transcript
  • minichromosome maintenance proteins.
• COG MCM2 699aa 1e-120 in ref transcript
  • Predicted ATPase involved in replication control, Cdc46/Mcm family [DNA replication, recombination, and repair].

MCM8

• refseq_MCM8.F3 refseq_MCM8.R3 105 153
• NCBIGene 36.3 84515
• Alternative 3-prime, size difference: 48
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_032485

• cd AAA 159aa 1e-04 in ref transcript
  • The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.
• Changed! smart MCM 543aa 1e-121 in ref transcript
  • minichromosome maintenance proteins.
• Changed! COG MCM2 699aa 1e-120 in ref transcript
  • Predicted ATPase involved in replication control, Cdc46/Mcm family [DNA replication, recombination, and repair].
• Changed! smart MCM 527aa 1e-116 in modified transcript
• Changed! COG MCM2 683aa 1e-116 in modified transcript

MECR

• refseq_MECR.F1 refseq_MECR.R1 233 360
• NCBIGene 36.3 51102
• Alternative 3-prime, size difference: 127
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_016011

• Changed! cd CBS_like 75aa 2e-05 in ref transcript
  • CBS_like: This subgroup includes Cystathionine beta-synthase (CBS) and Cysteine synthase. CBS is a unique heme-containing enzyme that catalyzes a pyridoxal 5'-phosphate (PLP)-dependent condensation of serine and homocysteine to give cystathionine. Deficiency of CBS leads to homocystinuria, an inherited disease of sulfur metabolism characterized by increased levels of the toxic metabolite homocysteine. Cysteine synthase on the other hand catalyzes the last step of cysteine biosynthesis. This subgroup also includes an O-Phosphoserine sulfhydrylase found in hyperthermophilic archaea which produces L-cysteine from sulfide and the more thermostable O-phospho-L-serine.
• Changed! smart PKS_ER 285aa 3e-26 in ref transcript
  • Enoylreductase. Enoylreductase in Polyketide synthases.
• Changed! COG Qor 330aa 6e-50 in ref transcript
  • NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only].

MED8

• refseq_MED8.F1 refseq_MED8.R1 106 167
• NCBIGene 36.2 112950
• Alternative 3-prime, size difference: 61
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_001001651

• Changed! pfam Arc32 178aa 3e-55 in ref transcript
  • Mediator of RNA polymerase II transcription. Arc32, or Med8, is one of the subunits of the Mediator complex of RNA polymerase II. The region conserved contains two alpha helices putatively necessary for binding to other subunits within the core of the Mediator complex.

MED8

• refseq_MED8.F3 refseq_MED8.R3 102 120
• NCBIGene 36.2 112950
• Alternative 3-prime, size difference: 18
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001001651

• pfam Arc32 178aa 3e-55 in ref transcript
  • Mediator of RNA polymerase II transcription. Arc32, or Med8, is one of the subunits of the Mediator complex of RNA polymerase II. The region conserved contains two alpha helices putatively necessary for binding to other subunits within the core of the Mediator complex.

MEIS2

• refseq_MEIS2.F2 refseq_MEIS2.R2 101 122
• NCBIGene 36.3 4212
• Alternative 3-prime, size difference: 21
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_170675

• cd homeodomain 54aa 2e-10 in ref transcript
  • Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
• smart HOX 54aa 2e-11 in ref transcript
  • Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes.

MEIS2

• refseq_MEIS2.F4 refseq_MEIS2.R4 299 395
• NCBIGene 36.3 4212
• Single exon skipping, size difference: 96
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_170675

• cd homeodomain 54aa 2e-10 in ref transcript
  • Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
• smart HOX 54aa 2e-11 in ref transcript
  • Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes.

MEIS2

• refseq_MEIS2.F5 refseq_MEIS2.R5 130 153
• NCBIGene 36.3 4212
• Alternative 3-prime, size difference: 23
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_170675

• Changed! cd homeodomain 54aa 2e-10 in ref transcript
  • Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
• Changed! smart HOX 54aa 2e-11 in ref transcript
  • Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes.

MEIS2

• refseq_MEIS2.F7 refseq_MEIS2.R7 174 251
• NCBIGene 36.2 4212
• Single exon skipping, size difference: 77
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_170675

• Changed! cd homeodomain 54aa 2e-10 in ref transcript
  • Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
• Changed! smart HOX 54aa 2e-11 in ref transcript
  • Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes.

MEIS3

• refseq_MEIS3.F2 refseq_MEIS3.R2 169 307
• NCBIGene 36.3 56917
• Alternative 3-prime, size difference: 138
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_020160

• Changed! cd homeodomain 37aa 2e-08 in ref transcript
  • Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
• Changed! smart HOX 37aa 9e-09 in ref transcript
  • Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes.
• Changed! cd homeodomain 56aa 1e-09 in modified transcript
• Changed! smart HOX 56aa 8e-11 in modified transcript

MEIS3

• refseq_MEIS3.F4 refseq_MEIS3.R4 141 192
• NCBIGene 36.3 56917
• Alternative 3-prime, size difference: 51
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_020160

• cd homeodomain 37aa 2e-08 in ref transcript
  • Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
• smart HOX 37aa 9e-09 in ref transcript
  • Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes.

MEN1

• refseq_MEN1.F1 refseq_MEN1.R1 109 355
• NCBIGene 36.3 4221
• Alternative 5-prime, size difference: 246
• Exclusion in 5'UTR
• Reference transcript: NM_130802

• pfam Menin 615aa 0.0 in ref transcript
  • Menin. MEN1, the gene responsible for multiple endocrine neoplasia type 1, is a tumour suppressor gene that encodes a protein called Menin which may be an atypical GTPase stimulated by nm23.

MEOX1

• refseq_MEOX1.F1 refseq_MEOX1.R1 227 400
• NCBIGene 36.3 4222
• Single exon skipping, size difference: 173
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_004527

• Changed! cd homeodomain 59aa 5e-18 in ref transcript
  • Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
• Changed! pfam Homeobox 57aa 8e-24 in ref transcript
  • Homeobox domain.
• Changed! COG COG5576 71aa 1e-08 in ref transcript
  • Homeodomain-containing transcription factor [Transcription].

METT11D1

• refseq_METT11D1.F2 refseq_METT11D1.R2 108 140
• NCBIGene 36.2 64745
• Alternative 3-prime, size difference: 32
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_001029991

• Changed! pfam Rsm22 267aa 5e-48 in ref transcript
  • Mitochondrial small ribosomal subunit Rsm22. Rsm22 has been identified as a mitochondrial small ribosomal subunit and is a methyltransferase. In Schizosaccharomyces pombe, Rsm22 is tandemly fused to Cox11 (a factor required for copper insertion into cytochrome oxidase) and the two proteins are proteolytically cleaved after import into the mitochondria.
• Changed! COG COG5459 263aa 1e-26 in ref transcript
  • Predicted rRNA methylase [Translation, ribosomal structure and biogenesis].

METTL1

• refseq_METTL1.F1 refseq_METTL1.R1 163 348
• NCBIGene 36.3 4234
• Single exon skipping, size difference: 185
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_005371

• Changed! pfam Methyltransf_4 200aa 2e-62 in ref transcript
  • Putative methyltransferase. This is a family of putative methyltransferases. The aligned region contains the GXGXG S-AdoMet binding site suggesting a putative methyltransferase activity.
• Changed! COG COG0220 243aa 3e-39 in ref transcript
  • Predicted S-adenosylmethionine-dependent methyltransferase [General function prediction only].
• Changed! COG COG0220 78aa 0.002 in modified transcript

MGA

• refseq_MGA.F1 refseq_MGA.R1 100 247
• NCBIGene 36.2 23269
• Alternative 3-prime, size difference: 147
• Exclusion in the protein (no frameshift)
• Reference transcript: XM_932720

• cd TBOX 191aa 9e-87 in ref transcript
  • T-box DNA binding domain of the T-box family of transcriptional regulators. The T-box family is an ancient group that appears to play a critical role in development in all animal species. These genes were uncovered on the basis of similarity to the DNA binding domain of murine Brachyury (T) gene product, the defining feature of the family. Common features shared by T-box family members are DNA-binding and transcriptional regulatory activity, a role in development and conserved expression patterns, most of the known genes in all species being expressed in mesoderm or mesoderm precursors.
• pfam T-box 186aa 2e-80 in ref transcript
  • T-box. The T-box encodes a 180 amino acid domain that binds to DNA. Genes encoding T-box proteins are found in a wide range of animals, but not in other kingdoms such as plants. Family members are all thought to bind to the DNA consensus sequence TCACACCT. they are found exclusively in the nucleus, and perform DNA-binding and transcriptional activation/repression roles. They are generally required for development of the specific tissues they are expressed in, and mutations in T-box genes are implicated in human conditions such as DiGeorge syndrome and X-linked cleft palate, which feature malformations.

C16orf13

• refseq_MGC13114.F1 refseq_MGC13114.R1 237 400
• NCBIGene 36.3 84326
• Single exon skipping, size difference: 163
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_001040160

• Changed! pfam DUF938 137aa 6e-48 in ref transcript
  • Protein of unknown function (DUF938). This family consists of several hypothetical proteins from both prokaryotes and eukaryotes. The function of this family is unknown.
• Changed! pfam DUF938 62aa 8e-21 in modified transcript
• Changed! pfam DUF938 40aa 2e-12 in modified transcript

C17orf91

• refseq_MGC14376.F1 refseq_MGC14376.R1 267 350
• NCBIGene 36.3 84981
• Single exon skipping, size difference: 83
• Exclusion in 5'UTR
• Reference transcript: NM_032895

MGC15875

• refseq_MGC15875.F2 refseq_MGC15875.R2 130 218
• NCBIGene 36.2 85007
• Alternative 3-prime, size difference: 88
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_153373

• Changed! cd OAT_like 404aa 1e-105 in ref transcript
  • Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase, alanine-glyoxylate aminotransferase, dialkylglycine decarboxylase, 4-aminobutyrate aminotransferase, beta-alanine-pyruvate aminotransferase, adenosylmethionine-8-amino-7-oxononanoate aminotransferase, and glutamate-1-semialdehyde 2,1-aminomutase. All the enzymes belonging to this family act on basic amino acids and their derivatives are involved in transamination or decarboxylation.
• Changed! pfam Aminotran_3 340aa 8e-65 in ref transcript
  • Aminotransferase class-III.
• Changed! PRK PRK06148 429aa 1e-153 in ref transcript
  • hypothetical protein; Provisional.
• Changed! cd OAT_like 205aa 1e-46 in modified transcript
• Changed! pfam Aminotran_3 201aa 2e-30 in modified transcript
• Changed! PRK PRK06148 227aa 2e-80 in modified transcript

MGC15875

• refseq_MGC15875.F3 refseq_MGC15875.R3 143 378
• NCBIGene 36.2 85007
• Multiple exon skipping, size difference: 235
• Exclusion in the protein causing a frameshift, Exclusion in the protein (no frameshift)
• Reference transcript: NM_153373

• Changed! cd OAT_like 404aa 1e-105 in ref transcript
  • Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase, alanine-glyoxylate aminotransferase, dialkylglycine decarboxylase, 4-aminobutyrate aminotransferase, beta-alanine-pyruvate aminotransferase, adenosylmethionine-8-amino-7-oxononanoate aminotransferase, and glutamate-1-semialdehyde 2,1-aminomutase. All the enzymes belonging to this family act on basic amino acids and their derivatives are involved in transamination or decarboxylation.
• Changed! pfam Aminotran_3 340aa 8e-65 in ref transcript
  • Aminotransferase class-III.
• Changed! PRK PRK06148 429aa 1e-153 in ref transcript
  • hypothetical protein; Provisional.
• Changed! cd OAT_like 31aa 5e-06 in modified transcript
• Changed! TIGR argD 28aa 6e-05 in modified transcript
  • Members of this family may also act on ornithine, like ornithine aminotransferase (EC 2.6.1.13) and on succinyldiaminopimelate, like N-succinyldiaminopmelate-aminotransferase (EC 2.6.1.17, DapC, an enzyme of lysine biosynthesis).
• Changed! PRK PRK06148 55aa 4e-09 in modified transcript

MGC15875

• refseq_MGC15875.F5 refseq_MGC15875.R5 106 197
• NCBIGene 36.2 85007
• Exon skipping and alternative 3-prime or 5-prime, size difference: 91
• Inclusion in the protein causing a frameshift, Exclusion in the protein (no frameshift)
• Reference transcript: NM_153373

• Changed! cd OAT_like 404aa 1e-105 in ref transcript
  • Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase, alanine-glyoxylate aminotransferase, dialkylglycine decarboxylase, 4-aminobutyrate aminotransferase, beta-alanine-pyruvate aminotransferase, adenosylmethionine-8-amino-7-oxononanoate aminotransferase, and glutamate-1-semialdehyde 2,1-aminomutase. All the enzymes belonging to this family act on basic amino acids and their derivatives are involved in transamination or decarboxylation.
• Changed! pfam Aminotran_3 340aa 8e-65 in ref transcript
  • Aminotransferase class-III.
• Changed! PRK PRK06148 429aa 1e-153 in ref transcript
  • hypothetical protein; Provisional.
• Changed! cd OAT_like 126aa 7e-35 in modified transcript
• Changed! pfam Aminotran_3 128aa 9e-22 in modified transcript
• Changed! PRK PRK06148 163aa 7e-60 in modified transcript

MGC19604

• refseq_MGC19604.F1 refseq_MGC19604.R1 181 218
• NCBIGene 36.2 112812
• Alternative 3-prime, size difference: 37
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_001031734

• Changed! cd fer2 90aa 7e-08 in ref transcript
  • 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis and ferredoxins, which participate in redox chains (from bacteria to mammals). Fold is ismilar to thioredoxin.
• Changed! TIGR fdx_isc 86aa 2e-16 in ref transcript
  • This family consists of proteobacterial ferredoxins associated with and essential to the ISC system of 2Fe-2S cluster assembly. This family is closely related to (but excludes) eukaryotic (mitochondrial) adrenodoxins, which are ferredoxins involved in electron transfer to P450 cytochromes.
• Changed! COG Fdx 102aa 2e-15 in ref transcript
  • Ferredoxin [Energy production and conversion].
• Changed! cd fer2 68aa 4e-05 in modified transcript
• Changed! TIGR fdx_isc 46aa 1e-07 in modified transcript
• Changed! COG Fdx 71aa 7e-07 in modified transcript

PRELID2

• refseq_MGC21644.F1 refseq_MGC21644.R1 140 343
• NCBIGene 36.3 153768
• Single exon skipping, size difference: 203
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_182960

• Changed! pfam PRELI 170aa 4e-39 in ref transcript
  • PRELI-like family. This family includes a conserved region found in the PRELI protein and yeast YLR168C gene MSF1 product. The function of this protein is unknown, though it is thought to be involved in intra-mitochondrial protein sorting. This region is also found in a number of other eukaryotic proteins.

PRELID2

• refseq_MGC21644.F2 refseq_MGC21644.R2 100 136
• NCBIGene 36.3 153768
• Single exon skipping, size difference: 36
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_182960

• Changed! pfam PRELI 170aa 4e-39 in ref transcript
  • PRELI-like family. This family includes a conserved region found in the PRELI protein and yeast YLR168C gene MSF1 product. The function of this protein is unknown, though it is thought to be involved in intra-mitochondrial protein sorting. This region is also found in a number of other eukaryotic proteins.
• Changed! pfam PRELI 158aa 1e-40 in modified transcript

MGC3207

• refseq_MGC3207.F1 refseq_MGC3207.R1 247 388
• NCBIGene 36.3 84245
• Exon skipping and alternative 3-prime or 5-prime, size difference: 141
• Inclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift, Exclusion in the protein (no frameshift)
• Reference transcript: NM_001031727

• Changed! TIGR salvage_mtnA 343aa 1e-122 in ref transcript
  • The delineation of this family was based in part on a discussion and neighbor-joining phylogenetic study, by Kyrpides and Woese, of archaeal and other proteins homologous to the alpha, beta, and delta subunits of eukaryotic initiation factor 2B (eIF-2B), a five-subunit molecule that catalyzes GTP recycling for eIF-2. This clade is now recognized to include the methionine salvage pathway enzyme MtnA.
• Changed! PRK mtnA 351aa 2e-84 in ref transcript
  • methylthioribose-1-phosphate isomerase; Reviewed.
• Changed! TIGR salvage_mtnA 146aa 1e-67 in modified transcript
• Changed! TIGR salvage_mtnA 93aa 5e-27 in modified transcript
• Changed! PRK mtnA 154aa 8e-58 in modified transcript
• Changed! COG COG0182 96aa 9e-13 in modified transcript
  • Predicted translation initiation factor 2B subunit, eIF-2B alpha/beta/delta family [Translation, ribosomal structure and biogenesis].

FAM133B

• refseq_MGC40405.F1 refseq_MGC40405.R1 160 259
• NCBIGene 36.3 257415
• Single exon skipping, size difference: 99
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_152789

MID1

• refseq_MID1.F2 refseq_MID1.R2 213 313
• NCBIGene 36.2 4281
• Alternative 5-prime and 3-prime, size difference: 100
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_000381

• cd FN3 100aa 9e-07 in ref transcript
  • Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.
• cd RING 55aa 2e-04 in ref transcript
  • RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H).
• cd BBOX 39aa 4e-04 in ref transcript
  • B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.
• Changed! smart SPRY 119aa 2e-25 in ref transcript
  • Domain in SPla and the RYanodine Receptor. Domain of unknown function. Distant homologues are domains in butyrophilin/marenostrin/pyrin homologues.
• smart BBC 126aa 1e-13 in ref transcript
  • B-Box C-terminal domain. Coiled coil region C-terminal to (some) B-Box domains.
• smart FN3 90aa 4e-08 in ref transcript
  • Fibronectin type 3 domain. One of three types of internal repeat within the plasma protein, fibronectin. The tenth fibronectin type III repeat contains a RGD cell recognition sequence in a flexible loop between 2 strands. Type III modules are present in both extracellular and intracellular proteins.
• smart BBOX 42aa 3e-06 in ref transcript
  • B-Box-type zinc finger.
• smart RING 50aa 3e-05 in ref transcript
  • Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s).
• smart PRY 38aa 0.002 in ref transcript
  • associated with SPRY domains.

MID2

• refseq_MID2.F1 refseq_MID2.R1 205 295
• NCBIGene 36.3 11043
• Alternative 5-prime, size difference: 90
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_012216

• cd RING 55aa 2e-04 in ref transcript
  • RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H).
• cd BBOX 38aa 5e-04 in ref transcript
  • B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.
• Changed! cd FN3 47aa 0.001 in ref transcript
  • Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.
• smart BBC 126aa 8e-29 in ref transcript
  • B-Box C-terminal domain. Coiled coil region C-terminal to (some) B-Box domains.
• smart SPRY 109aa 4e-24 in ref transcript
  • Domain in SPla and the RYanodine Receptor. Domain of unknown function. Distant homologues are domains in butyrophilin/marenostrin/pyrin homologues.
• pfam zf-B_box 42aa 2e-05 in ref transcript
  • B-box zinc finger.
• smart RING 50aa 2e-05 in ref transcript
  • Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s).
• Changed! smart FN3 120aa 1e-04 in ref transcript
  • Fibronectin type 3 domain. One of three types of internal repeat within the plasma protein, fibronectin. The tenth fibronectin type III repeat contains a RGD cell recognition sequence in a flexible loop between 2 strands. Type III modules are present in both extracellular and intracellular proteins.
• PRK PRK00409 124aa 1e-04 in ref transcript
  • recombination and DNA strand exchange inhibitor protein; Reviewed.
• Changed! cd FN3 100aa 1e-06 in modified transcript
• Changed! smart FN3 90aa 4e-08 in modified transcript

MINA

• refseq_MINA.F1 refseq_MINA.R1 264 368
• NCBIGene 36.2 84864
• Alternative 3-prime, size difference: 3
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_032778

• Changed! pfam Cupin_4 312aa 5e-89 in ref transcript
  • Cupin superfamily protein. This family contains many hypothetical proteins that belong to the cupin superfamily.
• COG COG2850 202aa 2e-10 in ref transcript
  • Uncharacterized conserved protein [Function unknown].
• Changed! pfam Cupin_4 313aa 3e-88 in modified transcript

MINA

• refseq_MINA.F1 refseq_MINA.R3 124 225
• NCBIGene 36.2 84864
• Single exon skipping, size difference: 101
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_032778

• Changed! pfam Cupin_4 312aa 5e-89 in ref transcript
  • Cupin superfamily protein. This family contains many hypothetical proteins that belong to the cupin superfamily.
• COG COG2850 202aa 2e-10 in ref transcript
  • Uncharacterized conserved protein [Function unknown].
• Changed! pfam Cupin_4 227aa 2e-71 in modified transcript

MINK1

• refseq_MINK1.F1 refseq_MINK1.R1 131 155
• NCBIGene 36.3 50488
• Single exon skipping, size difference: 24
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_153827

• cd STKc_MAP4K4_6 192aa 1e-114 in ref transcript
  • Serine/threonine kinases (STKs), mitogen-activated protein kinase (MAPK) kinase kinase kinase 4 (MAPKKKK4 or MAP4K4) and MAPKKKK6 (or MAP4K6) subfamily, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The MAP4K4/MAP4K6 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. Members of this subfamily contain an N-terminal catalytic domain and a C-terminal citron homology (CNH) regulatory domain. MAP4Ks (or MAPKKKKs) are involved in MAPK signaling pathways that are important in mediating cellular responses to extracellular signals by activating a MAPK kinase kinase (MAPKKK or MAP3K or MKKK). Each MAPK cascade is activated either by a small GTP-binding protein or by an adaptor protein, which transmits the signal either directly to a MAP3K to start the triple kinase core cascade or indirectly through a mediator kinase, a MAP4K. MAP4K4 is also called Nck Interacting kinase (NIK). It facilitates the activation of the MAPKs, extracellular signal-regulated kinase (ERK) 1, ERK2, and c-Jun N-terminal kinase (JNK), by phosphorylating and activating MEKK1. MAP4K4 plays a role in tumor necrosis factor (TNF) alpha-induced insulin resistance. MAP4K4 silencing in skeletal muscle cells from type II diabetic patients restores insulin-mediated glucose uptake. MAP4K4, through JNK, also plays a broad role in cell motility, which impacts inflammation, homeostasis, as well as the invasion and spread of cancer. MAP4K4 is found to be highly expressed in most tumor cell lines relative to normal tissue. MAP4K6 (also called MINK for Misshapen/NIKs-related kinase) is activated after Ras induction and mediates activation of p38 MAPK. MAP4K6 plays a role in cell cycle arrest, cytoskeleton organization, cell adhesion, and cell motility.
• smart CNH 299aa 9e-83 in ref transcript
  • Domain found in NIK1-like kinases, mouse citron and yeast ROM1, ROM2. Unpublished observations.
• smart S_TKc 188aa 2e-54 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• COG SPS1 205aa 2e-24 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].
• COG ROM1 286aa 3e-08 in ref transcript
  • RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms].

MINK1

• refseq_MINK1.F3 refseq_MINK1.R3 136 247
• NCBIGene 36.3 50488
• Single exon skipping, size difference: 111
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_153827

• cd STKc_MAP4K4_6 192aa 1e-114 in ref transcript
  • Serine/threonine kinases (STKs), mitogen-activated protein kinase (MAPK) kinase kinase kinase 4 (MAPKKKK4 or MAP4K4) and MAPKKKK6 (or MAP4K6) subfamily, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The MAP4K4/MAP4K6 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. Members of this subfamily contain an N-terminal catalytic domain and a C-terminal citron homology (CNH) regulatory domain. MAP4Ks (or MAPKKKKs) are involved in MAPK signaling pathways that are important in mediating cellular responses to extracellular signals by activating a MAPK kinase kinase (MAPKKK or MAP3K or MKKK). Each MAPK cascade is activated either by a small GTP-binding protein or by an adaptor protein, which transmits the signal either directly to a MAP3K to start the triple kinase core cascade or indirectly through a mediator kinase, a MAP4K. MAP4K4 is also called Nck Interacting kinase (NIK). It facilitates the activation of the MAPKs, extracellular signal-regulated kinase (ERK) 1, ERK2, and c-Jun N-terminal kinase (JNK), by phosphorylating and activating MEKK1. MAP4K4 plays a role in tumor necrosis factor (TNF) alpha-induced insulin resistance. MAP4K4 silencing in skeletal muscle cells from type II diabetic patients restores insulin-mediated glucose uptake. MAP4K4, through JNK, also plays a broad role in cell motility, which impacts inflammation, homeostasis, as well as the invasion and spread of cancer. MAP4K4 is found to be highly expressed in most tumor cell lines relative to normal tissue. MAP4K6 (also called MINK for Misshapen/NIKs-related kinase) is activated after Ras induction and mediates activation of p38 MAPK. MAP4K6 plays a role in cell cycle arrest, cytoskeleton organization, cell adhesion, and cell motility.
• smart CNH 299aa 9e-83 in ref transcript
  • Domain found in NIK1-like kinases, mouse citron and yeast ROM1, ROM2. Unpublished observations.
• smart S_TKc 188aa 2e-54 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• COG SPS1 205aa 2e-24 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].
• COG ROM1 286aa 3e-08 in ref transcript
  • RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms].
• Changed! PRK PRK07764 140aa 2e-04 in modified transcript
  • DNA polymerase III subunits gamma and tau; Validated.

MINK1

• refseq_MINK1.F5 refseq_MINK1.R5 246 306
• NCBIGene 36.3 50488
• Alternative 3-prime, size difference: 60
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_153827

• cd STKc_MAP4K4_6 192aa 1e-114 in ref transcript
  • Serine/threonine kinases (STKs), mitogen-activated protein kinase (MAPK) kinase kinase kinase 4 (MAPKKKK4 or MAP4K4) and MAPKKKK6 (or MAP4K6) subfamily, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The MAP4K4/MAP4K6 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. Members of this subfamily contain an N-terminal catalytic domain and a C-terminal citron homology (CNH) regulatory domain. MAP4Ks (or MAPKKKKs) are involved in MAPK signaling pathways that are important in mediating cellular responses to extracellular signals by activating a MAPK kinase kinase (MAPKKK or MAP3K or MKKK). Each MAPK cascade is activated either by a small GTP-binding protein or by an adaptor protein, which transmits the signal either directly to a MAP3K to start the triple kinase core cascade or indirectly through a mediator kinase, a MAP4K. MAP4K4 is also called Nck Interacting kinase (NIK). It facilitates the activation of the MAPKs, extracellular signal-regulated kinase (ERK) 1, ERK2, and c-Jun N-terminal kinase (JNK), by phosphorylating and activating MEKK1. MAP4K4 plays a role in tumor necrosis factor (TNF) alpha-induced insulin resistance. MAP4K4 silencing in skeletal muscle cells from type II diabetic patients restores insulin-mediated glucose uptake. MAP4K4, through JNK, also plays a broad role in cell motility, which impacts inflammation, homeostasis, as well as the invasion and spread of cancer. MAP4K4 is found to be highly expressed in most tumor cell lines relative to normal tissue. MAP4K6 (also called MINK for Misshapen/NIKs-related kinase) is activated after Ras induction and mediates activation of p38 MAPK. MAP4K6 plays a role in cell cycle arrest, cytoskeleton organization, cell adhesion, and cell motility.
• smart CNH 299aa 9e-83 in ref transcript
  • Domain found in NIK1-like kinases, mouse citron and yeast ROM1, ROM2. Unpublished observations.
• smart S_TKc 188aa 2e-54 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• COG SPS1 205aa 2e-24 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].
• COG ROM1 286aa 3e-08 in ref transcript
  • RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms].

MKNK1

• refseq_MKNK1.F2 refseq_MKNK1.R2 215 259
• NCBIGene 36.3 8569
• Single exon skipping, size difference: 44
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_003684

• cd S_TKc 322aa 3e-62 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• smart S_TKc 316aa 2e-66 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• Changed! COG SPS1 323aa 1e-33 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].
• Changed! COG SPS1 336aa 3e-34 in modified transcript

MKNK1

• refseq_MKNK1.F4 refseq_MKNK1.R4 132 255
• NCBIGene 36.3 8569
• Single exon skipping, size difference: 123
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_003684

• Changed! cd S_TKc 322aa 3e-62 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• Changed! smart S_TKc 316aa 2e-66 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• Changed! COG SPS1 323aa 1e-33 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].
• Changed! cd S_TKc 281aa 3e-67 in modified transcript
• Changed! smart S_TKc 275aa 2e-71 in modified transcript
• Changed! COG SPS1 282aa 4e-39 in modified transcript

MLH3

• refseq_MLH3.F1 refseq_MLH3.R1 153 225
• NCBIGene 36.3 27030
• Single exon skipping, size difference: 72
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001040108

• cd MutL_Trans_MLH3 144aa 4e-53 in ref transcript
  • MutL_Trans_MLH3: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to yeast and human MLH3 (MutL homologue 3). MLH3 belongs to the DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. MLH1 forms heterodimers with MLH3. The MLH1-MLH3 complex plays a role in meiosis. A role for hMLH1-hMLH3 in DNA mismatch repair (MMR) has not been established. It has been suggested that hMLH3 may be a low risk gene for colorectal cancer; however there is little evidence to support it having a role in classical HNPCC.
• TIGR mutl 269aa 1e-44 in ref transcript
  • All proteins in this family for which the functions are known are involved in the process of generalized mismatch repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
• Changed! smart MutL_C 174aa 4e-21 in ref transcript
  • MutL C terminal dimerisation domain. MutL and MutS are key components of the DNA repair machinery that corrects replication errors. MutS recognises mispaired or unpaired bases in a DNA duplex and in the presence of ATP, recruits MutL to form a DNA signaling complex for repair. The N terminal region of MutL contains the ATPase domain and the C terminal is involved in dimerisation.
• pfam DNA_mis_repair 134aa 1e-05 in ref transcript
  • DNA mismatch repair protein, C-terminal domain. This family represents the C-terminal domain of the mutL/hexB/PMS1 family. This domain has a ribosomal S5 domain 2-like fold.
• COG MutL 437aa 4e-45 in ref transcript
  • DNA mismatch repair enzyme (predicted ATPase) [DNA replication, recombination, and repair].
• Changed! PRK mutL 221aa 3e-22 in ref transcript
  • DNA mismatch repair protein; Reviewed.
• Changed! smart MutL_C 150aa 6e-11 in modified transcript
• Changed! COG MutL 152aa 6e-13 in modified transcript

MLL3

• refseq_MLL3.F1 refseq_MLL3.R1 229 400
• NCBIGene 36.2 58508
• Exon skipping and alternative 3-prime or 5-prime, size difference: 171
• Inclusion in the protein (no stop codon or frameshift), Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_170606

• pfam SET 129aa 5e-28 in ref transcript
  • SET domain. SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure.
• smart FYRC 88aa 2e-19 in ref transcript
  • "FY-rich" domain, C-terminal region. is sometimes closely juxtaposed with the N-terminal region (FYRN), but sometimes is far distant. Unknown function, but occurs frequently in chromatin-associated proteins.
• pfam FYRN 55aa 3e-16 in ref transcript
  • F/Y-rich N-terminus. This region is normally found in the trithorax/ALL1 family proteins. It is similar to SMART:SM00541.
• pfam PHD 47aa 9e-09 in ref transcript
  • PHD-finger. PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
• pfam PHD 49aa 5e-08 in ref transcript
• pfam PAT1 178aa 7e-08 in ref transcript
  • Topoisomerase II-associated protein PAT1. Members of this family are necessary for accurate chromosome transmission during cell division.
• pfam PHD 51aa 1e-07 in ref transcript
• pfam PHD 48aa 3e-06 in ref transcript
• pfam PHD 52aa 1e-05 in ref transcript
• smart HMG 52aa 4e-04 in ref transcript
  • high mobility group.
• pfam PHD 52aa 0.001 in ref transcript
• pfam ATG13 135aa 0.009 in ref transcript
  • Autophagy-related protein 13. Members of this family of phosphoproteins are involved in cytoplasm to vacuole transport (Cvt), and more specifically in Cvt vesicle formation. They are probably involved in the switching machinery regulating the conversion between the Cvt pathway and autophagy. Finally, ATG13 is also required for glycogen storage.
• COG COG2940 187aa 2e-18 in ref transcript
  • Proteins containing SET domain [General function prediction only].
• COG COG5141 115aa 0.001 in ref transcript
  • PHD zinc finger-containing protein [General function prediction only].
• COG COG5141 137aa 0.003 in ref transcript
• Changed! PRK PRK07003 331aa 0.010 in modified transcript
  • DNA polymerase III subunits gamma and tau; Validated.

MLL5

• refseq_MLL5.F2 refseq_MLL5.R2 249 397
• NCBIGene 36.3 55904
• Exon skipping and alternative 3-prime or 5-prime, size difference: 148
• Exclusion in 5'UTR, Exclusion in 5'UTR, Exclusion in 5'UTR
• Reference transcript: NM_182931

• pfam SET 128aa 5e-25 in ref transcript
  • SET domain. SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure.
• pfam PHD 46aa 2e-10 in ref transcript
  • PHD-finger. PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
• TIGR PABP-1234 119aa 0.003 in ref transcript
  • There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, and of unknown tissue range.
• pfam PAT1 113aa 0.003 in ref transcript
  • Topoisomerase II-associated protein PAT1. Members of this family are necessary for accurate chromosome transmission during cell division.
• COG COG2940 298aa 1e-04 in ref transcript
  • Proteins containing SET domain [General function prediction only].
• PRK PRK13729 87aa 0.007 in ref transcript
  • conjugal transfer pilus assembly protein TraB; Provisional.

MLLT10

• refseq_MLLT10.F1 refseq_MLLT10.R1 157 205
• NCBIGene 36.3 8028
• Single exon skipping, size difference: 48
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_004641

• pfam PHD 47aa 1e-06 in ref transcript
  • PHD-finger. PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
• smart PHD 59aa 0.005 in ref transcript
  • PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the R ING finger and the FY VE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent B ROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were R ING fingers misidentified as PHD fingers.
• COG COG5141 179aa 1e-37 in ref transcript
  • PHD zinc finger-containing protein [General function prediction only].

MLLT4

• refseq_MLLT4.F1 refseq_MLLT4.R1 158 203
• NCBIGene 36.3 4301
• Single exon skipping, size difference: 45
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001040001

• cd AF6_RA_repeat1 112aa 3e-53 in ref transcript
  • The AF-6 protein (also known as afadin and canoe) is a multidomain cell junction protein that contains two N-terminal Ras-associating (RA) domains in addition to FHA (forkhead-associated), DIL (class V myosin homology region), and PDZ domains and a proline-rich region. AF6 acts downstream of the Egfr (Epidermal Growth Factor-receptor)/Ras signalling pathway and provides a link from Egfr to cytoskeletal elements.
• cd AF6_RA_repeat2 100aa 2e-42 in ref transcript
  • The AF-6 protein (also known as afadin and canoe) is a multidomain cell junction protein that contains two N-terminal Ras-associating (RA) domains in addition to FHA (forkhead-associated), DIL (class V myosin homology region), and PDZ domains and a proline-rich region. AF6 acts downstream of the Egfr (Epidermal Growth Factor-receptor)/Ras signalling pathway and provides a link from Egfr to cytoskeletal elements.
• cd PDZ_signaling 84aa 3e-12 in ref transcript
  • PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of PDZ domains an N-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in proteases.
• Changed! cd FHA 90aa 2e-05 in ref transcript
  • Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins localize to the nucleus, where they participate in establishing or maintaining cell cycle checkpoints, DNA repair, or transcriptional regulation. Members of the FHA family include: Dun1, Rad53, Cds1, Mek1, KAPP(kinase-associated protein phosphatase),and Ki-67 (a human nuclear protein related to cell proliferation).
• pfam DIL 107aa 5e-26 in ref transcript
  • DIL domain. The DIL domain has no known function.
• smart RA 94aa 7e-17 in ref transcript
  • Ras association (RalGDS/AF-6) domain. RasGTP effectors (in cases of AF6, canoe and RalGDS); putative RasGTP effectors in other cases. Kalhammer et al. have shown that not all RA domains bind RasGTP. Predicted structure similar to that determined, and that of the RasGTP-binding domain of Raf kinase. Predicted RA domains in PLC210 and nore1 found to bind RasGTP. Included outliers (Grb7, Grb14, adenylyl cyclases etc.).
• smart PDZ 88aa 4e-14 in ref transcript
  • Domain present in PSD-95, Dlg, and ZO-1/2. Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities.
• smart RA 100aa 2e-13 in ref transcript
• smart FHA 52aa 4e-08 in ref transcript
  • Forkhead associated domain. Found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain.
• COG Prc 133aa 0.001 in ref transcript
  • Periplasmic protease [Cell envelope biogenesis, outer membrane].
• Changed! cd FHA 101aa 1e-05 in modified transcript

MLX

• refseq_MLX.F2 refseq_MLX.R2 115 277
• NCBIGene 36.3 6945
• Alternative 5-prime, size difference: 162
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_170607

• cd HLH 66aa 2e-10 in ref transcript
  • Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins.
• pfam HLH 59aa 1e-12 in ref transcript
  • Helix-loop-helix DNA-binding domain.

MLX

• refseq_MLX.F3 refseq_MLX.R3 125 215
• NCBIGene 36.3 6945
• Single exon skipping, size difference: 90
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_170607

• cd HLH 66aa 2e-10 in ref transcript
  • Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins.
• pfam HLH 59aa 1e-12 in ref transcript
  • Helix-loop-helix DNA-binding domain.

MLXIPL

• refseq_MLXIPL.F1 refseq_MLXIPL.R1 147 204
• NCBIGene 36.3 51085
• Alternative 3-prime, size difference: 57
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_032951

• Changed! cd HLH 61aa 3e-09 in ref transcript
  • Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins.
• Changed! pfam HLH 55aa 8e-09 in ref transcript
  • Helix-loop-helix DNA-binding domain.

MMP19

• refseq_MMP19.F1 refseq_MMP19.R1 101 448
• NCBIGene 36.2 4327
• Multiple exon skipping, size difference: 347
• Exclusion in the protein causing a frameshift, Exclusion in the protein (no frameshift)
• Reference transcript: NM_002429

• Changed! cd ZnMc_MMP 154aa 4e-53 in ref transcript
  • Zinc-dependent metalloprotease, matrix metalloproteinase (MMP) sub-family. MMPs are responsible for a great deal of pericellular proteolysis of extracellular matrix and cell surface molecules, playing crucial roles in morphogenesis, cell fate specification, cell migration, tissue repair, tumorigenesis, gain or loss of tissue-specific functions, and apoptosis. In many instances, they are anchored to cell membranes via trans-membrane domains, and their activity is controlled via TIMPs (tissue inhibitors of metalloproteinases).
• Changed! cd HX 186aa 7e-48 in ref transcript
  • Hemopexin-like repeats.; Hemopexin is a heme-binding protein that transports heme to the liver. Hemopexin-like repeats occur in vitronectin and some matrix metalloproteinases family (matrixins). The HX repeats of some matrixins bind tissue inhibitor of metalloproteinases (TIMPs). This CD contains 4 instances of the repeat.
• Changed! pfam Peptidase_M10 154aa 3e-57 in ref transcript
  • Matrixin. The members of this family are enzymes that cleave peptides. These proteases require zinc for catalysis.
• Changed! smart HX 39aa 2e-07 in ref transcript
  • Hemopexin-like repeats. Hemopexin is a heme-binding protein that transports heme to the liver. Hemopexin-like repeats occur in vitronectin and some matrix metalloproteinases family (matrixins). The HX repeats of some matrixins bind tissue inhibitor of metalloproteinases (TIMPs).
• Changed! smart HX 44aa 2e-06 in ref transcript
• Changed! pfam PG_binding_1 50aa 6e-05 in ref transcript
  • Putative peptidoglycan binding domain. This domain is composed of three alpha helices. This domain is found at the N or C terminus of a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function. This family is found N-terminal to the catalytic domain of matrixins.
• Changed! smart HX 43aa 4e-04 in ref transcript
• Changed! smart HX 47aa 0.010 in ref transcript

MMP23B

• refseq_MMP23B.F1 refseq_MMP23B.R1 112 252
• NCBIGene 36.2 8510
• Single exon skipping, size difference: 140
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_006983

• Changed! cd ZnMc_MMP 168aa 2e-48 in ref transcript
  • Zinc-dependent metalloprotease, matrix metalloproteinase (MMP) sub-family. MMPs are responsible for a great deal of pericellular proteolysis of extracellular matrix and cell surface molecules, playing crucial roles in morphogenesis, cell fate specification, cell migration, tissue repair, tumorigenesis, gain or loss of tissue-specific functions, and apoptosis. In many instances, they are anchored to cell membranes via trans-membrane domains, and their activity is controlled via TIMPs (tissue inhibitors of metalloproteinases).
• Changed! cd IGcam 61aa 0.004 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• Changed! pfam Peptidase_M10 168aa 7e-40 in ref transcript
  • Matrixin. The members of this family are enzymes that cleave peptides. These proteases require zinc for catalysis.
• Changed! smart IGc2 61aa 3e-04 in ref transcript
  • Immunoglobulin C-2 Type.
• Changed! smart ShKT 35aa 0.004 in ref transcript
  • ShK toxin domain. ShK toxin domain.

MOG

• refseq_MOG.F1 refseq_MOG.R1 120 370
• NCBIGene 36.3 4340
• Alternative 3-prime, size difference: 250
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_002433

• smart IGv 81aa 2e-12 in ref transcript
  • Immunoglobulin V-Type.

MOG

• refseq_MOG.F5 refseq_MOG.R5 275 413
• NCBIGene 36.2 4340
• Single exon skipping, size difference: 138
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_002433

• smart IGv 81aa 2e-12 in ref transcript
  • Immunoglobulin V-Type.

MORF4L1

• refseq_MORF4L1.F1 refseq_MORF4L1.R1 143 260
• NCBIGene 36.3 10933
• Single exon skipping, size difference: 117
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_206839

• Changed! pfam MRG 261aa 1e-81 in ref transcript
  • MRG. This family consists of three different eukaryotic proteins (mortality factor 4 (MORF4/MRG15), male-specific lethal 3(MSL-3) and ESA1-associated factor 3(EAF3)). It is thought that the MRG family is involved in transcriptional regulation via histone acetylation. It contains 2 chromo domains and a leucine zipper motif.
• Changed! cd CHROMO 49aa 0.003 in modified transcript
  • Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence implicates the chromo domain in the binding activity of these proteins to methylated histone tails and maybe RNA. May occur as single instance, in a tandem arrangement or followd by a related "chromo shadow" domain.
• Changed! pfam MRG 261aa 1e-81 in modified transcript

MOSPD3

• refseq_MOSPD3.F1 refseq_MOSPD3.R1 128 158
• NCBIGene 36.3 64598
• Alternative 3-prime, size difference: 30
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001040097

• Changed! pfam Motile_Sperm 64aa 1e-10 in ref transcript
  • MSP (Major sperm protein) domain. Major sperm proteins are involved in sperm motility. These proteins oligomerise to form filaments. This family contains many other proteins.
• Changed! pfam Motile_Sperm 54aa 9e-08 in modified transcript

MPG

• refseq_MPG.F2 refseq_MPG.R2 111 304
• NCBIGene 36.3 4350
• Single exon skipping, size difference: 193
• Exclusion of the protein initiation site
• Reference transcript: NM_002434

• cd AAG 190aa 3e-57 in ref transcript
  • Alkyladenine DNA glycosylase (AAG), also known as 3-methyladenine DNA glycosylase, catalyzes the first step in base excision repair (BER) by cleaving damaged DNA bases within double-stranded DNA to produce an abasic site. AAG bends DNA by intercalating between the base pairs, causing the damaged base to flip out of the double helix and into the enzyme active site for cleavage. Although AAG represents one of six DNA glycosylase classes, it lacks the helix-hairpin-helix active site motif associated with the other BER glycosylases and is structurally quite distinct from them.
• TIGR 3mg 201aa 1e-77 in ref transcript
  • This families are based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). All proteins in this family for which the function is known are involved in the base excision repair of alkylation damage to DNA. The exact specificty of the type of alkylation damage repaired by each of these varies somewhat between species. Substrates include 3-methyl adenine, 7-methyl-guanaine, and 3-methyl-guanine.
• PRK PRK00802 204aa 4e-53 in ref transcript
  • 3-methyladenine DNA glycosylase; Reviewed.

MPST

• refseq_MPST.F1 refseq_MPST.R1 237 413
• NCBIGene 36.3 4357
• Single exon skipping, size difference: 176
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_021126

• Changed! cd TST_Repeat_2 116aa 5e-38 in ref transcript
  • Thiosulfate sulfurtransferase (TST), C-terminal, catalytic domain. TST contains 2 copies of the Rhodanese Homology Domain; this is the second repeat. Only the second repeat contains the catalytically active Cys residue.
• Changed! cd TST_Repeat_1 130aa 9e-37 in ref transcript
  • Thiosulfate sulfurtransferase (TST), N-terminal, inactive domain. TST contains 2 copies of the Rhodanese Homology Domain; this is the 1st repeat, which does not contain the catalytically active Cys residue. The role of the 1st repeat is uncertain, but it is believed to be involved in protein interaction.
• Changed! pfam Rhodanese 118aa 3e-19 in ref transcript
  • Rhodanese-like domain. Rhodanese has an internal duplication. This Pfam represents a single copy of this duplicated domain. The domain is found as a single copy in other proteins, including phosphatases and ubiquitin C-terminal hydrolases.
• Changed! pfam Rhodanese 123aa 2e-16 in ref transcript
• Changed! COG SseA 284aa 4e-70 in ref transcript
  • Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism].

MPZL1

• refseq_MPZL1.F1 refseq_MPZL1.R1 146 249
• NCBIGene 36.3 9019
• Single exon skipping, size difference: 103
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_003953

• pfam V-set 114aa 6e-12 in ref transcript
  • Immunoglobulin V-set domain. This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.

MRE11A

• refseq_MRE11A.F1 refseq_MRE11A.R1 186 293
• NCBIGene 36.3 4361
• Alternative 5-prime, size difference: 107
• Inclusion in 5'UTR
• Reference transcript: NM_005591

• TIGR mre11 393aa 1e-140 in ref transcript
  • All proteins in this family for which functions are known are subunits of a nuclease complex made up of multiple proteins including MRE11 and RAD50 homologs. The functions of this nuclease complex include recombinational repair and non-homolgous end joining. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). The proteins in this family are distantly related to proteins in the SbcCD complex of bacteria.
• COG SbcD 309aa 2e-20 in ref transcript
  • DNA repair exonuclease [DNA replication, recombination, and repair].

MRPL10

• refseq_MRPL10.F2 refseq_MRPL10.R2 167 265
• NCBIGene 36.3 124995
• Single exon skipping, size difference: 98
• Exclusion of the protein initiation site
• Reference transcript: NM_148887

• cd Ribosomal_L10 132aa 9e-22 in ref transcript
  • Ribosomal protein L10 family, L10 subfamily; composed of bacterial 50S ribosomal protein and eukaryotic mitochondrial 39S ribosomal protein, L10. L10 occupies the L7/L12 stalk of the ribosome. The N-terminal domain (NTD) of L10 interacts with L11 protein and forms the base of the L7/L12 stalk, while the extended C-terminal helix binds to two or three dimers of the NTD of L7/L12 (L7 and L12 are identical except for an acetylated N-terminus). The L7/L12 stalk is known to contain the binding site for elongation factors G and Tu (EF-G and EF-Tu, respectively); however, there is disagreement as to whether or not L10 is involved in forming the binding site. The stalk is believed to be associated with GTPase activities in protein synthesis. In a neuroblastoma cell line, L10 has been shown to interact with the SH3 domain of Src and to activate the binding of the Nck1 adaptor protein with skeletal proteins such as the Wiskott-Aldrich Syndrome Protein (WASP) and the WASP-interacting protein (WIP). These bacteria and eukaryotic sequences have no additional C-terminal domain, present in other eukaryotic and archaeal orthologs.
• COG RplJ 128aa 3e-07 in ref transcript
  • Ribosomal protein L10 [Translation, ribosomal structure and biogenesis].

MRPL11

• refseq_MRPL11.F1 refseq_MRPL11.R1 148 226
• NCBIGene 36.3 65003
• Alternative 5-prime, size difference: 78
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_016050

• Changed! cd Ribosomal_L11 136aa 1e-36 in ref transcript
  • Ribosomal protein L11. Ribosomal protein L11, together with proteins L10 and L7/L12, and 23S rRNA, form the L7/L12 stalk on the surface of the large subunit of the ribosome. The homologous eukaryotic cytoplasmic protein is also called 60S ribosomal protein L12, which is distinct from the L12 involved in the formation of the L7/L12 stalk. The C-terminal domain (CTD) of L11 is essential for binding 23S rRNA, while the N-terminal domain (NTD) contains the binding site for the antibiotics thiostrepton and micrococcin. L11 and 23S rRNA form an essential part of the GTPase-associated region (GAR). Based on differences in the relative positions of the L11 NTD and CTD during the translational cycle, L11 is proposed to play a significant role in the binding of initiation factors, elongation factors, and release factors to the ribosome. Several factors, including the class I release factors RF1 and RF2, are known to interact directly with L11. In eukaryotes, L11 has been implicated in regulating the levels of ubiquinated p53 and MDM2 in the MDM2-p53 feedback loop, which is responsible for apoptosis in response to DNA damage. In bacteria, the "stringent response" to harsh conditions allows bacteria to survive, and ribosomes that lack L11 are deficient in stringent factor stimulation.
• Changed! smart RL11 137aa 8e-36 in ref transcript
  • Ribosomal protein L11/L12.
• Changed! PRK rplK 143aa 1e-27 in ref transcript
  • 50S ribosomal protein L11; Validated.
• Changed! cd Ribosomal_L11 114aa 8e-36 in modified transcript
• Changed! smart RL11 115aa 5e-35 in modified transcript
• Changed! PRK rplK 116aa 1e-26 in modified transcript

MRPL11

• refseq_MRPL11.F3 refseq_MRPL11.R3 193 287
• NCBIGene 36.3 65003
• Single exon skipping, size difference: 94
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_016050

• cd Ribosomal_L11 136aa 1e-36 in ref transcript
  • Ribosomal protein L11. Ribosomal protein L11, together with proteins L10 and L7/L12, and 23S rRNA, form the L7/L12 stalk on the surface of the large subunit of the ribosome. The homologous eukaryotic cytoplasmic protein is also called 60S ribosomal protein L12, which is distinct from the L12 involved in the formation of the L7/L12 stalk. The C-terminal domain (CTD) of L11 is essential for binding 23S rRNA, while the N-terminal domain (NTD) contains the binding site for the antibiotics thiostrepton and micrococcin. L11 and 23S rRNA form an essential part of the GTPase-associated region (GAR). Based on differences in the relative positions of the L11 NTD and CTD during the translational cycle, L11 is proposed to play a significant role in the binding of initiation factors, elongation factors, and release factors to the ribosome. Several factors, including the class I release factors RF1 and RF2, are known to interact directly with L11. In eukaryotes, L11 has been implicated in regulating the levels of ubiquinated p53 and MDM2 in the MDM2-p53 feedback loop, which is responsible for apoptosis in response to DNA damage. In bacteria, the "stringent response" to harsh conditions allows bacteria to survive, and ribosomes that lack L11 are deficient in stringent factor stimulation.
• smart RL11 137aa 8e-36 in ref transcript
  • Ribosomal protein L11/L12.
• PRK rplK 143aa 1e-27 in ref transcript
  • 50S ribosomal protein L11; Validated.

MRPL22

• refseq_MRPL22.F1 refseq_MRPL22.R1 188 306
• NCBIGene 36.3 29093
• Single exon skipping, size difference: 118
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_014180

• Changed! cd Ribosomal_L22 106aa 9e-23 in ref transcript
  • Ribosomal protein L22/L17e. L22 (L17 in eukaryotes) is a core protein of the large ribosomal subunit. It is the only ribosomal protein that interacts with all six domains of 23S rRNA, and is one of the proteins important for directing the proper folding and stabilizing the conformation of 23S rRNA. L22 is the largest protein contributor to the surface of the polypeptide exit channel, the tunnel through which the polypeptide product passes. L22 is also one of six proteins located at the putative translocon binding site on the exterior surface of the ribosome.
• Changed! pfam Ribosomal_L22 96aa 3e-09 in ref transcript
  • Ribosomal protein L22p/L17e. This family includes L22 from prokaryotes and chloroplasts and L17 from eukaryotes.
• Changed! PRK rplV 103aa 1e-14 in ref transcript
  • 50S ribosomal protein L22; Reviewed.

MRPL24

• refseq_MRPL24.F2 refseq_MRPL24.R2 183 224
• NCBIGene 36.3 79590
• Alternative 5-prime, size difference: 41
• Exclusion in 5'UTR
• Reference transcript: NM_145729

• TIGR rplX_bact 96aa 7e-15 in ref transcript
  • This model recognizes bacterial and organellar forms of ribosomal protein L24. It excludes eukaryotic and archaeal forms, designated L26 in eukaryotes.
• PRK rplX 96aa 2e-13 in ref transcript
  • 50S ribosomal protein L24; Reviewed.

MRPL33

• refseq_MRPL33.F2 refseq_MRPL33.R2 192 299
• NCBIGene 36.3 9553
• Single exon skipping, size difference: 107
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_004891

• Changed! TIGR rpmG_bact 49aa 0.002 in ref transcript
  • This model describes bacterial ribosomal protein L33 and its chloroplast and mitochondrial equivalents.
• Changed! PRK rpmG 51aa 3e-05 in ref transcript
  • 50S ribosomal protein L33; Validated.

MRPL43

• refseq_MRPL43.F2 refseq_MRPL43.R2 190 317
• NCBIGene 36.3 84545
• Single exon skipping, size difference: 127
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_176794

• pfam L51_S25_CI-B8 51aa 1e-10 in ref transcript
  • Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain. The proteins in this family are located in the mitochondrion. The family includes ribosomal protein L51, and S25. This family also includes mitochondrial NADH-ubiquinone oxidoreductase B8 subunit (CI-B8) EC:1.6.5.3. It is not known whether all members of this family form part of the NADH-ubiquinone oxidoreductase and whether they are also all ribosomal proteins.

MRPL47

• refseq_MRPL47.F2 refseq_MRPL47.R2 180 326
• NCBIGene 36.3 57129
• Single exon skipping, size difference: 146
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_020409

• Changed! pfam MRP-L47 86aa 3e-29 in ref transcript
  • Mitochondrial 39-S ribosomal protein L47 (MRP-L47). This family represents the N-terminal region (approximately 8 residues) of the eukaryotic mitochondrial 39-S ribosomal protein L47 (MRP-L47). Mitochondrial ribosomal proteins (MRPs) are the counterparts of the cytoplasmic ribosomal proteins, in that they fulfil similar functions in protein biosynthesis. However, they are distinct in number, features and primary structure.

MRPL48

• refseq_MRPL48.F2 refseq_MRPL48.R2 343 468
• NCBIGene 36.2 51642
• Single exon skipping, size difference: 125
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_016055

• Changed! pfam Ribosomal_S10 98aa 3e-16 in ref transcript
  • Ribosomal protein S10p/S20e. This family includes small ribosomal subunit S10 from prokaryotes and S20 from eukaryotes.

MRPL52

• refseq_MRPL52.F1 refseq_MRPL52.R1 101 175
• NCBIGene 36.3 122704
• Single exon skipping, size difference: 74
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_178336

MRPL55

• refseq_MRPL55.F1 refseq_MRPL55.R1 168 276
• NCBIGene 36.3 128308
• Single exon skipping, size difference: 108
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_181462

• Changed! pfam Mitoc_L55 118aa 1e-32 in ref transcript
  • Mitochondrial ribosomal protein L55. Members of this family are involved in mitochondrial biogenesis and G2/M phase cell cycle progression. They form a component of the mitochondrial ribosome large subunit (39S) which comprises a 16S rRNA and about 50 distinct proteins.
• Changed! pfam Mitoc_L55 119aa 3e-33 in modified transcript

MRPL55

• refseq_MRPL55.F3 refseq_MRPL55.R3 145 190
• NCBIGene 36.3 128308
• Exon skipping and alternative 3-prime or 5-prime, size difference: 45
• Inclusion in 5'UTR, Exclusion in 5'UTR
• Reference transcript: NM_181454

• pfam Mitoc_L55 119aa 3e-33 in ref transcript
  • Mitochondrial ribosomal protein L55. Members of this family are involved in mitochondrial biogenesis and G2/M phase cell cycle progression. They form a component of the mitochondrial ribosome large subunit (39S) which comprises a 16S rRNA and about 50 distinct proteins.

MRRF

• refseq_MRRF.F1 refseq_MRRF.R1 109 269
• NCBIGene 36.3 92399
• Single exon skipping, size difference: 160
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_138777

• Changed! cd RRF 178aa 3e-27 in ref transcript
  • Ribosome recycling factor (RRF). Ribosome recycling factor dissociates the posttermination complex, composed of the ribosome, deacylated tRNA, and mRNA, after termination of translation. Thus ribosomes are "recycled" and ready for another round of protein synthesis. RRF is believed to bind the ribosome at the A-site in a manner that mimics tRNA, but the specific mechanisms remain unclear. RRF is essential for bacterial growth. It is not necessary for cell growth in archaea or eukaryotes, but is found in mitochondria or chloroplasts of some eukaryotic species.
• Changed! pfam RRF 164aa 3e-22 in ref transcript
  • Ribosome recycling factor. The ribosome recycling factor (RRF / ribosome release factor) dissociates the ribosome from the mRNA after termination of translation, and is essential bacterial growth. Thus ribosomes are "recycled" and ready for another round of protein synthesis.
• Changed! PRK frr 183aa 7e-30 in ref transcript
  • ribosome recycling factor; Reviewed.
• Changed! cd RRF 109aa 2e-14 in modified transcript
• Changed! TIGR frr 103aa 2e-09 in modified transcript
  • This model finds only eubacterial proteins. Mitochondrial and/or chloroplast forms might be expected but are not currently known. This protein was previously called ribosome releasing factor. By releasing ribosomes from mRNA at the end of protein biosynthesis, it prevents inappropriate translation from 3-prime regions of the mRNA and frees the ribosome for new rounds of translation. EGAD|53116|YHR038W is part of the frr superfamily.
• Changed! PRK frr 114aa 1e-15 in modified transcript

MS4A1

• refseq_MS4A1.F2 refseq_MS4A1.R2 137 400
• NCBIGene 36.3 931
• Exon skipping and alternative 3-prime or 5-prime, size difference: 263
• Exclusion in 5'UTR, Exclusion in 5'UTR
• Reference transcript: NM_152866

• pfam CD20 167aa 2e-32 in ref transcript
  • CD20/IgE Fc receptor beta subunit family. This family includes the CD20 protein and the beta subunit of the high affinity receptor for IgE Fc. The high affinity receptor for IgE is a tetrameric structure consisting of a single IgE-binding alpha subunit, a single beta subunit, and two disulfide-linked gamma subunits. The alpha subunit of Fc epsilon RI and most Fc receptors are homologous members of the Ig superfamily. By contrast, the beta and gamma subunits from Fc epsilon RI are not homologous to the Ig superfamily. Both molecules have four putative transmembrane segments and a probably topology where both amino- and carboxy termini protrude into the cytoplasm.

MS4A3

• refseq_MS4A3.F1 refseq_MS4A3.R1 191 329
• NCBIGene 36.3 932
• Single exon skipping, size difference: 138
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_006138

• Changed! pfam CD20 148aa 7e-24 in ref transcript
  • CD20/IgE Fc receptor beta subunit family. This family includes the CD20 protein and the beta subunit of the high affinity receptor for IgE Fc. The high affinity receptor for IgE is a tetrameric structure consisting of a single IgE-binding alpha subunit, a single beta subunit, and two disulfide-linked gamma subunits. The alpha subunit of Fc epsilon RI and most Fc receptors are homologous members of the Ig superfamily. By contrast, the beta and gamma subunits from Fc epsilon RI are not homologous to the Ig superfamily. Both molecules have four putative transmembrane segments and a probably topology where both amino- and carboxy termini protrude into the cytoplasm.
• Changed! pfam CD20 106aa 1e-20 in modified transcript

MS4A6A

• refseq_MS4A6A.F2 refseq_MS4A6A.R2 141 245
• NCBIGene 36.3 64231
• Alternative 5-prime, size difference: 104
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_152852

• Changed! pfam CD20 163aa 3e-27 in ref transcript
  • CD20/IgE Fc receptor beta subunit family. This family includes the CD20 protein and the beta subunit of the high affinity receptor for IgE Fc. The high affinity receptor for IgE is a tetrameric structure consisting of a single IgE-binding alpha subunit, a single beta subunit, and two disulfide-linked gamma subunits. The alpha subunit of Fc epsilon RI and most Fc receptors are homologous members of the Ig superfamily. By contrast, the beta and gamma subunits from Fc epsilon RI are not homologous to the Ig superfamily. Both molecules have four putative transmembrane segments and a probably topology where both amino- and carboxy termini protrude into the cytoplasm.
• Changed! pfam CD20 101aa 1e-14 in modified transcript

MS4A7

• refseq_MS4A7.F1 refseq_MS4A7.R1 101 149
• NCBIGene 36.3 58475
• Alternative 5-prime, size difference: 48
• Exclusion in 5'UTR
• Reference transcript: NM_021201

• pfam CD20 162aa 6e-33 in ref transcript
  • CD20/IgE Fc receptor beta subunit family. This family includes the CD20 protein and the beta subunit of the high affinity receptor for IgE Fc. The high affinity receptor for IgE is a tetrameric structure consisting of a single IgE-binding alpha subunit, a single beta subunit, and two disulfide-linked gamma subunits. The alpha subunit of Fc epsilon RI and most Fc receptors are homologous members of the Ig superfamily. By contrast, the beta and gamma subunits from Fc epsilon RI are not homologous to the Ig superfamily. Both molecules have four putative transmembrane segments and a probably topology where both amino- and carboxy termini protrude into the cytoplasm.

MS4A7

• refseq_MS4A7.F4 refseq_MS4A7.R4 162 297
• NCBIGene 36.3 58475
• Single exon skipping, size difference: 135
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_206939

• Changed! pfam CD20 162aa 6e-33 in ref transcript
  • CD20/IgE Fc receptor beta subunit family. This family includes the CD20 protein and the beta subunit of the high affinity receptor for IgE Fc. The high affinity receptor for IgE is a tetrameric structure consisting of a single IgE-binding alpha subunit, a single beta subunit, and two disulfide-linked gamma subunits. The alpha subunit of Fc epsilon RI and most Fc receptors are homologous members of the Ig superfamily. By contrast, the beta and gamma subunits from Fc epsilon RI are not homologous to the Ig superfamily. Both molecules have four putative transmembrane segments and a probably topology where both amino- and carboxy termini protrude into the cytoplasm.
• Changed! pfam CD20 121aa 1e-21 in modified transcript

MSH5

• refseq_MSH5.F1 refseq_MSH5.R1 219 270
• NCBIGene 36.3 4439
• Alternative 3-prime, size difference: 51
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_025259

• cd ABC_MSH5_euk 207aa 5e-77 in ref transcript
  • MutS5 homolog in eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA structures or lesions results in ADP/ATP exchange.
• TIGR mutS1 529aa 9e-66 in ref transcript
• COG MutS 561aa 1e-84 in ref transcript
  • Mismatch repair ATPase (MutS family) [DNA replication, recombination, and repair].

MSH5

• refseq_MSH5.F4 refseq_MSH5.R4 114 272
• NCBIGene 36.3 4439
• Alternative 5-prime, size difference: 158
• Inclusion in 5'UTR
• Reference transcript: NM_025259

• cd ABC_MSH5_euk 207aa 5e-77 in ref transcript
  • MutS5 homolog in eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA structures or lesions results in ADP/ATP exchange.
• TIGR mutS1 529aa 9e-66 in ref transcript
• COG MutS 561aa 1e-84 in ref transcript
  • Mismatch repair ATPase (MutS family) [DNA replication, recombination, and repair].

MSL3L1

• refseq_MSL3L1.F2 refseq_MSL3L1.R2 139 222
• NCBIGene 36.3 10943
• Single exon skipping, size difference: 83
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_078629

• Changed! cd CHROMO 46aa 0.005 in ref transcript
  • Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence implicates the chromo domain in the binding activity of these proteins to methylated histone tails and maybe RNA. May occur as single instance, in a tandem arrangement or followd by a related "chromo shadow" domain.
• Changed! pfam MRG 110aa 5e-26 in ref transcript
  • MRG. This family consists of three different eukaryotic proteins (mortality factor 4 (MORF4/MRG15), male-specific lethal 3(MSL-3) and ESA1-associated factor 3(EAF3)). It is thought that the MRG family is involved in transcriptional regulation via histone acetylation. It contains 2 chromo domains and a leucine zipper motif.
• Changed! pfam MRG 57aa 5e-19 in ref transcript
• Changed! smart CHROMO 43aa 2e-04 in ref transcript
  • Chromatin organization modifier domain.

MSMB

• refseq_MSMB.F1 refseq_MSMB.R1 107 213
• NCBIGene 36.3 4477
• Single exon skipping, size difference: 106
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_002443

• Changed! pfam PSP94 114aa 2e-50 in ref transcript
  • Beta-microseminoprotein (PSP-94). This family consists of the mammalian specific protein beta-microseminoprotein. Prostatic secretory protein of 94 amino acids (PSP94), also called beta-microseminoprotein, is a small, nonglycosylated protein, rich in cysteine residues. It was first isolated as a major protein from human seminal plasma. The exact function of this protein is unknown.
• Changed! pfam PSP94 36aa 2e-13 in modified transcript

MSRB3

• refseq_MSRB3.F1 refseq_MSRB3.R1 177 304
• NCBIGene 36.3 253827
• Single exon skipping, size difference: 127
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_198080

• Changed! pfam SelR 123aa 3e-52 in ref transcript
  • SelR domain. Methionine sulfoxide reduction is an important process, by which cells regulate biological processes and cope with oxidative stress. MsrA, a protein involved in the reduction of methionine sulfoxides in proteins, has been known for four decades and has been extensively characterised with respect to structure and function. However, recent studies revealed that MsrA is only specific for methionine-S-sulfoxides. Because oxidised methionines occur in a mixture of R and S isomers in vivo, it was unclear how stereo-specific MsrA could be responsible for the reduction of all protein methionine sulfoxides. It appears that a second methionine sulfoxide reductase, SelR, evolved that is specific for methionine-R-sulfoxides, the activity that is different but complementary to that of MsrA. Thus, these proteins, working together, could reduce both stereoisomers of methionine sulfoxide. This domain is found both in SelR proteins and fused with the peptide methionine sulfoxide reductase enzymatic domain pfam01625. The domain has two conserved cysteine and histidines. The domain binds both selenium and zinc. The final cysteine is found to be replaced by the rare amino acid selenocysteine in some members of the family. This family has methionine-R-sulfoxide reductase activity.
• Changed! PRK PRK00222 129aa 3e-61 in ref transcript
  • methionine sulfoxide reductase B; Provisional.

MCAT

• refseq_MT.F1 refseq_MT.R1 110 328
• NCBIGene 36.3 27349
• Single exon skipping, size difference: 218
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_173467

• Changed! TIGR fabD 295aa 4e-53 in ref transcript
  • The seed alignment for this family of proteins contains a single member each from a number of bacterial species but also an additional pair of closely related, uncharacterized proteins from B. subtilis, one of which has a long C-terminal extension.
• Changed! COG FabD 299aa 1e-55 in ref transcript
  • (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism].
• Changed! TIGR fabD 107aa 6e-21 in modified transcript
• Changed! COG FabD 108aa 5e-19 in modified transcript

MTHFD2

• refseq_MTHFD2.F1 refseq_MTHFD2.R1 176 274
• NCBIGene 36.3 10797
• Single exon skipping, size difference: 98
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_006636

• Changed! cd NAD_bind_m-THF_DH_Cyclohyd 180aa 5e-67 in ref transcript
  • NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase. NADP binding domain of the Methylene-Tetrahydrofolate Dehydrogenase/cyclohydrolase (m-THF DH/cyclohydrolase) bifunctional enzyme. Tetrahydrofolate is a versatile carrier of activated one-carbon units. The major one-carbon folate donors are N-5 methyltetrahydrofolate, N5,N10-m-THF, and N10-formayltetrahydrofolate. The oxidation of metabolic intermediate m-THF to m-THF requires the enzyme m-THF DH. In addition, most DHs also have an associated cyclohydrolase activity which catalyzes its hydrolysis to N10-formyltetrahydrofolate. m-THF DH is typically found as part of a multifunctional protein in eukaryotes. NADP-dependent m-THF DH in mammals, birds and yeast are components of a trifunctional enzyme with DH, cyclohydrolase, and synthetase activities. Certain eukaryotic cells also contain homodimeric bifunctional DH/cyclodrolase form. In bacteria, monofucntional DH, as well as bifunctional m-THF m-THF DHm-THF DHDH/cyclodrolase are found. In addition, yeast (S. cerevisiae) also express an monofunctional DH. This family contains the bifunctional DH/cyclohydrolase. M-THF DH, like other amino acid DH-like NAD(P)-binding domains, is a member of the Rossmann fold superfamily which includes glutamate, leucine, and phenylalanine DHs, m-THF DH, methylene-tetrahydromethanopterin DH, m-THF DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids to keto acids with NAD(P)+ as a cofactor. The NAD(P)-binding Rossmann fold superfamily includes a wide variety of protein families including NAD(P)- binding domains of alcohol DHs, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate DH, lactate/malate DHs, formate/glycerate DHs, siroheme synthases, 6-phosphogluconate DH, amino acid DHs, repressor rex, NAD-binding potassium channel domain, CoA-binding, and ornithine cyclodeaminase-like domains.
• Changed! pfam THF_DHG_CYH_C 173aa 1e-64 in ref transcript
  • Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain.
• Changed! pfam THF_DHG_CYH 118aa 4e-35 in ref transcript
  • Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain.
• Changed! COG FolD 296aa 2e-83 in ref transcript
  • 5,10-methylene-tetrahydrofolate dehydrogenase/Methenyl tetrahydrofolate cyclohydrolase [Coenzyme metabolism].

MTIF2

• refseq_MTIF2.F2 refseq_MTIF2.R2 229 367
• NCBIGene 36.3 4528
• Single exon skipping, size difference: 138
• Exclusion in 5'UTR
• Reference transcript: NM_001005369

• cd IF2_eIF5B 165aa 2e-76 in ref transcript
  • IF2/eIF5B (initiation factors 2/ eukaryotic initiation factor 5B) subfamily. IF2/eIF5B contribute to ribosomal subunit joining and function as GTPases that are maximally activated by the presence of both ribosomal subunits. As seen in other GTPases, IF2/IF5B undergoes conformational changes between its GTP- and GDP-bound states. Eukaryotic IF2/eIF5Bs possess three characteristic segments, including a divergent N-terminal region followed by conserved central and C-terminal segments. This core region is conserved among all known eukaryotic and archaeal IF2/eIF5Bs and eubacterial IF2s.
• cd IF2_mtIF2_II 95aa 1e-32 in ref transcript
  • This family represents the domain II of bacterial Initiation Factor 2 (IF2) and its eukaryotic mitochondrial homologue mtIF2. IF2, the largest initiation factor is an essential GTP binding protein. In E. coli three natural forms of IF2 exist in the cell, IF2alpha, IF2beta1, and IF2beta2. Bacterial IF-2 is structurally and functionally related to eukaryotic mitochondrial mtIF-2.
• cd mtIF2_IVc 88aa 5e-22 in ref transcript
  • mtIF2_IVc: this family represents the C2 subdomain of domain IV of mitochondrial translation initiation factor 2 (mtIF2) which adopts a beta-barrel fold displaying a high degree of structural similarity with domain II of the translation elongation factor EF-Tu. The C-terminal part of mtIF2 contains the entire fMet-tRNAfmet binding site of IF-2 and is resistant to proteolysis. This C-terminal portion consists of two domains, IF2 C1 and IF2 C2. IF2 C2 been shown to contain all molecular determinants necessary and sufficient for the recognition and binding of fMet-tRNAfMet. Like IF2 from certain prokaryotes such as Thermus thermophilus, mtIF2lacks domain II which is thought to be involved in binding of E.coli IF-2 to 30S subunits.
• cd IF2_eIF5B 162aa 8e-04 in ref transcript
• TIGR IF-2 545aa 1e-146 in ref transcript
  • This model discriminates eubacterial (and mitochondrial) translation initiation factor 2 (IF-2), encoded by the infB gene in bacteria, from similar proteins in the Archaea and Eukaryotes. In the bacteria and in organelles, the initiator tRNA is charged with N-formyl-Met instead of Met. This translation factor acts in delivering the initator tRNA to the ribosome. It is one of a number of GTP-binding translation factors recognized by the pfam HMM GTP_EFTU.
• PRK infB 563aa 0.0 in ref transcript
  • translation initiation factor IF-2; Validated.

MTMR2

• refseq_MTMR2.F1 refseq_MTMR2.R1 102 225
• NCBIGene 36.3 8898
• Single exon skipping, size difference: 123
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_016156

• Changed! pfam Myotub-related 118aa 5e-54 in ref transcript
  • Myotubularin-related. This family represents a region within eukaryotic myotubularin-related proteins that is sometimes found with pfam02893. Myotubularin is a dual-specific lipid phosphatase that dephosphorylates phosphatidylinositol 3-phosphate and phosphatidylinositol (3,5)-bi-phosphate. Mutations in gene encoding myotubularin-related proteins have been associated with disease.
• Changed! pfam GRAM 62aa 5e-09 in ref transcript
  • GRAM domain. The GRAM domain is found in in glucosyltransferases, myotubularins and other putative membrane-associated proteins.
• Changed! smart PTPc_motif 107aa 6e-06 in ref transcript
  • Protein tyrosine phosphatase, catalytic domain motif.

MTMR2

• refseq_MTMR2.F2 refseq_MTMR2.R2 154 225
• NCBIGene 36.3 8898
• Single exon skipping, size difference: 71
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_016156

• Changed! pfam Myotub-related 118aa 5e-54 in ref transcript
  • Myotubularin-related. This family represents a region within eukaryotic myotubularin-related proteins that is sometimes found with pfam02893. Myotubularin is a dual-specific lipid phosphatase that dephosphorylates phosphatidylinositol 3-phosphate and phosphatidylinositol (3,5)-bi-phosphate. Mutations in gene encoding myotubularin-related proteins have been associated with disease.
• Changed! pfam GRAM 62aa 5e-09 in ref transcript
  • GRAM domain. The GRAM domain is found in in glucosyltransferases, myotubularins and other putative membrane-associated proteins.
• Changed! smart PTPc_motif 107aa 6e-06 in ref transcript
  • Protein tyrosine phosphatase, catalytic domain motif.

MTMR3

• refseq_MTMR3.F1 refseq_MTMR3.R1 138 165
• NCBIGene 36.3 8897
• Single exon skipping, size difference: 27
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_021090

• Changed! cd FYVE 55aa 4e-15 in ref transcript
  • FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;.
• pfam Myotub-related 163aa 5e-38 in ref transcript
  • Myotubularin-related. This family represents a region within eukaryotic myotubularin-related proteins that is sometimes found with pfam02893. Myotubularin is a dual-specific lipid phosphatase that dephosphorylates phosphatidylinositol 3-phosphate and phosphatidylinositol (3,5)-bi-phosphate. Mutations in gene encoding myotubularin-related proteins have been associated with disease.
• Changed! smart FYVE 66aa 4e-22 in ref transcript
  • Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the PHD finger and the RIN G finger. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. The FYVE finger functions in the membrane recruitment of cytosolic proteins by binding to phosphatidylinositol 3-phosphate (PI3P), which is prominent on endosomes. The R+HHC+XCG motif is critical for PI3P binding.
• smart PTPc_motif 40aa 7e-05 in ref transcript
  • Protein tyrosine phosphatase, catalytic domain motif.
• Changed! cd FYVE 64aa 8e-13 in modified transcript
• Changed! smart FYVE 75aa 8e-20 in modified transcript

MTMR3

• refseq_MTMR3.F3 refseq_MTMR3.R3 185 296
• NCBIGene 36.3 8897
• Single exon skipping, size difference: 111
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_021090

• cd FYVE 55aa 4e-15 in ref transcript
  • FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;.
• pfam Myotub-related 163aa 5e-38 in ref transcript
  • Myotubularin-related. This family represents a region within eukaryotic myotubularin-related proteins that is sometimes found with pfam02893. Myotubularin is a dual-specific lipid phosphatase that dephosphorylates phosphatidylinositol 3-phosphate and phosphatidylinositol (3,5)-bi-phosphate. Mutations in gene encoding myotubularin-related proteins have been associated with disease.
• smart FYVE 66aa 4e-22 in ref transcript
  • Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the PHD finger and the RIN G finger. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. The FYVE finger functions in the membrane recruitment of cytosolic proteins by binding to phosphatidylinositol 3-phosphate (PI3P), which is prominent on endosomes. The R+HHC+XCG motif is critical for PI3P binding.
• smart PTPc_motif 40aa 7e-05 in ref transcript
  • Protein tyrosine phosphatase, catalytic domain motif.

MTO1

• refseq_MTO1.F2 refseq_MTO1.R2 181 256
• NCBIGene 36.3 25821
• Single exon skipping, size difference: 75
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_133645

• Changed! TIGR gidA 652aa 0.0 in ref transcript
  • GidA, the longer of two forms of GidA-related proteins, appears to be present in all complete eubacterial genomes so far, as well as Saccharomyces cerevisiae. A subset of these organisms have a closely related protein. GidA is absent in the Archaea. It appears to act with MnmE, in an alpha2/beta2 heterotetramer, in the 5-carboxymethylaminomethyl modification of uridine 34 in certain tRNAs. The shorter, related protein, previously called gid or gidA(S), is now called TrmFO (see model TIGR00137).
• Changed! PRK PRK05192 657aa 0.0 in ref transcript
  • tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated.
• Changed! TIGR gidA 627aa 0.0 in modified transcript
• Changed! PRK PRK05192 632aa 0.0 in modified transcript

MTP18

• refseq_MTP18.F1 refseq_MTP18.R1 158 391
• NCBIGene 36.3 51537
• Single exon skipping, size difference: 233
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_016498

• Changed! pfam MTP18 130aa 1e-45 in ref transcript
  • Mitochondrial 18 KDa protein (MTP18). This family of proteins are mitochondrial 18KDa proteins that are often misannotated as carbonic anhydrases. It was shown that knockdown of MTP18 protein results in a cytochrome c release from mitochondria and consequently leads to apoptosis. Overexpression studies suggest that MTP18 is required for mitochondrial fission.
• Changed! pfam MTP18 54aa 1e-16 in modified transcript

MTRR

• refseq_MTRR.F2 refseq_MTRR.R2 114 140
• NCBIGene 36.3 4552
• Alternative 5-prime, size difference: 26
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_024010

• Changed! cd methionine_synthase_red 421aa 1e-164 in ref transcript
  • Human methionine synthase reductase (MSR) restores methionine sythase which is responsible for the regeneration of methionine from homocysteine, as well as the coversion of methyltetrahydrofolate to tetrahydrofolate. In MSR, electrons are transferred from NADPH to FAD to FMN to cob(II)alamin. MSR resembles proteins of the cytochrome p450 family including nitric oxide synthase, the alpha subunit of sulfite reductase, but contains an extended hinge region. NADPH cytochrome p450 reductase (CYPOR) serves as an electron donor in several oxygenase systems and is a component of nitric oxide synthases and methionine synthase reductases. CYPOR transfers two electrons from NADPH to the heme of cytochrome p450 via FAD and FMN. CYPORs resemble ferredoxin reductase (FNR) but have a connecting subdomain inserted within the flavin binding region, which helps orient the FMN binding doamin with the FNR module. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently bound FAD as a prosthetic group) are present in chloroplasts, mitochondria, and bacteria in which they participate in a wide variety of redox metabolic pathways. The C-terminal domain contains most of the NADP(H) binding residues and the N-terminal domain interacts non-covalently with the isoalloxazine rings of the flavin molecule which lies largely in a large gap betweed the two domains. Ferredoxin-NADP+ reductase first accepts one electron from reduced ferredoxin to form a flavin semiquinone intermediate. The enzyme then accepts a second electron to form FADH2 which then transfers two electrons and a proton to NADP+ to form NADPH.
• Changed! TIGR cysJ 414aa 4e-49 in ref transcript
  • This model describes an NADPH-dependent sulfite reductase flavoprotein subunit. Most members of this family are found in Cys biosynthesis gene clusters. The closest homologs below the trusted cutoff are designated as subunits nitrate reductase.
• Changed! pfam Flavodoxin_1 137aa 1e-29 in ref transcript
  • Flavodoxin.
• Changed! COG CysJ 432aa 1e-70 in ref transcript
  • Sulfite reductase, alpha subunit (flavoprotein) [Inorganic ion transport and metabolism].
• Changed! COG CysJ 188aa 1e-19 in ref transcript

MTUS1

• refseq_MTUS1.F2 refseq_MTUS1.R2 105 166
• NCBIGene 36.2 57509
• Single exon skipping, size difference: 61
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_001001924

• Changed! TIGR SMC_prok_B 297aa 3e-14 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• Changed! COG Smc 320aa 2e-11 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].

MTX1

• refseq_MTX1.F1 refseq_MTX1.R1 114 207
• NCBIGene 36.3 4580
• Single exon skipping, size difference: 93
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_002455

• Changed! cd GST_C_Metaxin1_3 137aa 3e-51 in ref transcript
  • GST_C family, Metaxin subfamily, Metaxin 1-like proteins; composed of metaxins 1 and 3, and similar proteins. Mammalian metaxin (or metaxin 1) is a component of the preprotein import complex of the mitochondrial outer membrane. Metaxin extends to the cytosol and is anchored to the mitochondrial membrane through its C-terminal domain. In mice, metaxin is required for embryonic development. Like the murine gene, the human metaxin gene is located downstream to the glucocerebrosidase (GBA) pseudogene and is convergently transcribed. Inherited deficiency of GBA results in Gaucher disease, which presents many diverse clinical phenotypes. Alterations in the metaxin gene, in addition to GBA mutations, may be associated with Gaucher disease. Genome sequencing shows that a third metaxin gene also exists in zebrafish, Xenopus, chicken, and mammals.
• Changed! cd GST_N_Metaxin1_like 74aa 7e-23 in ref transcript
  • GST_N family, Metaxin subfamily, Metaxin 1-like proteins; composed of metaxins 1 and 3, and similar proteins including Tom37 from fungi. Mammalian metaxin (or metaxin 1) and the fungal protein Tom37 are components of preprotein import complexes of the mitochondrial outer membrane. Metaxin extends to the cytosol and is anchored to the mitochondrial membrane through its C-terminal domain. In mice, metaxin is required for embryonic development. Like the murine gene, the human metaxin gene is located downstream to the glucocerebrosidase (GBA) pseudogene and is convergently transcribed. Inherited deficiency of GBA results in Gaucher disease, which presents many diverse clinical phenotypes. Alterations in the metaxin gene, in addition to GBA mutations, may be associated with Gaucher disease. Genome sequencing shows that a third metaxin gene also exists in zebrafish, Xenopus, chicken and mammals.
• Changed! pfam Tom37 219aa 4e-58 in ref transcript
  • Outer mitochondrial membrane transport complex protein. The TOM37 protein is one of the outer membrane proteins that make up the TOM complex for guiding cytosolic mitochondrial beta-barrel proteins from the cytosol across the outer mitochondrial membrane into the intramembrane space. In conjunction with TOM70 it guides peptides without an MTS into TOM40, the protein that forms the passage through the outer membrane. It has homology with Metaxin-1, also part of the outer mitochondrial membrane beta-barrel protein transport complex.
• Changed! cd GST_C_Metaxin1_3 134aa 3e-50 in modified transcript
• Changed! cd GST_N_Metaxin1_like 73aa 1e-22 in modified transcript
• Changed! pfam Tom37 188aa 8e-43 in modified transcript

MTX2

• refseq_MTX2.F1 refseq_MTX2.R1 153 357
• NCBIGene 36.3 10651
• Single exon skipping, size difference: 204
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_006554

• Changed! cd GST_C_Metaxin2 126aa 2e-62 in ref transcript
  • GST_C family, Metaxin subfamily, Metaxin 2; a metaxin 1 binding protein identified through a yeast two-hybrid system using metaxin 1 as the bait. Metaxin 2 shares sequence similarity with metaxin 1 but does not contain a C-terminal mitochondrial outer membrane signal-anchor domain. It associates with mitochondrial membranes through its interaction with metaxin 1, which is a component of the mitochondrial preprotein import complex of the outer membrane. The biological function of metaxin 2 is unknown. It is likely that it also plays a role in protein translocation into the mitochondria. However, this has not been experimentally validated. In a recent proteomics study, it has been shown that metaxin 2 is overexpressed in response to lipopolysaccharide-induced liver injury.
• Changed! cd GST_N_Metaxin2 74aa 8e-32 in ref transcript
  • GST_N family, Metaxin subfamily, Metaxin 2; a metaxin 1 binding protein identified through a yeast two-hybrid system using metaxin 1 as the bait. Metaxin 2 shares sequence similarity with metaxin 1 but does not contain a C-terminal mitochondrial outer membrane signal-anchor domain. It associates with mitochondrial membranes through its interaction with metaxin 1, which is a component of the mitochondrial preprotein import complex of the outer membrane. The biological function of metaxin 2 is unknown. It is likely that it also plays a role in protein translocation into the mitochondria. However, this has not been experimentally validated. In a recent proteomics study, it has been shown that metaxin 2 is overexpressed in response to lipopolysaccharide-induced liver injury.
• Changed! pfam Tom37 197aa 2e-11 in ref transcript
  • Outer mitochondrial membrane transport complex protein. The TOM37 protein is one of the outer membrane proteins that make up the TOM complex for guiding cytosolic mitochondrial beta-barrel proteins from the cytosol across the outer mitochondrial membrane into the intramembrane space. In conjunction with TOM70 it guides peptides without an MTS into TOM40, the protein that forms the passage through the outer membrane. It has homology with Metaxin-1, also part of the outer mitochondrial membrane beta-barrel protein transport complex.
• Changed! COG Gst 187aa 0.002 in ref transcript
  • Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones].

MXI1

• refseq_MXI1.F1 refseq_MXI1.R1 144 174
• NCBIGene 36.3 4601
• Single exon skipping, size difference: 30
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_130439

• Changed! cd HLH 60aa 2e-06 in ref transcript
  • Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins.
• Changed! smart HLH 53aa 1e-07 in ref transcript
  • helix loop helix domain.
• Changed! cd HLH 47aa 0.003 in modified transcript
• Changed! smart HLH 48aa 2e-05 in modified transcript

MXRA7

• refseq_MXRA7.F2 refseq_MXRA7.R2 307 388
• NCBIGene 36.3 439921
• Single exon skipping, size difference: 81
• Exclusion of the stop codon
• Reference transcript: NM_001008529

MYADM

• refseq_MYADM.F1 refseq_MYADM.R1 107 171
• NCBIGene 36.3 91663
• Alternative 3-prime, size difference: 64
• Inclusion in 5'UTR
• Reference transcript: NM_138373

• pfam MARVEL 108aa 2e-10 in ref transcript
  • Membrane-associating domain. MARVEL domain-containing proteins are often found in lipid-associating proteins - such as Occludin and MAL family proteins. It may be part of the machinery of membrane apposition events, such as transport vesicle biogenesis.
• pfam MARVEL 152aa 2e-07 in ref transcript

MYBPC1

• refseq_MYBPC1.F1 refseq_MYBPC1.R1 129 188
• NCBIGene 36.3 4604
• Single exon skipping, size difference: 59
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_002465

• cd IGcam 89aa 2e-15 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• cd FN3 84aa 1e-11 in ref transcript
  • Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.
• cd FN3 81aa 1e-10 in ref transcript
• cd FN3 85aa 2e-08 in ref transcript
• cd IGcam 80aa 4e-07 in ref transcript
• cd IGcam 90aa 1e-06 in ref transcript
• cd IGcam 70aa 0.001 in ref transcript
• cd IGcam 75aa 0.003 in ref transcript
• pfam I-set 90aa 1e-17 in ref transcript
  • Immunoglobulin I-set domain.
• smart FN3 83aa 2e-12 in ref transcript
  • Fibronectin type 3 domain. One of three types of internal repeat within the plasma protein, fibronectin. The tenth fibronectin type III repeat contains a RGD cell recognition sequence in a flexible loop between 2 strands. Type III modules are present in both extracellular and intracellular proteins.
• pfam I-set 78aa 6e-11 in ref transcript
• pfam I-set 85aa 4e-10 in ref transcript
• pfam I-set 69aa 2e-09 in ref transcript
• pfam I-set 84aa 8e-08 in ref transcript
• smart FN3 74aa 2e-07 in ref transcript
• smart IG_like 97aa 4e-07 in ref transcript
  • Immunoglobulin like. IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
• smart IG_like 82aa 3e-06 in ref transcript
• smart FN3 83aa 1e-04 in ref transcript

MYBPC1

• refseq_MYBPC1.F4 refseq_MYBPC1.R4 105 180
• NCBIGene 36.3 4604
• Multiple exon skipping, size difference: 75
• Exclusion in the protein (no frameshift), Exclusion in the protein (no frameshift)
• Reference transcript: NM_002465

• cd IGcam 89aa 2e-15 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• cd FN3 84aa 1e-11 in ref transcript
  • Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.
• cd FN3 81aa 1e-10 in ref transcript
• cd FN3 85aa 2e-08 in ref transcript
• cd IGcam 80aa 4e-07 in ref transcript
• cd IGcam 90aa 1e-06 in ref transcript
• cd IGcam 70aa 0.001 in ref transcript
• cd IGcam 75aa 0.003 in ref transcript
• pfam I-set 90aa 1e-17 in ref transcript
  • Immunoglobulin I-set domain.
• smart FN3 83aa 2e-12 in ref transcript
  • Fibronectin type 3 domain. One of three types of internal repeat within the plasma protein, fibronectin. The tenth fibronectin type III repeat contains a RGD cell recognition sequence in a flexible loop between 2 strands. Type III modules are present in both extracellular and intracellular proteins.
• pfam I-set 78aa 6e-11 in ref transcript
• pfam I-set 85aa 4e-10 in ref transcript
• pfam I-set 69aa 2e-09 in ref transcript
• pfam I-set 84aa 8e-08 in ref transcript
• smart FN3 74aa 2e-07 in ref transcript
• smart IG_like 97aa 4e-07 in ref transcript
  • Immunoglobulin like. IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
• smart IG_like 82aa 3e-06 in ref transcript
• smart FN3 83aa 1e-04 in ref transcript

MYBPC1

• refseq_MYBPC1.F5 refseq_MYBPC1.R5 190 244
• NCBIGene 36.3 4604
• Single exon skipping, size difference: 54
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_002465

• cd IGcam 89aa 2e-15 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• cd FN3 84aa 1e-11 in ref transcript
  • Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.
• cd FN3 81aa 1e-10 in ref transcript
• Changed! cd FN3 85aa 2e-08 in ref transcript
• cd IGcam 80aa 4e-07 in ref transcript
• cd IGcam 90aa 1e-06 in ref transcript
• cd IGcam 70aa 0.001 in ref transcript
• cd IGcam 75aa 0.003 in ref transcript
• pfam I-set 90aa 1e-17 in ref transcript
  • Immunoglobulin I-set domain.
• smart FN3 83aa 2e-12 in ref transcript
  • Fibronectin type 3 domain. One of three types of internal repeat within the plasma protein, fibronectin. The tenth fibronectin type III repeat contains a RGD cell recognition sequence in a flexible loop between 2 strands. Type III modules are present in both extracellular and intracellular proteins.
• pfam I-set 78aa 6e-11 in ref transcript
• pfam I-set 85aa 4e-10 in ref transcript
• pfam I-set 69aa 2e-09 in ref transcript
• pfam I-set 84aa 8e-08 in ref transcript
• smart FN3 74aa 2e-07 in ref transcript
• smart IG_like 97aa 4e-07 in ref transcript
  • Immunoglobulin like. IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
• smart IG_like 82aa 3e-06 in ref transcript
• Changed! smart FN3 83aa 1e-04 in ref transcript
• Changed! cd FN3 103aa 2e-05 in modified transcript
• Changed! smart FN3 101aa 0.001 in modified transcript

MYH11

• refseq_MYH11.F1 refseq_MYH11.R1 172 211
• NCBIGene 36.3 4629
• Single exon skipping, size difference: 39
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_001040114

• cd MYSc_type_II 709aa 0.0 in ref transcript
  • Myosin motor domain, type II myosins. Myosin II mediates cortical contraction in cell motility, and is the motor in smooth and skeletal muscle. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle.
• pfam Myosin_head 692aa 0.0 in ref transcript
  • Myosin head (motor domain).
• Changed! pfam Myosin_tail_1 820aa 1e-126 in ref transcript
  • Myosin tail. The myosin molecule is a multi-subunit complex made up of two heavy chains and four light chains it is a fundamental contractile protein found in all eukaryote cell types. This family consists of the coiled-coil myosin heavy chain tail region. The coiled-coil is composed of the tail from two molecules of myosin. These can then assemble into the macromolecular thick filament. The coiled-coil region provides the structural backbone the thick filament.
• pfam SMC_N 233aa 1e-09 in ref transcript
  • RecF/RecN/SMC N terminal domain. This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.
• pfam Myosin_N 43aa 1e-09 in ref transcript
  • Myosin N-terminal SH3-like domain. This domain has an SH3-like fold. It is found at the N-terminus of many but not all myosins. The function of this domain is unknown.
• COG COG5022 1265aa 0.0 in ref transcript
  • Myosin heavy chain [Cytoskeleton].
• Changed! COG Smc 392aa 2e-05 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].
• COG COG4372 227aa 2e-04 in ref transcript
  • Uncharacterized protein conserved in bacteria with the myosin-like domain [Function unknown].
• COG Smc 356aa 0.001 in ref transcript
• Changed! pfam Myosin_tail_1 819aa 1e-126 in modified transcript
• Changed! COG Smc 386aa 2e-05 in modified transcript

MYH11

• refseq_MYH11.F3 refseq_MYH11.R3 104 125
• NCBIGene 36.3 4629
• Single exon skipping, size difference: 21
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001040114

• Changed! cd MYSc_type_II 709aa 0.0 in ref transcript
  • Myosin motor domain, type II myosins. Myosin II mediates cortical contraction in cell motility, and is the motor in smooth and skeletal muscle. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle.
• Changed! pfam Myosin_head 692aa 0.0 in ref transcript
  • Myosin head (motor domain).
• pfam Myosin_tail_1 820aa 1e-126 in ref transcript
  • Myosin tail. The myosin molecule is a multi-subunit complex made up of two heavy chains and four light chains it is a fundamental contractile protein found in all eukaryote cell types. This family consists of the coiled-coil myosin heavy chain tail region. The coiled-coil is composed of the tail from two molecules of myosin. These can then assemble into the macromolecular thick filament. The coiled-coil region provides the structural backbone the thick filament.
• pfam SMC_N 233aa 1e-09 in ref transcript
  • RecF/RecN/SMC N terminal domain. This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.
• pfam Myosin_N 43aa 1e-09 in ref transcript
  • Myosin N-terminal SH3-like domain. This domain has an SH3-like fold. It is found at the N-terminus of many but not all myosins. The function of this domain is unknown.
• Changed! COG COG5022 1265aa 0.0 in ref transcript
  • Myosin heavy chain [Cytoskeleton].
• COG Smc 392aa 2e-05 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].
• COG COG4372 227aa 2e-04 in ref transcript
  • Uncharacterized protein conserved in bacteria with the myosin-like domain [Function unknown].
• COG Smc 356aa 0.001 in ref transcript
• Changed! cd MYSc_type_II 702aa 0.0 in modified transcript
• Changed! pfam Myosin_head 685aa 0.0 in modified transcript
• Changed! TIGR SMC_prok_A 236aa 0.001 in modified transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent.
• Changed! COG COG5022 1258aa 0.0 in modified transcript

MYL6

• refseq_MYL6.F2 refseq_MYL6.R2 241 286
• NCBIGene 36.3 4637
• Single exon skipping, size difference: 45
• Exclusion of the stop codon
• Reference transcript: NM_021019

• Changed! cd EFh 56aa 4e-05 in ref transcript
  • EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers.
• smart EFh 29aa 0.003 in ref transcript
  • EF-hand, calcium binding motif. EF-hands are calcium-binding motifs that occur at least in pairs. Links between disease states and genes encoding EF-hands, particularly the S100 subclass, are emerging. Each motif consists of a 12 residue loop flanked on either side by a 12 residue alpha-helix. EF-hands undergo a conformational change unpon binding calcium ions.
• Changed! PTZ PTZ00184 147aa 4e-30 in ref transcript
  • calmodulin; Provisional.
• Changed! cd EFh 56aa 1e-05 in modified transcript
• Changed! PTZ PTZ00184 147aa 6e-30 in modified transcript

MYL9

• refseq_MYL9.F2 refseq_MYL9.R2 261 423
• NCBIGene 36.3 10398
• Single exon skipping, size difference: 162
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_006097

• Changed! cd EFh 62aa 3e-04 in ref transcript
  • EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers.
• Changed! cd EFh 58aa 4e-04 in ref transcript
• smart EFh 29aa 0.002 in ref transcript
  • EF-hand, calcium binding motif. EF-hands are calcium-binding motifs that occur at least in pairs. Links between disease states and genes encoding EF-hands, particularly the S100 subclass, are emerging. Each motif consists of a 12 residue loop flanked on either side by a 12 residue alpha-helix. EF-hands undergo a conformational change unpon binding calcium ions.
• Changed! COG FRQ1 150aa 1e-26 in ref transcript
  • Ca2+-binding protein (EF-Hand superfamily) [Signal transduction mechanisms / Cytoskeleton / Cell division and chromosome partitioning / General function prediction only].
• Changed! cd EFh 78aa 6e-04 in modified transcript
• Changed! PTZ PTZ00184 85aa 2e-08 in modified transcript
  • calmodulin; Provisional.

MYLK

• refseq_MYLK.F2 refseq_MYLK.R2 155 375
• NCBIGene 36.2 4638
• Exon skipping and alternative 3-prime or 5-prime, size difference: 220
• Exclusion in the protein (no frameshift), Exclusion in the protein causing a frameshift
• Reference transcript: NM_053025

• Changed! cd S_TKc 256aa 7e-74 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• cd IGcam 88aa 1e-16 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• cd IGcam 90aa 9e-16 in ref transcript
• cd IGcam 90aa 5e-15 in ref transcript
• Changed! cd IGcam 90aa 9e-15 in ref transcript
• cd IGcam 90aa 2e-14 in ref transcript
• cd IGcam 89aa 3e-13 in ref transcript
• cd IGcam 86aa 3e-12 in ref transcript
• cd IGcam 88aa 1e-10 in ref transcript
• cd FN3 66aa 4e-09 in ref transcript
  • Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.
• cd IGcam 87aa 8e-05 in ref transcript
• Changed! smart S_TKc 245aa 4e-77 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• Changed! pfam I-set 91aa 2e-30 in ref transcript
  • Immunoglobulin I-set domain.
• pfam I-set 90aa 1e-23 in ref transcript
• pfam I-set 91aa 1e-21 in ref transcript
• pfam I-set 90aa 2e-21 in ref transcript
• pfam I-set 91aa 5e-19 in ref transcript
• pfam I-set 90aa 3e-18 in ref transcript
• pfam I-set 87aa 3e-18 in ref transcript
• pfam I-set 89aa 7e-15 in ref transcript
• pfam I-set 89aa 2e-13 in ref transcript
• pfam fn3 59aa 2e-06 in ref transcript
  • Fibronectin type III domain.
• Changed! COG SPS1 351aa 1e-38 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].

MYLK

• refseq_MYLK.F3 refseq_MYLK.R3 208 361
• NCBIGene 36.3 4638
• Single exon skipping, size difference: 153
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_053025

• Changed! cd S_TKc 256aa 7e-74 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• cd IGcam 88aa 1e-16 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• cd IGcam 90aa 9e-16 in ref transcript
• cd IGcam 90aa 5e-15 in ref transcript
• cd IGcam 90aa 9e-15 in ref transcript
• cd IGcam 90aa 2e-14 in ref transcript
• cd IGcam 89aa 3e-13 in ref transcript
• cd IGcam 86aa 3e-12 in ref transcript
• cd IGcam 88aa 1e-10 in ref transcript
• cd FN3 66aa 4e-09 in ref transcript
  • Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.
• cd IGcam 87aa 8e-05 in ref transcript
• Changed! smart S_TKc 245aa 4e-77 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• pfam I-set 91aa 2e-30 in ref transcript
  • Immunoglobulin I-set domain.
• pfam I-set 90aa 1e-23 in ref transcript
• pfam I-set 91aa 1e-21 in ref transcript
• pfam I-set 90aa 2e-21 in ref transcript
• pfam I-set 91aa 5e-19 in ref transcript
• pfam I-set 90aa 3e-18 in ref transcript
• pfam I-set 87aa 3e-18 in ref transcript
• pfam I-set 89aa 7e-15 in ref transcript
• pfam I-set 89aa 2e-13 in ref transcript
• pfam fn3 59aa 2e-06 in ref transcript
  • Fibronectin type III domain.
• Changed! COG SPS1 351aa 1e-38 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].
• Changed! cd S_TKc 220aa 3e-56 in modified transcript
• Changed! smart S_TKc 209aa 3e-59 in modified transcript
• Changed! COG SPS1 342aa 1e-29 in modified transcript

MYLK

• refseq_MYLK.F4 refseq_MYLK.R4 140 347
• NCBIGene 36.3 4638
• Single exon skipping, size difference: 207
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_053025

• cd S_TKc 256aa 7e-74 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• cd IGcam 88aa 1e-16 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• Changed! cd IGcam 90aa 9e-16 in ref transcript
• cd IGcam 90aa 5e-15 in ref transcript
• cd IGcam 90aa 9e-15 in ref transcript
• cd IGcam 90aa 2e-14 in ref transcript
• cd IGcam 89aa 3e-13 in ref transcript
• cd IGcam 86aa 3e-12 in ref transcript
• cd IGcam 88aa 1e-10 in ref transcript
• cd FN3 66aa 4e-09 in ref transcript
  • Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.
• cd IGcam 87aa 8e-05 in ref transcript
• smart S_TKc 245aa 4e-77 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• pfam I-set 91aa 2e-30 in ref transcript
  • Immunoglobulin I-set domain.
• pfam I-set 90aa 1e-23 in ref transcript
• pfam I-set 91aa 1e-21 in ref transcript
• pfam I-set 90aa 2e-21 in ref transcript
• Changed! pfam I-set 91aa 5e-19 in ref transcript
• pfam I-set 90aa 3e-18 in ref transcript
• pfam I-set 87aa 3e-18 in ref transcript
• pfam I-set 89aa 7e-15 in ref transcript
• pfam I-set 89aa 2e-13 in ref transcript
• pfam fn3 59aa 2e-06 in ref transcript
  • Fibronectin type III domain.
• COG SPS1 351aa 1e-38 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].

MYO18A

• refseq_MYO18A.F2 refseq_MYO18A.R2 255 300
• NCBIGene 36.3 399687
• Single exon skipping, size difference: 45
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_078471

• cd MYSc_type_XVIII 779aa 0.0 in ref transcript
  • Myosin motor domain, type XVIII myosins. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle.
• cd PDZ_signaling 80aa 6e-10 in ref transcript
  • PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of PDZ domains an N-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in proteases.
• smart MYSc 786aa 1e-105 in ref transcript
  • Myosin. Large ATPases. ATPase; molecular motor. Muscle contraction consists of a cyclical interaction between myosin and actin. The core of the myosin structure is similar in fold to that of kinesin.
• pfam Myosin_tail_1 527aa 1e-36 in ref transcript
  • Myosin tail. The myosin molecule is a multi-subunit complex made up of two heavy chains and four light chains it is a fundamental contractile protein found in all eukaryote cell types. This family consists of the coiled-coil myosin heavy chain tail region. The coiled-coil is composed of the tail from two molecules of myosin. These can then assemble into the macromolecular thick filament. The coiled-coil region provides the structural backbone the thick filament.
• Changed! TIGR SMC_prok_B 288aa 2e-11 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• smart PDZ 81aa 5e-08 in ref transcript
  • Domain present in PSD-95, Dlg, and ZO-1/2. Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities.
• COG COG5022 1200aa 1e-103 in ref transcript
  • Myosin heavy chain [Cytoskeleton].
• Changed! COG Smc 738aa 5e-21 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].
• Changed! TIGR SMC_prok_B 331aa 2e-08 in modified transcript
• Changed! COG Smc 691aa 1e-18 in modified transcript

MYOHD1

• refseq_MYOHD1.F2 refseq_MYOHD1.R2 115 165
• NCBIGene 36.2 80179
• Single exon skipping, size difference: 50
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_025109

• cd MYSc 402aa 1e-116 in ref transcript
  • Myosin motor domain. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle.
• Changed! cd MYSc_type_V 116aa 8e-08 in ref transcript
  • Myosin motor domain, type V myosins. Myosins V transport a variety of intracellular cargo processively along actin filaments, such as membraneous organelles and mRNA. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle.
• smart MYSc 404aa 1e-124 in ref transcript
  • Myosin. Large ATPases. ATPase; molecular motor. Muscle contraction consists of a cyclical interaction between myosin and actin. The core of the myosin structure is similar in fold to that of kinesin.
• Changed! smart MYSc 116aa 4e-07 in ref transcript
• COG COG5022 438aa 1e-107 in ref transcript
  • Myosin heavy chain [Cytoskeleton].
• Changed! COG COG5022 185aa 2e-11 in ref transcript
• Changed! cd MYSc_type_V 34aa 1e-07 in modified transcript
• Changed! smart MYSc 34aa 9e-07 in modified transcript
• Changed! COG COG5022 34aa 5e-07 in modified transcript

MZF1

• refseq_MZF1.F1 refseq_MZF1.R1 100 418
• NCBIGene 36.3 7593
• Alternative 5-prime, size difference: 318
• Exclusion in 5'UTR
• Reference transcript: NM_198055

• smart SCAN 113aa 2e-43 in ref transcript
  • leucine rich region.
• COG COG5048 165aa 6e-08 in ref transcript
  • FOG: Zn-finger [General function prediction only].

NLRP1

• refseq_NALP1.F2 refseq_NALP1.R2 184 316
• NCBIGene 36.3 22861
• Single exon skipping, size difference: 132
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_033004

• cd LRR_RI 179aa 8e-30 in ref transcript
  • Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1).
• cd AAA 95aa 0.009 in ref transcript
  • The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.
• pfam NACHT 170aa 5e-45 in ref transcript
  • NACHT domain. This NTPase domain is found in apoptosis proteins as well as those involved in MHC transcription activation. This family is closely related to pfam00931.
• pfam CARD 82aa 2e-16 in ref transcript
  • Caspase recruitment domain. Motif contained in proteins involved in apoptotic signaling. Predicted to possess a DEATH (pfam00531) domain-like fold.
• pfam PAAD_DAPIN 58aa 2e-08 in ref transcript
  • PAAD/DAPIN/Pyrin domain. This domain is predicted to contain 6 alpha helices and to have the same fold as the pfam00531 domain. This similarity may mean that this is a protein-protein interaction domain.
• smart LRR_RI 28aa 0.002 in ref transcript
  • Leucine rich repeat, ribonuclease inhibitor type.
• COG RNA1 142aa 0.004 in ref transcript
  • Ran GTPase-activating protein (RanGAP) involved in mRNA processing and transport [Signal transduction mechanisms / RNA processing and modification].

NLRP1

• refseq_NALP1.F3 refseq_NALP1.R3 178 268
• NCBIGene 36.3 22861
• Single exon skipping, size difference: 90
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_033004

• Changed! cd LRR_RI 179aa 8e-30 in ref transcript
  • Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1).
• cd AAA 95aa 0.009 in ref transcript
  • The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.
• pfam NACHT 170aa 5e-45 in ref transcript
  • NACHT domain. This NTPase domain is found in apoptosis proteins as well as those involved in MHC transcription activation. This family is closely related to pfam00931.
• pfam CARD 82aa 2e-16 in ref transcript
  • Caspase recruitment domain. Motif contained in proteins involved in apoptotic signaling. Predicted to possess a DEATH (pfam00531) domain-like fold.
• pfam PAAD_DAPIN 58aa 2e-08 in ref transcript
  • PAAD/DAPIN/Pyrin domain. This domain is predicted to contain 6 alpha helices and to have the same fold as the pfam00531 domain. This similarity may mean that this is a protein-protein interaction domain.
• smart LRR_RI 28aa 0.002 in ref transcript
  • Leucine rich repeat, ribonuclease inhibitor type.
• COG RNA1 142aa 0.004 in ref transcript
  • Ran GTPase-activating protein (RanGAP) involved in mRNA processing and transport [Signal transduction mechanisms / RNA processing and modification].
• Changed! cd LRR_RI 161aa 4e-27 in modified transcript

NLRP12

• refseq_NALP12.F1 refseq_NALP12.R1 206 377
• NCBIGene 36.3 91662
• Single exon skipping, size difference: 171
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_144687

• Changed! cd LRR_RI 319aa 6e-34 in ref transcript
  • Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1).
• Changed! cd LRR_RI 306aa 2e-23 in ref transcript
• pfam NACHT 170aa 1e-43 in ref transcript
  • NACHT domain. This NTPase domain is found in apoptosis proteins as well as those involved in MHC transcription activation. This family is closely related to pfam00931.
• pfam PAAD_DAPIN 81aa 5e-24 in ref transcript
  • PAAD/DAPIN/Pyrin domain. This domain is predicted to contain 6 alpha helices and to have the same fold as the pfam00531 domain. This similarity may mean that this is a protein-protein interaction domain.
• Changed! cd LRR_RI 286aa 3e-31 in modified transcript

NLRP12

• refseq_NALP12.F4 refseq_NALP12.R4 168 358
• NCBIGene 36.3 91662
• Single exon skipping, size difference: 190
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_144687

• Changed! cd LRR_RI 319aa 6e-34 in ref transcript
  • Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1).
• Changed! cd LRR_RI 306aa 2e-23 in ref transcript
• pfam NACHT 170aa 1e-43 in ref transcript
  • NACHT domain. This NTPase domain is found in apoptosis proteins as well as those involved in MHC transcription activation. This family is closely related to pfam00931.
• pfam PAAD_DAPIN 81aa 5e-24 in ref transcript
  • PAAD/DAPIN/Pyrin domain. This domain is predicted to contain 6 alpha helices and to have the same fold as the pfam00531 domain. This similarity may mean that this is a protein-protein interaction domain.
• Changed! cd LRR_RI 188aa 4e-05 in modified transcript

NLRP7

• refseq_NALP7.F2 refseq_NALP7.R2 200 284
• NCBIGene 36.3 199713
• Alternative 3-prime, size difference: 84
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_139176

• cd LRR_RI 266aa 7e-27 in ref transcript
  • Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1).
• pfam NACHT 168aa 1e-35 in ref transcript
  • NACHT domain. This NTPase domain is found in apoptosis proteins as well as those involved in MHC transcription activation. This family is closely related to pfam00931.
• pfam PAAD_DAPIN 67aa 3e-11 in ref transcript
  • PAAD/DAPIN/Pyrin domain. This domain is predicted to contain 6 alpha helices and to have the same fold as the pfam00531 domain. This similarity may mean that this is a protein-protein interaction domain.
• COG RNA1 165aa 5e-04 in ref transcript
  • Ran GTPase-activating protein (RanGAP) involved in mRNA processing and transport [Signal transduction mechanisms / RNA processing and modification].

NLRP7

• refseq_NALP7.F3 refseq_NALP7.R3 203 374
• NCBIGene 36.3 199713
• Single exon skipping, size difference: 171
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_139176

• Changed! cd LRR_RI 266aa 7e-27 in ref transcript
  • Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1).
• pfam NACHT 168aa 1e-35 in ref transcript
  • NACHT domain. This NTPase domain is found in apoptosis proteins as well as those involved in MHC transcription activation. This family is closely related to pfam00931.
• pfam PAAD_DAPIN 67aa 3e-11 in ref transcript
  • PAAD/DAPIN/Pyrin domain. This domain is predicted to contain 6 alpha helices and to have the same fold as the pfam00531 domain. This similarity may mean that this is a protein-protein interaction domain.
• Changed! COG RNA1 165aa 5e-04 in ref transcript
  • Ran GTPase-activating protein (RanGAP) involved in mRNA processing and transport [Signal transduction mechanisms / RNA processing and modification].
• Changed! cd LRR_RI 246aa 1e-23 in modified transcript

NASP

• refseq_NASP.F1 refseq_NASP.R1 140 213
• NCBIGene 36.3 4678
• Single exon skipping, size difference: 73
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_172164

• Changed! cd TPR 97aa 5e-04 in ref transcript
  • Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here.
• Changed! pfam SHNi-TPR 38aa 2e-07 in ref transcript
  • SHNi-TPR. SHNi-TPR family members contain a reiterated sequence motif that is an interrupted form of TPR repeat.
• Changed! TIGR 2A1904 189aa 0.001 in ref transcript
• Changed! COG MDN1 198aa 0.004 in ref transcript
  • AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only].

NAT5

• refseq_NAT5.F1 refseq_NAT5.R1 178 324
• NCBIGene 36.3 51126
• Single exon skipping, size difference: 146
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_016100

• Changed! cd GNAT 86aa 1e-07 in ref transcript
  • GCN5-related N-acetyltransferases (GNAT) represent a large superfamily of functionally diverse enzymes that catalyze the transfer of an acetyl group from acetyl-Coenzyme A to the primary amine of a wide range of acceptor substrates. Members of this superfamily include aminoglycoside N-acetyltransferases, serotonin N-acetyltransferase, glucosamine-6-phosphate N-acetyltransferase, the histone acetyltransferases, mycothiol synthase, and the Fem family of amino acyl transferases.
• Changed! pfam Acetyltransf_1 79aa 2e-12 in ref transcript
  • Acetyltransferase (GNAT) family. This family contains proteins with N-acetyltransferase functions such as Elp3-related proteins.
• Changed! COG RimI 156aa 1e-19 in ref transcript
  • Acetyltransferases [General function prediction only].
• Changed! pfam Acetyltransf_1 44aa 3e-04 in modified transcript
• Changed! COG RimI 93aa 1e-09 in modified transcript

NAV2

• refseq_NAV2.F2 refseq_NAV2.R2 165 264
• NCBIGene 36.3 89797
• Single exon skipping, size difference: 99
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_182964

• cd CH 102aa 4e-12 in ref transcript
  • Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav).
• pfam CH 102aa 5e-14 in ref transcript
  • Calponin homology (CH) domain. The CH domain is found in both cytoskeletal proteins and signal transduction proteins. The CH domain is involved in actin binding in some members of the family. However in calponins there is evidence that the CH domain is not involved in its actin binding activity. Most proteins have two copies of the CH domain, however some proteins such as calponin have only a single copy.
• smart AAA 109aa 0.001 in ref transcript
  • ATPases associated with a variety of cellular activities. AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.
• COG SAC6 98aa 3e-08 in ref transcript
  • Ca2+-binding actin-bundling protein fimbrin/plastin (EF-Hand superfamily) [Cytoskeleton].
• PRK PRK06835 104aa 0.006 in ref transcript
  • DNA replication protein DnaC; Validated.

NAV2

• refseq_NAV2.F4 refseq_NAV2.R4 341 410
• NCBIGene 36.3 89797
• Single exon skipping, size difference: 69
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_182964

• cd CH 102aa 4e-12 in ref transcript
  • Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav).
• pfam CH 102aa 5e-14 in ref transcript
  • Calponin homology (CH) domain. The CH domain is found in both cytoskeletal proteins and signal transduction proteins. The CH domain is involved in actin binding in some members of the family. However in calponins there is evidence that the CH domain is not involved in its actin binding activity. Most proteins have two copies of the CH domain, however some proteins such as calponin have only a single copy.
• smart AAA 109aa 0.001 in ref transcript
  • ATPases associated with a variety of cellular activities. AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.
• COG SAC6 98aa 3e-08 in ref transcript
  • Ca2+-binding actin-bundling protein fimbrin/plastin (EF-Hand superfamily) [Cytoskeleton].
• PRK PRK06835 104aa 0.006 in ref transcript
  • DNA replication protein DnaC; Validated.

NBR1

• refseq_NBR1.F1 refseq_NBR1.R1 103 435
• NCBIGene 36.3 4077
• Alternative 5-prime, size difference: 332
• Exclusion in 5'UTR
• Reference transcript: NM_031858

• cd PB1_NBR1 81aa 1e-35 in ref transcript
  • The PB1 domain is an essential part of NBR1 protein, next to BRCA1, a scaffold protein mediating specific protein-protein interaction with both titin protein kinase and with another scaffold protein p62. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. The NBR1 protein contains a type I PB1 domain.
• cd ZZ_NBR1_like 45aa 6e-12 in ref transcript
  • Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
• smart PB1 80aa 1e-12 in ref transcript
  • PB1 domain. Phox and Bem1p domain, present in many eukaryotic cytoplasmic signalling proteins. The domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pairs associate.
• smart ZnF_ZZ 45aa 9e-11 in ref transcript
  • Zinc-binding domain, present in Dystrophin, CREB-binding protein. Putative zinc-binding domain present in dystrophin-like proteins, and CREB-binding protein/p300 homologues. The ZZ in dystrophin appears to bind calmodulin. A missense mutation of one of the conserved cysteines in dystrophin results in a patient with Duchenne muscular dystrophy [3].

NCAM1

• refseq_NCAM1.F1 refseq_NCAM1.R1 154 184
• NCBIGene 36.3 4684
• Single exon skipping, size difference: 30
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_181351

• cd IGcam 91aa 5e-12 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• cd IGcam 87aa 8e-10 in ref transcript
• Changed! cd IGcam 104aa 1e-09 in ref transcript
• cd IGcam 73aa 2e-09 in ref transcript
• cd FN3 98aa 5e-07 in ref transcript
  • Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.
• cd FN3 88aa 2e-04 in ref transcript
• pfam I-set 83aa 1e-15 in ref transcript
  • Immunoglobulin I-set domain.
• Changed! smart IG_like 91aa 2e-11 in ref transcript
  • Immunoglobulin like. IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
• smart IGc2 69aa 8e-10 in ref transcript
  • Immunoglobulin C-2 Type.
• smart IG_like 85aa 2e-08 in ref transcript
• pfam fn3 89aa 7e-08 in ref transcript
  • Fibronectin type III domain.
• pfam fn3 83aa 1e-06 in ref transcript
• Changed! cd IGcam 94aa 9e-11 in modified transcript
• Changed! smart IG_like 81aa 2e-12 in modified transcript

NCKAP1

• refseq_NCKAP1.F1 refseq_NCKAP1.R1 102 120
• NCBIGene 36.3 10787
• Single exon skipping, size difference: 18
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_205842

• Changed! pfam Nckap1 1123aa 0.0 in ref transcript
  • Membrane-associated apoptosis protein. Expression of this protein was found to be markedly reduced in patients with Alzheimer's disease. It is involved in the regulation of actin polymerisation in the brain as part of a WAVE2 signalling complex.
• Changed! pfam Nckap1 1117aa 0.0 in modified transcript

NCKIPSD

• refseq_NCKIPSD.F1 refseq_NCKIPSD.R1 107 128
• NCBIGene 36.3 51517
• Alternative 3-prime, size difference: 21
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_016453

• cd SH3 55aa 4e-09 in ref transcript
  • Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
• pfam DUF2013 117aa 2e-33 in ref transcript
  • Protein of unknown function (DUF2013). This region is found at the C terminal of a group of cytoskeletal proteins.
• smart SH3 56aa 7e-10 in ref transcript
  • Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.

NCOA1

• refseq_NCOA1.F1 refseq_NCOA1.R1 114 174
• NCBIGene 36.3 8648
• Exon skipping and alternative 3-prime or 5-prime, size difference: 60
• Inclusion in the protein causing a new stop codon, Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_147233

• cd PAS 94aa 2e-08 in ref transcript
  • PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.
• cd HLH 58aa 4e-05 in ref transcript
  • Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins.
• pfam Nuc_rec_co-act 47aa 8e-13 in ref transcript
  • Nuclear receptor coactivator. This region is found on eukaryotic nuclear receptor coactivators and forms an alpha helical structure.
• pfam SRC-1 79aa 7e-10 in ref transcript
  • Steroid receptor coactivator. This domain is found in steroid/nuclear receptor coactivators and contains two LXXLL motifs that are involved in receptor binding. The family includes SRC-1/NcoA-1, NcoA-2/TIF2, pCIP/ACTR/GRIP-1/AIB1.
• smart PAS 58aa 8e-09 in ref transcript
  • PAS domain. PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels ([1]; Ponting & Aravind, in press).
• smart HLH 55aa 3e-06 in ref transcript
  • helix loop helix domain.
• pfam DUF1518 38aa 0.001 in ref transcript
  • Domain of unknown function (DUF1518). This domain, which is usually found tandemly repeated, is found various receptor co-activating proteins.

NDEL1

• refseq_NDEL1.F2 refseq_NDEL1.R2 130 165
• NCBIGene 36.3 81565
• Single exon skipping, size difference: 35
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_030808

• pfam NUDE_C 181aa 5e-32 in ref transcript
  • NUDE protein, C-terminal conserved region. This family represents the C-terminal conserved region of the NUDE proteins. NUDE proteins are involved in nuclear migration.

NDRG2

• refseq_NDRG2.F1 refseq_NDRG2.R1 140 182
• NCBIGene 36.3 57447
• Single exon skipping, size difference: 42
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_201537

• pfam Ndr 279aa 1e-124 in ref transcript
  • Ndr family. This family consists of proteins from different gene families: Ndr1/RTP/Drg1, Ndr2, and Ndr3. Their similarity was previously noted. The precise molecular and cellular function of members of this family is still unknown. Yet, they are known to be involved in cellular differentiation events. The Ndr1 group was the first to be discovered. Their expression is repressed by the proto-oncogenes N-myc and c-myc, and in line with this observation, Ndr1 protein expression is down-regulated in neoplastic cells, and is reactivated when differentiation is induced by chemicals such as retinoic acid. Ndr2 and Ndr3 expression is not under the control of N-myc or c-myc. Ndr1 expression is also activated by several chemicals: tunicamycin and homocysteine induce Ndr1 in human umbilical endothelial cells; nickel induces Ndr1 in several cell types. Members of this family are found in wide variety of multicellular eukaryotes, including an Ndr1 type protein in Helianthus annuus (sunflower), known as Sf21. Interestingly, the highest scoring matches in the noise are all alpha/beta hydrolases pfam00561, suggesting that this family may have an enzymatic function (Bateman A pers. obs.).
• COG MhpC 259aa 3e-05 in ref transcript
  • Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only].

NDRG2

• refseq_NDRG2.F3 refseq_NDRG2.R3 106 173
• NCBIGene 36.3 57447
• Single exon skipping, size difference: 67
• Exclusion in 5'UTR
• Reference transcript: NM_201540

• pfam Ndr 279aa 1e-124 in ref transcript
  • Ndr family. This family consists of proteins from different gene families: Ndr1/RTP/Drg1, Ndr2, and Ndr3. Their similarity was previously noted. The precise molecular and cellular function of members of this family is still unknown. Yet, they are known to be involved in cellular differentiation events. The Ndr1 group was the first to be discovered. Their expression is repressed by the proto-oncogenes N-myc and c-myc, and in line with this observation, Ndr1 protein expression is down-regulated in neoplastic cells, and is reactivated when differentiation is induced by chemicals such as retinoic acid. Ndr2 and Ndr3 expression is not under the control of N-myc or c-myc. Ndr1 expression is also activated by several chemicals: tunicamycin and homocysteine induce Ndr1 in human umbilical endothelial cells; nickel induces Ndr1 in several cell types. Members of this family are found in wide variety of multicellular eukaryotes, including an Ndr1 type protein in Helianthus annuus (sunflower), known as Sf21. Interestingly, the highest scoring matches in the noise are all alpha/beta hydrolases pfam00561, suggesting that this family may have an enzymatic function (Bateman A pers. obs.).
• COG MhpC 259aa 3e-05 in ref transcript
  • Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only].

NDRG2

• refseq_NDRG2.F5 refseq_NDRG2.R3 130 197
• NCBIGene 36.3 57447
• Single exon skipping, size difference: 67
• Exclusion in 5'UTR
• Reference transcript: NM_201535

• pfam Ndr 279aa 1e-124 in ref transcript
  • Ndr family. This family consists of proteins from different gene families: Ndr1/RTP/Drg1, Ndr2, and Ndr3. Their similarity was previously noted. The precise molecular and cellular function of members of this family is still unknown. Yet, they are known to be involved in cellular differentiation events. The Ndr1 group was the first to be discovered. Their expression is repressed by the proto-oncogenes N-myc and c-myc, and in line with this observation, Ndr1 protein expression is down-regulated in neoplastic cells, and is reactivated when differentiation is induced by chemicals such as retinoic acid. Ndr2 and Ndr3 expression is not under the control of N-myc or c-myc. Ndr1 expression is also activated by several chemicals: tunicamycin and homocysteine induce Ndr1 in human umbilical endothelial cells; nickel induces Ndr1 in several cell types. Members of this family are found in wide variety of multicellular eukaryotes, including an Ndr1 type protein in Helianthus annuus (sunflower), known as Sf21. Interestingly, the highest scoring matches in the noise are all alpha/beta hydrolases pfam00561, suggesting that this family may have an enzymatic function (Bateman A pers. obs.).
• COG MhpC 259aa 3e-05 in ref transcript
  • Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only].

NDRG3

• refseq_NDRG3.F1 refseq_NDRG3.R1 119 155
• NCBIGene 36.3 57446
• Single exon skipping, size difference: 36
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_032013

• pfam Ndr 286aa 1e-123 in ref transcript
  • Ndr family. This family consists of proteins from different gene families: Ndr1/RTP/Drg1, Ndr2, and Ndr3. Their similarity was previously noted. The precise molecular and cellular function of members of this family is still unknown. Yet, they are known to be involved in cellular differentiation events. The Ndr1 group was the first to be discovered. Their expression is repressed by the proto-oncogenes N-myc and c-myc, and in line with this observation, Ndr1 protein expression is down-regulated in neoplastic cells, and is reactivated when differentiation is induced by chemicals such as retinoic acid. Ndr2 and Ndr3 expression is not under the control of N-myc or c-myc. Ndr1 expression is also activated by several chemicals: tunicamycin and homocysteine induce Ndr1 in human umbilical endothelial cells; nickel induces Ndr1 in several cell types. Members of this family are found in wide variety of multicellular eukaryotes, including an Ndr1 type protein in Helianthus annuus (sunflower), known as Sf21. Interestingly, the highest scoring matches in the noise are all alpha/beta hydrolases pfam00561, suggesting that this family may have an enzymatic function (Bateman A pers. obs.).
• COG MhpC 275aa 4e-08 in ref transcript
  • Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only].

NDUFB6

• refseq_NDUFB6.F1 refseq_NDUFB6.R1 225 270
• NCBIGene 36.3 4712
• Single exon skipping, size difference: 45
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_002493

• Changed! pfam NDUF_B6 128aa 2e-45 in ref transcript
  • NADH:ubiquinone oxidoreductase, NDUFB6/B17 subunit. Members of this family mediate the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone, the reaction that occurs being: NADH + ubiquinone = NAD(+) + ubiquinol.
• Changed! pfam NDUF_B6 113aa 2e-36 in modified transcript

NEBL

• refseq_NEBL.F1 refseq_NEBL.R1 131 374
• NCBIGene 36.3 10529
• Multiple exon skipping, size difference: 243
• Exclusion in the protein (no frameshift), Exclusion in the protein (no frameshift)
• Reference transcript: NM_006393

• cd SH3 54aa 1e-11 in ref transcript
  • Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
• smart SH3 57aa 2e-13 in ref transcript
  • Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.
• pfam Nebulin 29aa 4e-04 in ref transcript
  • Nebulin repeat.
• smart NEBU 30aa 7e-04 in ref transcript
  • The Nebulin repeat is present also in Las1. Tandem arrays of these repeats are known to bind actin.
• pfam Nebulin 28aa 0.002 in ref transcript
• smart NEBU 26aa 0.003 in ref transcript
• pfam Nebulin 29aa 0.005 in ref transcript

NF2

• refseq_NF2.F1 refseq_NF2.R1 217 343
• NCBIGene 36.3 4771
• Single exon skipping, size difference: 126
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000268

• cd FERM_C 93aa 2e-22 in ref transcript
  • The FERM_C domain is the third structural domain within the FERM domain. The FERM domain is found in the cytoskeletal-associated proteins such as ezrin, moesin, radixin, 4.1R, and merlin. These proteins provide a link between the membrane and cytoskeleton and are involved in signal transduction pathways. The FERM_C domain is also found in protein tyrosine phosphatases (PTPs) , the tryosine kinases FAKand JAK, in addition to other proteins involved in signaling. This domain is structuraly similar to the PH and PTB domains and consequently is capable of binding to both peptides and phospholipids at different sites.
• Changed! smart B41 204aa 6e-53 in ref transcript
  • Band 4.1 homologues. Also known as ezrin/radixin/moesin (ERM) protein domains. Present in myosins, ezrin, radixin, moesin, protein tyrosine phosphatases. Plasma membrane-binding domain. These proteins play structural and regulatory roles in the assembly and stabilization of specialized plasmamembrane domains. Some PDZ domain containing proteins bind one or more of this family. Now includes JAKs.
• pfam ERM 234aa 1e-35 in ref transcript
  • Ezrin/radixin/moesin family. This family of proteins contain a band 4.1 domain (pfam00373), at their amino terminus. This family represents the rest of these proteins.
• pfam FERM_C 87aa 1e-32 in ref transcript
  • FERM C-terminal PH-like domain.
• Changed! smart B41 143aa 9e-36 in modified transcript

NF2

• refseq_NF2.F2 refseq_NF2.R2 100 223
• NCBIGene 36.3 4771
• Single exon skipping, size difference: 123
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000268

• cd FERM_C 93aa 2e-22 in ref transcript
  • The FERM_C domain is the third structural domain within the FERM domain. The FERM domain is found in the cytoskeletal-associated proteins such as ezrin, moesin, radixin, 4.1R, and merlin. These proteins provide a link between the membrane and cytoskeleton and are involved in signal transduction pathways. The FERM_C domain is also found in protein tyrosine phosphatases (PTPs) , the tryosine kinases FAKand JAK, in addition to other proteins involved in signaling. This domain is structuraly similar to the PH and PTB domains and consequently is capable of binding to both peptides and phospholipids at different sites.
• Changed! smart B41 204aa 6e-53 in ref transcript
  • Band 4.1 homologues. Also known as ezrin/radixin/moesin (ERM) protein domains. Present in myosins, ezrin, radixin, moesin, protein tyrosine phosphatases. Plasma membrane-binding domain. These proteins play structural and regulatory roles in the assembly and stabilization of specialized plasmamembrane domains. Some PDZ domain containing proteins bind one or more of this family. Now includes JAKs.
• pfam ERM 234aa 1e-35 in ref transcript
  • Ezrin/radixin/moesin family. This family of proteins contain a band 4.1 domain (pfam00373), at their amino terminus. This family represents the rest of these proteins.
• pfam FERM_C 87aa 1e-32 in ref transcript
  • FERM C-terminal PH-like domain.
• Changed! smart B41 163aa 2e-38 in modified transcript

NFAT5

• refseq_NFAT5.F1 refseq_NFAT5.R1 262 324
• NCBIGene 36.3 10725
• Single exon skipping, size difference: 62
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_138713

• Changed! cd IPT_NFAT 100aa 5e-36 in ref transcript
  • IPT domain of the NFAT family of transcription factors. NFAT transcription complexes are a target of calcineurin, a calcium dependent phosphatase, and activate genes mainly involved in cell-cell-interaction.
• Changed! pfam RHD 158aa 9e-20 in ref transcript
  • Rel homology domain (RHD). Proteins containing the Rel homology domain (RHD) are eukaryotic transcription factors. The RHD is composed of two structural domains. This is the N-terminal domain that is similar to that found in P53. The C-terminal domain has an immunoglobulin-like fold (See pfam01833) that binds to DNA.
• Changed! smart IPT 98aa 4e-08 in ref transcript
  • ig-like, plexins, transcription factors.
• Changed! pfam PAT1 225aa 2e-04 in ref transcript
  • Topoisomerase II-associated protein PAT1. Members of this family are necessary for accurate chromosome transmission during cell division.

NFAT5

• refseq_NFAT5.F3 refseq_NFAT5.R3 112 166
• NCBIGene 36.3 10725
• Single exon skipping, size difference: 54
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_138713

• cd IPT_NFAT 100aa 5e-36 in ref transcript
  • IPT domain of the NFAT family of transcription factors. NFAT transcription complexes are a target of calcineurin, a calcium dependent phosphatase, and activate genes mainly involved in cell-cell-interaction.
• pfam RHD 158aa 9e-20 in ref transcript
  • Rel homology domain (RHD). Proteins containing the Rel homology domain (RHD) are eukaryotic transcription factors. The RHD is composed of two structural domains. This is the N-terminal domain that is similar to that found in P53. The C-terminal domain has an immunoglobulin-like fold (See pfam01833) that binds to DNA.
• smart IPT 98aa 4e-08 in ref transcript
  • ig-like, plexins, transcription factors.
• pfam PAT1 225aa 2e-04 in ref transcript
  • Topoisomerase II-associated protein PAT1. Members of this family are necessary for accurate chromosome transmission during cell division.

NFATC1

• refseq_NFATC1.F1 refseq_NFATC1.R1 181 488
• NCBIGene 36.3 4772
• Alternative 5-prime, size difference: 307
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_172387

• cd IPT_NFAT 101aa 5e-33 in ref transcript
  • IPT domain of the NFAT family of transcription factors. NFAT transcription complexes are a target of calcineurin, a calcium dependent phosphatase, and activate genes mainly involved in cell-cell-interaction.
• pfam RHD 161aa 6e-30 in ref transcript
  • Rel homology domain (RHD). Proteins containing the Rel homology domain (RHD) are eukaryotic transcription factors. The RHD is composed of two structural domains. This is the N-terminal domain that is similar to that found in P53. The C-terminal domain has an immunoglobulin-like fold (See pfam01833) that binds to DNA.
• pfam TIG 98aa 8e-09 in ref transcript
  • IPT/TIG domain. This family consists of a domain that has an immunoglobulin like fold. These domains are found in cell surface receptors such as Met and Ron as well as in intracellular transcription factors where it is involved in DNA binding. CAUTION: This family does not currently recognise a significant number of members.

NFATC2

• refseq_NFATC2.F2 refseq_NFATC2.R2 230 318
• NCBIGene 36.3 4773
• Single exon skipping, size difference: 88
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_173091

• cd IPT_NFAT 101aa 1e-40 in ref transcript
  • IPT domain of the NFAT family of transcription factors. NFAT transcription complexes are a target of calcineurin, a calcium dependent phosphatase, and activate genes mainly involved in cell-cell-interaction.
• pfam RHD 161aa 9e-26 in ref transcript
  • Rel homology domain (RHD). Proteins containing the Rel homology domain (RHD) are eukaryotic transcription factors. The RHD is composed of two structural domains. This is the N-terminal domain that is similar to that found in P53. The C-terminal domain has an immunoglobulin-like fold (See pfam01833) that binds to DNA.
• smart IPT 100aa 3e-10 in ref transcript
  • ig-like, plexins, transcription factors.

NFIC

• refseq_NFIC.F1 refseq_NFIC.R1 107 347
• NCBIGene 36.3 4782
• Multiple exon skipping, size difference: 240
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_205843

• cd MH1 114aa 5e-17 in ref transcript
  • MH1 is a small DNA binding domain, binding in an unusal way involving a beta hairpin structure binding to the major groove. MH1 is present in Smad proteins, an important family of proteins involved in TGF-beta signalling and frequent targets of tumorigenic mutations. Also known as Domain A in dwarfin family proteins.
• Changed! pfam CTF_NFI 292aa 1e-107 in ref transcript
  • CTF/NF-I family transcription modulation region.
• pfam NfI_DNAbd_pre-N 38aa 5e-19 in ref transcript
  • Nuclear factor I protein pre-N-terminus. The Nuclear factor I (NFI) family of site-specific DNA-binding proteins (also known as CTF or CAAT box transcription factor) functions both in viral DNA replication and in the regulation of gene expression in higher organisms. The N-terminal 200 residues contains the DNA-binding and dimerisation domain, but also has an 8-47 residue highly conserved region 5' of this, whose function is not known. Deletion of the N-terminal 200 amino acids removes the DNA-binding activity, dimerisation-ability and the stimulation of adenovirus DNA replication.
• smart DWA 102aa 9e-15 in ref transcript
  • Domain A in dwarfin family proteins.
• Changed! pfam CTF_NFI 207aa 2e-85 in modified transcript

NFKBIB

• refseq_NFKBIB.F2 refseq_NFKBIB.R2 213 269
• NCBIGene 36.3 4793
• Alternative 3-prime, size difference: 56
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_002503

• Changed! cd ANK 97aa 3e-15 in ref transcript
  • ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats.
• Changed! cd ANK 86aa 7e-12 in ref transcript
• Changed! cd ANK 139aa 2e-07 in ref transcript
• Changed! TIGR trp 68aa 2e-07 in ref transcript
  • after chronic exposure to capsaicin. (McCleskey and Gold, 1999).
• Changed! COG Arp 85aa 2e-09 in ref transcript
  • FOG: Ankyrin repeat [General function prediction only].
• Changed! COG Arp 94aa 7e-09 in ref transcript
• Changed! COG Arp 210aa 6e-06 in ref transcript

NFYA

• refseq_NFYA.F1 refseq_NFYA.R1 212 299
• NCBIGene 36.3 4800
• Single exon skipping, size difference: 87
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_002505

• smart CBF 60aa 9e-27 in ref transcript
  • CCAAT-Binding transcription Factor.
• COG HAP2 64aa 1e-10 in ref transcript
  • CCAAT-binding factor, subunit B [Transcription].

NGFRAP1

• refseq_NGFRAP1.F2 refseq_NGFRAP1.R2 241 288
• NCBIGene 36.3 27018
• Alternative 3-prime, size difference: 47
• Exclusion of the protein initiation site
• Reference transcript: NM_206915

• Changed! pfam BEX 91aa 2e-20 in ref transcript
  • Brain expressed X-linked like family.
• Changed! pfam BEX 100aa 3e-22 in modified transcript

ISCU

• refseq_NIFUN.F1 refseq_NIFUN.R1 125 221
• NCBIGene 36.3 23479
• Single exon skipping, size difference: 96
• Exclusion of the protein initiation site
• Reference transcript: NM_014301

• Changed! TIGR iscU 123aa 1e-60 in ref transcript
  • This model represents IscU, a homolog of the N-terminal region of NifU, an Fe-S cluster assembly protein found mostly in nitrogen-fixing bacteria. IscU is considered part of the IscSUA-hscAB-fdx system of Fe-S assembly, whereas NifU is found in nitrogenase-containing (nitrogen-fixing) species. A NifU-type protein is also found in Helicobacter and Campylobacter. IscU and NifU are considered scaffold proteins on which Fe-S clusters are assembled before transfer to apoproteins. This model excludes true NifU proteins as in Klebsiella pneumoniae and Anabaena sp. as well as archaeal homologs. It includes largely proteobacterial and eukaryotic forms.
• Changed! PRK PRK11325 123aa 1e-66 in ref transcript
  • scaffold protein; Provisional.
• Changed! TIGR iscU 86aa 9e-40 in modified transcript
• Changed! PRK PRK11325 86aa 2e-43 in modified transcript

NIPA2

• refseq_NIPA2.F1 refseq_NIPA2.R1 125 247
• NCBIGene 36.3 81614
• Single exon skipping, size difference: 122
• Exclusion in 5'UTR
• Reference transcript: NM_030922

• pfam DUF803 301aa 7e-96 in ref transcript
  • Protein of unknown function (DUF803). This family consists of several eukaryotic proteins of unknown function.

NIPA2

• refseq_NIPA2.F4 refseq_NIPA2.R4 189 246
• NCBIGene 36.3 81614
• Single exon skipping, size difference: 57
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001008860

• Changed! pfam DUF803 301aa 7e-96 in ref transcript
  • Protein of unknown function (DUF803). This family consists of several eukaryotic proteins of unknown function.
• Changed! pfam DUF803 224aa 2e-81 in modified transcript

NKTR

• refseq_NKTR.F2 refseq_NKTR.R2 139 167
• NCBIGene 36.2 4820
• Single exon skipping, size difference: 28
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_005385

• Changed! cd cyclophilin_ABH_like 168aa 8e-58 in ref transcript
  • cyclophilin_ABH_like: Cyclophilin A, B and H-like cyclophilin-type peptidylprolyl cis- trans isomerase (PPIase) domain. This family represents the archetypal cystolic cyclophilin similar to human cyclophilins A, B and H. PPIase is an enzyme which accelerates protein folding by catalyzing the cis-trans isomerization of the peptide bonds preceding proline residues. These enzymes have been implicated in protein folding processes which depend on catalytic /chaperone-like activities. As cyclophilins, Human hCyP-A, human cyclophilin-B (hCyP-19), S. cerevisiae Cpr1 and C. elegans Cyp-3, are inhibited by the immunosuppressive drug cyclopsporin A (CsA). CsA binds to the PPIase active site. Cyp-3. S. cerevisiae Cpr1 interacts with the Rpd3 - Sin3 complex and in addition is a component of the Set3 complex. S. cerevisiae Cpr1 has also been shown to have a role in Zpr1p nuclear transport. Human cyclophilin H associates with the [U4/U6.U5] tri-snRNP particles of the splicesome.
• Changed! pfam Pro_isomerase 169aa 8e-72 in ref transcript
  • Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD. The peptidyl-prolyl cis-trans isomerases, also known as cyclophilins, share this domain of about 109 amino acids. Cyclophilins have been found in all organisms studied so far and catalyse peptidyl-prolyl isomerisation during which the peptide bond preceding proline (the peptidyl-prolyl bond) is stabilised in the cis conformation. Mammalian cyclophilin A (CypA) is a major cellular target for the immunosuppressive drug cyclosporin A (CsA). Other roles for cyclophilins may include chaperone and cell signalling function.
• Changed! PTZ PTZ00060 171aa 1e-51 in ref transcript
  • cyclophilin; Provisional.
• Changed! cd cyclophilin_ABH_like 88aa 1e-22 in modified transcript
• Changed! pfam Pro_isomerase 89aa 4e-27 in modified transcript
• Changed! PTZ PTZ00060 91aa 7e-22 in modified transcript

NKTR

• refseq_NKTR.F3 refseq_NKTR.R3 148 176
• NCBIGene 36.2 4820
• Single exon skipping, size difference: 28
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_005385

• Changed! cd cyclophilin_ABH_like 168aa 8e-58 in ref transcript
  • cyclophilin_ABH_like: Cyclophilin A, B and H-like cyclophilin-type peptidylprolyl cis- trans isomerase (PPIase) domain. This family represents the archetypal cystolic cyclophilin similar to human cyclophilins A, B and H. PPIase is an enzyme which accelerates protein folding by catalyzing the cis-trans isomerization of the peptide bonds preceding proline residues. These enzymes have been implicated in protein folding processes which depend on catalytic /chaperone-like activities. As cyclophilins, Human hCyP-A, human cyclophilin-B (hCyP-19), S. cerevisiae Cpr1 and C. elegans Cyp-3, are inhibited by the immunosuppressive drug cyclopsporin A (CsA). CsA binds to the PPIase active site. Cyp-3. S. cerevisiae Cpr1 interacts with the Rpd3 - Sin3 complex and in addition is a component of the Set3 complex. S. cerevisiae Cpr1 has also been shown to have a role in Zpr1p nuclear transport. Human cyclophilin H associates with the [U4/U6.U5] tri-snRNP particles of the splicesome.
• Changed! pfam Pro_isomerase 169aa 8e-72 in ref transcript
  • Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD. The peptidyl-prolyl cis-trans isomerases, also known as cyclophilins, share this domain of about 109 amino acids. Cyclophilins have been found in all organisms studied so far and catalyse peptidyl-prolyl isomerisation during which the peptide bond preceding proline (the peptidyl-prolyl bond) is stabilised in the cis conformation. Mammalian cyclophilin A (CypA) is a major cellular target for the immunosuppressive drug cyclosporin A (CsA). Other roles for cyclophilins may include chaperone and cell signalling function.
• Changed! PTZ PTZ00060 171aa 1e-51 in ref transcript
  • cyclophilin; Provisional.
• Changed! cd cyclophilin_ABH_like 126aa 2e-39 in modified transcript
• Changed! pfam Pro_isomerase 121aa 1e-45 in modified transcript
• Changed! PTZ PTZ00060 126aa 2e-38 in modified transcript

NME1

• refseq_NME1.F2 refseq_NME1.R2 167 387
• NCBIGene 36.3 4830
• Single exon skipping, size difference: 220
• Exclusion of the protein initiation site
• Reference transcript: NM_198175

• cd NDPk_I 130aa 1e-65 in ref transcript
  • Nucleoside diphosphate kinase Group I (NDPk_I)-like: NDP kinase domains are present in a large family of structurally and functionally conserved proteins from bacteria to humans that generally catalyze the transfer of gamma-phosphates of a nucleoside triphosphate (NTP) donor onto a nucleoside diphosphate (NDP) acceptor through a phosphohistidine intermediate. The mammalian nm23/NDP kinase gene family can be divided into two distinct groups. The group I genes encode proteins that generally have highly homologous counterparts in other organisms and possess the classic enzymatic activity of a kinase. This group includes vertebrate NDP kinases A-D (Nm23- H1 to -H4), and its counterparts in bacteria, archea and other eukaryotes. NDP kinases exist in two different quaternary structures; all known eukaryotic enzymes are hexamers, while some bacterial enzymes are tetramers, as in Myxococcus. They possess the NDP kinase active site motif (NXXH[G/A]SD) and the nine residues that are most essential for catalysis.
• pfam NDK 135aa 2e-72 in ref transcript
  • Nucleoside diphosphate kinase.
• PTZ PTZ00093 147aa 2e-72 in ref transcript
  • nucleoside diphosphate kinase; Provisional.

NME7

• refseq_NME7.F1 refseq_NME7.R1 141 172
• NCBIGene 36.3 29922
• Alternative 3-prime, size difference: 31
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_013330

• Changed! cd NDPk7A 131aa 3e-63 in ref transcript
  • Nucleoside diphosphate kinase 7 domain A (NDPk7A): The nm23-H7 class of nucleoside diphosphate kinase (NDPk7) consists of an N-terminal DM10 domain and two functional catalytic NDPk modules, NDPk7A and NDPk7B. The function of the DM10 domain, which also occurs in multiple copies in other proteins, is unknown. NDPk7 is predominantly expressed in testes, although appreciable amount are also found in liver, heart, brain, ovary, small intestine and spleen. The nm23-H7 gene is located in or near the hereditary prostrate cancer susceptibility locus. Nm23-H7 may be involved in the development of colon and gastric carcinoma, the latter possibly in a type-specific manner.
• Changed! cd NDPk7B 134aa 3e-62 in ref transcript
  • Nucleoside diphosphate kinase 7 domain B (NDPk7B): The nm23-H7 class of nucleoside diphosphate kinase (NDPk7) consists of an N-terminal DM10 domain and two functional catalytic NDPk modules, NDPk7A and NDPk7B. The function of the DM10 domain, which also occurs in multiple copies in other proteins, is unknown. NDPk7 is predominantly expressed in testes, although appreciable amount are also found in liver, heart, brain, ovary, small intestine and spleen. The nm23-H7 gene is located in or near the hereditary prostrate cancer susceptibility locus. Nm23-H7 may be involved in the development of colon and gastric carcinoma, the latter possibly in a type-specific manner.
• Changed! smart NDK 134aa 4e-47 in ref transcript
  • These are enzymes that catalyze nonsubstrate specific conversions of nucleoside diphosphates to nucleoside triphosphates. These enzymes play important roles in bacterial growth, signal transduction and pathogenicity.
• Changed! smart NDK 138aa 1e-44 in ref transcript
• Changed! smart DM10 89aa 6e-25 in ref transcript
  • Domains in hypothetical proteins in Drosophila, C. elegans and mammals. Occurs singly in some nucleoside diphosphate kinases.
• Changed! COG Ndk 134aa 4e-31 in ref transcript
  • Nucleoside diphosphate kinase [Nucleotide transport and metabolism].
• Changed! COG Ndk 133aa 3e-22 in ref transcript

NNAT

• refseq_NNAT.F1 refseq_NNAT.R1 316 397
• NCBIGene 36.3 4826
• Single exon skipping, size difference: 81
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_005386

NOL1

• refseq_NOL1.F1 refseq_NOL1.R1 116 184
• NCBIGene 36.3 4839
• Alternative 5-prime, size difference: 68
• Exclusion in 5'UTR
• Reference transcript: NM_001033714

• cd AdoMet_MTases 129aa 1e-05 in ref transcript
  • S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.).
• pfam Nol1_Nop2_Fmu 286aa 8e-92 in ref transcript
  • NOL1/NOP2/sun family.
• COG Sun 330aa 2e-79 in ref transcript
  • tRNA and rRNA cytosine-C5-methylases [Translation, ribosomal structure and biogenesis].

NOLA1

• refseq_NOLA1.F1 refseq_NOLA1.R1 117 376
• NCBIGene 36.3 54433
• Alternative 5-prime, size difference: 259
• Exclusion in 5'UTR
• Reference transcript: NM_018983

• pfam Gar1 104aa 3e-36 in ref transcript
  • Gar1 protein RNA binding region. Gar1 is a small nucleolar RNP that is required for pre-mRNA processing and pseudouridylation. It is co-immunoprecipitated with the H/ACA families of snoRNAs. This family represents the conserved central region of Gar1. This region is necessary and sufficient for normal cell growth, and specifically binds two snoRNAs snR10 and snR30. This region is also necessary for nucleolar targeting, and it is thought that the protein is co-transported to the nucleolus as part of a nucleoprotein complex. In humans, Gar1 is also component of telomerase in vivo.
• COG GAR1 78aa 4e-12 in ref transcript
  • RNA-binding protein involved in rRNA processing [Translation, ribosomal structure and biogenesis].

NOLA2

• refseq_NOLA2.F2 refseq_NOLA2.R2 269 375
• NCBIGene 36.3 55651
• Single exon skipping, size difference: 106
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_017838

• Changed! pfam Ribosomal_L7Ae 94aa 1e-18 in ref transcript
  • Ribosomal protein L7Ae/L30e/S12e/Gadd45 family. This family includes: Ribosomal L7A from metazoa, Ribosomal L8-A and L8-B from fungi, 30S ribosomal protein HS6 from archaebacteria, 40S ribosomal protein S12 from eukaryotes, Ribosomal protein L30 from eukaryotes and archaebacteria. Gadd45 and MyD118.
• Changed! COG RPL8A 114aa 2e-16 in ref transcript
  • Ribosomal protein HS6-type (S12/L30/L7a) [Translation, ribosomal structure and biogenesis].
• Changed! pfam Ribosomal_L7Ae 32aa 0.003 in modified transcript

NOSTRIN

• refseq_NOSTRIN.F1 refseq_NOSTRIN.R1 122 208
• NCBIGene 36.3 115677
• Single exon skipping, size difference: 86
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_001039724

• Changed! cd SH3 52aa 1e-14 in ref transcript
  • Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
• Changed! smart SH3 57aa 9e-17 in ref transcript
  • Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.

NOX1

• refseq_NOX1.F1 refseq_NOX1.R1 165 312
• NCBIGene 36.3 27035
• Single exon skipping, size difference: 147
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_007052

• Changed! cd NOX_Duox_like_FAD_NADP 268aa 3e-42 in ref transcript
  • NADPH oxidase (NOX) catalyzes the generation of reactive oxygen species (ROS) such as superoxide and hydrogen peroxide. ROS were originally identified as bactericidal agents in phagocytes, but are now also implicated in cell signaling and metabolism. NOX has a 6-alpha helix heme-binding transmembrane domain fused to a flavoprotein with the nucleotide binding domain located in the cytoplasm. Duox enzymes link a peroxidase domain to the NOX domain via a single transmembrane and EF-hand Ca2+ binding sites. The flavoprotein module has a ferredoxin like FAD/NADPH binding domain. In classical phagocytic NOX2, electron transfer occurs from NADPH to FAD to the heme of cytb to oxygen leading to superoxide formation.
• Changed! pfam NAD_binding_6 150aa 5e-27 in ref transcript
  • Ferric reductase NAD binding domain.
• pfam FAD_binding_8 95aa 6e-21 in ref transcript
  • FAD-binding domain.
• pfam Ferric_reduct 156aa 2e-18 in ref transcript
  • Ferric reductase like transmembrane component. This family includes a common region in the transmembrane proteins mammalian cytochrome B-245 heavy chain (gp91-phox), ferric reductase transmembrane component in yeast and respiratory burst oxidase from mouse-ear cress. This may be a family of flavocytochromes capable of moving electrons across the plasma membrane. The Frp1 protein from S. pombe is a ferric reductase component and is required for cell surface ferric reductase activity, mutants in frp1 are deficient in ferric iron uptake. Cytochrome B-245 heavy chain is a FAD-dependent dehydrogenase it is also has electron transferase activity which reduces molecular oxygen to superoxide anion, a precursor in the production of microbicidal oxidants. Mutations in the sequence of cytochrome B-245 heavy chain (gp91-phox) lead to the X-linked chronic granulomatous disease. The bacteriocidal ability of phagocytic cells is reduced and is characterised by the absence of a functional plasma membrane associated NADPH oxidase. The chronic granulomatous disease gene codes for the beta chain of cytochrome B-245 and cytochrome B-245 is missing from patients with the disease.
• Changed! COG COG4097 263aa 9e-09 in ref transcript
  • Predicted ferric reductase [Inorganic ion transport and metabolism].
• Changed! cd NOX_Duox_like_FAD_NADP 219aa 6e-34 in modified transcript
• Changed! pfam NAD_binding_6 101aa 4e-12 in modified transcript
• Changed! COG COG4097 214aa 6e-10 in modified transcript

NPAS3

• refseq_NPAS3.F1 refseq_NPAS3.R1 147 204
• NCBIGene 36.3 64067
• Exon skipping and alternative 3-prime or 5-prime, size difference: 57
• Exclusion in the protein (no frameshift), Exclusion in the protein (no frameshift)
• Reference transcript: NM_173159

• cd PAS 81aa 1e-09 in ref transcript
  • PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.
• cd PAS 53aa 3e-07 in ref transcript
• cd HLH 58aa 3e-06 in ref transcript
  • Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins.
• pfam PAS_3 69aa 1e-10 in ref transcript
  • PAS fold. The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs. The PAS fold appears in archaea, eubacteria and eukarya.
• smart PAS 59aa 6e-09 in ref transcript
  • PAS domain. PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels ([1]; Ponting & Aravind, in press).
• smart HLH 46aa 1e-05 in ref transcript
  • helix loop helix domain.

NPTN

• refseq_NPTN.F1 refseq_NPTN.R1 103 451
• NCBIGene 36.3 27020
• Single exon skipping, size difference: 348
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_012428

• cd IGcam 77aa 6e-07 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• Changed! cd IGcam 89aa 1e-05 in ref transcript
• pfam I-set 96aa 5e-10 in ref transcript
  • Immunoglobulin I-set domain.
• Changed! pfam I-set 88aa 1e-07 in ref transcript

NR1I2

• refseq_NR1I2.F1 refseq_NR1I2.R1 265 376
• NCBIGene 36.3 8856
• Alternative 3-prime, size difference: 111
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_022002

• Changed! cd NR_LBD_PXR_like 193aa 1e-102 in ref transcript
  • The ligand binding domain of xenobiotic receptors:pregnane X receptor and constitutive androstane receptor. The ligand binding domain of xenobiotic receptors: This xenobiotic receptor family includes pregnane X receptor (PXR), constitutive androstane receptor (CAR) and other related nuclear receptors. They function as sensors of toxic byproducts of cell metabolism and of exogenous chemicals, to facilitate their elimination. The nuclear receptor pregnane X receptor (PXR) is a ligand-regulated transcription factor that responds to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. The ligand binding domain of PXR shows remarkable flexibility to accommodate both large and small molecules. PXR functions as a heterodimer with retinoic X receptor-alpha (RXRa) and binds to a variety of response elements in the promoter regions of a diverse set of target genes involved in the metabolism, transport, and elimination of these molecules from the cell. Constitutive androstane receptor (CAR) is a closest mammalian relative of PXR, which has also been proposed to function as a xenosensor. CAR is activated by some of the same ligands as PXR and regulates a subset of common genes. The sequence homology and functional similarity suggests that the CAR gene arose from a duplication of an ancestral PXR gene. Like other nuclear receptors, xenobiotic receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
• Changed! cd NR_LBD_PXR_like 33aa 1e-09 in ref transcript
• pfam Hormone_recep 181aa 2e-32 in ref transcript
  • Ligand-binding domain of nuclear hormone receptor. This all helical domain is involved in binding the hormone in these receptors.
• pfam zf-C4 74aa 1e-30 in ref transcript
  • Zinc finger, C4 type (two domains). In nearly all cases, this is the DNA binding domain of a nuclear hormone receptor. The alignment contains two Zinc finger domains that are too dissimilar to be aligned with each other.
• Changed! cd NR_LBD_PXR_like 249aa 1e-113 in modified transcript

NR4A1

• refseq_NR4A1.F1 refseq_NR4A1.R1 140 290
• NCBIGene 36.3 3164
• Single exon skipping, size difference: 150
• Exclusion in 5'UTR
• Reference transcript: NM_002135

• cd NR_LBD_NGFI-B 238aa 1e-138 in ref transcript
  • The ligand binding domain of Nurr1, a member of conserved family of nuclear receptors. The ligand binding domain of Nerve growth factor-induced-B (NGFI-B): NGFI-B is a member of the nuclear#steroid receptor superfamily. NGFI-B is classified as an orphan receptor because no ligand has yet been identified. NGFI-B is an early immediate gene product of the embryo development that is rapidly produced in response to a variety of cellular signals including nerve growth factor. It is involved in T-cell-mediated apoptosis, as well as neuronal differentiation and function. NGFI-B regulates transcription by binding to a specific DNA target upstream of its target genes and regulating the rate of transcriptional initiation. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, NGFI-B has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
• pfam Hormone_recep 179aa 4e-36 in ref transcript
  • Ligand-binding domain of nuclear hormone receptor. This all helical domain is involved in binding the hormone in these receptors.
• pfam zf-C4 74aa 1e-28 in ref transcript
  • Zinc finger, C4 type (two domains). In nearly all cases, this is the DNA binding domain of a nuclear hormone receptor. The alignment contains two Zinc finger domains that are too dissimilar to be aligned with each other.

NR4A2

• refseq_NR4A2.F1 refseq_NR4A2.R1 162 216
• NCBIGene 36.3 4929
• Alternative 3-prime, size difference: 54
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_006186

• Changed! cd NR_LBD_Nurr1 235aa 1e-137 in ref transcript
  • The ligand binding domain of Nurr1, a member of conserved family of nuclear receptors. The ligand binding domain of nuclear receptor Nurr1: Nurr1 belongs to the conserved family of nuclear receptors. It is a transcription factor that is expressed in the embryonic ventral midbrain and is critical for the development of dopamine (DA) neurons. Structural studies have shown that the ligand binding pocket of Nurr1 is filled by bulky hydrophobic residues, making it unable to bind to ligands. Therefore, it belongs to the class of orphan receptors. However, Nurr1 forms heterodimers with RXR and can promote signaling via its partner, RXR. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, Nurr1 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
• pfam zf-C4 75aa 1e-39 in ref transcript
  • Zinc finger, C4 type (two domains). In nearly all cases, this is the DNA binding domain of a nuclear hormone receptor. The alignment contains two Zinc finger domains that are too dissimilar to be aligned with each other.
• Changed! pfam Hormone_recep 175aa 8e-34 in ref transcript
  • Ligand-binding domain of nuclear hormone receptor. This all helical domain is involved in binding the hormone in these receptors.
• Changed! cd NR_LBD_Nurr1 217aa 1e-122 in modified transcript
• Changed! pfam Hormone_recep 157aa 2e-28 in modified transcript

NR4A2

• refseq_NR4A2.F2 refseq_NR4A2.R2 115 293
• NCBIGene 36.3 4929
• Alternative 3-prime, size difference: 178
• Exclusion of the protein initiation site
• Reference transcript: NM_006186

• cd NR_LBD_Nurr1 235aa 1e-137 in ref transcript
  • The ligand binding domain of Nurr1, a member of conserved family of nuclear receptors. The ligand binding domain of nuclear receptor Nurr1: Nurr1 belongs to the conserved family of nuclear receptors. It is a transcription factor that is expressed in the embryonic ventral midbrain and is critical for the development of dopamine (DA) neurons. Structural studies have shown that the ligand binding pocket of Nurr1 is filled by bulky hydrophobic residues, making it unable to bind to ligands. Therefore, it belongs to the class of orphan receptors. However, Nurr1 forms heterodimers with RXR and can promote signaling via its partner, RXR. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, Nurr1 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
• pfam zf-C4 75aa 1e-39 in ref transcript
  • Zinc finger, C4 type (two domains). In nearly all cases, this is the DNA binding domain of a nuclear hormone receptor. The alignment contains two Zinc finger domains that are too dissimilar to be aligned with each other.
• pfam Hormone_recep 175aa 8e-34 in ref transcript
  • Ligand-binding domain of nuclear hormone receptor. This all helical domain is involved in binding the hormone in these receptors.

NR5A2

• refseq_NR5A2.F1 refseq_NR5A2.R1 124 262
• NCBIGene 36.3 2494
• Single exon skipping, size difference: 138
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_205860

• cd NR_LBD_Lrh-1 241aa 1e-140 in ref transcript
  • The ligand binding domain of the liver receptor homolog-1, a member of nuclear receptor superfamily,. The ligand binding domain (LBD) of the liver receptor homolog-1 (LRH-1): LRH-1 belongs to nuclear hormone receptor superfamily, and is expressed mainly in the liver, intestine, exocrine pancreas, and ovary. Most nuclear receptors function as homodimer or heterodimers. However, LRH-1 binds DNA as a monomer, and is a regulator of bile-acid homeostasis, steroidogenesis, reverse cholesterol transport and the initial stages of embryonic development. Recently, phospholipids have been identified as potential ligand for LRH-1 and steroidogenic factor-1 (SF-1). Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, LRH-1 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
• pfam Hormone_recep 186aa 1e-41 in ref transcript
  • Ligand-binding domain of nuclear hormone receptor. This all helical domain is involved in binding the hormone in these receptors.
• pfam zf-C4 76aa 4e-38 in ref transcript
  • Zinc finger, C4 type (two domains). In nearly all cases, this is the DNA binding domain of a nuclear hormone receptor. The alignment contains two Zinc finger domains that are too dissimilar to be aligned with each other.

NRAP

• refseq_NRAP.F2 refseq_NRAP.R2 124 229
• NCBIGene 36.3 4892
• Single exon skipping, size difference: 105
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_198060

• pfam LIM 52aa 2e-08 in ref transcript
  • LIM domain. This family represents two copies of the LIM structural domain.
• smart NEBU 31aa 7e-05 in ref transcript
  • The Nebulin repeat is present also in Las1. Tandem arrays of these repeats are known to bind actin.
• smart NEBU 31aa 7e-04 in ref transcript
• smart NEBU 31aa 0.001 in ref transcript
• smart NEBU 31aa 0.002 in ref transcript
• pfam Nebulin 29aa 0.002 in ref transcript
  • Nebulin repeat.
• smart NEBU 31aa 0.003 in ref transcript
• smart NEBU 31aa 0.005 in ref transcript

NRCAM

• refseq_NRCAM.F2 refseq_NRCAM.R2 150 180
• NCBIGene 36.3 4897
• Single exon skipping, size difference: 30
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001037132

• cd IGcam 94aa 7e-14 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• cd IGcam 88aa 5e-13 in ref transcript
• Changed! cd FN3 90aa 8e-12 in ref transcript
  • Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.
• cd IGcam 88aa 4e-10 in ref transcript
• cd IGcam 89aa 4e-10 in ref transcript
• cd FN3 96aa 6e-10 in ref transcript
• cd FN3 100aa 5e-09 in ref transcript
• cd IGcam 74aa 4e-07 in ref transcript
• cd FN3 88aa 4e-04 in ref transcript
• cd FN3 77aa 0.004 in ref transcript
• pfam I-set 89aa 2e-12 in ref transcript
  • Immunoglobulin I-set domain.
• pfam I-set 89aa 1e-11 in ref transcript
• smart IGc2 63aa 1e-11 in ref transcript
  • Immunoglobulin C-2 Type.
• Changed! pfam fn3 85aa 5e-11 in ref transcript
  • Fibronectin type III domain.
• pfam fn3 86aa 6e-11 in ref transcript
• pfam fn3 93aa 4e-10 in ref transcript
• pfam I-set 87aa 1e-09 in ref transcript
• pfam I-set 71aa 2e-09 in ref transcript
• pfam fn3 83aa 4e-05 in ref transcript
• pfam fn3 78aa 2e-04 in ref transcript
• Changed! cd FN3 91aa 1e-12 in modified transcript
• Changed! pfam fn3 87aa 1e-11 in modified transcript

NRCAM

• refseq_NRCAM.F4 refseq_NRCAM.R4 102 120
• NCBIGene 36.3 4897
• Single exon skipping, size difference: 18
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001037132

• cd IGcam 94aa 7e-14 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• cd IGcam 88aa 5e-13 in ref transcript
• cd FN3 90aa 8e-12 in ref transcript
  • Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.
• cd IGcam 88aa 4e-10 in ref transcript
• cd IGcam 89aa 4e-10 in ref transcript
• cd FN3 96aa 6e-10 in ref transcript
• cd FN3 100aa 5e-09 in ref transcript
• cd IGcam 74aa 4e-07 in ref transcript
• cd FN3 88aa 4e-04 in ref transcript
• cd FN3 77aa 0.004 in ref transcript
• pfam I-set 89aa 2e-12 in ref transcript
  • Immunoglobulin I-set domain.
• pfam I-set 89aa 1e-11 in ref transcript
• smart IGc2 63aa 1e-11 in ref transcript
  • Immunoglobulin C-2 Type.
• pfam fn3 85aa 5e-11 in ref transcript
  • Fibronectin type III domain.
• pfam fn3 86aa 6e-11 in ref transcript
• pfam fn3 93aa 4e-10 in ref transcript
• pfam I-set 87aa 1e-09 in ref transcript
• pfam I-set 71aa 2e-09 in ref transcript
• pfam fn3 83aa 4e-05 in ref transcript
• pfam fn3 78aa 2e-04 in ref transcript

NRCAM

• refseq_NRCAM.F5 refseq_NRCAM.R5 153 468
• NCBIGene 36.3 4897
• Multiple exon skipping, size difference: 315
• Exclusion in the protein (no frameshift), Exclusion in the protein (no frameshift), Exclusion in the protein (no frameshift)
• Reference transcript: NM_001037132

• cd IGcam 94aa 7e-14 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• cd IGcam 88aa 5e-13 in ref transcript
• cd FN3 90aa 8e-12 in ref transcript
  • Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.
• cd IGcam 88aa 4e-10 in ref transcript
• cd IGcam 89aa 4e-10 in ref transcript
• cd FN3 96aa 6e-10 in ref transcript
• cd FN3 100aa 5e-09 in ref transcript
• cd IGcam 74aa 4e-07 in ref transcript
• cd FN3 88aa 4e-04 in ref transcript
• Changed! cd FN3 77aa 0.004 in ref transcript
• pfam I-set 89aa 2e-12 in ref transcript
  • Immunoglobulin I-set domain.
• pfam I-set 89aa 1e-11 in ref transcript
• smart IGc2 63aa 1e-11 in ref transcript
  • Immunoglobulin C-2 Type.
• pfam fn3 85aa 5e-11 in ref transcript
  • Fibronectin type III domain.
• pfam fn3 86aa 6e-11 in ref transcript
• pfam fn3 93aa 4e-10 in ref transcript
• pfam I-set 87aa 1e-09 in ref transcript
• pfam I-set 71aa 2e-09 in ref transcript
• pfam fn3 83aa 4e-05 in ref transcript
• Changed! pfam fn3 78aa 2e-04 in ref transcript

NRXN2

• refseq_NRXN2.F2 refseq_NRXN2.R2 153 180
• NCBIGene 36.3 9379
• Single exon skipping, size difference: 27
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_015080

• cd LamG 154aa 3e-24 in ref transcript
  • Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules.
• cd LamG 171aa 3e-20 in ref transcript
• cd LamG 168aa 1e-19 in ref transcript
• cd LamG 174aa 2e-12 in ref transcript
• cd LamG 157aa 4e-11 in ref transcript
• Changed! cd LamG 157aa 6e-11 in ref transcript
• cd EGF_CA 34aa 0.001 in ref transcript
  • Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements.
• smart LamG 136aa 2e-28 in ref transcript
  • Laminin G domain.
• smart LamG 151aa 2e-24 in ref transcript
• smart LamG 147aa 8e-24 in ref transcript
• Changed! pfam Laminin_G_2 128aa 6e-16 in ref transcript
  • Laminin G domain. This family includes the Thrombospondin N-terminal-like domain, a Laminin G subfamily.
• smart LamG 154aa 3e-13 in ref transcript
• smart LamG 139aa 2e-11 in ref transcript
• pfam FAP 88aa 0.009 in ref transcript
  • Fibronectin-attachment protein (FAP). This family contains bacterial fibronectin-attachment proteins (FAP). Family members are rich in alanine and proline, are approximately 300 long, and seem to be restricted to mycobacteria. These proteins contain a fibronectin-binding motif that allows mycobacteria to bind to fibronectin in the extracellular matrix.
• Changed! cd LamG 148aa 7e-14 in modified transcript
• Changed! smart LamG 128aa 2e-18 in modified transcript

NRXN2

• refseq_NRXN2.F3 refseq_NRXN2.R3 229 301
• NCBIGene 36.3 9379
• Single exon skipping, size difference: 72
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_015080

• cd LamG 154aa 3e-24 in ref transcript
  • Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules.
• cd LamG 171aa 3e-20 in ref transcript
• cd LamG 168aa 1e-19 in ref transcript
• cd LamG 174aa 2e-12 in ref transcript
• cd LamG 157aa 4e-11 in ref transcript
• cd LamG 157aa 6e-11 in ref transcript
• cd EGF_CA 34aa 0.001 in ref transcript
  • Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements.
• smart LamG 136aa 2e-28 in ref transcript
  • Laminin G domain.
• smart LamG 151aa 2e-24 in ref transcript
• smart LamG 147aa 8e-24 in ref transcript
• pfam Laminin_G_2 128aa 6e-16 in ref transcript
  • Laminin G domain. This family includes the Thrombospondin N-terminal-like domain, a Laminin G subfamily.
• smart LamG 154aa 3e-13 in ref transcript
• smart LamG 139aa 2e-11 in ref transcript
• pfam FAP 88aa 0.009 in ref transcript
  • Fibronectin-attachment protein (FAP). This family contains bacterial fibronectin-attachment proteins (FAP). Family members are rich in alanine and proline, are approximately 300 long, and seem to be restricted to mycobacteria. These proteins contain a fibronectin-binding motif that allows mycobacteria to bind to fibronectin in the extracellular matrix.

NRXN2

• refseq_NRXN2.F5 refseq_NRXN2.R5 220 310
• NCBIGene 36.3 9379
• Single exon skipping, size difference: 90
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_015080

• cd LamG 154aa 3e-24 in ref transcript
  • Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules.
• cd LamG 171aa 3e-20 in ref transcript
• cd LamG 168aa 1e-19 in ref transcript
• Changed! cd LamG 174aa 2e-12 in ref transcript
• cd LamG 157aa 4e-11 in ref transcript
• cd LamG 157aa 6e-11 in ref transcript
• cd EGF_CA 34aa 0.001 in ref transcript
  • Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements.
• smart LamG 136aa 2e-28 in ref transcript
  • Laminin G domain.
• smart LamG 151aa 2e-24 in ref transcript
• smart LamG 147aa 8e-24 in ref transcript
• pfam Laminin_G_2 128aa 6e-16 in ref transcript
  • Laminin G domain. This family includes the Thrombospondin N-terminal-like domain, a Laminin G subfamily.
• Changed! smart LamG 154aa 3e-13 in ref transcript
• smart LamG 139aa 2e-11 in ref transcript
• Changed! pfam FAP 88aa 0.009 in ref transcript
  • Fibronectin-attachment protein (FAP). This family contains bacterial fibronectin-attachment proteins (FAP). Family members are rich in alanine and proline, are approximately 300 long, and seem to be restricted to mycobacteria. These proteins contain a fibronectin-binding motif that allows mycobacteria to bind to fibronectin in the extracellular matrix.
• Changed! cd LamG 144aa 2e-14 in modified transcript
• Changed! smart LamG 124aa 8e-17 in modified transcript

NRXN2

• refseq_NRXN2.F7 refseq_NRXN2.R7 102 123
• NCBIGene 36.3 9379
• Alternative 5-prime, size difference: 21
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_015080

• cd LamG 154aa 3e-24 in ref transcript
  • Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules.
• cd LamG 171aa 3e-20 in ref transcript
• Changed! cd LamG 168aa 1e-19 in ref transcript
• cd LamG 174aa 2e-12 in ref transcript
• cd LamG 157aa 4e-11 in ref transcript
• cd LamG 157aa 6e-11 in ref transcript
• cd EGF_CA 34aa 0.001 in ref transcript
  • Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements.
• smart LamG 136aa 2e-28 in ref transcript
  • Laminin G domain.
• smart LamG 151aa 2e-24 in ref transcript
• Changed! smart LamG 147aa 8e-24 in ref transcript
• pfam Laminin_G_2 128aa 6e-16 in ref transcript
  • Laminin G domain. This family includes the Thrombospondin N-terminal-like domain, a Laminin G subfamily.
• smart LamG 154aa 3e-13 in ref transcript
• smart LamG 139aa 2e-11 in ref transcript
• pfam FAP 88aa 0.009 in ref transcript
  • Fibronectin-attachment protein (FAP). This family contains bacterial fibronectin-attachment proteins (FAP). Family members are rich in alanine and proline, are approximately 300 long, and seem to be restricted to mycobacteria. These proteins contain a fibronectin-binding motif that allows mycobacteria to bind to fibronectin in the extracellular matrix.
• Changed! cd LamG 161aa 1e-20 in modified transcript
• Changed! smart LamG 140aa 1e-24 in modified transcript

NSFL1C

• refseq_NSFL1C.F1 refseq_NSFL1C.R1 142 335
• NCBIGene 36.3 55968
• Alternative 3-prime, size difference: 95
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_016143

• Changed! cd p47_UBX 79aa 3e-32 in ref transcript
  • p47_UBX p47 is an adaptor molecule of the cytosolic AAA ATPase p97. The principal role of the p97-p47 complex is to regulate membrane fusion events. Mono-ubiquitin recognition by p47 is crucial for p97-p47-mediated Golgi membrane fusion events. p47 has carboxy-terminal SEP and UBX domains. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.
• Changed! smart SEP 93aa 2e-38 in ref transcript
  • Domain present in Saccharomyces cerevisiae Shp1, Drosophila melanogaster eyes closed gene (eyc), and vertebrate p47.
• Changed! pfam UBX 80aa 2e-15 in ref transcript
  • UBX domain. This domain is present in ubiquitin-regulatory proteins and is a general Cdc48-interacting module.

NSFL1C

• refseq_NSFL1C.F4 refseq_NSFL1C.R4 102 195
• NCBIGene 36.3 55968
• Single exon skipping, size difference: 93
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_016143

• cd p47_UBX 79aa 3e-32 in ref transcript
  • p47_UBX p47 is an adaptor molecule of the cytosolic AAA ATPase p97. The principal role of the p97-p47 complex is to regulate membrane fusion events. Mono-ubiquitin recognition by p47 is crucial for p97-p47-mediated Golgi membrane fusion events. p47 has carboxy-terminal SEP and UBX domains. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.
• Changed! smart SEP 93aa 2e-38 in ref transcript
  • Domain present in Saccharomyces cerevisiae Shp1, Drosophila melanogaster eyes closed gene (eyc), and vertebrate p47.
• pfam UBX 80aa 2e-15 in ref transcript
  • UBX domain. This domain is present in ubiquitin-regulatory proteins and is a general Cdc48-interacting module.
• Changed! smart SEP 92aa 9e-38 in modified transcript

NSUN5B

• refseq_NSUN5B.F1 refseq_NSUN5B.R1 139 247
• NCBIGene 36.3 155400
• Alternative 5-prime, size difference: 108
• Exclusion in 5'UTR
• Reference transcript: NM_001039575

• TIGR nop2p 71aa 2e-04 in ref transcript
• COG Sun 101aa 1e-09 in ref transcript
  • tRNA and rRNA cytosine-C5-methylases [Translation, ribosomal structure and biogenesis].

NT5C1B

• refseq_NT5C1B.F1 refseq_NT5C1B.R1 151 331
• NCBIGene 36.3 93034
• Single exon skipping, size difference: 180
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001002006

• pfam 5-nucleotidase 261aa 1e-116 in ref transcript
  • 5'-nucleotidase. This family consists of both eukaryotic and prokaryotic 5'-nucleotidase sequences (EC:3.1.3.5).

NT5C3

• refseq_NT5C3.F1 refseq_NT5C3.R1 243 298
• NCBIGene 36.3 51251
• Single exon skipping, size difference: 55
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_001002010

• Changed! TIGR HAD-SF-IE 275aa 1e-134 in ref transcript
  • This group of sequences was found during searches for members of the haloacid dehalogenase (HAD) superfamily. All of the conserved catalytic motifs are found. The placement of the variable domain between motifs 1 and 2 indicates membership in subfamily I of the superfamily, but these sequences are sufficiently different from any of the branches (IA, TIGR01493, TIGR01509, TIGR01549; IB, TIGR01488; IC, TIGR01494; ID, TIGR01658; IF TIGR01545) of that subfamily as to constitute a separate branch to now be called IE. Considering that the closest identifiable hit outside of the noise range is to a phosphoserine phosphatase, this group may be considered to be most closely allied to subfamily IB.
• Changed! COG SerB 122aa 0.009 in ref transcript
  • Phosphoserine phosphatase [Amino acid transport and metabolism].

NTRK2

• refseq_NTRK2.F2 refseq_NTRK2.R2 147 195
• NCBIGene 36.3 4915
• Single exon skipping, size difference: 48
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_006180

• cd PTKc_TrkB 288aa 0.0 in ref transcript
  • Catalytic Domain of the Protein Tyrosine Kinase, Tropomyosin Related Kinase B. Protein Tyrosine Kinase (PTK) family; Tropomyosin related kinase B (TrkB); catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. TrkB is a member of the Trk subfamily of proteins, which are receptor tyr kinases (RTKs) containing an extracellular region with arrays of leucine-rich motifs flanked by two cysteine-rich clusters followed by two immunoglobulin-like domains, a transmembrane segment, and an intracellular catalytic domain. Binding of TrkB to its ligands, brain-derived neurotrophic factor (BDNF) or neurotrophin 4 (NT4), results in receptor oligomerization and activation of the catalytic domain. TrkB is broadly expressed in the nervous system and in some non-neural tissues. It plays important roles in cell proliferation, differentiation, and survival. BDNF/Trk signaling plays a key role in regulating activity-dependent synaptic plasticity. TrkB also contributes to protection against gp120-induced neuronal cell death. TrkB overexpression is associated with poor prognosis in neuroblastoma (NB) and other human cancers. It acts as a suppressor of anoikis (detachment-induced apoptosis) and contributes to tumor metastasis.
• cd IGcam 79aa 4e-08 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• cd IGcam 69aa 3e-04 in ref transcript
• pfam Pkinase_Tyr 270aa 1e-115 in ref transcript
  • Protein tyrosine kinase.
• pfam I-set 79aa 3e-12 in ref transcript
  • Immunoglobulin I-set domain.
• pfam I-set 67aa 4e-06 in ref transcript
• smart LRRCT 46aa 8e-05 in ref transcript
  • Leucine rich repeat C-terminal domain.
• pfam LRRNT 30aa 0.006 in ref transcript
  • Leucine rich repeat N-terminal domain. Leucine Rich Repeats pfam00560 are short sequence motifs present in a number of proteins with diverse functions and cellular locations. Leucine Rich Repeats are often flanked by cysteine rich domains. This domain is often found at the N-terminus of tandem leucine rich repeats.
• COG SPS1 262aa 4e-24 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].

NTRK3

• refseq_NTRK3.F1 refseq_NTRK3.R1 194 236
• NCBIGene 36.3 4916
• Single exon skipping, size difference: 42
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001012338

• Changed! cd PTKc_TrkC 305aa 1e-179 in ref transcript
  • Catalytic Domain of the Protein Tyrosine Kinase, Tropomyosin Related Kinase C. Protein Tyrosine Kinase (PTK) family; Tropomyosin related kinase C (TrkC); catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. TrkC is a member of the Trk subfamily of proteins, which are receptor tyr kinases (RTKs) containing an extracellular region with arrays of leucine-rich motifs flanked by two cysteine-rich clusters followed by two immunoglobulin-like domains, a transmembrane segment, and an intracellular catalytic domain. Binding of TrkC to its ligand, neurotrophin 3 (NT3), results in receptor oligomerization and activation of the catalytic domain. TrkC is broadly expressed in the nervous system and in some non-neural tissues including the developing heart. NT3/TrkC signaling plays an important role in the innervation of the cardiac conducting system and the development of smooth muscle cells. Mice deficient with NT3 and TrkC have multiple heart defects. NT3/TrkC signaling is also critical for the development and maintenance of enteric neurons that are important for the control of gut peristalsis.
• cd IGcam 89aa 7e-07 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• cd IGcam 89aa 2e-05 in ref transcript
• Changed! pfam Pkinase_Tyr 287aa 1e-108 in ref transcript
  • Protein tyrosine kinase.
• smart IG_like 85aa 2e-10 in ref transcript
  • Immunoglobulin like. IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
• smart LRRCT 46aa 1e-07 in ref transcript
  • Leucine rich repeat C-terminal domain.
• pfam I-set 68aa 5e-07 in ref transcript
  • Immunoglobulin I-set domain.
• Changed! COG SPS1 283aa 3e-23 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].
• Changed! cd PTKc_TrkC 291aa 0.0 in modified transcript
• Changed! pfam Pkinase_Tyr 273aa 1e-111 in modified transcript
• Changed! COG SPS1 269aa 1e-23 in modified transcript

NUDT1

• refseq_NUDT1.F1 refseq_NUDT1.R1 113 186
• NCBIGene 36.3 4521
• Alternative 5-prime, size difference: 73
• Exclusion of the protein initiation site
• Reference transcript: NM_198949

• cd MTH1 136aa 5e-30 in ref transcript
  • MutT homolog-1 (MTH1) is a member of the Nudix hydrolase superfamily. MTH1, the mammalian counterpart of MutT, hydrolyzes oxidized purine nucleoside triphosphates, such as 8-oxo-dGTP and 2-hydroxy-ATP, to monophosphates, thereby preventing the incorporation of such oxygen radicals during replication. This is an important step in the repair mechanism in genomic and mitochondrial DNA. Like other members of the Nudix family, it requires a divalent cation, such as Mg2+ or Mn2+, for activity, and contain the Nudix motif, a highly conserved 23-residue block (GX5EX7REUXEEXGU, where U = I, L or V), that functions as a metal binding and catalytic site. MTH1 is predominantly localized in the cytoplasm and mitochondria. Structurally, this enzyme adopts a similar fold to MutT despite low sequence similarity outside the conserved nudix motif. The most distinctive structural difference between MutT and MTH1 is the presence of a beta-hairpin, which is absent in MutT. This results in a much deeper and narrower substrate binding pocket. Mechanistically, MTH1 contains dual specificity for nucleotides that contain 2-OH-adenine bases and those that contain 8-oxo-guanine bases.
• pfam NUDIX 93aa 1e-14 in ref transcript
  • NUDIX domain.
• COG COG1051 76aa 4e-05 in ref transcript
  • ADP-ribose pyrophosphatase [Nucleotide transport and metabolism].

NUDT2

• refseq_NUDT2.F2 refseq_NUDT2.R2 116 187
• NCBIGene 36.3 318
• Alternative 3-prime, size difference: 71
• Inclusion in 5'UTR
• Reference transcript: NM_147172

• cd Ap4A_hydrolase_human_like 139aa 4e-43 in ref transcript
  • Diadenosine tetraphosphate (Ap4A) hydrolase is a member of the Nudix hydrolase superfamily. Ap4A hydrolases are well represented in a variety of prokaryotic and eukaryotic organisms. Phylogenetic analysis reveals two distinct subgroups where plant enzymes fall into one subfamily and fungi/animals/archaea enzymes, represented by this subfamily, fall into another. Bacterial enzymes are found in both subfamilies. Ap4A is a potential by-product of aminoacyl tRNA synthesis, and accumulation of Ap4A has been implicated in a range of biological events, such as DNA replication, cellular differentiation, heat shock, metabolic stress, and apoptosis. Ap4A hydrolase cleaves Ap4A asymmetrically into ATP and AMP. It is important in the invasive properties of bacteria and thus presents a potential target for inhibition of such invasive bacteria. Besides the signature nudix motif (G[X5]E[X7]REUXEEXGU, where U is Ile, Leu, or Val) that functions as a metal binding and catalytic site, and a required divalent cation, Ap4A hydrolase is structurally similar to the other members of the nudix superfamily with some degree of variation. Several regions in the sequences are poorly defined and substrate and metal binding sites are only predicted based on kinetic studies.
• pfam NUDIX 112aa 5e-16 in ref transcript
  • NUDIX domain.
• COG MutT 121aa 3e-07 in ref transcript
  • NTP pyrophosphohydrolases including oxidative damage repair enzymes [DNA replication, recombination, and repair / General function prediction only].

NUDT9

• refseq_NUDT9.F1 refseq_NUDT9.R1 109 446
• NCBIGene 36.3 53343
• Alternative 5-prime, size difference: 337
• Exclusion of the protein initiation site
• Reference transcript: NM_024047

• cd ADPRase_NUDT9 187aa 9e-77 in ref transcript
  • ADP-ribose pyrophosphatase (ADPRase) catalyzes the hydrolysis of ADP-ribose to AMP and ribose-5-P. Like other members of the Nudix hydrolase superfamily of enzymes, it is thought to require a divalent cation, such as Mg2+, for its activity. It also contains a 23-residue Nudix motif (GX5EX7REUXEEXGU, where U = I, L or V) which functions as a metal binding site/catalytic site. In addition to the Nudix motif, there are additional conserved amino acid residues, distal from the signature sequence, that correlate with substrate specificity. In humans, there are four distinct ADPRase activities, three putative cytosolic (ADPRase-I, -II, and -Mn) and a single mitochondrial enzyme (ADPRase-m). ADPRase-m is also known as NUDT9. It can be distinugished from the cytosolic ADPRase by a N-terminal target sequence unique to mitochondrial ADPRase. NUDT9 functions as a monomer.
• pfam NUDIX 38aa 2e-05 in ref transcript
  • NUDIX domain.
• COG COG1051 135aa 7e-06 in ref transcript
  • ADP-ribose pyrophosphatase [Nucleotide transport and metabolism].

NUMB

• refseq_NUMB.F1 refseq_NUMB.R1 127 271
• NCBIGene 36.3 8650
• Single exon skipping, size difference: 144
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001005743

• cd Numb 149aa 2e-72 in ref transcript
  • Numb Phosphotyrosine-binding (PTB) domain. Numb is a membrane associated adaptor protein, which is a determinant of asymmetric cell division. Numb has an N-terminal PTB domain. PTB domains have a PH-like fold and are found in various eukaryotic signaling molecules. They were initially identified based upon their ability to recognize phosphorylated tyrosine residues. In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. More recent studies have found that some types of PTB domains can bind to peptides which are not tyrosine phosphorylated or lack tyrosine residues altogether.
• pfam PID 134aa 7e-34 in ref transcript
  • Phosphotyrosine interaction domain (PTB/PID).
• pfam NumbF 82aa 8e-32 in ref transcript
  • NUMB domain. This presumed domain is found in the Numb family of proteins adjacent to the PTB domain.

NUP35

• refseq_NUP35.F1 refseq_NUP35.R1 217 359
• NCBIGene 36.2 129401
• Single exon skipping, size difference: 142
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_138285

• Changed! pfam MPPN 84aa 9e-33 in ref transcript
  • MPPN (rrm-like) domain. The MPPN (Mitotic PhosphoProtein N' end) family is uncharacterised however it probably plays a role in the cell cycle because the family includes mitotic phosphoproteins. This family also includes a suppressor of thermosensitive mutations in the DNA polymerase delta gene (Pol III). The conserved central region appears to be distantly related to the pfam00076 domain, suggesting an RNA binding function for this protein (Bateman A. pers obs).

NUP62

• refseq_NUP62.F1 refseq_NUP62.R1 140 173
• NCBIGene 36.3 23636
• Alternative 3-prime, size difference: 33
• Inclusion in 5'UTR
• Reference transcript: NM_016553

• pfam Nsp1_C 102aa 8e-39 in ref transcript
  • Nsp1-like C-terminal region. This family probably forms a coiled-coil. This important region of Nsp1 is involved in binding Nup82.

NUPL1

• refseq_NUPL1.F2 refseq_NUPL1.R2 156 192
• NCBIGene 36.3 9818
• Single exon skipping, size difference: 36
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_014089

NVL

• refseq_NVL.F1 refseq_NVL.R1 189 263
• NCBIGene 36.3 4931
• Single exon skipping, size difference: 74
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_002533

• Changed! cd AAA 141aa 2e-24 in ref transcript
  • The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.
• Changed! cd AAA 137aa 1e-23 in ref transcript
• Changed! TIGR CDC48 614aa 1e-161 in ref transcript
  • This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.
• Changed! COG SpoVK 557aa 1e-117 in ref transcript
  • ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones].

NXF5

• refseq_NXF5.F1 refseq_NXF5.R1 191 380
• NCBIGene 36.2 55998
• Multiple exon skipping, size difference: 189
• Exclusion in the protein (no frameshift), Exclusion in the protein (no frameshift)
• Reference transcript: NM_032946

• Changed! pfam Tap-RNA_bind 88aa 5e-39 in ref transcript
  • Tap, RNA-binding. Members of this family adopt a structure consisting of an alpha+beta sandwich with an antiparallel beta-sheet, arranged in a 2(beta-alpha-beta) motif. They are mainly found in mRNA export factors, and mediate the sequence nonspecific nuclear export of cellular mRNAs as well as the sequence-specific export of retroviral mRNAs bearing the constitutive transport element.

NXF5

• refseq_NXF5.F5 refseq_NXF5.R5 224 288
• NCBIGene 36.2 55998
• Alternative 3-prime, size difference: 64
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_032946

• pfam Tap-RNA_bind 88aa 5e-39 in ref transcript
  • Tap, RNA-binding. Members of this family adopt a structure consisting of an alpha+beta sandwich with an antiparallel beta-sheet, arranged in a 2(beta-alpha-beta) motif. They are mainly found in mRNA export factors, and mediate the sequence nonspecific nuclear export of cellular mRNAs as well as the sequence-specific export of retroviral mRNAs bearing the constitutive transport element.

OAS1

• refseq_OAS1.F1 refseq_OAS1.R1 201 299
• NCBIGene 36.3 4938
• Alternative 3-prime, size difference: 98
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_001032409

• Changed! pfam OAS1_C 182aa 1e-100 in ref transcript
  • 2'-5'-oligoadenylate synthetase 1, domain 2, C-terminus. This is the largely alpha-helical, C-terminal half of 2'-5'-oligoadenylate synthetase 1, being described as domain 2 of the enzyme and homologous to a tandem ubiquitin repeat. It carries the region of enzymic activity between 320 and 344 at the extreme C-terminal end. Oligoadenylate synthetases are antiviral enzymes that counteract vial attack by degrading viral RNA. The enzyme uses ATP in 2'-specific nucleotidyl transfer reactions to synthesise 2'.5'-oligoadenylates, which activate latent ribonuclease, resulting in degradation of viral RNA and inhibition of virus replication. This domain is often associated with NTP_transf_2 pfam01909.
• Changed! pfam OAS1_C 187aa 1e-100 in modified transcript

OASL

• refseq_OASL.F1 refseq_OASL.R1 106 348
• NCBIGene 36.3 8638
• Single exon skipping, size difference: 242
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_003733

• Changed! cd OASL_repeat1 80aa 5e-34 in ref transcript
  • OASL_repeat1 (2'-5' oligoadenylate synthetase-like protein) belongs to a family of interferon-induced 2'-5' oligoadenylate synthetases which are important for the antiviral activity of interferons. While each member of this famliy has a conserved N-terminal OAS catalytic domain, only OASL has two tandem ubiquitin-like repeats located at the C-terminus and this CD represents one of those repeats.
• Changed! pfam OAS1_C 187aa 2e-76 in ref transcript
  • 2'-5'-oligoadenylate synthetase 1, domain 2, C-terminus. This is the largely alpha-helical, C-terminal half of 2'-5'-oligoadenylate synthetase 1, being described as domain 2 of the enzyme and homologous to a tandem ubiquitin repeat. It carries the region of enzymic activity between 320 and 344 at the extreme C-terminal end. Oligoadenylate synthetases are antiviral enzymes that counteract vial attack by degrading viral RNA. The enzyme uses ATP in 2'-specific nucleotidyl transfer reactions to synthesise 2'.5'-oligoadenylates, which activate latent ribonuclease, resulting in degradation of viral RNA and inhibition of virus replication. This domain is often associated with NTP_transf_2 pfam01909.
• Changed! pfam ubiquitin 67aa 6e-07 in ref transcript
  • Ubiquitin family. This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue), Nedd8, Elongin B, Rub1, and Parkin. A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites.
• Changed! pfam OAS1_C 66aa 8e-22 in modified transcript

OATL1

• refseq_OATL1.F1 refseq_OATL1.R1 230 385
• NCBIGene 36.2 4943
• Single exon skipping, size difference: 155
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_002536

• Changed! smart TBC 212aa 2e-46 in ref transcript
  • Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs. Widespread domain present in Gyp6 and Gyp7, thereby giving rise to the notion that it performs a GTP-activator activity on Rab-like GTPases.
• Changed! COG COG5210 215aa 1e-26 in ref transcript
  • GTPase-activating protein [General function prediction only].

OCIAD2

• refseq_OCIAD2.F1 refseq_OCIAD2.R1 101 219
• NCBIGene 36.3 132299
• Single exon skipping, size difference: 118
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_001014446

• Changed! pfam OCIA 118aa 1e-34 in ref transcript
  • Ovarian carcinoma immunoreactive antigen (OCIA). This family consists of several ovarian carcinoma immunoreactive antigen (OCIA) and related eukaryotic sequences. The function of this family is unknown.
• Changed! pfam OCIA 86aa 7e-27 in modified transcript

OCRL

• refseq_OCRL.F1 refseq_OCRL.R1 123 147
• NCBIGene 36.3 4952
• Single exon skipping, size difference: 24
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000276

• Changed! cd RhoGAP_OCRL1 229aa 6e-65 in ref transcript
  • RhoGAP_OCRL1: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in OCRL1-like proteins. OCRL1 (oculocerebrorenal syndrome of Lowe 1)-like proteins contain two conserved domains: a central inositol polyphosphate 5-phosphatase domain and a C-terminal Rho GAP domain, this GAP domain lacks the catalytic residue and therefore maybe inactive. OCRL-like proteins are type II inositol polyphosphate 5-phosphatases that can hydrolyze lipid PI(4,5)P2 and PI(3,4,5)P3 and soluble Ins(1,4,5)P3 and Ins(1,3,4,5)P4, but their individual specificities vary. The functionality of the RhoGAP domain is still unclear. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
• smart IPPc 302aa 1e-112 in ref transcript
  • Inositol polyphosphate phosphatase, catalytic domain homologues. Mg(2+)-dependent/Li(+)-sensitive enzymes.
• smart RhoGAP 162aa 1e-34 in ref transcript
  • GTPase-activator protein for Rho-like GTPases. GTPase activator proteins towards Rho/Rac/Cdc42-like small GTPases. etter domain limits and outliers.
• COG COG5411 318aa 7e-53 in ref transcript
  • Phosphatidylinositol 5-phosphate phosphatase [Signal transduction mechanisms].
• Changed! cd RhoGAP_OCRL1 221aa 7e-66 in modified transcript

ODF2

• refseq_ODF2.F2 refseq_ODF2.R2 115 374
• NCBIGene 36.3 4957
• Multiple exon skipping, size difference: 259
• Exclusion in 5'UTR, Exclusion of the protein initiation site
• Reference transcript: NM_002540

• TIGR SMC_prok_B 601aa 2e-14 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• COG Smc 329aa 5e-11 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].
• COG Smc 353aa 5e-09 in ref transcript

ODF2L

• refseq_ODF2L.F1 refseq_ODF2L.R1 188 321
• NCBIGene 36.3 57489
• Single exon skipping, size difference: 133
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_020729

• Changed! pfam SMC_N 255aa 7e-05 in ref transcript
  • RecF/RecN/SMC N terminal domain. This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.
• Changed! TIGR SMC_prok_B 198aa 0.006 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.

ODZ3

• refseq_ODZ3.F1 refseq_ODZ3.R1 102 123
• NCBIGene 36.2 55714
• Single exon skipping, size difference: 21
• Exclusion in the protein (no frameshift)
• Reference transcript: XM_931600

• pfam Ten_N 279aa 4e-63 in ref transcript
  • Teneurin Intracellular Region. This family is found in the intracellular N-terminal region of the Teneurin family of proteins. These proteins are 'pair-rule' genes and are involved in tissue patterning, specifically probably neural patterning. The intracellular domain is cleaved in response to homophilic interaction of the extracellular domain, and translocates to the nucleus. Here it probably carries out to some transcriptional regulatory activity. The length of this region and the conservation suggests that there may be two structural domains here (personal obs:C Yeats).
• pfam Keratin_B2 153aa 0.005 in ref transcript
  • Keratin, high sulfur B2 protein. High sulfur proteins are cysteine-rich proteins synthesised during the differentiation of hair matrix cells, and form hair fibres in association with hair keratin intermediate filaments. This family has been divided up into four regions, with the second region containing 8 copies of a short repeat. This family is also known as B2 or KAP1.
• COG RhsA 630aa 1e-07 in ref transcript
  • Rhs family protein [Cell envelope biogenesis, outer membrane].

ODZ3

• refseq_ODZ3.F3 refseq_ODZ3.R3 101 128
• NCBIGene 36.2 55714
• Single exon skipping, size difference: 27
• Exclusion in the protein (no frameshift)
• Reference transcript: XM_931600

• pfam Ten_N 279aa 4e-63 in ref transcript
  • Teneurin Intracellular Region. This family is found in the intracellular N-terminal region of the Teneurin family of proteins. These proteins are 'pair-rule' genes and are involved in tissue patterning, specifically probably neural patterning. The intracellular domain is cleaved in response to homophilic interaction of the extracellular domain, and translocates to the nucleus. Here it probably carries out to some transcriptional regulatory activity. The length of this region and the conservation suggests that there may be two structural domains here (personal obs:C Yeats).
• pfam Keratin_B2 153aa 0.005 in ref transcript
  • Keratin, high sulfur B2 protein. High sulfur proteins are cysteine-rich proteins synthesised during the differentiation of hair matrix cells, and form hair fibres in association with hair keratin intermediate filaments. This family has been divided up into four regions, with the second region containing 8 copies of a short repeat. This family is also known as B2 or KAP1.
• COG RhsA 630aa 1e-07 in ref transcript
  • Rhs family protein [Cell envelope biogenesis, outer membrane].

OGT

• refseq_OGT.F2 refseq_OGT.R2 106 136
• NCBIGene 36.3 8473
• Alternative 3-prime, size difference: 30
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_181672

• cd TPR 100aa 4e-18 in ref transcript
  • Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here.
• cd TPR 100aa 4e-18 in ref transcript
• cd TPR 100aa 9e-18 in ref transcript
• cd TPR 96aa 1e-16 in ref transcript
• cd TPR 95aa 1e-14 in ref transcript
• cd TPR 98aa 2e-08 in ref transcript
• Changed! TIGR PEP_TPR_lipo 444aa 5e-39 in ref transcript
  • This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of tetratricopeptide repeats (TPR) suggests protein-protein interaction, possibly for the regulation of PEP-CTERM protein expression, since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator.
• COG Spy 199aa 8e-46 in ref transcript
  • Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational modification, protein turnover, chaperones].
• COG Spy 396aa 1e-38 in ref transcript
• COG NrfG 211aa 1e-15 in ref transcript
  • FOG: TPR repeat [General function prediction only].
• COG TadD 199aa 2e-11 in ref transcript
  • Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking and secretion].
• Changed! TIGR PEP_TPR_lipo 433aa 5e-39 in modified transcript

OSGIN1

• refseq_OKL38.F1 refseq_OKL38.R1 110 270
• NCBIGene 36.3 29948
• Single exon skipping, size difference: 160
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_013370

• Changed! pfam Pyr_redox_2 208aa 3e-06 in ref transcript
  • Pyridine nucleotide-disulphide oxidoreductase. This family includes both class I and class II oxidoreductases and also NADH oxidases and peroxidases. This domain is actually a small NADH binding domain within a larger FAD binding domain.
• Changed! PRK PRK12770 80aa 4e-07 in ref transcript
  • putative glutamate synthase subunit beta; Provisional.
• Changed! COG GltD 205aa 8e-07 in ref transcript
  • NADPH-dependent glutamate synthase beta chain and related oxidoreductases [Amino acid transport and metabolism / General function prediction only].
• Changed! COG TrkA 202aa 0.003 in ref transcript
  • Predicted flavoprotein involved in K+ transport [Inorganic ion transport and metabolism].

OLAH

• refseq_OLAH.F1 refseq_OLAH.R1 227 386
• NCBIGene 36.3 55301
• Single exon skipping, size difference: 159
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_018324

• Changed! pfam Thioesterase 282aa 9e-26 in ref transcript
  • Thioesterase domain. Peptide synthetases are involved in the non-ribosomal synthesis of peptide antibiotics. Next to the operons encoding these enzymes, in almost all cases, are genes that encode proteins that have similarity to the type II fatty acid thioesterases of vertebrates. There are also modules within the peptide synthetases that also share this similarity. With respect to antibiotic production, thioesterases are required for the addition of the last amino acid to the peptide antibiotic, thereby forming a cyclic antibiotic. Thioesterases (non-integrated) have molecular masses of 25-29 kDa.
• Changed! COG GrsT 278aa 8e-34 in ref transcript
  • Predicted thioesterase involved in non-ribosomal peptide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism].
• Changed! pfam Thioesterase 229aa 4e-33 in modified transcript
• Changed! COG GrsT 225aa 4e-42 in modified transcript

OPA1

• refseq_OPA1.F1 OPA1.u.r.6 129 183
• NCBIGene 36.3 4976
• Single exon skipping, size difference: 54
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_130837

• pfam Dynamin_N 179aa 4e-38 in ref transcript
  • Dynamin family.

OPN3

• refseq_OPN3.F2 refseq_OPN3.R2 206 366
• NCBIGene 36.2 23596
• Alternative 5-prime, size difference: 160
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_014322

• Changed! pfam 7tm_1 243aa 6e-23 in ref transcript
  • 7 transmembrane receptor (rhodopsin family). This family contains, amongst other G-protein-coupled receptors (GCPRs), members of the opsin family, which have been considered to be typical members of the rhodopsin superfamily. They share several motifs, mainly the seven transmembrane helices, GCPRs of the rhodopsin superfamily. All opsins bind a chromophore, such as 11-cis-retinal. The function of most opsins other than the photoisomerases is split into two steps: light absorption and G-protein activation. Photoisomerases, on the other hand, are not coupled to G-proteins - they are thought to generate and supply the chromophore that is used by visual opsins.
• Changed! pfam 7tm_1 115aa 2e-08 in modified transcript

OPN4

• refseq_OPN4.F1 refseq_OPN4.R1 142 175
• NCBIGene 36.3 94233
• Single exon skipping, size difference: 33
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001030015

• Changed! pfam 7tm_1 257aa 6e-41 in ref transcript
  • 7 transmembrane receptor (rhodopsin family). This family contains, amongst other G-protein-coupled receptors (GCPRs), members of the opsin family, which have been considered to be typical members of the rhodopsin superfamily. They share several motifs, mainly the seven transmembrane helices, GCPRs of the rhodopsin superfamily. All opsins bind a chromophore, such as 11-cis-retinal. The function of most opsins other than the photoisomerases is split into two steps: light absorption and G-protein activation. Photoisomerases, on the other hand, are not coupled to G-proteins - they are thought to generate and supply the chromophore that is used by visual opsins.
• Changed! pfam 7tm_1 258aa 8e-43 in modified transcript

OPN5

• refseq_OPN5.F2 refseq_OPN5.R2 242 322
• NCBIGene 36.3 221391
• Single exon skipping, size difference: 80
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_181744

• Changed! pfam 7tm_1 248aa 1e-25 in ref transcript
  • 7 transmembrane receptor (rhodopsin family). This family contains, amongst other G-protein-coupled receptors (GCPRs), members of the opsin family, which have been considered to be typical members of the rhodopsin superfamily. They share several motifs, mainly the seven transmembrane helices, GCPRs of the rhodopsin superfamily. All opsins bind a chromophore, such as 11-cis-retinal. The function of most opsins other than the photoisomerases is split into two steps: light absorption and G-protein activation. Photoisomerases, on the other hand, are not coupled to G-proteins - they are thought to generate and supply the chromophore that is used by visual opsins.
• Changed! pfam 7tm_1 79aa 5e-10 in modified transcript

OPRL1

• refseq_OPRL1.F1 refseq_OPRL1.R1 134 285
• NCBIGene 36.3 4987
• Single exon skipping, size difference: 151
• Exclusion in 5'UTR
• Reference transcript: NM_182647

• pfam 7tm_1 246aa 4e-38 in ref transcript
  • 7 transmembrane receptor (rhodopsin family). This family contains, amongst other G-protein-coupled receptors (GCPRs), members of the opsin family, which have been considered to be typical members of the rhodopsin superfamily. They share several motifs, mainly the seven transmembrane helices, GCPRs of the rhodopsin superfamily. All opsins bind a chromophore, such as 11-cis-retinal. The function of most opsins other than the photoisomerases is split into two steps: light absorption and G-protein activation. Photoisomerases, on the other hand, are not coupled to G-proteins - they are thought to generate and supply the chromophore that is used by visual opsins.

OPRS1

• refseq_OPRS1.F2 refseq_OPRS1.R2 140 248
• NCBIGene 36.2 10280
• Alternative 5-prime, size difference: 66
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_005866

• Changed! pfam ERG2_Sigma1R 189aa 3e-73 in ref transcript
  • ERG2 and Sigma1 receptor like protein. This family consists of the fungal C-8 sterol isomerase and mammalian sigma1 receptor. C-8 sterol isomerase (delta-8-delta-7 sterol isomerase), catalyses a reaction in ergosterol biosynthesis, which results in unsaturation at C-7 in the B ring of sterols. Sigma 1 receptor is a low molecular mass mammalian protein located in the endoplasmic reticulum, which interacts with endogenous steroid hormones, such as progesterone and testosterone. It also binds the sigma ligands, which are are a set of chemically unrelated drugs including haloperidol, pentazocine, and ditolylguanidine. Sigma1 effectors are not well understood, but sigma1 agonists have been observed to affect NMDA receptor function, the alpha-adrenergic system and opioid analgesia.
• Changed! pfam ERG2_Sigma1R 167aa 7e-67 in modified transcript

OPRS1

• refseq_OPRS1.F3 refseq_OPRS1.R3 129 222
• NCBIGene 36.3 10280
• Single exon skipping, size difference: 93
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_005866

• Changed! pfam ERG2_Sigma1R 189aa 3e-73 in ref transcript
  • ERG2 and Sigma1 receptor like protein. This family consists of the fungal C-8 sterol isomerase and mammalian sigma1 receptor. C-8 sterol isomerase (delta-8-delta-7 sterol isomerase), catalyses a reaction in ergosterol biosynthesis, which results in unsaturation at C-7 in the B ring of sterols. Sigma 1 receptor is a low molecular mass mammalian protein located in the endoplasmic reticulum, which interacts with endogenous steroid hormones, such as progesterone and testosterone. It also binds the sigma ligands, which are are a set of chemically unrelated drugs including haloperidol, pentazocine, and ditolylguanidine. Sigma1 effectors are not well understood, but sigma1 agonists have been observed to affect NMDA receptor function, the alpha-adrenergic system and opioid analgesia.
• Changed! pfam ERG2_Sigma1R 158aa 3e-54 in modified transcript

ORC4L

• refseq_ORC4L.F2 refseq_ORC4L.R2 133 158
• NCBIGene 36.3 5000
• Alternative 5-prime, size difference: 25
• Exclusion in 5'UTR
• Reference transcript: NM_002552

• cd AAA 168aa 5e-08 in ref transcript
  • The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.
• TIGR TIGR02928 182aa 6e-14 in ref transcript
  • Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.
• COG CDC6 176aa 2e-16 in ref transcript
  • Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones].

OS9

• refseq_OS9.F1 refseq_OS9.R1 300 465
• NCBIGene 36.3 10956
• Single exon skipping, size difference: 165
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_006812

• pfam PRKCSH 69aa 5e-13 in ref transcript
  • Glucosidase II beta subunit-like protein. The sequences found in this family are similar to a region found in the beta-subunit of glucosidase II, which is also known as protein kinase C substrate 80K-H (PRKCSH). The enzyme catalyses the sequential removal of two alpha-1,3-linked glucose residues in the second step of N-linked oligosaccharide processing. The beta subunit is required for the solubility and stability of the heterodimeric enzyme, and is involved in retaining the enzyme within the endoplasmic reticulum. Mutations in the gene coding for PRKCSH have been found to be involved in the development of autosomal dominant polycystic liver disease (ADPLD), but the precise role the protein has in the pathogenesis of this disease is unknown. This family also includes an ER sensor for misfolded glycoproteins and is therefore likely to be a generic sugar binding domain.

OS9

• refseq_OS9.F3 refseq_OS9.R3 214 259
• NCBIGene 36.3 10956
• Alternative 5-prime, size difference: 45
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_006812

• pfam PRKCSH 69aa 5e-13 in ref transcript
  • Glucosidase II beta subunit-like protein. The sequences found in this family are similar to a region found in the beta-subunit of glucosidase II, which is also known as protein kinase C substrate 80K-H (PRKCSH). The enzyme catalyses the sequential removal of two alpha-1,3-linked glucose residues in the second step of N-linked oligosaccharide processing. The beta subunit is required for the solubility and stability of the heterodimeric enzyme, and is involved in retaining the enzyme within the endoplasmic reticulum. Mutations in the gene coding for PRKCSH have been found to be involved in the development of autosomal dominant polycystic liver disease (ADPLD), but the precise role the protein has in the pathogenesis of this disease is unknown. This family also includes an ER sensor for misfolded glycoproteins and is therefore likely to be a generic sugar binding domain.

OSBPL1A

• refseq_OSBPL1A.F2 refseq_OSBPL1A.R2 105 174
• NCBIGene 36.2 114876
• Alternative 5-prime and 3-prime, size difference: 69
• Exclusion in the protein (no frameshift), Exclusion in the protein (no frameshift)
• Reference transcript: NM_080597

• cd ANK 154aa 2e-19 in ref transcript
  • ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats.
• cd ANK 74aa 3e-07 in ref transcript
• cd PH_oxysterol_bp 95aa 3e-06 in ref transcript
  • Oxysterol binding protein (OSBP) Pleckstrin homology (PH) domain. Oxysterol binding proteins are a multigene family that is conserved in yeast, flies, worms, mammals and plants. They all contain a C-terminal oxysterol binding domain, and most contain an N-terminal PH domain. OSBP PH domains bind to membrane phosphoinositides and thus likely play an important role in intracellular targeting. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
• Changed! pfam Oxysterol_BP 402aa 2e-72 in ref transcript
  • Oxysterol-binding protein.
• pfam Ank 32aa 1e-06 in ref transcript
  • Ankyrin repeat. There's no clear separation between noise and signal on the HMM search Ankyrin repeats generally consist of a beta, alpha, alpha, beta order of secondary structures. The repeats associate to form a higher order structure.
• pfam Ank 32aa 4e-05 in ref transcript
• pfam Ank 31aa 3e-04 in ref transcript
• smart PH 97aa 0.001 in ref transcript
  • Pleckstrin homology domain. Domain commonly found in eukaryotic signalling proteins. The domain family possesses multiple functions including the abilities to bind inositol phosphates, and various proteins. PH domains have been found to possess inserted domains (such as in PLC gamma, syntrophins) and to be inserted within other domains. Mutations in Brutons tyrosine kinase (Btk) within its PH domain cause X-linked agammaglobulinaemia (XLA) in patients. Point mutations cluster into the positively charged end of the molecule around the predicted binding site for phosphatidylinositol lipids.
• PTZ PTZ00322 96aa 9e-10 in ref transcript
  • 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase; Provisional.
• COG Arp 169aa 5e-09 in ref transcript
  • FOG: Ankyrin repeat [General function prediction only].
• Changed! pfam Oxysterol_BP 379aa 5e-58 in modified transcript

OSBPL3

• refseq_OSBPL3.F2 refseq_OSBPL3.R2 102 195
• NCBIGene 36.3 26031
• Single exon skipping, size difference: 93
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_015550

• cd PH_oxysterol_bp 91aa 2e-18 in ref transcript
  • Oxysterol binding protein (OSBP) Pleckstrin homology (PH) domain. Oxysterol binding proteins are a multigene family that is conserved in yeast, flies, worms, mammals and plants. They all contain a C-terminal oxysterol binding domain, and most contain an N-terminal PH domain. OSBP PH domains bind to membrane phosphoinositides and thus likely play an important role in intracellular targeting. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
• pfam Oxysterol_BP 300aa 2e-56 in ref transcript
  • Oxysterol-binding protein.
• smart PH 91aa 3e-09 in ref transcript
  • Pleckstrin homology domain. Domain commonly found in eukaryotic signalling proteins. The domain family possesses multiple functions including the abilities to bind inositol phosphates, and various proteins. PH domains have been found to possess inserted domains (such as in PLC gamma, syntrophins) and to be inserted within other domains. Mutations in Brutons tyrosine kinase (Btk) within its PH domain cause X-linked agammaglobulinaemia (XLA) in patients. Point mutations cluster into the positively charged end of the molecule around the predicted binding site for phosphatidylinositol lipids.

OSBPL5

• refseq_OSBPL5.F1 refseq_OSBPL5.R1 112 316
• NCBIGene 36.3 114879
• Single exon skipping, size difference: 204
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_020896

• Changed! cd PH_oxysterol_bp 114aa 4e-20 in ref transcript
  • Oxysterol binding protein (OSBP) Pleckstrin homology (PH) domain. Oxysterol binding proteins are a multigene family that is conserved in yeast, flies, worms, mammals and plants. They all contain a C-terminal oxysterol binding domain, and most contain an N-terminal PH domain. OSBP PH domains bind to membrane phosphoinositides and thus likely play an important role in intracellular targeting. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
• pfam Oxysterol_BP 332aa 1e-52 in ref transcript
  • Oxysterol-binding protein.
• Changed! smart PH 117aa 4e-08 in ref transcript
  • Pleckstrin homology domain. Domain commonly found in eukaryotic signalling proteins. The domain family possesses multiple functions including the abilities to bind inositol phosphates, and various proteins. PH domains have been found to possess inserted domains (such as in PLC gamma, syntrophins) and to be inserted within other domains. Mutations in Brutons tyrosine kinase (Btk) within its PH domain cause X-linked agammaglobulinaemia (XLA) in patients. Point mutations cluster into the positively charged end of the molecule around the predicted binding site for phosphatidylinositol lipids.

OSBPL6

• refseq_OSBPL6.F2 refseq_OSBPL6.R2 241 316
• NCBIGene 36.3 114880
• Single exon skipping, size difference: 75
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_145739

• cd PH_oxysterol_bp 91aa 7e-15 in ref transcript
  • Oxysterol binding protein (OSBP) Pleckstrin homology (PH) domain. Oxysterol binding proteins are a multigene family that is conserved in yeast, flies, worms, mammals and plants. They all contain a C-terminal oxysterol binding domain, and most contain an N-terminal PH domain. OSBP PH domains bind to membrane phosphoinositides and thus likely play an important role in intracellular targeting. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
• pfam Oxysterol_BP 342aa 3e-58 in ref transcript
  • Oxysterol-binding protein.
• smart PH 89aa 8e-08 in ref transcript
  • Pleckstrin homology domain. Domain commonly found in eukaryotic signalling proteins. The domain family possesses multiple functions including the abilities to bind inositol phosphates, and various proteins. PH domains have been found to possess inserted domains (such as in PLC gamma, syntrophins) and to be inserted within other domains. Mutations in Brutons tyrosine kinase (Btk) within its PH domain cause X-linked agammaglobulinaemia (XLA) in patients. Point mutations cluster into the positively charged end of the molecule around the predicted binding site for phosphatidylinositol lipids.

OSBPL8

• refseq_OSBPL8.F1 refseq_OSBPL8.R1 188 234
• NCBIGene 36.3 114882
• Exon skipping and alternative 3-prime or 5-prime, size difference: 46
• Exclusion in the protein causing a frameshift, Exclusion in the protein (no frameshift)
• Reference transcript: NM_020841

• Changed! cd PH_oxysterol_bp 114aa 2e-19 in ref transcript
  • Oxysterol binding protein (OSBP) Pleckstrin homology (PH) domain. Oxysterol binding proteins are a multigene family that is conserved in yeast, flies, worms, mammals and plants. They all contain a C-terminal oxysterol binding domain, and most contain an N-terminal PH domain. OSBP PH domains bind to membrane phosphoinositides and thus likely play an important role in intracellular targeting. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
• Changed! pfam Oxysterol_BP 333aa 3e-51 in ref transcript
  • Oxysterol-binding protein.
• Changed! smart PH 117aa 2e-08 in ref transcript
  • Pleckstrin homology domain. Domain commonly found in eukaryotic signalling proteins. The domain family possesses multiple functions including the abilities to bind inositol phosphates, and various proteins. PH domains have been found to possess inserted domains (such as in PLC gamma, syntrophins) and to be inserted within other domains. Mutations in Brutons tyrosine kinase (Btk) within its PH domain cause X-linked agammaglobulinaemia (XLA) in patients. Point mutations cluster into the positively charged end of the molecule around the predicted binding site for phosphatidylinositol lipids.

OSBPL9

• refseq_OSBPL9.F1 refseq_OSBPL9.R1 104 143
• NCBIGene 36.3 114883
• Single exon skipping, size difference: 39
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_148909

• cd PH_oxysterol_bp 93aa 1e-28 in ref transcript
  • Oxysterol binding protein (OSBP) Pleckstrin homology (PH) domain. Oxysterol binding proteins are a multigene family that is conserved in yeast, flies, worms, mammals and plants. They all contain a C-terminal oxysterol binding domain, and most contain an N-terminal PH domain. OSBP PH domains bind to membrane phosphoinositides and thus likely play an important role in intracellular targeting. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
• pfam Oxysterol_BP 342aa 2e-49 in ref transcript
  • Oxysterol-binding protein.
• smart PH 95aa 6e-13 in ref transcript
  • Pleckstrin homology domain. Domain commonly found in eukaryotic signalling proteins. The domain family possesses multiple functions including the abilities to bind inositol phosphates, and various proteins. PH domains have been found to possess inserted domains (such as in PLC gamma, syntrophins) and to be inserted within other domains. Mutations in Brutons tyrosine kinase (Btk) within its PH domain cause X-linked agammaglobulinaemia (XLA) in patients. Point mutations cluster into the positively charged end of the molecule around the predicted binding site for phosphatidylinositol lipids.

OSBPL9

• refseq_OSBPL9.F2 refseq_OSBPL9.R2 303 399
• NCBIGene 36.3 114883
• Single exon skipping, size difference: 96
• Exclusion in 5'UTR
• Reference transcript: NM_148904

• pfam Oxysterol_BP 342aa 1e-49 in ref transcript
  • Oxysterol-binding protein.

OSBPL9

• refseq_OSBPL9.F4 refseq_OSBPL9.R4 173 252
• NCBIGene 36.3 114883
• Single exon skipping, size difference: 79
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_148909

• Changed! cd PH_oxysterol_bp 93aa 1e-28 in ref transcript
  • Oxysterol binding protein (OSBP) Pleckstrin homology (PH) domain. Oxysterol binding proteins are a multigene family that is conserved in yeast, flies, worms, mammals and plants. They all contain a C-terminal oxysterol binding domain, and most contain an N-terminal PH domain. OSBP PH domains bind to membrane phosphoinositides and thus likely play an important role in intracellular targeting. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
• Changed! pfam Oxysterol_BP 342aa 2e-49 in ref transcript
  • Oxysterol-binding protein.
• Changed! smart PH 95aa 6e-13 in ref transcript
  • Pleckstrin homology domain. Domain commonly found in eukaryotic signalling proteins. The domain family possesses multiple functions including the abilities to bind inositol phosphates, and various proteins. PH domains have been found to possess inserted domains (such as in PLC gamma, syntrophins) and to be inserted within other domains. Mutations in Brutons tyrosine kinase (Btk) within its PH domain cause X-linked agammaglobulinaemia (XLA) in patients. Point mutations cluster into the positively charged end of the molecule around the predicted binding site for phosphatidylinositol lipids.
• Changed! cd PH_oxysterol_bp 49aa 2e-13 in modified transcript
• Changed! smart PH 51aa 0.001 in modified transcript

OSBPL9

• refseq_OSBPL9.F6 refseq_OSBPL9.R6 130 253
• NCBIGene 36.3 114883
• Alternative 5-prime, size difference: 123
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_148907

• Changed! pfam Oxysterol_BP 342aa 1e-49 in ref transcript
  • Oxysterol-binding protein.

OSCAR

• refseq_OSCAR.F1 refseq_OSCAR.R1 134 158
• NCBIGene 36.2 126014
• Alternative 5-prime and 3-prime, size difference: 24
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_206818

OTOF

• refseq_OTOF.F1 refseq_OTOF.R1 117 315
• NCBIGene 36.3 9381
• Single exon skipping, size difference: 198
• Exclusion of the stop codon
• Reference transcript: NM_194248

• cd C2 90aa 5e-14 in ref transcript
  • Protein kinase C conserved region 2 (CalB); Ca2+-binding motif present in phospholipases, protein kinases C, and synaptotagmins (among others). Some do not appear to contain Ca2+-binding sites. Particular C2s appear to bind phospholipids, inositol polyphosphates,and intracellular proteins. Synaptotagmin and PLC C2s are permuted in sequence with respect to N- and C-terminal beta strands.
• cd C2 91aa 5e-09 in ref transcript
• cd C2 110aa 7e-09 in ref transcript
• cd C2 100aa 4e-05 in ref transcript
• cd C2 99aa 0.006 in ref transcript
• pfam FerB 78aa 2e-32 in ref transcript
  • FerB (NUC096) domain. This is central domain B in proteins of the Ferlin family.
• pfam FerI 72aa 3e-31 in ref transcript
  • FerI (NUC094) domain. This domain is present in proteins of the Ferlin family. It is often located between two C2 domains.
• pfam C2 84aa 2e-15 in ref transcript
  • C2 domain.
• pfam C2 90aa 6e-11 in ref transcript
• smart C2 103aa 5e-10 in ref transcript
  • Protein kinase C conserved region 2 (CalB). Ca2+-binding motif present in phospholipases, protein kinases C, and synaptotamins (among others). Some do not appear to contain Ca2+-binding sites. Particular C2s appear to bind phospholipids, inositol polyphosphates, and intracellular proteins. Unusual occurrence in perforin. Synaptotagmin and PLC C2s are permuted in sequence with respect to N- and C-terminal beta strands. SMART detects C2 domains using one or both of two profiles.
• smart C2 97aa 4e-07 in ref transcript
• smart C2 105aa 0.001 in ref transcript
• COG COG5038 88aa 9e-11 in ref transcript
  • Ca2+-dependent lipid-binding protein, contains C2 domain [General function prediction only].
• COG COG5038 107aa 8e-04 in ref transcript

OTOF

• refseq_OTOF.F3 refseq_OTOF.R3 136 196
• NCBIGene 36.3 9381
• Alternative 3-prime, size difference: 60
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_194248

• cd C2 90aa 5e-14 in ref transcript
  • Protein kinase C conserved region 2 (CalB); Ca2+-binding motif present in phospholipases, protein kinases C, and synaptotagmins (among others). Some do not appear to contain Ca2+-binding sites. Particular C2s appear to bind phospholipids, inositol polyphosphates,and intracellular proteins. Synaptotagmin and PLC C2s are permuted in sequence with respect to N- and C-terminal beta strands.
• cd C2 91aa 5e-09 in ref transcript
• cd C2 110aa 7e-09 in ref transcript
• cd C2 100aa 4e-05 in ref transcript
• cd C2 99aa 0.006 in ref transcript
• pfam FerB 78aa 2e-32 in ref transcript
  • FerB (NUC096) domain. This is central domain B in proteins of the Ferlin family.
• pfam FerI 72aa 3e-31 in ref transcript
  • FerI (NUC094) domain. This domain is present in proteins of the Ferlin family. It is often located between two C2 domains.
• pfam C2 84aa 2e-15 in ref transcript
  • C2 domain.
• pfam C2 90aa 6e-11 in ref transcript
• smart C2 103aa 5e-10 in ref transcript
  • Protein kinase C conserved region 2 (CalB). Ca2+-binding motif present in phospholipases, protein kinases C, and synaptotamins (among others). Some do not appear to contain Ca2+-binding sites. Particular C2s appear to bind phospholipids, inositol polyphosphates, and intracellular proteins. Unusual occurrence in perforin. Synaptotagmin and PLC C2s are permuted in sequence with respect to N- and C-terminal beta strands. SMART detects C2 domains using one or both of two profiles.
• smart C2 97aa 4e-07 in ref transcript
• smart C2 105aa 0.001 in ref transcript
• COG COG5038 88aa 9e-11 in ref transcript
  • Ca2+-dependent lipid-binding protein, contains C2 domain [General function prediction only].
• COG COG5038 107aa 8e-04 in ref transcript

OTX2

• refseq_OTX2.F1 refseq_OTX2.R1 125 149
• NCBIGene 36.3 5015
• Alternative 3-prime, size difference: 24
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_021728

• cd homeodomain 56aa 3e-16 in ref transcript
  • Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
• pfam Homeobox 56aa 2e-21 in ref transcript
  • Homeobox domain.
• pfam TF_Otx 66aa 5e-20 in ref transcript
  • Otx1 transcription factor.
• COG COG5576 59aa 5e-11 in ref transcript
  • Homeodomain-containing transcription factor [Transcription].

P2RX2

• refseq_P2RX2.F1 refseq_P2RX2.R1 154 222
• NCBIGene 36.3 22953
• Alternative 5-prime, size difference: 68
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_170683

• Changed! TIGR P2X 392aa 1e-178 in ref transcript
  • ACC channels are probably hetero- or homomultimers and transport small monovalent cations (Me+). Some also transport Ca2+; a few also transport small metabolites.
• Changed! TIGR P2X 32aa 6e-06 in modified transcript

P2RX2

• refseq_P2RX2.F2 refseq_P2RX2.R2 136 208
• NCBIGene 36.3 22953
• Single exon skipping, size difference: 72
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_170683

• Changed! TIGR P2X 392aa 1e-178 in ref transcript
  • ACC channels are probably hetero- or homomultimers and transport small monovalent cations (Me+). Some also transport Ca2+; a few also transport small metabolites.
• Changed! TIGR P2X 368aa 1e-163 in modified transcript

P2RX5

• refseq_P2RX5.F1 refseq_P2RX5.R1 294 369
• NCBIGene 36.3 5026
• Single exon skipping, size difference: 72
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_002561

• Changed! pfam P2X_receptor 344aa 0.0 in ref transcript
  • ATP P2X receptor.
• Changed! pfam P2X_receptor 320aa 1e-169 in modified transcript

P2RX5

• refseq_P2RX5.F2 refseq_P2RX5.R3 126 198
• NCBIGene 36.3 5026
• Single exon skipping, size difference: 72
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_002561

• Changed! pfam P2X_receptor 344aa 0.0 in ref transcript
  • ATP P2X receptor.
• Changed! pfam P2X_receptor 320aa 1e-169 in modified transcript

P2RY10

• refseq_P2RY10.F2 refseq_P2RY10.R2 187 379
• NCBIGene 36.3 27334
• Multiple exon skipping, size difference: 192
• Exclusion in 5'UTR, Exclusion in 5'UTR
• Reference transcript: NM_014499

• pfam 7tm_1 230aa 1e-27 in ref transcript
  • 7 transmembrane receptor (rhodopsin family). This family contains, amongst other G-protein-coupled receptors (GCPRs), members of the opsin family, which have been considered to be typical members of the rhodopsin superfamily. They share several motifs, mainly the seven transmembrane helices, GCPRs of the rhodopsin superfamily. All opsins bind a chromophore, such as 11-cis-retinal. The function of most opsins other than the photoisomerases is split into two steps: light absorption and G-protein activation. Photoisomerases, on the other hand, are not coupled to G-proteins - they are thought to generate and supply the chromophore that is used by visual opsins.

P2RY2

• refseq_P2RY2.F1 refseq_P2RY2.R1 106 240
• NCBIGene 36.3 5029
• Alternative 3-prime, size difference: 134
• Inclusion in 5'UTR
• Reference transcript: NM_002564

• pfam 7tm_1 251aa 2e-33 in ref transcript
  • 7 transmembrane receptor (rhodopsin family). This family contains, amongst other G-protein-coupled receptors (GCPRs), members of the opsin family, which have been considered to be typical members of the rhodopsin superfamily. They share several motifs, mainly the seven transmembrane helices, GCPRs of the rhodopsin superfamily. All opsins bind a chromophore, such as 11-cis-retinal. The function of most opsins other than the photoisomerases is split into two steps: light absorption and G-protein activation. Photoisomerases, on the other hand, are not coupled to G-proteins - they are thought to generate and supply the chromophore that is used by visual opsins.

P2RY6

• refseq_P2RY6.F1 refseq_P2RY6.R1 114 274
• NCBIGene 36.3 5031
• Single exon skipping, size difference: 160
• Exclusion in 5'UTR
• Reference transcript: NM_176796

• pfam 7tm_1 250aa 2e-22 in ref transcript
  • 7 transmembrane receptor (rhodopsin family). This family contains, amongst other G-protein-coupled receptors (GCPRs), members of the opsin family, which have been considered to be typical members of the rhodopsin superfamily. They share several motifs, mainly the seven transmembrane helices, GCPRs of the rhodopsin superfamily. All opsins bind a chromophore, such as 11-cis-retinal. The function of most opsins other than the photoisomerases is split into two steps: light absorption and G-protein activation. Photoisomerases, on the other hand, are not coupled to G-proteins - they are thought to generate and supply the chromophore that is used by visual opsins.

P2RY6

• refseq_P2RY6.F3 refseq_P2RY6.R3 130 216
• NCBIGene 36.3 5031
• Single exon skipping, size difference: 86
• Exclusion in 5'UTR
• Reference transcript: NM_176796

• pfam 7tm_1 250aa 2e-22 in ref transcript
  • 7 transmembrane receptor (rhodopsin family). This family contains, amongst other G-protein-coupled receptors (GCPRs), members of the opsin family, which have been considered to be typical members of the rhodopsin superfamily. They share several motifs, mainly the seven transmembrane helices, GCPRs of the rhodopsin superfamily. All opsins bind a chromophore, such as 11-cis-retinal. The function of most opsins other than the photoisomerases is split into two steps: light absorption and G-protein activation. Photoisomerases, on the other hand, are not coupled to G-proteins - they are thought to generate and supply the chromophore that is used by visual opsins.

PAEP

• refseq_PAEP.F1 refseq_PAEP.R1 146 175
• NCBIGene 36.3 5047
• Alternative 5-prime, size difference: 29
• Exclusion in 3'UTR
• Reference transcript: NM_001018049

• pfam Lipocalin 142aa 2e-24 in ref transcript
  • Lipocalin / cytosolic fatty-acid binding protein family. Lipocalins are transporters for small hydrophobic molecules, such as lipids, steroid hormones, bilins, and retinoids. The family also encompasses the enzyme prostaglandin D synthase (EC:5.3.99.2). Alignment subsumes both the lipocalin and fatty acid binding protein signatures from PROSITE. This is supported on structural and functional grounds. The structure is an eight-stranded beta barrel.

PAGE5

• refseq_PAGE5.F2 refseq_PAGE5.R2 107 306
• NCBIGene 36.3 90737
• Alternative 5-prime, size difference: 199
• Exclusion of the protein initiation site
• Reference transcript: NM_130467

• pfam GAGE 103aa 8e-06 in ref transcript
  • GAGE protein. This family consists of several GAGE and XAGE proteins which are found exclusively in humans. The function of this family is unknown although they have been implicated in human cancers.

PAIP1

• refseq_PAIP1.F1 refseq_PAIP1.R1 160 397
• NCBIGene 36.3 10605
• Alternative 5-prime, size difference: 237
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_006451

• smart MIF4G 217aa 2e-30 in ref transcript
  • Middle domain of eukaryotic initiation factor 4G (eIF4G). Also occurs in NMD2p and CBP80. The domain is rich in alpha-helices and may contain multiple alpha-helical repeats. In eIF4G, this domain binds eIF4A, eIF3, RNA and DNA. Ponting (TiBS) "Novel eIF4G domain homologues (in press).

PAK4

• refseq_PAK4.F1 refseq_PAK4.R1 110 336
• NCBIGene 36.3 10298
• Exon skipping and alternative 3-prime or 5-prime, size difference: 226
• Exclusion in 5'UTR, Exclusion in 5'UTR
• Reference transcript: NM_001014831

• cd STKc_PAK_II 285aa 1e-173 in ref transcript
  • Serine/threonine kinases (STKs), p21-activated kinase (PAK) subfamily, Group II, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The PAK subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. PAKs are Rho family GTPase-regulated kinases that serve as important mediators in the function of Cdc42 (cell division cycle 42) and Rac. PAKs from higher eukaryotes are classified into two groups (I and II), according to their biochemical and structural features. Group II PAKs, also called non-conventional PAKs, include PAK4, PAK5, and PAK6. Group II PAKs contain PBD (p21-binding domain) and catalytic domains, but lack other motifs found in group I PAKs, such as an AID (autoinhibitory domain) and SH3 binding sites. Since group II PAKs do not contain an obvious AID, they may be regulated differently from group I PAKs. While group I PAKs interact with the SH3 containing proteins Nck, Grb2 and PIX, no such binding has been demonstrated for group II PAKs. Some known substrates of group II PAKs are also substrates of group I PAKs such as Raf, BAD, LIMK and GEFH1. Unique group II substrates include MARK/Par-1 and PDZ-RhoGEF. Group II PAKs play important roles in filopodia formation, neuron extension, cytoskeletal organization, and cell survival.
• cd CRIB_PAK_like 39aa 4e-11 in ref transcript
  • PAK (p21 activated kinase) Binding Domain (PBD), binds Cdc42p- and/or Rho-like small GTPases; also known as the Cdc42/Rac interactive binding (CRIB) motif; has been shown to inhibit transcriptional activation and cell transformation mediated by the Ras-Rac pathway. This subgroup of CRIB/PBD-domains is found N-terminal of Serine/Threonine kinase domains in PAK and PAK-like proteins.
• smart S_TKc 242aa 5e-76 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• pfam PBD 55aa 1e-11 in ref transcript
  • P21-Rho-binding domain. Small domains that bind Cdc42p- and/or Rho-like small GTPases. Also known as the Cdc42/Rac interactive binding (CRIB).
• COG SPS1 248aa 2e-35 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].

PAK7

• refseq_PAK7.F1 refseq_PAK7.R1 159 308
• NCBIGene 36.3 57144
• Single exon skipping, size difference: 149
• Exclusion in 5'UTR
• Reference transcript: NM_020341

• cd STKc_PAK_II 285aa 1e-175 in ref transcript
  • Serine/threonine kinases (STKs), p21-activated kinase (PAK) subfamily, Group II, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The PAK subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. PAKs are Rho family GTPase-regulated kinases that serve as important mediators in the function of Cdc42 (cell division cycle 42) and Rac. PAKs from higher eukaryotes are classified into two groups (I and II), according to their biochemical and structural features. Group II PAKs, also called non-conventional PAKs, include PAK4, PAK5, and PAK6. Group II PAKs contain PBD (p21-binding domain) and catalytic domains, but lack other motifs found in group I PAKs, such as an AID (autoinhibitory domain) and SH3 binding sites. Since group II PAKs do not contain an obvious AID, they may be regulated differently from group I PAKs. While group I PAKs interact with the SH3 containing proteins Nck, Grb2 and PIX, no such binding has been demonstrated for group II PAKs. Some known substrates of group II PAKs are also substrates of group I PAKs such as Raf, BAD, LIMK and GEFH1. Unique group II substrates include MARK/Par-1 and PDZ-RhoGEF. Group II PAKs play important roles in filopodia formation, neuron extension, cytoskeletal organization, and cell survival.
• cd CRIB_PAK_like 47aa 2e-11 in ref transcript
  • PAK (p21 activated kinase) Binding Domain (PBD), binds Cdc42p- and/or Rho-like small GTPases; also known as the Cdc42/Rac interactive binding (CRIB) motif; has been shown to inhibit transcriptional activation and cell transformation mediated by the Ras-Rac pathway. This subgroup of CRIB/PBD-domains is found N-terminal of Serine/Threonine kinase domains in PAK and PAK-like proteins.
• smart S_TKc 242aa 3e-75 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• pfam PBD 58aa 1e-12 in ref transcript
  • P21-Rho-binding domain. Small domains that bind Cdc42p- and/or Rho-like small GTPases. Also known as the Cdc42/Rac interactive binding (CRIB).
• PTZ PTZ00263 245aa 3e-34 in ref transcript
  • protein kinase A catalytic subunit; Provisional.

PALM

• refseq_PALM.F1 refseq_PALM.R1 146 278
• NCBIGene 36.3 5064
• Single exon skipping, size difference: 132
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_002579

• Changed! pfam Paralemmin 318aa 1e-102 in ref transcript
  • Paralemmin.
• Changed! pfam Paralemmin 274aa 5e-74 in modified transcript

PALM2-AKAP2

• refseq_PALM2-AKAP2.F2 refseq_PALM2-AKAP2.R2 216 255
• NCBIGene 36.3 445815
• Single exon skipping, size difference: 39
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_007203

PALM2

• refseq_PALM2.F1 refseq_PALM2.R1 170 272
• NCBIGene 36.3 114299
• Single exon skipping, size difference: 102
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_053016

• Changed! pfam Paralemmin 336aa 3e-34 in ref transcript
  • Paralemmin.
• Changed! pfam Paralemmin 302aa 6e-33 in modified transcript

PAM

• refseq_PAM.F1 refseq_PAM.R1 100 421
• NCBIGene 36.3 5066
• Single exon skipping, size difference: 321
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000919

• pfam Cu2_monoox_C 154aa 1e-69 in ref transcript
  • Copper type II ascorbate-dependent monooxygenase, C-terminal domain. The N and C-terminal domains of members of this family adopt the same PNGase F-like fold.
• pfam Cu2_monooxygen 138aa 2e-59 in ref transcript
  • Copper type II ascorbate-dependent monooxygenase, N-terminal domain. The N and C-terminal domains of members of this family adopt the same PNGase F-like fold.
• pfam NHL 28aa 8e-04 in ref transcript
  • NHL repeat. The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in the peptidyl-glycine alpha-amidating monooxygenase (PAM), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. The human tripartite motif-containing protein 32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats.
• pfam NHL 28aa 0.006 in ref transcript
• pfam NHL 30aa 0.007 in ref transcript
• COG COG3391 247aa 6e-07 in ref transcript
  • Uncharacterized conserved protein [Function unknown].
• Changed! pfam NHL 29aa 0.010 in modified transcript

PANK1

• refseq_PANK1.F1 refseq_PANK1.R1 152 329
• NCBIGene 36.3 53354
• Single exon skipping, size difference: 177
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_148977

• Changed! pfam Fumble 356aa 1e-131 in ref transcript
  • Fumble. Fumble is required for cell division in Drosophila. Mutants lacking fumble exhibit abnormalities in bipolar spindle organisation, chromosome segregation, and contractile ring formation. Analyses have demonstrated that encodes three protein isoforms, all of which contain a domain with high similarity to the pantothenate kinases of A. nidulans and mouse. A role of fumble in membrane synthesis has been proposed.
• Changed! COG PanK 350aa 8e-45 in ref transcript
  • Pantothenate kinase, acetyl-CoA regulated [Coenzyme metabolism].
• Changed! pfam Fumble 297aa 8e-94 in modified transcript
• Changed! COG PanK 291aa 5e-22 in modified transcript

PAOX

• refseq_PAOX.F2 refseq_PAOX.R2 159 317
• NCBIGene 36.3 196743
• Single exon skipping, size difference: 158
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_152911

• Changed! pfam Amino_oxidase 455aa 5e-52 in ref transcript
  • Flavin containing amine oxidoreductase. This family consists of various amine oxidases, including maze polyamine oxidase (PAO) and various flavin containing monoamine oxidases (MAO). The aligned region includes the flavin binding site of these enzymes. The family also contains phytoene dehydrogenases and related enzymes. In vertebrates MAO plays an important role regulating the intracellular levels of amines via there oxidation; these include various neurotransmitters, neurotoxins and trace amines. In lower eukaryotes such as aspergillus and in bacteria the main role of amine oxidases is to provide a source of ammonium. PAOs in plants, bacteria and protozoa oxidase spermidine and spermine to an aminobutyral, diaminopropane and hydrogen peroxide and are involved in the catabolism of polyamines. Other members of this family include tryptophan 2-monooxygenase, putrescine oxidase, corticosteroid binding proteins and antibacterial glycoproteins.
• Changed! COG COG1231 232aa 8e-12 in ref transcript
  • Monoamine oxidase [Amino acid transport and metabolism].
• Changed! pfam Amino_oxidase 391aa 9e-35 in modified transcript
• Changed! COG COG1231 88aa 6e-08 in modified transcript

PAOX

• refseq_PAOX.F4 refseq_PAOX.R4 105 358
• NCBIGene 36.3 196743
• Single exon skipping, size difference: 253
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_152911

• Changed! pfam Amino_oxidase 455aa 5e-52 in ref transcript
  • Flavin containing amine oxidoreductase. This family consists of various amine oxidases, including maze polyamine oxidase (PAO) and various flavin containing monoamine oxidases (MAO). The aligned region includes the flavin binding site of these enzymes. The family also contains phytoene dehydrogenases and related enzymes. In vertebrates MAO plays an important role regulating the intracellular levels of amines via there oxidation; these include various neurotransmitters, neurotoxins and trace amines. In lower eukaryotes such as aspergillus and in bacteria the main role of amine oxidases is to provide a source of ammonium. PAOs in plants, bacteria and protozoa oxidase spermidine and spermine to an aminobutyral, diaminopropane and hydrogen peroxide and are involved in the catabolism of polyamines. Other members of this family include tryptophan 2-monooxygenase, putrescine oxidase, corticosteroid binding proteins and antibacterial glycoproteins.
• Changed! COG COG1231 232aa 8e-12 in ref transcript
  • Monoamine oxidase [Amino acid transport and metabolism].
• Changed! pfam Amino_oxidase 267aa 5e-18 in modified transcript

PAPD5

• refseq_PAPD5.F2 refseq_PAPD5.R2 252 393
• NCBIGene 36.3 64282
• Alternative 3-prime, size difference: 141
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001040284

• pfam PAP_assoc 61aa 3e-14 in ref transcript
  • Poly(A) polymerase. This domain is found in poly(A) polymerases and has been shown to have polynucleotide adenylyltransferase activity. Proteins in this family have been located to both the nucleus and cytoplasm.
• pfam NTP_transf_2 77aa 2e-09 in ref transcript
  • Nucleotidyltransferase domain. Members of this family belong to a large family of nucleotidyltransferases. This family includes kanamycin nucleotidyltransferase (KNTase) which is a plasmid-coded enzyme responsible for some types of bacterial resistance to aminoglycosides. KNTase in-activates antibiotics by catalysing the addition of a nucleotidyl group onto the drug.
• COG TRF4 262aa 3e-44 in ref transcript
  • DNA polymerase sigma [DNA replication, recombination, and repair].

PAQR6

• refseq_PAQR6.F1 refseq_PAQR6.R1 104 146
• NCBIGene 36.3 79957
• Alternative 5-prime, size difference: 42
• Exclusion in 5'UTR
• Reference transcript: NM_024897

• pfam HlyIII 149aa 1e-04 in ref transcript
  • Haemolysin-III related. Members of this family are integral membrane proteins. This family includes a protein with hemolytic activity from Bacillus cereus. It is not clear if all the members of this family are hemolysins. It has been proposed that YOL002c encodes a Saccharomyces cerevisiae protein that plays a key role in metabolic pathways that regulate lipid and phosphate metabolism.

PAQR6

• refseq_PAQR6.F3 refseq_PAQR6.R3 103 174
• NCBIGene 36.3 79957
• Alternative 5-prime, size difference: 71
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_024897

• Changed! pfam HlyIII 149aa 1e-04 in ref transcript
  • Haemolysin-III related. Members of this family are integral membrane proteins. This family includes a protein with hemolytic activity from Bacillus cereus. It is not clear if all the members of this family are hemolysins. It has been proposed that YOL002c encodes a Saccharomyces cerevisiae protein that plays a key role in metabolic pathways that regulate lipid and phosphate metabolism.
• Changed! pfam HlyIII 165aa 3e-10 in modified transcript

PARL

• refseq_PARL.F2 refseq_PARL.R2 252 402
• NCBIGene 36.3 55486
• Single exon skipping, size difference: 150
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_018622

• Changed! pfam Rhomboid 142aa 1e-21 in ref transcript
  • Rhomboid family. This family contains integral membrane proteins that are related to Drosophila rhomboid protein. Members of this family are found in bacteria and eukaryotes. Rhomboid promotes the cleavage of the membrane-anchored TGF-alpha-like growth factor Spitz, allowing it to activate the Drosophila EGF receptor. Analysis has shown that Rhomboid-1 is an intramembrane serine protease (EC:3.4.21.105). Parasite-encoded rhomboid enzymes are also important for invasion of host cells by Toxoplasma and the malaria parasite.
• Changed! COG GlpG 198aa 2e-13 in ref transcript
  • Uncharacterized membrane protein (homolog of Drosophila rhomboid) [General function prediction only].
• Changed! pfam Rhomboid 100aa 4e-09 in modified transcript
• Changed! COG GlpG 119aa 5e-04 in modified transcript

PARP3

• refseq_PARP3.F2 refseq_PARP3.R2 263 385
• NCBIGene 36.3 10039
• Exon skipping and alternative 3-prime or 5-prime, size difference: 122
• Inclusion in the protein causing a new stop codon, Inclusion in the protein causing a frameshift
• Reference transcript: NM_001003931

• Changed! cd parp_like 351aa 1e-99 in ref transcript
  • Poly(ADP-ribose) polymerase (parp) catalytic domain catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active. Poly(ADP-ribose)-like polymerases (PARPS 1-3, VPARP, tankyrase) catalyze the addition of up to 100 ADP_ribose units from NAD+. PARPs 1 and 2 are localized in the nucleaus, bind DNA, and are activated by DNA damage. VPARP is part of the vault ribonucleoprotein complex. Tankyrases regulates telomere length through interactions with telomere repeat binding factor 1.
• Changed! pfam PARP 211aa 5e-53 in ref transcript
  • Poly(ADP-ribose) polymerase catalytic domain. Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active.
• Changed! pfam WGR 64aa 2e-22 in ref transcript
  • WGR domain. This domain is found in a variety of polyA polymerases as well as the Escherichia coli molybdate metabolism regulator and other proteins of unknown function. I have called this domain WGR after the most conserved central motif of the domain. The domain is found in isolation in some proteins and is between 70 and 80 residues in length. I propose that this may be a nucleic acid binding domain.
• Changed! pfam PARP_reg 136aa 2e-20 in ref transcript
  • Poly(ADP-ribose) polymerase, regulatory domain. Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active.
• Changed! COG COG3831 66aa 1e-04 in ref transcript
  • Uncharacterized conserved protein [Function unknown].

PAX2

• refseq_PAX2.F1 refseq_PAX2.R1 149 232
• NCBIGene 36.3 5076
• Single exon skipping, size difference: 83
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_003990

• cd PAX 127aa 2e-62 in ref transcript
  • Paired Box domain.
• smart PAX 125aa 1e-69 in ref transcript
  • Paired Box domain.
• COG COG3415 92aa 0.003 in ref transcript
  • Transposase and inactivated derivatives [DNA replication, recombination, and repair].

PAX2

• refseq_PAX2.F4 refseq_PAX2.R4 105 124
• NCBIGene 36.3 5076
• Alternative 3-prime, size difference: 19
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_003990

• cd PAX 127aa 2e-62 in ref transcript
  • Paired Box domain.
• smart PAX 125aa 1e-69 in ref transcript
  • Paired Box domain.
• COG COG3415 92aa 0.003 in ref transcript
  • Transposase and inactivated derivatives [DNA replication, recombination, and repair].

PAX2

• refseq_PAX2.F5 refseq_PAX2.R5 162 231
• NCBIGene 36.3 5076
• Single exon skipping, size difference: 69
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_003990

• cd PAX 127aa 2e-62 in ref transcript
  • Paired Box domain.
• smart PAX 125aa 1e-69 in ref transcript
  • Paired Box domain.
• COG COG3415 92aa 0.003 in ref transcript
  • Transposase and inactivated derivatives [DNA replication, recombination, and repair].

PAX6

• refseq_PAX6.F1 refseq_PAX6.R1 237 335
• NCBIGene 36.3 5080
• Alternative 5-prime, size difference: 98
• Inclusion in 5'UTR
• Reference transcript: NM_001604

• cd PAX 141aa 2e-58 in ref transcript
  • Paired Box domain.
• cd homeodomain 57aa 1e-15 in ref transcript
  • Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
• smart PAX 139aa 2e-63 in ref transcript
  • Paired Box domain.
• pfam Homeobox 55aa 1e-21 in ref transcript
  • Homeobox domain.
• COG COG5576 66aa 2e-08 in ref transcript
  • Homeodomain-containing transcription factor [Transcription].

PAX6

• refseq_PAX6.F4 refseq_PAX6.R4 111 153
• NCBIGene 36.3 5080
• Single exon skipping, size difference: 42
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001604

• Changed! cd PAX 141aa 2e-58 in ref transcript
  • Paired Box domain.
• cd homeodomain 57aa 1e-15 in ref transcript
  • Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
• Changed! smart PAX 139aa 2e-63 in ref transcript
  • Paired Box domain.
• pfam Homeobox 55aa 1e-21 in ref transcript
  • Homeobox domain.
• COG COG5576 66aa 2e-08 in ref transcript
  • Homeodomain-containing transcription factor [Transcription].
• Changed! cd PAX 127aa 4e-61 in modified transcript
• Changed! smart PAX 125aa 7e-66 in modified transcript

PAX8

• refseq_PAX8.F2 refseq_PAX8.R2 153 232
• NCBIGene 36.3 7849
• Alternative 3-prime, size difference: 79
• Inclusion in 3'UTR
• Reference transcript: NM_013952

• cd PAX 127aa 4e-59 in ref transcript
  • Paired Box domain.
• smart PAX 125aa 5e-65 in ref transcript
  • Paired Box domain.
• COG COG3415 92aa 0.004 in ref transcript
  • Transposase and inactivated derivatives [DNA replication, recombination, and repair].

PBRM1

• refseq_PB1.F1 refseq_PB1.R1 220 295
• NCBIGene 36.3 55193
• Alternative 3-prime, size difference: 75
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_018165

• cd Bromo_polybromo_I 109aa 3e-53 in ref transcript
  • Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.
• cd Bromo_polybromo_VI 108aa 1e-51 in ref transcript
  • Bromodomain, polybromo repeat VI. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.
• cd Bromo_polybromo_V 105aa 5e-49 in ref transcript
  • Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.
• cd Bromo_polybromo_III 102aa 8e-49 in ref transcript
  • Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.
• Changed! cd BAH_polybromo 118aa 3e-48 in ref transcript
  • BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2. The human polybromo protein (BAF180) is a component of the SWI/SNF chromatin-remodeling complex PBAF. It is thought that polybromo participates in transcriptional regulation. Saccharomyces cerevisiae RSC1 and RSC2 are part of the 15-subunit nucleosome remodeling RSC complex. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
• cd Bromo_polybromo_II 103aa 3e-46 in ref transcript
  • Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.
• cd BAH_polybromo 119aa 2e-44 in ref transcript
• cd Bromo_polybromo_IV 95aa 2e-35 in ref transcript
  • Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.
• cd HMG-box 44aa 2e-06 in ref transcript
  • High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4; and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions.
• Changed! pfam BAH 119aa 2e-33 in ref transcript
  • BAH domain. This domain has been called BAH (Bromo adjacent homology) domain and has also been called ELM1 and BAM (Bromo adjacent motif) domain. The function of this domain is unknown but may be involved in protein-protein interaction.
• smart BROMO 113aa 9e-26 in ref transcript
  • bromo domain.
• smart BAH 116aa 6e-25 in ref transcript
  • Bromo adjacent homology domain.
• smart BROMO 107aa 3e-23 in ref transcript
• smart BROMO 104aa 5e-22 in ref transcript
• smart BROMO 103aa 1e-21 in ref transcript
• pfam Bromodomain 87aa 3e-14 in ref transcript
  • Bromodomain. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
• smart BROMO 101aa 2e-13 in ref transcript
• smart HMG 44aa 5e-07 in ref transcript
  • high mobility group.
• COG COG5076 281aa 4e-20 in ref transcript
  • Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription].
• COG COG5076 205aa 2e-16 in ref transcript
• COG COG5076 136aa 4e-16 in ref transcript
• Changed! COG COG5076 392aa 4e-09 in ref transcript
• Changed! cd BAH_polybromo 93aa 3e-29 in modified transcript
• Changed! pfam BAH 94aa 8e-20 in modified transcript

PBRM1

• refseq_PB1.F3 refseq_PB1.R3 158 314
• NCBIGene 36.3 55193
• Single exon skipping, size difference: 156
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_018165

• cd Bromo_polybromo_I 109aa 3e-53 in ref transcript
  • Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.
• cd Bromo_polybromo_VI 108aa 1e-51 in ref transcript
  • Bromodomain, polybromo repeat VI. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.
• cd Bromo_polybromo_V 105aa 5e-49 in ref transcript
  • Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.
• cd Bromo_polybromo_III 102aa 8e-49 in ref transcript
  • Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.
• cd BAH_polybromo 118aa 3e-48 in ref transcript
  • BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2. The human polybromo protein (BAF180) is a component of the SWI/SNF chromatin-remodeling complex PBAF. It is thought that polybromo participates in transcriptional regulation. Saccharomyces cerevisiae RSC1 and RSC2 are part of the 15-subunit nucleosome remodeling RSC complex. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
• cd Bromo_polybromo_II 103aa 3e-46 in ref transcript
  • Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.
• cd BAH_polybromo 119aa 2e-44 in ref transcript
• cd Bromo_polybromo_IV 95aa 2e-35 in ref transcript
  • Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.
• Changed! cd HMG-box 44aa 2e-06 in ref transcript
  • High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4; and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions.
• pfam BAH 119aa 2e-33 in ref transcript
  • BAH domain. This domain has been called BAH (Bromo adjacent homology) domain and has also been called ELM1 and BAM (Bromo adjacent motif) domain. The function of this domain is unknown but may be involved in protein-protein interaction.
• smart BROMO 113aa 9e-26 in ref transcript
  • bromo domain.
• smart BAH 116aa 6e-25 in ref transcript
  • Bromo adjacent homology domain.
• smart BROMO 107aa 3e-23 in ref transcript
• smart BROMO 104aa 5e-22 in ref transcript
• smart BROMO 103aa 1e-21 in ref transcript
• pfam Bromodomain 87aa 3e-14 in ref transcript
  • Bromodomain. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
• smart BROMO 101aa 2e-13 in ref transcript
• Changed! smart HMG 44aa 5e-07 in ref transcript
  • high mobility group.
• COG COG5076 281aa 4e-20 in ref transcript
  • Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription].
• COG COG5076 205aa 2e-16 in ref transcript
• COG COG5076 136aa 4e-16 in ref transcript
• COG COG5076 392aa 4e-09 in ref transcript
• Changed! cd HMG-box 47aa 2e-07 in modified transcript
• Changed! smart HMG 47aa 4e-08 in modified transcript

PBRM1

• refseq_PB1.F5 refseq_PB1.R5 292 373
• NCBIGene 36.3 55193
• Alternative 5-prime, size difference: 81
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_018165

• cd Bromo_polybromo_I 109aa 3e-53 in ref transcript
  • Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.
• cd Bromo_polybromo_VI 108aa 1e-51 in ref transcript
  • Bromodomain, polybromo repeat VI. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.
• cd Bromo_polybromo_V 105aa 5e-49 in ref transcript
  • Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.
• cd Bromo_polybromo_III 102aa 8e-49 in ref transcript
  • Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.
• cd BAH_polybromo 118aa 3e-48 in ref transcript
  • BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2. The human polybromo protein (BAF180) is a component of the SWI/SNF chromatin-remodeling complex PBAF. It is thought that polybromo participates in transcriptional regulation. Saccharomyces cerevisiae RSC1 and RSC2 are part of the 15-subunit nucleosome remodeling RSC complex. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
• cd Bromo_polybromo_II 103aa 3e-46 in ref transcript
  • Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.
• cd BAH_polybromo 119aa 2e-44 in ref transcript
• cd Bromo_polybromo_IV 95aa 2e-35 in ref transcript
  • Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.
• cd HMG-box 44aa 2e-06 in ref transcript
  • High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4; and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions.
• pfam BAH 119aa 2e-33 in ref transcript
  • BAH domain. This domain has been called BAH (Bromo adjacent homology) domain and has also been called ELM1 and BAM (Bromo adjacent motif) domain. The function of this domain is unknown but may be involved in protein-protein interaction.
• smart BROMO 113aa 9e-26 in ref transcript
  • bromo domain.
• smart BAH 116aa 6e-25 in ref transcript
  • Bromo adjacent homology domain.
• smart BROMO 107aa 3e-23 in ref transcript
• smart BROMO 104aa 5e-22 in ref transcript
• smart BROMO 103aa 1e-21 in ref transcript
• pfam Bromodomain 87aa 3e-14 in ref transcript
  • Bromodomain. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
• smart BROMO 101aa 2e-13 in ref transcript
• smart HMG 44aa 5e-07 in ref transcript
  • high mobility group.
• COG COG5076 281aa 4e-20 in ref transcript
  • Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription].
• COG COG5076 205aa 2e-16 in ref transcript
• COG COG5076 136aa 4e-16 in ref transcript
• COG COG5076 392aa 4e-09 in ref transcript

PBRM1

• refseq_PB1.F7 refseq_PB1.R7 150 246
• NCBIGene 36.3 55193
• Single exon skipping, size difference: 96
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_018165

• cd Bromo_polybromo_I 109aa 3e-53 in ref transcript
  • Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.
• cd Bromo_polybromo_VI 108aa 1e-51 in ref transcript
  • Bromodomain, polybromo repeat VI. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.
• cd Bromo_polybromo_V 105aa 5e-49 in ref transcript
  • Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.
• cd Bromo_polybromo_III 102aa 8e-49 in ref transcript
  • Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.
• cd BAH_polybromo 118aa 3e-48 in ref transcript
  • BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2. The human polybromo protein (BAF180) is a component of the SWI/SNF chromatin-remodeling complex PBAF. It is thought that polybromo participates in transcriptional regulation. Saccharomyces cerevisiae RSC1 and RSC2 are part of the 15-subunit nucleosome remodeling RSC complex. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
• cd Bromo_polybromo_II 103aa 3e-46 in ref transcript
  • Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.
• cd BAH_polybromo 119aa 2e-44 in ref transcript
• cd Bromo_polybromo_IV 95aa 2e-35 in ref transcript
  • Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.
• cd HMG-box 44aa 2e-06 in ref transcript
  • High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4; and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions.
• pfam BAH 119aa 2e-33 in ref transcript
  • BAH domain. This domain has been called BAH (Bromo adjacent homology) domain and has also been called ELM1 and BAM (Bromo adjacent motif) domain. The function of this domain is unknown but may be involved in protein-protein interaction.
• smart BROMO 113aa 9e-26 in ref transcript
  • bromo domain.
• smart BAH 116aa 6e-25 in ref transcript
  • Bromo adjacent homology domain.
• smart BROMO 107aa 3e-23 in ref transcript
• smart BROMO 104aa 5e-22 in ref transcript
• smart BROMO 103aa 1e-21 in ref transcript
• pfam Bromodomain 87aa 3e-14 in ref transcript
  • Bromodomain. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
• smart BROMO 101aa 2e-13 in ref transcript
• smart HMG 44aa 5e-07 in ref transcript
  • high mobility group.
• COG COG5076 281aa 4e-20 in ref transcript
  • Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription].
• COG COG5076 205aa 2e-16 in ref transcript
• COG COG5076 136aa 4e-16 in ref transcript
• COG COG5076 392aa 4e-09 in ref transcript

PCDH11X

• refseq_PCDH11X.F1 refseq_PCDH11X.R1 105 135
• NCBIGene 36.3 27328
• Single exon skipping, size difference: 30
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_032968

• cd CA 194aa 1e-45 in ref transcript
  • Cadherin repeat domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion; these domains occur as repeats in the extracellular regions which are thought to mediate cell-cell contact when bound to calcium; plays a role in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-,CNR-,proto-,and FAT-family cadherin, desmocollin, and desmoglein, exists as monomers or dimers (hetero- and homo-); two copies of the repeat are present here.
• cd CA 201aa 6e-40 in ref transcript
• cd CA 196aa 1e-37 in ref transcript
• cd CA 197aa 2e-35 in ref transcript
• pfam Protocadherin 199aa 6e-67 in ref transcript
  • Protocadherin. The structure of protocadherins is similar to that of classic cadherins (pfam00028), but particularly on the cytoplasmic domains they also have some unique features. They are expressed in a variety of organisms and are found in high concentrations in the brain where they seem to be localised mainly at cell-cell contact sites. Their expression seems to be developmentally regulated.
• smart CA 77aa 5e-19 in ref transcript
  • Cadherin repeats. Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. Cadherin domains occur as repeats in the extracellular regions which are thought to mediate cell-cell contact when bound to calcium.
• smart CA 77aa 7e-19 in ref transcript
• pfam Cadherin 80aa 7e-16 in ref transcript
  • Cadherin domain.
• smart CA 84aa 7e-13 in ref transcript
• pfam Cadherin 82aa 1e-10 in ref transcript
• smart CA 79aa 2e-09 in ref transcript
• pfam Cadherin_2 85aa 6e-06 in ref transcript
  • Cadherin-like. This cadherin domain is usually the most N-terminal copy of the domain.

PCDH8

• refseq_PCDH8.F2 refseq_PCDH8.R2 126 417
• NCBIGene 36.3 5100
• Alternative 5-prime, size difference: 291
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_002590

• cd CA 201aa 4e-43 in ref transcript
  • Cadherin repeat domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion; these domains occur as repeats in the extracellular regions which are thought to mediate cell-cell contact when bound to calcium; plays a role in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-,CNR-,proto-,and FAT-family cadherin, desmocollin, and desmoglein, exists as monomers or dimers (hetero- and homo-); two copies of the repeat are present here.
• cd CA 206aa 2e-33 in ref transcript
• cd CA 238aa 2e-28 in ref transcript
• cd CA 200aa 5e-20 in ref transcript
• smart CA 86aa 6e-19 in ref transcript
  • Cadherin repeats. Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. Cadherin domains occur as repeats in the extracellular regions which are thought to mediate cell-cell contact when bound to calcium.
• smart CA 78aa 5e-17 in ref transcript
• smart CA 79aa 1e-13 in ref transcript
• smart CA 84aa 5e-13 in ref transcript
• pfam Cadherin_2 79aa 6e-09 in ref transcript
  • Cadherin-like. This cadherin domain is usually the most N-terminal copy of the domain.
• pfam Cadherin 81aa 2e-07 in ref transcript
  • Cadherin domain.

PCDH9

• refseq_PCDH9.F1 refseq_PCDH9.R1 293 395
• NCBIGene 36.3 5101
• Single exon skipping, size difference: 102
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_203487

• cd CA 195aa 1e-45 in ref transcript
  • Cadherin repeat domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion; these domains occur as repeats in the extracellular regions which are thought to mediate cell-cell contact when bound to calcium; plays a role in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-,CNR-,proto-,and FAT-family cadherin, desmocollin, and desmoglein, exists as monomers or dimers (hetero- and homo-); two copies of the repeat are present here.
• cd CA 201aa 4e-39 in ref transcript
• cd CA 195aa 1e-38 in ref transcript
• cd CA 204aa 8e-38 in ref transcript
• cd CA 204aa 5e-35 in ref transcript
• cd CA 212aa 6e-22 in ref transcript
• pfam Protocadherin 225aa 9e-65 in ref transcript
  • Protocadherin. The structure of protocadherins is similar to that of classic cadherins (pfam00028), but particularly on the cytoplasmic domains they also have some unique features. They are expressed in a variety of organisms and are found in high concentrations in the brain where they seem to be localised mainly at cell-cell contact sites. Their expression seems to be developmentally regulated.
• smart CA 77aa 2e-20 in ref transcript
  • Cadherin repeats. Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. Cadherin domains occur as repeats in the extracellular regions which are thought to mediate cell-cell contact when bound to calcium.
• smart CA 77aa 2e-19 in ref transcript
• pfam Cadherin 92aa 2e-17 in ref transcript
  • Cadherin domain.
• smart CA 84aa 7e-14 in ref transcript
• smart CA 79aa 1e-11 in ref transcript
• smart CA 79aa 1e-07 in ref transcript
• pfam Cadherin_2 90aa 4e-07 in ref transcript
  • Cadherin-like. This cadherin domain is usually the most N-terminal copy of the domain.

PCGF6

• refseq_PCGF6.F2 refseq_PCGF6.R2 129 354
• NCBIGene 36.3 84108
• Multiple exon skipping, size difference: 225
• Exclusion in the protein causing a frameshift, Exclusion in the protein (no frameshift), Exclusion in the protein causing a frameshift
• Reference transcript: NM_001011663

• cd RING 43aa 4e-06 in ref transcript
  • RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H).
• pfam zf-C3HC4 39aa 1e-06 in ref transcript
  • Zinc finger, C3HC4 type (RING finger). The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid. Many proteins containing a RING finger play a key role in the ubiquitination pathway.
• COG RAD18 49aa 1e-04 in ref transcript
  • RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms].

PCNXL3

• refseq_PCNXL3.F1 refseq_PCNXL3.R1 149 365
• NCBIGene 36.2 399909
• Single exon skipping, size difference: 216
• Exclusion in the protein (no frameshift)
• Reference transcript: XM_934366

• pfam Pecanex_C 231aa 1e-125 in ref transcript
  • Pecanex protein (C-terminus). This family consists of C terminal region of the pecanex protein homologues. The pecanex protein is a maternal-effect neurogenic gene found in Drosophila.

MED15

• refseq_PCQAP.F1 refseq_PCQAP.R1 146 266
• NCBIGene 36.3 51586
• Single exon skipping, size difference: 120
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001003891

• pfam ARC105_Med_act 65aa 7e-29 in ref transcript
  • ARC105 domain. The approx. 70 residue ARC105 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, ARC105 is a critical transducer of gene activation signals that control early metazoan development.

PCTK3

• refseq_PCTK3.F1 refseq_PCTK3.R1 148 238
• NCBIGene 36.3 5129
• Alternative 5-prime, size difference: 90
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_212503

• cd S_TKc 282aa 3e-64 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• smart S_TKc 272aa 1e-68 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• PTZ PTZ00024 284aa 1e-44 in ref transcript
  • cyclin-dependent protein kinase; Provisional.

PDCD4

• refseq_PDCD4.F1 refseq_PDCD4.R1 290 374
• NCBIGene 36.3 27250
• Single exon skipping, size difference: 84
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_014456

• Changed! smart MA3 114aa 1e-29 in ref transcript
  • Domain in DAP-5, eIF4G, MA-3 and other proteins. Highly alpha-helical. May contain repeats and/or regions similar to MIF4G domains Ponting (TIBS) "Novel eIF4G domain homologues" in press.
• Changed! smart MA3 112aa 8e-28 in ref transcript

PDE8A

• refseq_PDE8A.F1 refseq_PDE8A.R1 169 367
• NCBIGene 36.2 5151
• Single exon skipping, size difference: 198
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_002605

• Changed! cd PAS 99aa 3e-06 in ref transcript
  • PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.
• Changed! cd HDc 195aa 4e-05 in ref transcript
  • Metal dependent phosphohydrolases with conserved 'HD' motif.
• Changed! pfam PDEase_I 255aa 2e-55 in ref transcript
  • 3'5'-cyclic nucleotide phosphodiesterase.
• Changed! pfam PAS 106aa 2e-07 in ref transcript
  • PAS fold. The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs. The PAS fold appears in archaea, eubacteria and eukarya.
• pfam Response_reg 117aa 5e-07 in ref transcript
  • Response regulator receiver domain. This domain receives the signal from the sensor partner in bacterial two-component systems. It is usually found N-terminal to a DNA binding effector domain.
• Changed! COG AtoS 113aa 1e-04 in ref transcript
  • FOG: PAS/PAC domain [Signal transduction mechanisms].

PDE8B

• refseq_PDE8B.F2 refseq_PDE8B.R2 168 309
• NCBIGene 36.3 8622
• Single exon skipping, size difference: 141
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_003719

• Changed! cd PAS 98aa 3e-07 in ref transcript
  • PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.
• cd HDc 191aa 0.001 in ref transcript
  • Metal dependent phosphohydrolases with conserved 'HD' motif.
• pfam PDEase_I 251aa 3e-52 in ref transcript
  • 3'5'-cyclic nucleotide phosphodiesterase.
• pfam PDE8 52aa 2e-23 in ref transcript
  • PDE8 phosphodiesterase. This region is found in members of the PDE8 phosphodiesterase family. It is found with pfam00233.
• pfam Response_reg 118aa 1e-12 in ref transcript
  • Response regulator receiver domain. This domain receives the signal from the sensor partner in bacterial two-component systems. It is usually found N-terminal to a DNA binding effector domain.
• Changed! TIGR nifL_nitrog 106aa 5e-08 in ref transcript
  • NifL is a modulator of the nitrogen fixation positive regulator protein NifA, and is therefore a negative regulator. It binds NifA. NifA and NifL are encoded by adjacent genes.
• Changed! COG AtoS 209aa 5e-05 in ref transcript
  • FOG: PAS/PAC domain [Signal transduction mechanisms].

PDE8B

• refseq_PDE8B.F3 refseq_PDE8B.R3 104 269
• NCBIGene 36.3 8622
• Single exon skipping, size difference: 165
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_003719

• cd PAS 98aa 3e-07 in ref transcript
  • PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.
• cd HDc 191aa 0.001 in ref transcript
  • Metal dependent phosphohydrolases with conserved 'HD' motif.
• pfam PDEase_I 251aa 3e-52 in ref transcript
  • 3'5'-cyclic nucleotide phosphodiesterase.
• pfam PDE8 52aa 2e-23 in ref transcript
  • PDE8 phosphodiesterase. This region is found in members of the PDE8 phosphodiesterase family. It is found with pfam00233.
• pfam Response_reg 118aa 1e-12 in ref transcript
  • Response regulator receiver domain. This domain receives the signal from the sensor partner in bacterial two-component systems. It is usually found N-terminal to a DNA binding effector domain.
• TIGR nifL_nitrog 106aa 5e-08 in ref transcript
  • NifL is a modulator of the nitrogen fixation positive regulator protein NifA, and is therefore a negative regulator. It binds NifA. NifA and NifL are encoded by adjacent genes.
• COG AtoS 209aa 5e-05 in ref transcript
  • FOG: PAS/PAC domain [Signal transduction mechanisms].

PDE8B

• refseq_PDE8B.F5 refseq_PDE8B.R5 337 397
• NCBIGene 36.3 8622
• Single exon skipping, size difference: 60
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_003719

• cd PAS 98aa 3e-07 in ref transcript
  • PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.
• cd HDc 191aa 0.001 in ref transcript
  • Metal dependent phosphohydrolases with conserved 'HD' motif.
• pfam PDEase_I 251aa 3e-52 in ref transcript
  • 3'5'-cyclic nucleotide phosphodiesterase.
• pfam PDE8 52aa 2e-23 in ref transcript
  • PDE8 phosphodiesterase. This region is found in members of the PDE8 phosphodiesterase family. It is found with pfam00233.
• pfam Response_reg 118aa 1e-12 in ref transcript
  • Response regulator receiver domain. This domain receives the signal from the sensor partner in bacterial two-component systems. It is usually found N-terminal to a DNA binding effector domain.
• TIGR nifL_nitrog 106aa 5e-08 in ref transcript
  • NifL is a modulator of the nitrogen fixation positive regulator protein NifA, and is therefore a negative regulator. It binds NifA. NifA and NifL are encoded by adjacent genes.
• COG AtoS 209aa 5e-05 in ref transcript
  • FOG: PAS/PAC domain [Signal transduction mechanisms].

PDE9A

• refseq_PDE9A.F1 refseq_PDE9A.R9 104 180
• NCBIGene 36.3 5152
• Single exon skipping, size difference: 76
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_002606

• Changed! cd HDc 174aa 6e-10 in ref transcript
  • Metal dependent phosphohydrolases with conserved 'HD' motif.
• Changed! pfam PDEase_I 223aa 8e-56 in ref transcript
  • 3'5'-cyclic nucleotide phosphodiesterase.

PDE9A

• refseq_PDE9A.F2 refseq_PDE9A.R2 113 293
• NCBIGene 36.3 5152
• Single exon skipping, size difference: 180
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_002606

• cd HDc 174aa 6e-10 in ref transcript
  • Metal dependent phosphohydrolases with conserved 'HD' motif.
• pfam PDEase_I 223aa 8e-56 in ref transcript
  • 3'5'-cyclic nucleotide phosphodiesterase.

PDE9A

• refseq_PDE9A.F3 refseq_PDE9A.R3 140 211
• NCBIGene 36.3 5152
• Single exon skipping, size difference: 71
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_002606

• Changed! cd HDc 174aa 6e-10 in ref transcript
  • Metal dependent phosphohydrolases with conserved 'HD' motif.
• Changed! pfam PDEase_I 223aa 8e-56 in ref transcript
  • 3'5'-cyclic nucleotide phosphodiesterase.

PDE9A

• refseq_PDE9A.F5 refseq_PDE9A.R5 116 201
• NCBIGene 36.3 5152
• Single exon skipping, size difference: 85
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_002606

• Changed! cd HDc 174aa 6e-10 in ref transcript
  • Metal dependent phosphohydrolases with conserved 'HD' motif.
• Changed! pfam PDEase_I 223aa 8e-56 in ref transcript
  • 3'5'-cyclic nucleotide phosphodiesterase.

PDE9A

• refseq_PDE9A.F8 refseq_PDE9A.R8 113 191
• NCBIGene 36.3 5152
• Single exon skipping, size difference: 78
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_002606

• cd HDc 174aa 6e-10 in ref transcript
  • Metal dependent phosphohydrolases with conserved 'HD' motif.
• pfam PDEase_I 223aa 8e-56 in ref transcript
  • 3'5'-cyclic nucleotide phosphodiesterase.

PDGFA

• refseq_PDGFA.F1 refseq_PDGFA.R1 143 212
• NCBIGene 36.3 5154
• Single exon skipping, size difference: 69
• Exclusion of the stop codon
• Reference transcript: NM_002607

• cd PDGF 89aa 3e-18 in ref transcript
  • Platelet-derived and vascular endothelial growth factors (PDGF, VEGF) family domain; PDGF is a potent activator for cells of mesenchymal origin; PDGF-A and PDGF-B form AA and BB homodimers and an AB heterodimer; VEGF is a potent mitogen in embryonic and somatic angiogenesis with a unique specificity for vascular endothelial cells; VEGF forms homodimers and exists in 4 different isoforms; overall, the VEGF monomer resembles that of PDGF, but its N-terminal segment is helical rather than extended; the cysteine knot motif is a common feature of this domain.
• pfam PDGF 84aa 3e-33 in ref transcript
  • Platelet-derived growth factor (PDGF).
• pfam PDGF_N 75aa 3e-25 in ref transcript
  • Platelet-derived growth factor, N terminal region. This family consists of the amino terminal regions of platelet-derived growth factor (PDGF, pfam00341) A and B chains.

PDGFD

• refseq_PDGFD.F1 refseq_PDGFD.R1 100 118
• NCBIGene 36.3 80310
• Alternative 3-prime, size difference: 18
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_025208

• cd CUB 114aa 2e-19 in ref transcript
  • CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.
• cd PDGF 96aa 2e-17 in ref transcript
  • Platelet-derived and vascular endothelial growth factors (PDGF, VEGF) family domain; PDGF is a potent activator for cells of mesenchymal origin; PDGF-A and PDGF-B form AA and BB homodimers and an AB heterodimer; VEGF is a potent mitogen in embryonic and somatic angiogenesis with a unique specificity for vascular endothelial cells; VEGF forms homodimers and exists in 4 different isoforms; overall, the VEGF monomer resembles that of PDGF, but its N-terminal segment is helical rather than extended; the cysteine knot motif is a common feature of this domain.
• smart CUB 106aa 5e-19 in ref transcript
  • Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. This domain is found mostly among developmentally-regulated proteins. Spermadhesins contain only this domain.
• smart PDGF 92aa 0.002 in ref transcript
  • Platelet-derived and vascular endothelial growth factors (PDGF, VEGF) family. Platelet-derived growth factor is a potent activator for cells of mesenchymal origin. PDGF-A and PDGF-B form AA and BB homodimers and an AB heterodimer. Members of the VEGF family are homologues of PDGF.

PDLIM2

• refseq_PDLIM2.F1 refseq_PDLIM2.R1 106 224
• NCBIGene 36.3 64236
• Single exon skipping, size difference: 118
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_176871

• cd PDZ_signaling 77aa 6e-15 in ref transcript
  • PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of PDZ domains an N-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in proteases.
• smart PDZ 74aa 1e-14 in ref transcript
  • Domain present in PSD-95, Dlg, and ZO-1/2. Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities.
• Changed! pfam LIM 45aa 0.001 in ref transcript
  • LIM domain. This family represents two copies of the LIM structural domain.
• COG Prc 62aa 6e-04 in ref transcript
  • Periplasmic protease [Cell envelope biogenesis, outer membrane].

PDLIM5

• refseq_PDLIM5.F1 refseq_PDLIM5.R1 106 433
• NCBIGene 36.3 10611
• Alternative 3-prime, size difference: 327
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_006457

• cd PDZ_signaling 73aa 6e-16 in ref transcript
  • PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of PDZ domains an N-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in proteases.
• smart PDZ 74aa 2e-17 in ref transcript
  • Domain present in PSD-95, Dlg, and ZO-1/2. Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities.
• pfam LIM 56aa 7e-12 in ref transcript
  • LIM domain. This family represents two copies of the LIM structural domain.
• pfam LIM 53aa 3e-09 in ref transcript
• pfam LIM 56aa 4e-09 in ref transcript
• COG Prc 59aa 6e-06 in ref transcript
  • Periplasmic protease [Cell envelope biogenesis, outer membrane].

PDLIM5

• refseq_PDLIM5.F1 refseq_PDLIM5.R3 312 372
• NCBIGene 36.3 10611
• Mutually exclusive exon skipping, size difference: 60
• Inclusion in the protein causing a frameshift, Inclusion in the protein (no stop codon or frameshift), Exclusion in the protein causing a frameshift
• Reference transcript: NM_001011515

• cd PDZ_signaling 73aa 2e-15 in ref transcript
  • PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of PDZ domains an N-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in proteases.
• smart PDZ 74aa 1e-16 in ref transcript
  • Domain present in PSD-95, Dlg, and ZO-1/2. Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities.
• COG Prc 59aa 1e-05 in ref transcript
  • Periplasmic protease [Cell envelope biogenesis, outer membrane].

PDLIM5

• refseq_PDLIM5.F4 refseq_PDLIM5.R5 100 118
• NCBIGene 36.3 10611
• Single exon skipping, size difference: 18
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_006457

• cd PDZ_signaling 73aa 6e-16 in ref transcript
  • PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of PDZ domains an N-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in proteases.
• smart PDZ 74aa 2e-17 in ref transcript
  • Domain present in PSD-95, Dlg, and ZO-1/2. Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities.
• pfam LIM 56aa 7e-12 in ref transcript
  • LIM domain. This family represents two copies of the LIM structural domain.
• pfam LIM 53aa 3e-09 in ref transcript
• pfam LIM 56aa 4e-09 in ref transcript
• COG Prc 59aa 6e-06 in ref transcript
  • Periplasmic protease [Cell envelope biogenesis, outer membrane].

PDLIM7

• refseq_PDLIM7.F2 refseq_PDLIM7.R2 160 262
• NCBIGene 36.3 9260
• Mutually exclusive exon skipping, size difference: 102
• Inclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_005451

• cd PDZ_signaling 75aa 9e-10 in ref transcript
  • PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of PDZ domains an N-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in proteases.
• pfam LIM 56aa 1e-11 in ref transcript
  • LIM domain. This family represents two copies of the LIM structural domain.
• pfam LIM 52aa 5e-11 in ref transcript
• smart PDZ 80aa 3e-10 in ref transcript
  • Domain present in PSD-95, Dlg, and ZO-1/2. Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities.
• pfam LIM 53aa 4e-09 in ref transcript
• Changed! PRK PRK12323 140aa 0.001 in ref transcript
  • DNA polymerase III subunits gamma and tau; Provisional.

PDPK1

• refseq_PDPK1.F1 refseq_PDPK1.R1 100 481
• NCBIGene 36.3 5170
• Multiple exon skipping, size difference: 381
• Exclusion in the protein (no frameshift), Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_002613

• Changed! cd STKc_PDK1 263aa 1e-120 in ref transcript
  • STKc_PDK1: Serine/Threonine Kinases (STKs), Phosphoinositide-dependent kinase 1 (PDK1) subfamily, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The PDK1 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase (PI3K). PDK1 carries an N-terminal catalytic domain and a C-terminal pleckstrin homology (PH) domain that binds phosphoinositides. It phosphorylates the activation loop of AGC kinases that are regulated by PI3K such as PKB, SGK, and PKC, among others, and is crucial for their activation. Thus, it contributes in regulating many processes including metabolism, growth, proliferation, and survival. PDK1 also has the ability to autophosphorylate and is constitutively active in mammalian cells. PDK1 is essential for normal embryo development and is important in regulating cell volume.
• cd PH_PDK1 88aa 6e-36 in ref transcript
  • 3-Phosphoinositide dependent protein kinase 1 (PDK1) pleckstrin homology (PH) domain. PDK1 contains an N-terminal serine/threonine kinase domain followed by a PH domain. Following binding of the PH domain to PtdIns(3,4,5)P3 and PtdIns(3,4)P2, PDK1 activates kinases such as Akt (PKB). PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
• Changed! smart S_TKc 251aa 1e-78 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• Changed! PTZ PTZ00263 276aa 1e-64 in ref transcript
  • protein kinase A catalytic subunit; Provisional.
• Changed! cd STKc_PDK1 135aa 8e-46 in modified transcript
• Changed! smart S_TKc 118aa 6e-26 in modified transcript
• Changed! smart STYKc 28aa 8e-04 in modified transcript
  • Protein kinase; unclassified specificity. Phosphotransferases. The specificity of this class of kinases can not be predicted. Possible dual-specificity Ser/Thr/Tyr kinase.
• Changed! PTZ PTZ00263 134aa 5e-20 in modified transcript

PECI

• refseq_PECI.F2 refseq_PECI.R2 144 215
• NCBIGene 36.3 10455
• Single exon skipping, size difference: 71
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_006117

• Changed! cd crotonase-like 195aa 5e-47 in ref transcript
  • Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase. Many of these play important roles in fatty acid metabolism. In addition to a conserved structural core and the formation of trimers (or dimers of trimers), a common feature in this superfamily is the stabilization of an enolate anion intermediate derived from an acyl-CoA substrate. This is accomplished by two conserved backbone NH groups in active sites that form an oxyanion hole.
• cd ACBP 76aa 5e-23 in ref transcript
  • Acyl CoA binding protein (ACBP) binds thiol esters of long fatty acids and coenzyme A in a one-to-one binding mode with high specificity and affinity. Acyl-CoAs are important intermediates in fatty lipid synthesis and fatty acid degradation and play a role in regulation of intermediary metabolism and gene regulation. The suggested role of ACBP is to act as a intracellular acyl-CoA transporter and pool former. ACBPs are present in a large group of eukaryotic species and several tissue-specific isoforms have been detected.
• Changed! TIGR PaaB1 216aa 1e-22 in ref transcript
  • This family of proteins are found within apparent operons for the degradation of phenylacetic acid. These proteins contain the enoyl-CoA hydratase domain as detected by pfam00378. This activity is consistent with current hypotheses for the degradation pathway which involve the ligation of phenylacetate with coenzyme A (paaF), hydroxylation (paaGHIJK), ring-opening (paaN) and degradation of the resulting fatty acid-like compound to a Krebs cycle intermediate (paaABCDE).
• pfam ACBP 76aa 2e-21 in ref transcript
  • Acyl CoA binding protein.
• Changed! PRK PRK06688 232aa 3e-46 in ref transcript
  • enoyl-CoA hydratase; Provisional.
• COG ACB 75aa 2e-16 in ref transcript
  • Acyl-CoA-binding protein [Lipid metabolism].
• Changed! cd crotonase-like 26aa 0.002 in modified transcript
• Changed! PRK PRK06688 31aa 0.002 in modified transcript

PER2

• refseq_PER2.F1 refseq_PER2.R1 110 217
• NCBIGene 36.2 8864
• Single exon skipping, size difference: 107
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_022817

• Changed! cd PAS 102aa 2e-08 in ref transcript
  • PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.
• Changed! pfam PAS_3 85aa 2e-08 in ref transcript
  • PAS fold. The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs. The PAS fold appears in archaea, eubacteria and eukarya.

PEX10

• refseq_PEX10.F1 refseq_PEX10.R1 222 282
• NCBIGene 36.3 5192
• Alternative 3-prime, size difference: 60
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_153818

• cd RING 42aa 1e-07 in ref transcript
  • RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H).
• Changed! pfam Pex2_Pex12 169aa 1e-16 in ref transcript
  • Pex2 / Pex12 amino terminal region. This region is found at the N terminal of a number of known and predicted peroxins including Pex2, Pex10 and Pex12. This conserved region is usually associated with a C terminal ring finger (pfam00097) domain.
• smart RING 38aa 2e-08 in ref transcript
  • Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s).
• COG PEX10 55aa 7e-12 in ref transcript
  • RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones].
• Changed! pfam Pex2_Pex12 175aa 3e-19 in modified transcript

PFDN5

• refseq_PFDN5.F1 refseq_PFDN5.R1 142 277
• NCBIGene 36.3 5204
• Multiple exon skipping, size difference: 135
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_002624

• Changed! cd Prefoldin_alpha 128aa 2e-25 in ref transcript
  • Prefoldin alpha subunit; Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils.
• Changed! TIGR TIGR00293 127aa 2e-31 in ref transcript
  • This model finds a set of small proteins from the Archaea and from Aquifex aeolicus that may represent two orthologous groups. The proteins are predicted to be mostly coiled coil, and builds of HMMs for the seed alignment with less selective parameters lead to significant hits to large numbers of proteins that contain coiled coil regions. This model is built with a more selective usage of Dirichlet priors.
• Changed! COG GIM5 130aa 3e-16 in ref transcript
  • Predicted prefoldin, molecular chaperone implicated in de novo protein folding [Posttranslational modification, protein turnover, chaperones].
• Changed! cd Prefoldin_alpha 79aa 5e-13 in modified transcript
• Changed! TIGR TIGR00293 70aa 2e-16 in modified transcript
• Changed! COG GIM5 67aa 2e-06 in modified transcript

PFN2

• refseq_PFN2.F2 refseq_PFN2.R2 100 422
• NCBIGene 36.3 5217
• Alternative 3-prime, size difference: 322
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_002628

• Changed! cd PROF 137aa 2e-26 in ref transcript
  • Profilin binds actin monomers, membrane polyphosphoinositides such as PI(4,5)P2, and poly-L-proline. Profilin can inhibit actin polymerization into F-actin by binding to monomeric actin (G-actin) and terminal F-actin subunits, but - as a regulator of the cytoskeleton - it may also promote actin polymerization. It plays a role in the assembly of branched actin filament networks, by activating WASP via binding to WASP's proline rich domain. Profilin may link the cytoskeleton with major signalling pathways by interacting with components of the phosphatidylinositol cycle and Ras pathway.
• Changed! smart PROF 138aa 2e-33 in ref transcript
  • Profilin. Binds actin monomers, membrane polyphosphoinositides and poly-L-proline.
• Changed! cd PROF 138aa 2e-25 in modified transcript
• Changed! smart PROF 139aa 2e-32 in modified transcript

CBY1

• refseq_PGEA1.F1 refseq_PGEA1.R1 151 291
• NCBIGene 36.3 25776
• Single exon skipping, size difference: 140
• Exclusion of the protein initiation site
• Reference transcript: NM_001002880

PHACTR3

• refseq_PHACTR3.F2 refseq_PHACTR3.R2 115 325
• NCBIGene 36.3 116154
• Single exon skipping, size difference: 210
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_080672

PHF1

• refseq_PHF1.F1 refseq_PHF1.R1 299 394
• NCBIGene 36.3 5252
• Single exon skipping, size difference: 95
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_024165

• smart TUDOR 52aa 1e-06 in ref transcript
  • Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).
• pfam PHD 53aa 4e-06 in ref transcript
  • PHD-finger. PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
• Changed! COG COG5141 84aa 0.009 in ref transcript
  • PHD zinc finger-containing protein [General function prediction only].

PHF1

• refseq_PHF1.F3 refseq_PHF1.R3 285 391
• NCBIGene 36.3 5252
• Single exon skipping, size difference: 95
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_024165

• smart TUDOR 52aa 1e-06 in ref transcript
  • Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).
• pfam PHD 53aa 4e-06 in ref transcript
  • PHD-finger. PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
• Changed! COG COG5141 84aa 0.009 in ref transcript
  • PHD zinc finger-containing protein [General function prediction only].

PHF2

• refseq_PHF2.F1 refseq_PHF2.R1 100 136
• NCBIGene 36.2 5253
• Exon skipping and alternative 3-prime or 5-prime, size difference: 36
• Inclusion in the protein causing a frameshift, Inclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_005392

• pfam JmjC 101aa 2e-17 in ref transcript
  • JmjC domain. The JmjC domain belongs to the Cupin superfamily. JmjC-domain proteins may be protein hydroxylases that catalyse a novel histone modification.
• Changed! smart PHD 47aa 1e-08 in ref transcript
  • PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the R ING finger and the FY VE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent B ROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were R ING fingers misidentified as PHD fingers.
• smart JmjC 64aa 5e-06 in ref transcript
  • A domain family that is part of the cupin metalloenzyme superfamily. Probable enzymes, but of unknown functions, that regulate chromatin reorganisation processes (Clissold and Ponting, in press).
• Changed! COG TNG2 51aa 0.006 in ref transcript
  • Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics].

PHF20L1

• refseq_PHF20L1.F2 refseq_PHF20L1.R2 193 271
• NCBIGene 36.3 51105
• Single exon skipping, size difference: 78
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_016018

• cd TUDOR 46aa 2e-06 in ref transcript
  • Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal.
• smart TUDOR 54aa 3e-06 in ref transcript
  • Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).
• smart MBT 66aa 3e-05 in ref transcript
  • Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2. Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2. These proteins are involved in transcriptional regulation.
• pfam PHD 44aa 1e-04 in ref transcript
  • PHD-finger. PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.

PHF7

• refseq_PHF7.F2 refseq_PHF7.R2 276 393
• NCBIGene 36.3 51533
• Single exon skipping, size difference: 117
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_016483

PHKB

• refseq_PHKB.F1 refseq_PHKB.R1 113 225
• NCBIGene 36.3 5257
• Single exon skipping, size difference: 112
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_000293

• Changed! pfam PHK_AB 1040aa 0.0 in ref transcript
  • Phosphorylase kinase alpha/beta. This family consists of several eukaryotic phosphorylase kinase alpha and beta subunits. Phosphorylase kinase (PHK) is a regulatory enzyme in glycogen metabolism. Mutations in the gene encoding the alpha subunit of PHK (PHKA2) have been shown to be responsible for X-linked liver glycogenosis (XLG). XLG, a frequent type of glycogen storage disease, is characterised by hepatomegaly and growth retardation.

PIB5PA

• refseq_PIB5PA.F1 refseq_PIB5PA.R1 111 289
• NCBIGene 36.3 27124
• Single exon skipping, size difference: 178
• Exclusion of the protein initiation site
• Reference transcript: NM_014422

• Changed! smart IPPc 308aa 9e-74 in ref transcript
  • Inositol polyphosphate phosphatase, catalytic domain homologues. Mg(2+)-dependent/Li(+)-sensitive enzymes.
• pfam CALCOCO1 96aa 0.003 in ref transcript
  • Calcium binding and coiled-coil domain (CALCOCO1) like. Proteins found in this family are similar to the coiled-coil transcriptional coactivator protein coexpressed by Mus musculus (CoCoA/CALCOCO1). This protein binds to a highly conserved N-terminal domain of p160 coactivators, such as GRIP1, and thus enhances transcriptional activation by a number of nuclear receptors. CALCOCO1 has a central coiled-coil region with three leucine zipper motifs, which is required for its interaction with GRIP1 and may regulate the autonomous transcriptional activation activity of the C-terminal region.
• Changed! COG COG5411 328aa 5e-40 in ref transcript
  • Phosphatidylinositol 5-phosphate phosphatase [Signal transduction mechanisms].
• Changed! smart IPPc 305aa 2e-73 in modified transcript
• Changed! COG COG5411 283aa 2e-39 in modified transcript

PICALM

• refseq_PICALM.F2 refseq_PICALM.R2 103 127
• NCBIGene 36.3 8301
• Single exon skipping, size difference: 24
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_007166

• cd ANTH_AP180_CALM 117aa 1e-37 in ref transcript
  • ANTH domain family; composed of adaptor protein 180 (AP180), clathrin assembly lymphoid myeloid leukemia protein (CALM) and similar proteins. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to as an AP180 N-terminal homology (ANTH) domain. AP180 and CALM play important roles in clathrin-mediated endocytosis. AP180 is a brain-specific clathrin-binding protein which stimulates clathrin assembly during the recycling of synaptic vesicles. The ANTH domain is structurally similar to the VHS domain and is composed of a superhelix of eight alpha helices. ANTH domains bind both inositol phospholipids and proteins, and contribute to the nucleation and formation of clathrin coats on membranes. ANTH-bearing proteins have recently been shown to function with adaptor protein-1 and GGA adaptors at the trans-Golgi network, which suggests that the ANTH domain is a universal component of the machinery for clathrin-mediated membrane budding.
• pfam ANTH 265aa 7e-80 in ref transcript
  • ANTH domain. AP180 is an endocytotic accessory proteins that has been implicated in the formation of clathrin-coated pits. The domain is involved in phosphatidylinositol 4,5-bisphosphate binding and is a universal adaptor for nucleation of clathrin coats.

PICK1

• refseq_PICK1.F1 refseq_PICK1.R1 173 226
• NCBIGene 36.3 9463
• Alternative 5-prime, size difference: 53
• Exclusion in 5'UTR
• Reference transcript: NM_001039583

• cd Arfaptin 215aa 2e-68 in ref transcript
  • Arfaptin domain; arfaptin is a ubiquitously expressed protein implicated in mediating cross-talk between Rac, a member of the Rho family, and Arf small GTPases; Arfaptin binds to GTP-bound Arf1 and Arf6, but binds Rac.GTP and Rac.GDP with similar affinities. Structures of Arfaptin with Rac bound to either GDP or the slowly hydrolysable analogue GMPPNP show that the switch regions adopt similar conformations in both complexes. Arf1 and Arf6 are thought to bind to the same surface as Rac.
• cd PDZ_signaling 77aa 5e-11 in ref transcript
  • PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of PDZ domains an N-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in proteases.
• pfam Arfaptin 216aa 2e-74 in ref transcript
  • Arfaptin-like domain. Arfaptin interacts with ARF1, a small GTPase involved in vesicle budding at the Golgi complex and immature secretory granules. The structure of arfaptin shows that upon binding to a small GTPase, arfaptin forms a an elongated, crescent-shaped dimer of three-helix coiled-coils. The N-terminal region of ICA69 is similar to arfaptin.
• smart PDZ 81aa 2e-12 in ref transcript
  • Domain present in PSD-95, Dlg, and ZO-1/2. Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities.
• COG Prc 64aa 5e-04 in ref transcript
  • Periplasmic protease [Cell envelope biogenesis, outer membrane].

PIGC

• refseq_PIGC.F1 refseq_PIGC.R1 117 140
• NCBIGene 36.3 5279
• Alternative 3-prime, size difference: 23
• Inclusion in 5'UTR
• Reference transcript: NM_153747

• pfam GPI2 210aa 2e-70 in ref transcript
  • Phosphatidylinositol N-acetylglucosaminyltransferase. Glycosylphosphatidylinositol (GPI) represents an important anchoring molecule for cell surface proteins. The first step in its synthesis is the transfer of N-acetylglucosamine (GlcNAc) from UDP-N-acetylglucosamine to phosphatidylinositol (PI). This step involves products of three or four genes in both yeast (GPI1, GPI2 and GPI3) and mammals (GPI1, PIG A, PIG H and PIG C), respectively.

PIGF

• refseq_PIGF.F1 refseq_PIGF.R1 206 311
• NCBIGene 36.3 5281
• Single exon skipping, size difference: 105
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_002643

• Changed! pfam PIG-F 206aa 2e-59 in ref transcript
  • GPI biosynthesis protein family Pig-F. PIG-F is involved in glycosylphosphatidylinositol (GPI) anchor biosynthesis.
• Changed! pfam PIG-F 182aa 5e-51 in modified transcript

PIGN

• refseq_PIGN.F1 refseq_PIGN.R1 272 349
• NCBIGene 36.3 23556
• Single exon skipping, size difference: 77
• Exclusion in 5'UTR
• Reference transcript: NM_176787

• pfam PigN 188aa 5e-43 in ref transcript
  • Phosphatidylinositolglycan class N (PIG-N). Phosphatidylinositolglycan class N (PIG-N) is a mammalian homologue of the yeast protein MCD4P and is expressed in the endoplasmic reticulum. PIG-N is essential for glycosylphosphatidylinositol anchor synthesis. Glycosylphosphatidylinositol (GPI)-anchored proteins are cell surface-localised proteins that serve many important cellular functions.
• pfam PigN 202aa 5e-38 in ref transcript

PIGQ

• refseq_PIGQ.F1 refseq_PIGQ.R1 298 360
• NCBIGene 36.3 9091
• Single exon skipping, size difference: 62
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_148920

• pfam Gpi1 172aa 1e-58 in ref transcript
  • N-acetylglucosaminyl transferase component (Gpi1). Glycosylphosphatidylinositol (GPI) represents an important anchoring molecule for cell surface proteins.The first step in its synthesis is the transfer of N-acetylglucosamine (GlcNAc) from UDP-N-acetylglucosamine to phosphatidylinositol (PI). This chemically simple step is genetically complex because three or four genes are required in both yeast (GPI1, GPI2 and GPI3) and mammals (GPI1, PIG A, PIG H and PIG C), respectively.

PILRA

• refseq_PILRA.F1 refseq_PILRA.R1 118 337
• NCBIGene 36.3 29992
• Single exon skipping, size difference: 219
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_013439

• pfam V-set 115aa 9e-05 in ref transcript
  • Immunoglobulin V-set domain. This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.

PILRB

• refseq_PILRB.F1 refseq_PILRB.R1 150 218
• NCBIGene 36.3 29990
• Alternative 3-prime, size difference: 68
• Inclusion in 5'UTR
• Reference transcript: NM_013440

• pfam V-set 92aa 3e-05 in ref transcript
  • Immunoglobulin V-set domain. This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.

PILRB

• refseq_PILRB.F3 refseq_PILRB.R3 114 213
• NCBIGene 36.3 29990
• Alternative 3-prime, size difference: 99
• Exclusion in 5'UTR
• Reference transcript: NM_013440

• pfam V-set 92aa 3e-05 in ref transcript
  • Immunoglobulin V-set domain. This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.

PIP5K1B

• refseq_PIP5K1B.F1 refseq_PIP5K1B.R1 258 379
• NCBIGene 36.2 8395
• Single exon skipping, size difference: 121
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_003558

• Changed! cd PIPKc 252aa 4e-81 in ref transcript
  • Phosphatidylinositol phosphate kinases (PIPK) catalyze the phosphorylation of phosphatidylinositol phosphate on the fourth or fifth hydroxyl of the inositol ring, to form phosphatidylinositol bisphosphate. CD alignment includes type II phosphatidylinositol phosphate kinases (PIPKII-beta), type I andII PIPK (-alpha, -beta, and -gamma) kinases and related yeast Fab1p and Mss4p kinases. Signaling by phosphorylated species of phosphatidylinositol regulates secretion, vesicular trafficking, membrane translocation, cell adhesion, chemotaxis, DNA synthesis, and cell cycling. The catalytic core domains of PIPKs are structurally similar to PI3K, PI4K, and cAMP-dependent protein kinases (PKA), the dimerization region is a unique feature of the PIPKs.
• Changed! cd PIPKc 57aa 5e-15 in ref transcript
• Changed! pfam PIP5K 289aa 1e-119 in ref transcript
  • Phosphatidylinositol-4-phosphate 5-Kinase. This family contains a region from the common kinase core found in the type I phosphatidylinositol-4-phosphate 5-kinase (PIP5K) family. The family consists of various type I, II and III PIP5K enzymes. PIP5K catalyses the formation of phosphoinositol-4,5-bisphosphate via the phosphorylation of phosphatidylinositol-4-phosphate a precursor in the phosphinositide signaling pathway.
• Changed! COG MSS4 327aa 4e-27 in ref transcript
  • Phosphatidylinositol-4-phosphate 5-kinase [Signal transduction mechanisms].

PIP5K3

• refseq_PIP5K3.F2 refseq_PIP5K3.R2 221 393
• NCBIGene 36.2 200576
• Single exon skipping, size difference: 172
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_015040

• Changed! cd Fab1_TCP 245aa 1e-104 in ref transcript
  • TCP-1 like domain of the eukaryotic phosphatidylinositol 3-phosphate (PtdIns3P) 5-kinase Fab1. Fab1p is important for vacuole size regulation, presumably by modulating PtdIns(3,5)P2 effector activity. In the human homolog p235/PIKfyve deletion of this domain leads to loss of catalytic activity. However no exact function this domain has been defined. In general, chaperonins are involved in productive folding of proteins.
• Changed! cd PIPKc 314aa 5e-98 in ref transcript
  • Phosphatidylinositol phosphate kinases (PIPK) catalyze the phosphorylation of phosphatidylinositol phosphate on the fourth or fifth hydroxyl of the inositol ring, to form phosphatidylinositol bisphosphate. CD alignment includes type II phosphatidylinositol phosphate kinases (PIPKII-beta), type I andII PIPK (-alpha, -beta, and -gamma) kinases and related yeast Fab1p and Mss4p kinases. Signaling by phosphorylated species of phosphatidylinositol regulates secretion, vesicular trafficking, membrane translocation, cell adhesion, chemotaxis, DNA synthesis, and cell cycling. The catalytic core domains of PIPKs are structurally similar to PI3K, PI4K, and cAMP-dependent protein kinases (PKA), the dimerization region is a unique feature of the PIPKs.
• Changed! cd DEP_PIKfyve 82aa 1e-38 in ref transcript
  • DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in fungal RhoGEF (GDP/GTP exchange factor) PIKfyve-like proteins. PIKfyve contains N-terminal Fyve finger and DEP domains, a central chaperonin-like domain and a C-terminal PIPK (phosphatidylinositol phosphate kinase) domain. PIKfyve-like proteins are important phosphatidylinositol (3)-monophosphate (PtdIns(3)P)-5-kinases, producing PtdIns(3,5)P2, which plays a major role in multivesicular body (MVB) sorting and control of retrograde traffic from the vacuole back to the endosome and/or Golgi. PIKfyve itself has been shown to be play a role in regulating early-endosome-to-trans-Golgi network (TGN) retrograde trafficking.
• Changed! cd FYVE 53aa 2e-15 in ref transcript
  • FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;.
• Changed! smart PIPKc 238aa 5e-72 in ref transcript
  • Phosphatidylinositol phosphate kinases.
• Changed! TIGR chap_CCT_gamma 224aa 8e-32 in ref transcript
  • Members of this family, all eukaryotic, are part of the group II chaperonin complex called CCT (chaperonin containing TCP-1) or TRiC. The archaeal equivalent group II chaperonin is often called the thermosome. Both are somewhat related to the group I chaperonin of bacterial, GroEL/GroES. This family consists exclusively of the CCT gamma chain (part of a paralogous family) from animals, plants, fungi, and other eukaryotes.
• Changed! pfam FYVE 60aa 9e-20 in ref transcript
  • FYVE zinc finger. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn++ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. We have included members which do not conserve these histidine residues but are clearly related.
• Changed! smart DEP 73aa 3e-17 in ref transcript
  • Domain found in Dishevelled, Egl-10, and Pleckstrin. Domain of unknown function present in signalling proteins that contain PH, rasGEF, rhoGEF, rhoGAP, RGS, PDZ domains. DEP domain in Drosophila dishevelled is essential to rescue planar polarity defects and induce JNK signalling (Cell 94, 109-118).
• Changed! smart PIPKc 56aa 6e-17 in ref transcript
• Changed! COG MSS4 288aa 9e-54 in ref transcript
  • Phosphatidylinositol-4-phosphate 5-kinase [Signal transduction mechanisms].
• Changed! COG GroL 219aa 2e-17 in ref transcript
  • Chaperonin GroEL (HSP60 family) [Posttranslational modification, protein turnover, chaperones].

PIR

• refseq_PIR.F1 FIGF.R4 192 226
• NCBIGene 36.3 8544
• Alternative 5-prime, size difference: 34
• Exclusion in 5'UTR
• Reference transcript: NM_003662

• pfam Pirin 98aa 3e-33 in ref transcript
  • Pirin. This family consists of Pirin proteins from both eukaryotes and prokaryotes. The function of Pirin is unknown but the gene coding for this protein is known to be expressed in all tissues in the human body although it is expressed most strongly in the liver and heart. Pirin is known to be a nuclear protein, exclusively localised within the nucleoplasma and predominantly concentrated within dot-like subnuclear structures. A tomato homologue of human Pirin has been found to be induced during programmed cell death. Human Pirin interacts with Bcl-3 and NFI and hence is probably involved in the regulation of DNA transcription and replication. It appears to be an Fe(II)-containing member of the Cupin superfamily.
• pfam Pirin_C 107aa 5e-33 in ref transcript
  • Pirin C-terminal cupin domain. This region is found the C-terminal half of the Pirin protein.
• COG COG1741 275aa 2e-53 in ref transcript
  • Pirin-related protein [General function prediction only].

PITPNC1

• refseq_PITPNC1.F2 refseq_PITPNC1.R2 263 382
• NCBIGene 36.3 26207
• Single exon skipping, size difference: 119
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_012417

• Changed! pfam IP_trans 244aa 1e-73 in ref transcript
  • Phosphatidylinositol transfer protein. Along with the structurally unrelated Sec14p family (found in pfam00650), this family can bind/exchange one molecule of phosphatidylinositol (PI) or phosphatidylcholine (PC) and thus aids their transfer between different membrane compartments. There are three sub-families - all share an N-terminal PITP-like domain, whose sequence is highly conserved. It is described as consisting of three regions. The N-terminal region is thought to bind the lipid and contains two helices and an eight-stranded, mostly antiparallel beta-sheet. An intervening loop region, which is thought to play a role in protein-protein interactions, separates this from the C-terminal region, which exhibits the greatest sequence variation and may be involved in membrane binding. PITP alpha has a 16-fold greater affinity for PI than PC. Together with PITP beta, it is expressed ubiquitously in all tissues.
• Changed! pfam IP_trans 239aa 4e-73 in modified transcript

PITX2

• refseq_PITX2.F2 refseq_PITX2.R2 122 260
• NCBIGene 36.3 5308
• Single exon skipping, size difference: 138
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_153426

• cd homeodomain 59aa 9e-15 in ref transcript
  • Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
• pfam Homeobox 57aa 5e-21 in ref transcript
  • Homeobox domain.
• pfam OAR 21aa 0.001 in ref transcript
  • OAR domain.
• Changed! COG COG5576 114aa 2e-08 in ref transcript
  • Homeodomain-containing transcription factor [Transcription].
• Changed! COG COG5576 89aa 6e-08 in modified transcript

PJA1

• refseq_PJA1.F2 refseq_PJA1.R2 100 426
• NCBIGene 36.3 64219
• Alternative 3-prime, size difference: 326
• Exclusion of the protein initiation site
• Reference transcript: NM_145119

• cd RING 43aa 5e-08 in ref transcript
  • RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H).
• smart RING 41aa 3e-07 in ref transcript
  • Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s).
• COG COG5540 48aa 1e-08 in ref transcript
  • RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones].

PKD1L2

• refseq_PKD1L2.F1 refseq_PKD1L2.R1 192 397
• NCBIGene 36.2 114780
• Single exon skipping, size difference: 205
• Exclusion in 3'UTR
• Reference transcript: NM_052892

• cd PLAT_polycystin 120aa 2e-51 in ref transcript
  • PLAT/LH2 domain of polycystin-1 like proteins. Polycystins are a large family of membrane proteins composed of multiple domains, present in fish, invertebrates, mammals, and humans that are widely expressed in various cell types and whose biological functions remain poorly defined. In human, mutations in polycystin-1 (PKD1) and polycystin-2 (PKD2) have been shown to be the cause for autosomal dominant polycystic kidney disease (ADPKD). The generally proposed function of PLAT/LH2 domains is to mediate interaction with lipids or membrane bound proteins.
• cd CLECT 116aa 2e-17 in ref transcript
  • CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs. Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice. Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis; P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration. CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose. Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors. C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces. Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model. In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer. A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome. Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model.
• smart CLECT 126aa 6e-21 in ref transcript
  • C-type lectin (CTL) or carbohydrate-recognition domain (CRD). Many of these domains function as calcium-dependent carbohydrate binding modules.
• pfam PLAT 105aa 7e-15 in ref transcript
  • PLAT/LH2 domain. This domain is found in a variety of membrane or lipid associated proteins. It is called the PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology) domain. The known structure of pancreatic lipase shows this domain binds to procolipase pfam01114, which mediates membrane association. So it appears possible that this domain mediates membrane attachment via other protein binding partners. The structure of this domain is known for many members of the family and is composed of a beta sandwich.
• pfam GPS 40aa 2e-10 in ref transcript
  • Latrophilin/CL-1-like GPS domain. Domain present in latrophilin/CL-1, sea urchin REJ and polycystin.
• pfam REJ 203aa 2e-06 in ref transcript
  • REJ domain. The REJ (Receptor for Egg Jelly) domain is found in PKD1, and the sperm receptor for egg jelly. The function of this domain is unknown. The domain is 600 amino acids long so is probably composed of multiple structural domains. There are six completely conserved cysteine residues that may form disulphide bridges.

PKIA

• refseq_PKIA.F1 refseq_PKIA.R1 228 357
• NCBIGene 36.3 5569
• Single exon skipping, size difference: 129
• Exclusion in 5'UTR
• Reference transcript: NM_006823

• pfam PKI 74aa 9e-19 in ref transcript
  • cAMP-dependent protein kinase inhibitor. Members of this family are extremely potent competitive inhibitors of camp-dependent protein kinase activity. These proteins interact with the catalytic subunit of the enzyme after the cAMP-induced dissociation of its regulatory chains.

PKIB

• refseq_PKIB.F2 refseq_PKIB.R2 249 316
• NCBIGene 36.3 5570
• Single exon skipping, size difference: 67
• Exclusion in 5'UTR
• Reference transcript: NM_181795

• pfam PKI 46aa 2e-08 in ref transcript
  • cAMP-dependent protein kinase inhibitor. Members of this family are extremely potent competitive inhibitors of camp-dependent protein kinase activity. These proteins interact with the catalytic subunit of the enzyme after the cAMP-induced dissociation of its regulatory chains.

PKIG

• refseq_PKIG.F1 refseq_PKIG.R1 275 380
• NCBIGene 36.3 11142
• Single exon skipping, size difference: 105
• Exclusion in 5'UTR
• Reference transcript: NM_181805

• pfam PKI 74aa 1e-19 in ref transcript
  • cAMP-dependent protein kinase inhibitor. Members of this family are extremely potent competitive inhibitors of camp-dependent protein kinase activity. These proteins interact with the catalytic subunit of the enzyme after the cAMP-induced dissociation of its regulatory chains.

PKM2

• refseq_PKM2.F1 refseq_PKM2.R1 145 361
• NCBIGene 36.3 5315
• Alternative 5-prime, size difference: 216
• Exclusion in 5'UTR
• Reference transcript: NM_182470

• cd Pyruvate_Kinase 489aa 0.0 in ref transcript
  • Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low affinity T state. PK exists as several different isozymes, depending on organism and tissue type. In mammals, there are four PK isozymes: R, found in red blood cells, L, found in liver, M1, found in skeletal muscle, and M2, found in kidney, adipose tissue, and lung. PK forms a homotetramer, with each subunit containing three domains. The T state to R state transition of PK is more complex than in most allosteric enzymes, involving a concerted rotation of all 3 domains of each monomer in the homotetramer.
• TIGR pyruv_kin 485aa 0.0 in ref transcript
  • This enzyme is a homotetramer. Some forms are active only in the presence of fructose-1,6-bisphosphate or similar phosphorylated sugars.
• PRK PRK05826 472aa 1e-158 in ref transcript
  • pyruvate kinase; Provisional.

PKMYT1

• refseq_PKMYT1.F1 refseq_PKMYT1.R1 106 144
• NCBIGene 36.3 9088
• Alternative 3-prime, size difference: 38
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_004203

• cd S_TKc 248aa 4e-50 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• pfam Pkinase 250aa 2e-48 in ref transcript
  • Protein kinase domain.
• COG SPS1 261aa 8e-30 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].

PKP1

• refseq_PKP1.F1 refseq_PKP1.R1 120 183
• NCBIGene 36.3 5317
• Single exon skipping, size difference: 63
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000299

• cd ARM 113aa 6e-20 in ref transcript
  • Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model.
• cd ARM 129aa 4e-07 in ref transcript
• smart ARM 41aa 3e-07 in ref transcript
  • Armadillo/beta-catenin-like repeats. Approx. 40 amino acid repeat. Tandem repeats form superhelix of helices that is proposed to mediate interaction of beta-catenin with its ligands. Involved in transducing the Wingless/Wnt signal. In plakoglobin arm repeats bind alpha-catenin and N-cadherin.

PKP2

• refseq_PKP2.F2 refseq_PKP2.R2 184 316
• NCBIGene 36.3 5318
• Single exon skipping, size difference: 132
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_004572

• Changed! cd ARM 118aa 3e-11 in ref transcript
  • Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model.
• cd ARM 130aa 6e-06 in ref transcript
• Changed! cd ARM 118aa 3e-13 in modified transcript
• Changed! pfam Arm 42aa 0.001 in modified transcript
  • Armadillo/beta-catenin-like repeat. Approx. 40 amino acid repeat. Tandem repeats form super-helix of helices that is proposed to mediate interaction of beta-catenin with its ligands. CAUTION: This family does not contain all known armadillo repeats.

PKP4

• refseq_PKP4.F2 refseq_PKP4.R2 271 400
• NCBIGene 36.3 8502
• Single exon skipping, size difference: 129
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_003628

• cd ARM 123aa 3e-25 in ref transcript
  • Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model.
• cd ARM 129aa 1e-11 in ref transcript
• cd ARM 142aa 1e-04 in ref transcript
• smart ARM 41aa 4e-07 in ref transcript
  • Armadillo/beta-catenin-like repeats. Approx. 40 amino acid repeat. Tandem repeats form superhelix of helices that is proposed to mediate interaction of beta-catenin with its ligands. Involved in transducing the Wingless/Wnt signal. In plakoglobin arm repeats bind alpha-catenin and N-cadherin.
• smart ARM 36aa 2e-05 in ref transcript
• smart ARM 42aa 3e-05 in ref transcript

PLA2G6

• refseq_PLA2G6.F1 refseq_PLA2G6.R1 109 271
• NCBIGene 36.3 8398
• Single exon skipping, size difference: 162
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_003560

• cd Pat_PNPLA9 314aa 1e-164 in ref transcript
  • Patatin-like phospholipase domain containing protein 9. PNPLA9 is a Ca-independent phospholipase that catalyzes the hydrolysis of glycerophospholipids at the sn-2 position. PNPLA9 is also known as PLA2G6 (phospholipase A2 group VI) or iPLA2beta. PLA2G6 is stimulated by ATP and inhibited by bromoenol lactone (BEL). In humans, PNPLA9 in expressed ubiquitously and is involved in signal transduction, cell proliferation, and apoptotic cell death. Mutations in human PLA2G6 leads to infantile neuroaxonal dystrophy (INAD) and idiopathic neurodegeneration with brain iron accumulation (NBIA). This family includes PLA2G6 from Homo sapiens and Rattus norvegicus.
• Changed! cd ANK 119aa 1e-24 in ref transcript
  • ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats.
• cd ANK 126aa 9e-20 in ref transcript
• pfam Patatin 185aa 1e-33 in ref transcript
  • Patatin-like phospholipase. This family consists of various patatin glycoproteins from plants. The patatin protein accounts for up to 40% of the total soluble protein in potato tubers. Patatin is a storage protein but it also has the enzymatic activity of lipid acyl hydrolase, catalysing the cleavage of fatty acids from membrane lipids. Members of this family have been found also in vertebrates.
• Changed! TIGR trp 146aa 1e-04 in ref transcript
  • after chronic exposure to capsaicin. (McCleskey and Gold, 1999).
• COG COG3621 227aa 6e-19 in ref transcript
  • Patatin [General function prediction only].
• COG Arp 204aa 2e-11 in ref transcript
  • FOG: Ankyrin repeat [General function prediction only].
• Changed! PTZ PTZ00322 110aa 3e-06 in ref transcript
  • 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase; Provisional.
• COG Arp 196aa 6e-06 in ref transcript
• Changed! cd ANK 111aa 4e-24 in modified transcript
• Changed! TIGR trp 101aa 1e-04 in modified transcript
• Changed! pfam Ank 30aa 0.002 in modified transcript
  • Ankyrin repeat. There's no clear separation between noise and signal on the HMM search Ankyrin repeats generally consist of a beta, alpha, alpha, beta order of secondary structures. The repeats associate to form a higher order structure.
• Changed! TIGR trp 234aa 0.008 in modified transcript

PLCB1

• refseq_PLCB1.F1 refseq_PLCB1.R1 234 352
• NCBIGene 36.3 23236
• Single exon skipping, size difference: 118
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_015192

• cd PLCc 149aa 6e-42 in ref transcript
  • Phospholipase C, catalytic domain; Phosphoinositide-specific phospholipases C catalyze hydrolysis of phosphatidylinositol-4,5-bisphosphate (PIP2) to D-myo-inositol-1,4,5-trisphosphate (1,4,5-IP3) and sn-1,2-diacylglycerol (DAG). Both products function as second messengers in eukaryotic signal transduction cascades. 1,4,5-IP3 triggers inflow of calcium from intracellular stores; the membrane resident product DAG controls cellular protein phosphorylation states by activating various protein kinase C isozymes. The enzyme comprises 2 regions (X and Y) connected via a linker which may contain inserted domains, X and Y together form a TIM barrel-like structure containing the active site residues.
• cd PH_PLC 121aa 2e-25 in ref transcript
  • Phospholipase C (PLC) pleckstrin homology (PH) domain. There are several isozymes of PLC (beta, gamma, delta, epsilon. zeta). While, PLC beta, gamma and delta all have N-terminal PH domains, lipid binding specificity is not conserved between them. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
• cd PLCc 102aa 2e-19 in ref transcript
• cd C2_2 118aa 5e-09 in ref transcript
  • Protein kinase C conserved region 2, subgroup 2; C2 Ca2+-binding motif present in phospholipases, protein kinases C, and synaptotagmins (amongst others); some PKCs lack calcium dependence. Particular C2s appear to bind phospholipids, inositol polyphosphates,and intracellular proteins. Two distinct C2 topologies generated by permutation of the sequence with respect to the N- and C-terminal beta strands are seen. In this subgroup, containing phospholipases C and D( PLC-1, PLD) and specific protein kinases C (PKC) subtypes, the C-terminal beta strand occupies the position of what is the N-terminal strand in subgroup 1.
• pfam PI-PLC-Y 118aa 1e-59 in ref transcript
  • Phosphatidylinositol-specific phospholipase C, Y domain. This associates with pfam00388 to form a single structural unit.
• pfam PI-PLC-X 147aa 2e-55 in ref transcript
  • Phosphatidylinositol-specific phospholipase C, X domain. This associates with pfam00387 to form a single structural unit.
• Changed! pfam PLC-beta_C 165aa 1e-41 in ref transcript
  • PLC-beta C terminal. This domain corresponds to the alpha helical C terminal domain of phospholipase C beta.
• pfam efhand_like 92aa 9e-22 in ref transcript
  • Phosphoinositide-specific phospholipase C, efhand-like. Members of this family are predominantly found in phosphoinositide-specific phospholipase C. They adopt a structure consisting of a core of four alpha helices, in an EF like fold, and are required for functioning of the enzyme.
• smart C2 100aa 7e-10 in ref transcript
  • Protein kinase C conserved region 2 (CalB). Ca2+-binding motif present in phospholipases, protein kinases C, and synaptotamins (among others). Some do not appear to contain Ca2+-binding sites. Particular C2s appear to bind phospholipids, inositol polyphosphates, and intracellular proteins. Unusual occurrence in perforin. Synaptotagmin and PLC C2s are permuted in sequence with respect to N- and C-terminal beta strands. SMART detects C2 domains using one or both of two profiles.
• Changed! pfam PLC-beta_C 118aa 7e-31 in modified transcript

PLOD2

• refseq_PLOD2.F1 refseq_PLOD2.R1 113 176
• NCBIGene 36.3 5352
• Single exon skipping, size difference: 63
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_182943

• smart P4Hc 173aa 1e-18 in ref transcript
  • Prolyl 4-hydroxylase alpha subunit homologues. Mammalian enzymes catalyse hydroxylation of collagen, for example. Prokaryotic enzymes might catalyse hydroxylation of antibiotic peptides. These are 2-oxoglutarate-dependent dioxygenases, requiring 2-oxoglutarate and dioxygen as cosubstrates and ferrous iron as a cofactor.

PLP1

• refseq_PLP1.F1 refseq_PLP1.R1 218 323
• NCBIGene 36.3 5354
• Alternative 5-prime, size difference: 105
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000533

• Changed! pfam Myelin_PLP 276aa 1e-108 in ref transcript
  • Myelin proteolipid protein (PLP or lipophilin).
• Changed! pfam Myelin_PLP 241aa 1e-109 in modified transcript

PLTP

• refseq_PLTP.F1 refseq_PLTP.R1 149 305
• NCBIGene 36.3 5360
• Single exon skipping, size difference: 156
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_006227

• Changed! cd BPI1 219aa 2e-56 in ref transcript
  • BPI/LBP/CETP N-terminal domain; Bactericidal permeability-increasing protein (BPI) / Lipopolysaccharide-binding protein (LBP) / Cholesteryl ester transfer protein (CETP) N-terminal domain; binds to and neutralizes lipopolysaccharides from the outer membrane of Gram-negative bacteria.; Apolar pockets on the concave surface bind a molecule of phosphatidylcholine, primarily by interacting with their acyl chains; this suggests that the pockets may also bind the acyl chains of lipopolysaccharide.
• cd BPI2 201aa 1e-47 in ref transcript
  • BPI/LBP/CETP C-terminal domain; Bactericidal permeability-increasing protein (BPI) / Lipopolysaccharide-binding protein (LBP) / Cholesteryl ester transfer protein (CETP) C-terminal domain; binds to and neutralizes lipopolysaccharides from the outer membrane of Gram-negative bacteria.; Apolar pockets on the concave surface bind a molecule of phosphatidylcholine, primarily by interacting with their acyl chains; this suggests that the pockets may also bind the acyl chains of lipopolysaccharide.
• pfam LBP_BPI_CETP_C 237aa 7e-78 in ref transcript
  • LBP / BPI / CETP family, C-terminal domain. The N and C terminal domains of the LBP/BPI/CETP family are structurally similar.
• Changed! smart BPI1 219aa 5e-53 in ref transcript
  • BPI/LBP/CETP N-terminal domain. Bactericidal permeability-increasing protein (BPI) / Lipopolysaccharide-binding protein (LBP) / Cholesteryl ester transfer protein (CETP) N-terminal domain.
• Changed! cd BPI1 167aa 9e-33 in modified transcript
• Changed! smart BPI1 167aa 9e-35 in modified transcript

PLUNC

• refseq_PLUNC.F1 refseq_PLUNC.R1 184 239
• NCBIGene 36.3 51297
• Alternative 3-prime, size difference: 55
• Inclusion in 3'UTR
• Reference transcript: NM_016583

• cd BPI1 138aa 0.001 in ref transcript
  • BPI/LBP/CETP N-terminal domain; Bactericidal permeability-increasing protein (BPI) / Lipopolysaccharide-binding protein (LBP) / Cholesteryl ester transfer protein (CETP) N-terminal domain; binds to and neutralizes lipopolysaccharides from the outer membrane of Gram-negative bacteria.; Apolar pockets on the concave surface bind a molecule of phosphatidylcholine, primarily by interacting with their acyl chains; this suggests that the pockets may also bind the acyl chains of lipopolysaccharide.
• pfam LBP_BPI_CETP 141aa 3e-24 in ref transcript
  • LBP / BPI / CETP family, N-terminal domain. The N and C terminal domains of the LBP/BPI/CETP family are structurally similar.

PML

• refseq_PML.F2 refseq_PML.R2 139 283
• NCBIGene 36.3 5371
• Single exon skipping, size difference: 144
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_033238

• smart RING 35aa 3e-04 in ref transcript
  • Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s).
• pfam zf-B_box 43aa 0.003 in ref transcript
  • B-box zinc finger.
• TIGR rad18 73aa 0.003 in ref transcript
  • This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
• Changed! pfam zf-B_box 40aa 0.009 in ref transcript

POGZ

• refseq_POGZ.F1 refseq_POGZ.R1 200 359
• NCBIGene 36.3 23126
• Single exon skipping, size difference: 159
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_015100

• pfam DDE 165aa 2e-15 in ref transcript
  • DDE superfamily endonuclease. This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction. Interestingly this family also includes the CENP-B protein. This domain in that protein appears to have lost the metal binding residues and is unlikely to have endonuclease activity. Centromere Protein B (CENP-B) is a DNA-binding protein localised to the centromere.
• smart CENPB 62aa 6e-12 in ref transcript
  • Putative DNA-binding domain in centromere protein B, mouse jerky and transposases.

POLDIP3

• refseq_POLDIP3.F1 refseq_POLDIP3.R1 301 388
• NCBIGene 36.3 84271
• Single exon skipping, size difference: 87
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_032311

• cd RRM 65aa 1e-09 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• smart RRM 64aa 8e-09 in ref transcript
  • RNA recognition motif.
• COG COG0724 133aa 2e-04 in ref transcript
  • RNA-binding proteins (RRM domain) [General function prediction only].

POLR3H

• refseq_POLR3H.F1 refseq_POLR3H.R1 126 181
• NCBIGene 36.2 171568
• Alternative 5-prime, size difference: 55
• Exclusion in 5'UTR
• Reference transcript: NM_001018051

POMC

• refseq_POMC.F1 refseq_POMC.R1 145 195
• NCBIGene 36.3 5443
• Single exon skipping, size difference: 50
• Exclusion in 5'UTR
• Reference transcript: NM_001035256

• pfam NPP 45aa 8e-16 in ref transcript
  • Pro-opiomelanocortin, N-terminal region. This family features the N-terminal peptide of pro-opiomelanocortin (NPP). It is thought to represent an important pituitary peptide, given its high yield from pituitary glands, and exhibits a potent in vitro aldosterone-stimulating activity.
• pfam Op_neuropeptide 29aa 2e-07 in ref transcript
  • Opioids neuropeptide. This family corresponds to the conserved YGG motif that is found in a wide variety of opioid neuropeptides such as enkephalin.
• pfam ACTH_domain 39aa 1e-04 in ref transcript
  • Corticotropin ACTH domain.

POMZP3

• refseq_POMZP3.F1 refseq_POMZP3.R1 186 416
• NCBIGene 36.3 22932
• Multiple exon skipping, size difference: 230
• Exclusion in the protein causing a frameshift, Exclusion of the stop codon
• Reference transcript: NM_012230

• Changed! smart ZP 65aa 9e-09 in ref transcript
  • Zona pellucida (ZP) domain. ZP proteins are responsible for sperm-adhesion fo the zona pellucida. ZP domains are also present in multidomain transmembrane proteins such as glycoprotein GP2, uromodulin and TGF-beta receptor type III (betaglycan).

POP5

• refseq_POP5.F1 refseq_POP5.R1 182 332
• NCBIGene 36.3 51367
• Single exon skipping, size difference: 150
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_015918

• Changed! pfam RNase_P_Rpp14 111aa 4e-21 in ref transcript
  • Rpp14/Pop5 family. tRNA processing enzyme ribonuclease P (RNase P) consists of an RNA molecule associated with at least eight protein subunits, hPop1, Rpp14, Rpp20, Rpp25, Rpp29, Rpp30, Rpp38, and Rpp40. This protein is known as Pop5 in eukaryotes.
• Changed! COG POP5 114aa 8e-06 in ref transcript
  • RNase P/RNase MRP subunit POP5 [Translation, ribosomal structure and biogenesis].

PORCN

• refseq_PORCN.F1 refseq_PORCN.R1 155 226
• NCBIGene 36.3 64840
• Alternative 3-prime, size difference: 71
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_203475

• Changed! pfam MBOAT 288aa 8e-29 in ref transcript
  • MBOAT family. The MBOAT (membrane bound O-acyl transferase) family of membrane proteins contains a variety of acyltransferase enzymes. A conserved histidine has been suggested to be the active site residue.
• Changed! COG COG5202 336aa 5e-09 in ref transcript
  • Predicted membrane protein [Function unknown].

PPA2

• refseq_PPA2.F2 refseq_PPA2.R2 286 340
• NCBIGene 36.3 27068
• Single exon skipping, size difference: 54
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_176869

• Changed! cd pyrophosphatase 184aa 1e-48 in ref transcript
  • Inorganic pyrophosphatase. These enzymes hydrolyze inorganic pyrophosphate (PPi) to two molecules of orthophosphates (Pi). The reaction requires bivalent cations. The enzymes in general exist as homooligomers.
• Changed! pfam Pyrophosphatase 185aa 3e-55 in ref transcript
  • Inorganic pyrophosphatase.
• Changed! COG Ppa 216aa 7e-33 in ref transcript
  • Inorganic pyrophosphatase [Energy production and conversion].
• Changed! cd pyrophosphatase 178aa 1e-40 in modified transcript
• Changed! pfam Pyrophosphatase 171aa 3e-50 in modified transcript
• Changed! COG Ppa 198aa 7e-29 in modified transcript

PPA2

• refseq_PPA2.F3 refseq_PPA2.R3 188 275
• NCBIGene 36.3 27068
• Single exon skipping, size difference: 87
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_176869

• Changed! cd pyrophosphatase 184aa 1e-48 in ref transcript
  • Inorganic pyrophosphatase. These enzymes hydrolyze inorganic pyrophosphate (PPi) to two molecules of orthophosphates (Pi). The reaction requires bivalent cations. The enzymes in general exist as homooligomers.
• Changed! pfam Pyrophosphatase 185aa 3e-55 in ref transcript
  • Inorganic pyrophosphatase.
• Changed! COG Ppa 216aa 7e-33 in ref transcript
  • Inorganic pyrophosphatase [Energy production and conversion].
• Changed! cd pyrophosphatase 155aa 5e-39 in modified transcript
• Changed! pfam Pyrophosphatase 156aa 4e-45 in modified transcript
• Changed! COG Ppa 187aa 2e-25 in modified transcript

PPAP2C

• refseq_PPAP2C.F1 refseq_PPAP2C.R1 127 168
• NCBIGene 36.3 8612
• Alternative 5-prime, size difference: 41
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_003712

• Changed! cd PAP2_wunen 131aa 2e-48 in ref transcript
  • PAP2, wunen subfamily. Most likely a family of membrane associated phosphatidic acid phosphatases. Wunen is a drosophila protein expressed in the central nervous system, which provides repellent activity towards primordial germ cells (PGCs), controls the survival of PGCs and is essential in the migration process of these cells towards the somatic gonadal precursors.
• Changed! pfam PAP2 123aa 4e-19 in ref transcript
  • PAP2 superfamily. This family includes the enzyme type 2 phosphatidic acid phosphatase (PAP2), Glucose-6-phosphatase EC:3.1.3.9, Phosphatidylglycerophosphatase B EC:3.1.3.27 and bacterial acid phosphatase EC:3.1.3.2. The family also includes a variety of haloperoxidases that function by oxidising halides in the presence of hydrogen peroxide to form the corresponding hypohalous acids.
• Changed! COG PgpB 134aa 0.003 in ref transcript
  • Membrane-associated phospholipid phosphatase [Lipid metabolism].

PPEF1

• refseq_PPEF1.F1 refseq_PPEF1.R1 195 381
• NCBIGene 36.3 5475
• Single exon skipping, size difference: 186
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_006240

• Changed! cd PP2Ac 318aa 5e-63 in ref transcript
  • Protein phosphatase 2A homologues, catalytic domain. Large family of serine/threonine phosphatases, including PP1, PP2A and PP2B (calcineurin) family members.
• cd EFh 66aa 2e-07 in ref transcript
  • EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers.
• Changed! smart PP2Ac 322aa 2e-91 in ref transcript
  • Protein phosphatase 2A homologues, catalytic domain. Large family of serine/threonine phosphatases, that includes PP1, PP2A and PP2B (calcineurin) family members.
• pfam PPP5 62aa 3e-07 in ref transcript
  • PPP5. This domain is specific to the PPP5 subfamily of serine/threonine phosphatases.
• smart EH 67aa 0.001 in ref transcript
  • Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
• Changed! PTZ PTZ00244 314aa 5e-30 in ref transcript
  • serine/threonine-protein phosphatase PP1; Provisional.
• COG FRQ1 68aa 2e-05 in ref transcript
  • Ca2+-binding protein (EF-Hand superfamily) [Signal transduction mechanisms / Cytoskeleton / Cell division and chromosome partitioning / General function prediction only].
• Changed! cd PP2Ac 256aa 2e-42 in modified transcript
• Changed! smart PP2Ac 260aa 1e-64 in modified transcript
• Changed! PTZ PTZ00244 176aa 5e-22 in modified transcript

PPEF1

• refseq_PPEF1.F1 refseq_PPEF1.R2 219 303
• NCBIGene 36.3 5475
• Alternative 5-prime, size difference: 84
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_006240

• Changed! cd PP2Ac 318aa 5e-63 in ref transcript
  • Protein phosphatase 2A homologues, catalytic domain. Large family of serine/threonine phosphatases, including PP1, PP2A and PP2B (calcineurin) family members.
• cd EFh 66aa 2e-07 in ref transcript
  • EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers.
• Changed! smart PP2Ac 322aa 2e-91 in ref transcript
  • Protein phosphatase 2A homologues, catalytic domain. Large family of serine/threonine phosphatases, that includes PP1, PP2A and PP2B (calcineurin) family members.
• pfam PPP5 62aa 3e-07 in ref transcript
  • PPP5. This domain is specific to the PPP5 subfamily of serine/threonine phosphatases.
• smart EH 67aa 0.001 in ref transcript
  • Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
• Changed! PTZ PTZ00244 314aa 5e-30 in ref transcript
  • serine/threonine-protein phosphatase PP1; Provisional.
• COG FRQ1 68aa 2e-05 in ref transcript
  • Ca2+-binding protein (EF-Hand superfamily) [Signal transduction mechanisms / Cytoskeleton / Cell division and chromosome partitioning / General function prediction only].
• Changed! cd PP2Ac 290aa 2e-65 in modified transcript
• Changed! smart PP2Ac 294aa 8e-93 in modified transcript
• Changed! PTZ PTZ00244 286aa 7e-33 in modified transcript
• Changed! PTZ PTZ00184 148aa 0.010 in modified transcript
  • calmodulin; Provisional.

PPHLN1

• refseq_PPHLN1.F1 refseq_PPHLN1.R1 118 283
• NCBIGene 36.3 51535
• Single exon skipping, size difference: 165
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_016488

PPHLN1

• refseq_PPHLN1.F4 refseq_PPHLN1.R4 112 155
• NCBIGene 36.3 51535
• Single exon skipping, size difference: 43
• Inclusion in 5'UTR
• Reference transcript: NM_016488

PPIL2

• refseq_PPIL2.F1 refseq_PPIL2.R1 110 248
• NCBIGene 36.3 23759
• Alternative 3-prime, size difference: 138
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_148176

• cd cyclophilin_RING 160aa 9e-76 in ref transcript
  • cyclophilin_RING: cyclophilin-type peptidylprolyl cis- trans isomerases (cyclophilins) having a modified RING finger domain. This group includes the nuclear proteins, Human hCyP-60 and Caenorhabditis elegans MOG-6 which, compared to the archetypal cyclophilin Human cyclophilin A exhibit reduced peptidylprolyl cis- trans isomerase activity and lack a residue important for cyclophilin binding. Human hCyP-60 has been shown to physically interact with the proteinase inhibitor peptide eglin c and; C. elegans MOG-6 to physically interact with MEP-1, a nuclear zinc finger protein. MOG-6 has been shown to function in germline sex determination.
• pfam Pro_isomerase 140aa 4e-35 in ref transcript
  • Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD. The peptidyl-prolyl cis-trans isomerases, also known as cyclophilins, share this domain of about 109 amino acids. Cyclophilins have been found in all organisms studied so far and catalyse peptidyl-prolyl isomerisation during which the peptide bond preceding proline (the peptidyl-prolyl bond) is stabilised in the cis conformation. Mammalian cyclophilin A (CypA) is a major cellular target for the immunosuppressive drug cyclosporin A (CsA). Other roles for cyclophilins may include chaperone and cell signalling function.
• smart Ubox 60aa 1e-12 in ref transcript
  • Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
• COG PpiB 153aa 8e-40 in ref transcript
  • Peptidyl-prolyl cis-trans isomerase (rotamase) - cyclophilin family [Posttranslational modification, protein turnover, chaperones].
• COG COG1723 117aa 0.010 in ref transcript
  • Uncharacterized conserved protein [Function unknown].

PPIL2

• refseq_PPIL2.F2 refseq_PPIL2.R2 237 379
• NCBIGene 36.3 23759
• Alternative 3-prime, size difference: 4
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_148176

• cd cyclophilin_RING 160aa 9e-76 in ref transcript
  • cyclophilin_RING: cyclophilin-type peptidylprolyl cis- trans isomerases (cyclophilins) having a modified RING finger domain. This group includes the nuclear proteins, Human hCyP-60 and Caenorhabditis elegans MOG-6 which, compared to the archetypal cyclophilin Human cyclophilin A exhibit reduced peptidylprolyl cis- trans isomerase activity and lack a residue important for cyclophilin binding. Human hCyP-60 has been shown to physically interact with the proteinase inhibitor peptide eglin c and; C. elegans MOG-6 to physically interact with MEP-1, a nuclear zinc finger protein. MOG-6 has been shown to function in germline sex determination.
• pfam Pro_isomerase 140aa 4e-35 in ref transcript
  • Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD. The peptidyl-prolyl cis-trans isomerases, also known as cyclophilins, share this domain of about 109 amino acids. Cyclophilins have been found in all organisms studied so far and catalyse peptidyl-prolyl isomerisation during which the peptide bond preceding proline (the peptidyl-prolyl bond) is stabilised in the cis conformation. Mammalian cyclophilin A (CypA) is a major cellular target for the immunosuppressive drug cyclosporin A (CsA). Other roles for cyclophilins may include chaperone and cell signalling function.
• smart Ubox 60aa 1e-12 in ref transcript
  • Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
• COG PpiB 153aa 8e-40 in ref transcript
  • Peptidyl-prolyl cis-trans isomerase (rotamase) - cyclophilin family [Posttranslational modification, protein turnover, chaperones].
• Changed! COG COG1723 117aa 0.010 in ref transcript
  • Uncharacterized conserved protein [Function unknown].

PPIL2

• refseq_PPIL2.F3 refseq_PPIL2.R3 256 398
• NCBIGene 36.3 23759
• Alternative 3-prime, size difference: 4
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_148176

• cd cyclophilin_RING 160aa 9e-76 in ref transcript
  • cyclophilin_RING: cyclophilin-type peptidylprolyl cis- trans isomerases (cyclophilins) having a modified RING finger domain. This group includes the nuclear proteins, Human hCyP-60 and Caenorhabditis elegans MOG-6 which, compared to the archetypal cyclophilin Human cyclophilin A exhibit reduced peptidylprolyl cis- trans isomerase activity and lack a residue important for cyclophilin binding. Human hCyP-60 has been shown to physically interact with the proteinase inhibitor peptide eglin c and; C. elegans MOG-6 to physically interact with MEP-1, a nuclear zinc finger protein. MOG-6 has been shown to function in germline sex determination.
• pfam Pro_isomerase 140aa 4e-35 in ref transcript
  • Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD. The peptidyl-prolyl cis-trans isomerases, also known as cyclophilins, share this domain of about 109 amino acids. Cyclophilins have been found in all organisms studied so far and catalyse peptidyl-prolyl isomerisation during which the peptide bond preceding proline (the peptidyl-prolyl bond) is stabilised in the cis conformation. Mammalian cyclophilin A (CypA) is a major cellular target for the immunosuppressive drug cyclosporin A (CsA). Other roles for cyclophilins may include chaperone and cell signalling function.
• smart Ubox 60aa 1e-12 in ref transcript
  • Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
• COG PpiB 153aa 8e-40 in ref transcript
  • Peptidyl-prolyl cis-trans isomerase (rotamase) - cyclophilin family [Posttranslational modification, protein turnover, chaperones].
• Changed! COG COG1723 117aa 0.010 in ref transcript
  • Uncharacterized conserved protein [Function unknown].

PPIL3

• refseq_PPIL3.F2 refseq_PPIL3.R2 105 396
• NCBIGene 36.3 53938
• Alternative 5-prime and 3-prime, size difference: 291
• Inclusion in 5'UTR, Inclusion in 5'UTR
• Reference transcript: NM_032472

• cd Cyclophilin_PPIL3_like 158aa 2e-55 in ref transcript
  • Cyclophilin_PPIL3_like. Proteins similar to Human cyclophilin-like peptidylprolyl cis- trans isomerase (PPIL3). Members of this family lack a key residue important for cyclosporin binding: the tryptophan residue corresponding to W121 in human hCyP-18a; most members have a histidine at this position. The exact function of the protein is not known.
• pfam Pro_isomerase 152aa 5e-26 in ref transcript
  • Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD. The peptidyl-prolyl cis-trans isomerases, also known as cyclophilins, share this domain of about 109 amino acids. Cyclophilins have been found in all organisms studied so far and catalyse peptidyl-prolyl isomerisation during which the peptide bond preceding proline (the peptidyl-prolyl bond) is stabilised in the cis conformation. Mammalian cyclophilin A (CypA) is a major cellular target for the immunosuppressive drug cyclosporin A (CsA). Other roles for cyclophilins may include chaperone and cell signalling function.
• COG PpiB 157aa 2e-24 in ref transcript
  • Peptidyl-prolyl cis-trans isomerase (rotamase) - cyclophilin family [Posttranslational modification, protein turnover, chaperones].

PPM1A

• refseq_PPM1A.F2 refseq_PPM1A.R2 279 381
• NCBIGene 36.3 5494
• Single exon skipping, size difference: 102
• Inclusion in 5'UTR
• Reference transcript: NM_021003

• cd PP2Cc 269aa 5e-71 in ref transcript
  • Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence similarity.
• smart PP2Cc 273aa 1e-82 in ref transcript
  • Serine/threonine phosphatases, family 2C, catalytic domain. The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence similarity.
• pfam PP2C_C 80aa 1e-32 in ref transcript
  • Protein serine/threonine phosphatase 2C, C-terminal domain. Protein phosphatase 2C (PP2C) is involved in regulating cellular responses to stress in various eukaryotes. It consists of two domains: an N-terminal catalytic domain and a C-terminal domain characteristic of mammalian PP2Cs. This domain consists of three antiparallel alpha helices, one of which packs against two corresponding alpha-helices of the N-terminal domain. The C-terminal domain does not seem to play a role in catalysis, but it may provide protein substrate specificity due to the cleft that is created between it and the catalytic domain.
• PTZ PTZ00224 293aa 2e-45 in ref transcript
  • protein phosphatase 2C; Provisional.

PPP1CA

• refseq_PPP1CA.F2 refseq_PPP1CA.R2 129 162
• NCBIGene 36.3 5499
• Alternative 3-prime, size difference: 33
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001008709

• cd PP2Ac 267aa 1e-116 in ref transcript
  • Protein phosphatase 2A homologues, catalytic domain. Large family of serine/threonine phosphatases, including PP1, PP2A and PP2B (calcineurin) family members.
• smart PP2Ac 270aa 1e-121 in ref transcript
  • Protein phosphatase 2A homologues, catalytic domain. Large family of serine/threonine phosphatases, that includes PP1, PP2A and PP2B (calcineurin) family members.
• Changed! PTZ PTZ00244 281aa 1e-118 in ref transcript
  • serine/threonine-protein phosphatase PP1; Provisional.
• Changed! PTZ PTZ00244 289aa 1e-120 in modified transcript

PPP1CB

• refseq_PPP1CB.F2 refseq_PPP1CB.R2 118 405
• NCBIGene 36.2 5500
• Multiple exon skipping, size difference: 287
• Exclusion in the protein causing a frameshift, Exclusion in the protein (no frameshift)
• Reference transcript: NM_206876

• Changed! cd PP2Ac 267aa 1e-114 in ref transcript
  • Protein phosphatase 2A homologues, catalytic domain. Large family of serine/threonine phosphatases, including PP1, PP2A and PP2B (calcineurin) family members.
• Changed! smart PP2Ac 271aa 1e-120 in ref transcript
  • Protein phosphatase 2A homologues, catalytic domain. Large family of serine/threonine phosphatases, that includes PP1, PP2A and PP2B (calcineurin) family members.
• Changed! PTZ PTZ00244 288aa 1e-117 in ref transcript
  • serine/threonine-protein phosphatase PP1; Provisional.
• Changed! cd PP2Ac 168aa 2e-69 in modified transcript
• Changed! smart PP2Ac 168aa 4e-73 in modified transcript
• Changed! PTZ PTZ00244 192aa 7e-72 in modified transcript

PPP1R12B

• refseq_PPP1R12B.F1 refseq_PPP1R12B.R1 133 314
• NCBIGene 36.3 4660
• Single exon skipping, size difference: 181
• Exclusion of the stop codon
• Reference transcript: NM_032105

• cd ANK 103aa 2e-25 in ref transcript
  • ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats.
• cd ANK 152aa 7e-20 in ref transcript
• cd ANK 58aa 1e-06 in ref transcript
• pfam Ank 33aa 4e-06 in ref transcript
  • Ankyrin repeat. There's no clear separation between noise and signal on the HMM search Ankyrin repeats generally consist of a beta, alpha, alpha, beta order of secondary structures. The repeats associate to form a higher order structure.
• pfam Ank 32aa 2e-05 in ref transcript
• pfam Ank 31aa 1e-04 in ref transcript
• TIGR trp 170aa 8e-04 in ref transcript
  • after chronic exposure to capsaicin. (McCleskey and Gold, 1999).
• pfam Ank 33aa 0.005 in ref transcript
• COG Arp 125aa 1e-12 in ref transcript
  • FOG: Ankyrin repeat [General function prediction only].
• PTZ PTZ00322 77aa 6e-06 in ref transcript
  • 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase; Provisional.

PPP1R8

• refseq_PPP1R8.F2 refseq_PPP1R8.R2 257 377
• NCBIGene 36.3 5511
• Alternative 5-prime, size difference: 120
• Inclusion in 5'UTR
• Reference transcript: NM_138558

PPP1R8

• refseq_PPP1R8.F3 refseq_PPP1R8.R3 145 366
• NCBIGene 36.3 5511
• Single exon skipping, size difference: 221
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_014110

• Changed! cd FHA 100aa 3e-12 in ref transcript
  • Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins localize to the nucleus, where they participate in establishing or maintaining cell cycle checkpoints, DNA repair, or transcriptional regulation. Members of the FHA family include: Dun1, Rad53, Cds1, Mek1, KAPP(kinase-associated protein phosphatase),and Ki-67 (a human nuclear protein related to cell proliferation).
• Changed! pfam FHA 69aa 8e-13 in ref transcript
  • FHA domain. The FHA (Forkhead-associated) domain is a phosphopeptide binding motif.
• Changed! COG COG1716 89aa 0.001 in ref transcript
  • FOG: FHA domain [Signal transduction mechanisms].
• Changed! cd FHA 65aa 2e-06 in modified transcript
• Changed! pfam FHA 42aa 2e-07 in modified transcript

PPP2R2B

• refseq_PPP2R2B.F1 refseq_PPP2R2B.R1 100 294
• NCBIGene 36.3 5521
• Single exon skipping, size difference: 194
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_181674

• Changed! cd WD40 347aa 4e-07 in ref transcript
  • WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.
• Changed! pfam PP2A_B_N 71aa 1e-28 in ref transcript
  • Serine-threonine phosphatase 2A subunit B alpha and beta N-terminal domain. Protein phosphatase 2A (PP2A) is a serine/threonine phosphatase involved in many aspects of cellular function including the regulation of metabolic enzymes and proteins involved in signal transduction. PP2A is a trimeric enzyme consisting of a central catalytic core, and two subunits, A and B. This is the N-terminal domain of subunit B that is thought to perform substrate recognition function or be responsible for targeting the enzyme complex to the appropriate subcellular compartment. Changes in intracellular PP2A subunit composition have been found modulate micro-tubule dynamics. It would appear that reduced amounts of neuronal B-alpha-containing PP2A heterotrimers contribute to micro-tubule destabilisation in Alzheimer's disease.
• Changed! pfam PP2A_B_subs_rcg 61aa 5e-27 in ref transcript
  • Serine-threonine phosphatase 2A subunit B alpha and beta central domain. Protein phosphatase 2A (PP2A) is a serine/threonine phosphatase involved in many aspects of cellular function including the regulation of metabolic enzymes and proteins involved in signal transduction. PP2A is a trimeric enzyme consisting of a central catalytic core, and two subunits, A and B. This is a central highly conserved region of subunit B that is thought to perform a substrate recognition function or to be be responsible for targeting the enzyme complex to the appropriate subcellular compartment. Changes in intracellular PP2A subunit composition have been found to modulate micro-tubule dynamics. It would appear that reduced amounts of neuronal B-alpha-containing PP2A heterotrimers contribute to micro-tubule destabilisation in Alzheimer's disease.
• Changed! COG CDC55 417aa 1e-122 in ref transcript
  • Serine/threonine protein phosphatase 2A, regulatory subunit [Signal transduction mechanisms].

PPP2R2D

• refseq_PPP2R2D.F1 refseq_PPP2R2D.R1 177 304
• NCBIGene 36.3 55844
• Alternative 3-prime, size difference: 127
• Exclusion of the protein initiation site
• Reference transcript: NM_018461

• Changed! pfam PP2A_B_subs_rcg 61aa 3e-26 in ref transcript
  • Serine-threonine phosphatase 2A subunit B alpha and beta central domain. Protein phosphatase 2A (PP2A) is a serine/threonine phosphatase involved in many aspects of cellular function including the regulation of metabolic enzymes and proteins involved in signal transduction. PP2A is a trimeric enzyme consisting of a central catalytic core, and two subunits, A and B. This is a central highly conserved region of subunit B that is thought to perform a substrate recognition function or to be be responsible for targeting the enzyme complex to the appropriate subcellular compartment. Changes in intracellular PP2A subunit composition have been found to modulate micro-tubule dynamics. It would appear that reduced amounts of neuronal B-alpha-containing PP2A heterotrimers contribute to micro-tubule destabilisation in Alzheimer's disease.
• Changed! COG CDC55 282aa 9e-80 in ref transcript
  • Serine/threonine protein phosphatase 2A, regulatory subunit [Signal transduction mechanisms].
• Changed! COG CDC55 221aa 2e-52 in modified transcript

PPP2R2D

• refseq_PPP2R2D.F2 refseq_PPP2R2D.R2 242 355
• NCBIGene 36.3 55844
• Single exon skipping, size difference: 113
• Inclusion in 5'UTR
• Reference transcript: NM_018461

• pfam PP2A_B_subs_rcg 61aa 3e-26 in ref transcript
  • Serine-threonine phosphatase 2A subunit B alpha and beta central domain. Protein phosphatase 2A (PP2A) is a serine/threonine phosphatase involved in many aspects of cellular function including the regulation of metabolic enzymes and proteins involved in signal transduction. PP2A is a trimeric enzyme consisting of a central catalytic core, and two subunits, A and B. This is a central highly conserved region of subunit B that is thought to perform a substrate recognition function or to be be responsible for targeting the enzyme complex to the appropriate subcellular compartment. Changes in intracellular PP2A subunit composition have been found to modulate micro-tubule dynamics. It would appear that reduced amounts of neuronal B-alpha-containing PP2A heterotrimers contribute to micro-tubule destabilisation in Alzheimer's disease.
• COG CDC55 282aa 9e-80 in ref transcript
  • Serine/threonine protein phosphatase 2A, regulatory subunit [Signal transduction mechanisms].

PPP2R4

• refseq_PPP2R4.F1 refseq_PPP2R4.R1 121 226
• NCBIGene 36.3 5524
• Single exon skipping, size difference: 105
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_021131

• Changed! cd PTPA 266aa 1e-116 in ref transcript
  • Phosphotyrosyl phosphatase activator (PTPA) is also known as protein phosphatase 2A (PP2A) phosphatase activator. PTPA is an essential, well conserved protein that stimulates the tyrosyl phosphatase activity of PP2A. It also reactivates the serine/threonine phosphatase activity of an inactive form of PP2A. Together, PTPA and PP2A constitute an ATPase. It has been suggested that PTPA alters the relative specificity of PP2A from phosphoserine/phosphothreonine substrates to phosphotyrosine substrates in an ATP-hydrolysis-dependent manner. Basal expression of PTPA is controlled by the transcription factor Yin Yang1 (YY1). PTPA has been suggested to play a role in the insertion of metals to the PP2A catalytic subunit (PP2Ac) active site, to act as a chaperone, and more recently, to have peptidyl prolyl cis/trans isomerase activity that specifically targets human PP2Ac.
• Changed! pfam PTPA 299aa 1e-142 in ref transcript
  • Phosphotyrosyl phosphate activator (PTPA) protein. Phosphotyrosyl phosphatase activator (PTPA) proteins stimulate the phosphotyrosyl phosphatase (PTPase) activity of the dimeric form of protein phosphatase 2A (PP2A). PTPase activity in PP2A (in vitro) is relatively low when compared to the better recognised phosphoserine/ threonine protein phosphorylase activity. The specific biological role of PTPA is unknown, Basal expression of PTPA depends on the activity of a ubiquitous transcription factor, Yin Yang 1 (YY1). The tumour suppressor protein p53 can inhibit PTPA expression through an unknown mechanism that negatively controls YY1.
• Changed! COG LAG1 301aa 3e-85 in ref transcript
  • Phosphotyrosyl phosphatase activator [Cell division and chromosome partitioning / Signal transduction mechanisms].
• Changed! cd PTPA 301aa 1e-112 in modified transcript
• Changed! pfam PTPA 334aa 1e-138 in modified transcript
• Changed! COG LAG1 336aa 2e-82 in modified transcript

PPP2R5C

• refseq_PPP2R5C.F2 refseq_PPP2R5C.R2 287 404
• NCBIGene 36.3 5527
• Single exon skipping, size difference: 117
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_002719

• pfam B56 409aa 1e-170 in ref transcript
  • Protein phosphatase 2A regulatory B subunit (B56 family). Protein phosphatase 2A (PP2A) is a major intracellular protein phosphatase that regulates multiple aspects of cell growth and metabolism. The ability of this widely distributed heterotrimeric enzyme to act on a diverse array of substrates is largely controlled by the nature of its regulatory B subunit. There are multiple families of B subunits (See also pfam01240), this family is called the B56 family.

PQBP1

• refseq_PQBP1.F1 refseq_PQBP1.R1 183 316
• NCBIGene 36.2 10084
• Alternative 5-prime, size difference: 133
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_001032381

• pfam WW 31aa 0.004 in ref transcript
  • WW domain. The WW domain is a protein module with two highly conserved tryptophans that binds proline-rich peptide motifs in vitro.

PQLC2

• refseq_PQLC2.F2 refseq_PQLC2.R2 159 401
• NCBIGene 36.3 54896
• Single exon skipping, size difference: 242
• Exclusion of the protein initiation site
• Reference transcript: NM_001040125

• pfam PQ-loop 57aa 4e-06 in ref transcript
  • PQ loop repeat. Members of this family are all membrane bound proteins possessing a pair of repeats each spanning two transmembrane helices connected by a loop. The PQ motif found on loop 2 is critical for the localisation of cystinosin to lysosomes. However, the PQ motif appears not to be a general lysosome-targeting motif. It is thought likely to possess a more general function. Most probably this involves a glutamine residue.

PRAME

• refseq_PRAME.F1 refseq_PRAME.R1 112 133
• NCBIGene 36.3 23532
• Alternative 3-prime, size difference: 21
• Inclusion in 5'UTR
• Reference transcript: NM_206956

PRC1

• refseq_PRC1.F2 refseq_PRC1.R2 154 196
• NCBIGene 36.3 9055
• Single exon skipping, size difference: 42
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_003981

• Changed! pfam MAP65_ASE1 579aa 1e-159 in ref transcript
  • Microtubule associated protein (MAP65/ASE1 family).
• Changed! pfam MAP65_ASE1 565aa 1e-153 in modified transcript

PRCC

• refseq_PRCC.F1 refseq_PRCC.R1 126 222
• NCBIGene 36.3 5546
• Single exon skipping, size difference: 96
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_005973

• pfam PRCC_Cterm 41aa 2e-13 in ref transcript
  • Mitotic checkpoint protein PRCC_Cterm. This is the highly conserved C-terminal domain of the renal papillary carcinoma protein PRCC. The function of this domain is not known.

PRCP

• refseq_PRCP.F2 refseq_PRCP.R2 137 200
• NCBIGene 36.3 5547
• Single exon skipping, size difference: 63
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_199418

• Changed! pfam Peptidase_S28 421aa 1e-84 in ref transcript
  • Serine carboxypeptidase S28. These serine proteases include several eukaryotic enzymes such as lysosomal Pro-X carboxypeptidase, dipeptidyl-peptidase II, and thymus-specific serine peptidase.
• Changed! pfam Peptidase_S28 423aa 9e-86 in modified transcript

PRDM10

• refseq_PRDM10.F1 refseq_PRDM10.R1 120 159
• NCBIGene 36.3 56980
• Alternative 5-prime, size difference: 39
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_020228

PRDM15

• refseq_PRDM15.F2 refseq_PRDM15.R2 179 377
• NCBIGene 36.3 63977
• Single exon skipping, size difference: 198
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_022115

• smart SET 109aa 0.003 in ref transcript
  • SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain. Putative methyl transferase, based on outlier plant homologues.
• COG COG5048 170aa 0.002 in ref transcript
  • FOG: Zn-finger [General function prediction only].

PRDM16

• refseq_PRDM16.F1 refseq_PRDM16.R1 226 283
• NCBIGene 36.3 63976
• Alternative 3-prime, size difference: 57
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_022114

• smart SET 124aa 9e-09 in ref transcript
  • SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain. Putative methyl transferase, based on outlier plant homologues.
• pfam zf-C2H2 23aa 0.003 in ref transcript
  • Zinc finger, C2H2 type. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter.
• COG COG5048 70aa 0.007 in ref transcript
  • FOG: Zn-finger [General function prediction only].

PRDX1

• refseq_PRDX1.F1 refseq_PRDX1.R1 118 144
• NCBIGene 36.3 5052
• Alternative 5-prime, size difference: 26
• Exclusion in 5'UTR
• Reference transcript: NM_002574

• cd PRX_Typ2cys 173aa 2e-87 in ref transcript
  • Peroxiredoxin (PRX) family, Typical 2-Cys PRX subfamily; PRXs are thiol-specific antioxidant (TSA) proteins, which confer a protective role in cells through its peroxidase activity by reducing hydrogen peroxide, peroxynitrite, and organic hydroperoxides. The functional unit of typical 2-cys PRX is a homodimer. A unique intermolecular redox-active disulfide center is utilized for its activity. Upon reaction with peroxides, its peroxidatic cysteine is oxidized into a sulfenic acid intermediate which is resolved by bonding with the resolving cysteine from the other subunit of the homodimer. This intermolecular disulfide bond is then reduced by thioredoxin, tryparedoxin or AhpF. Typical 2-cys PRXs, like 1-cys PRXs, form decamers which are stabilized by reduction of the active site cysteine. Typical 2-cys PRX interacts through beta strands at one edge of the monomer (B-type interface) to form the functional homodimer, and uses an A-type interface (similar to the dimeric interface in atypical 2-cys PRX and PRX5) at the opposite end of the monomer to form the stable decameric (pentamer of dimers) structure.
• TIGR AhpC 179aa 1e-46 in ref transcript
  • This gene contains two invariant cysteine residues, one near the N-terminus and one near the C-terminus, each followed immediately by a proline residue.
• PTZ PTZ00253 196aa 5e-85 in ref transcript
  • tryparedoxin peroxidase; Provisional.

PRDX2

• refseq_PRDX2.F1 refseq_PRDX2.R1 188 342
• NCBIGene 36.2 7001
• Single exon skipping, size difference: 154
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_005809

• Changed! cd PRX_Typ2cys 172aa 1e-85 in ref transcript
  • Peroxiredoxin (PRX) family, Typical 2-Cys PRX subfamily; PRXs are thiol-specific antioxidant (TSA) proteins, which confer a protective role in cells through its peroxidase activity by reducing hydrogen peroxide, peroxynitrite, and organic hydroperoxides. The functional unit of typical 2-cys PRX is a homodimer. A unique intermolecular redox-active disulfide center is utilized for its activity. Upon reaction with peroxides, its peroxidatic cysteine is oxidized into a sulfenic acid intermediate which is resolved by bonding with the resolving cysteine from the other subunit of the homodimer. This intermolecular disulfide bond is then reduced by thioredoxin, tryparedoxin or AhpF. Typical 2-cys PRXs, like 1-cys PRXs, form decamers which are stabilized by reduction of the active site cysteine. Typical 2-cys PRX interacts through beta strands at one edge of the monomer (B-type interface) to form the functional homodimer, and uses an A-type interface (similar to the dimeric interface in atypical 2-cys PRX and PRX5) at the opposite end of the monomer to form the stable decameric (pentamer of dimers) structure.
• Changed! TIGR AhpC 181aa 5e-51 in ref transcript
  • This gene contains two invariant cysteine residues, one near the N-terminus and one near the C-terminus, each followed immediately by a proline residue.
• Changed! PTZ PTZ00253 195aa 2e-80 in ref transcript
  • tryparedoxin peroxidase; Provisional.
• Changed! cd PRX_Typ2cys 28aa 7e-07 in modified transcript
• Changed! pfam AhpC-TSA 29aa 7e-04 in modified transcript
  • AhpC/TSA family. This family contains proteins related to alkyl hydroperoxide reductase (AhpC) and thiol specific antioxidant (TSA).
• Changed! PTZ PTZ00253 35aa 1e-04 in modified transcript

PRDX3

• refseq_PRDX3.F2 refseq_PRDX3.R2 107 161
• NCBIGene 36.3 10935
• Alternative 5-prime and 3-prime, size difference: 54
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_006793

• Changed! cd PRX_Typ2cys 172aa 8e-84 in ref transcript
  • Peroxiredoxin (PRX) family, Typical 2-Cys PRX subfamily; PRXs are thiol-specific antioxidant (TSA) proteins, which confer a protective role in cells through its peroxidase activity by reducing hydrogen peroxide, peroxynitrite, and organic hydroperoxides. The functional unit of typical 2-cys PRX is a homodimer. A unique intermolecular redox-active disulfide center is utilized for its activity. Upon reaction with peroxides, its peroxidatic cysteine is oxidized into a sulfenic acid intermediate which is resolved by bonding with the resolving cysteine from the other subunit of the homodimer. This intermolecular disulfide bond is then reduced by thioredoxin, tryparedoxin or AhpF. Typical 2-cys PRXs, like 1-cys PRXs, form decamers which are stabilized by reduction of the active site cysteine. Typical 2-cys PRX interacts through beta strands at one edge of the monomer (B-type interface) to form the functional homodimer, and uses an A-type interface (similar to the dimeric interface in atypical 2-cys PRX and PRX5) at the opposite end of the monomer to form the stable decameric (pentamer of dimers) structure.
• Changed! TIGR AhpC 181aa 7e-55 in ref transcript
  • This gene contains two invariant cysteine residues, one near the N-terminus and one near the C-terminus, each followed immediately by a proline residue.
• Changed! PTZ PTZ00253 197aa 4e-77 in ref transcript
  • tryparedoxin peroxidase; Provisional.
• Changed! cd PRX_Typ2cys 169aa 6e-83 in modified transcript
• Changed! TIGR AhpC 177aa 2e-55 in modified transcript
• Changed! PTZ PTZ00253 190aa 2e-76 in modified transcript

PRDX5

• refseq_PRDX5.F2 refseq_PRDX5.R2 196 328
• NCBIGene 36.3 25824
• Single exon skipping, size difference: 132
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_012094

• Changed! cd PRX5_like 155aa 8e-51 in ref transcript
  • Peroxiredoxin (PRX) family, PRX5-like subfamily; members are similar to the human protein, PRX5, a homodimeric TRX peroxidase, widely expressed in tissues and found cellularly in mitochondria, peroxisomes and the cytosol. The cellular location of PRX5 suggests that it may have an important antioxidant role in organelles that are major sources of reactive oxygen species (ROS), as well as a role in the control of signal transduction. PRX5 has been shown to reduce hydrogen peroxide, alkyl hydroperoxides and peroxynitrite. As with all other PRXs, the N-terminal peroxidatic cysteine of PRX5 is oxidized into a sulfenic acid intermediate upon reaction with peroxides. Human PRX5 is able to resolve this intermediate by forming an intramolecular disulfide bond with its C-terminal cysteine (the resolving cysteine), which can then be reduced by TRX, just like an atypical 2-cys PRX. This resolving cysteine, however, is not conserved in other members of the subfamily. In such cases, it is assumed that the oxidized cysteine is directly resolved by an external small-molecule or protein reductant, typical of a 1-cys PRX. In the case of the H. influenza PRX5 hybrid, the resolving glutaredoxin domain is on the same protein chain as PRX. PRX5 homodimers show an A-type interface, similar to atypical 2-cys PRXs.
• Changed! pfam Redoxin 145aa 1e-30 in ref transcript
  • Redoxin. This family of redoxins includes peroxiredoxin, thioredoxin and glutaredoxin proteins.
• Changed! COG AHP1 159aa 3e-39 in ref transcript
  • Peroxiredoxin [Posttranslational modification, protein turnover, chaperones].
• Changed! cd PRX5_like 111aa 4e-26 in modified transcript
• Changed! pfam Redoxin 101aa 2e-12 in modified transcript
• Changed! COG AHP1 115aa 7e-17 in modified transcript

PRKAA1

• refseq_PRKAA1.F1 refseq_PRKAA1.R1 182 227
• NCBIGene 36.3 5562
• Single exon skipping, size difference: 45
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_206907

• Changed! cd S_TKc 269aa 6e-70 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• Changed! smart S_TKc 249aa 1e-76 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• Changed! PTZ PTZ00263 272aa 6e-37 in ref transcript
  • protein kinase A catalytic subunit; Provisional.
• Changed! cd S_TKc 254aa 1e-72 in modified transcript
• Changed! smart S_TKc 234aa 2e-79 in modified transcript
• Changed! PTZ PTZ00263 257aa 2e-39 in modified transcript

PRKAG1

• refseq_PRKAG1.F1 refseq_PRKAG1.R1 151 200
• NCBIGene 36.3 5571
• Alternative 3-prime, size difference: 49
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_002733

• Changed! cd CBS_pair_28 120aa 4e-41 in ref transcript
  • The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase).
• Changed! cd CBS_pair_5 130aa 2e-29 in ref transcript
  • The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase).
• Changed! cd CBS_pair_14 123aa 1e-11 in ref transcript
  • The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase).
• Changed! pfam CBS 121aa 1e-16 in ref transcript
  • CBS domain pair. CBS domains are small intracellular modules that pair together to form a stable globular domain. This family represents a pair of CBS domains, that has been termed a Bateman domain. CBS domains have been shown to bind ligands with an adenosyl group such as AMP, ATP and S-AdoMet. CBS domains are found attached to a wide range of other protein domains suggesting that CBS domains may play a regulatory role making proteins sensitive to adenosyl carrying ligands. The region containing the CBS domains in Cystathionine-beta synthase is involved in regulation by S-AdoMet. CBS domain pairs from AMPK bind AMP or ATP. The CBS domains from IMPDH and the chloride channel CLC2 bind ATP.
• Changed! pfam CBS 132aa 7e-12 in ref transcript
• Changed! PRK PRK05567 109aa 2e-08 in ref transcript
  • inositol-5'-monophosphate dehydrogenase; Reviewed.
• Changed! COG COG3448 120aa 3e-06 in ref transcript
  • CBS-domain-containing membrane protein [Signal transduction mechanisms].
• Changed! COG COG2905 128aa 5e-05 in ref transcript
  • Predicted signal-transduction protein containing cAMP-binding and CBS domains [Signal transduction mechanisms].

PRKAR1A

• refseq_PRKAR1A.F1 refseq_PRKAR1A.R1 169 200
• NCBIGene 36.3 5573
• Alternative 5-prime, size difference: 31
• Exclusion in 5'UTR
• Reference transcript: NM_212472

• cd CAP_ED 116aa 1e-21 in ref transcript
  • effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels. Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels.
• cd CAP_ED 110aa 4e-20 in ref transcript
• smart cNMP 119aa 2e-22 in ref transcript
  • Cyclic nucleotide-monophosphate binding domain. Catabolite gene activator protein (CAP) is a prokaryotic homologue of eukaryotic cNMP-binding domains, present in ion channels, and cNMP-dependent kinases.
• smart cNMP 115aa 4e-21 in ref transcript
• smart RIIa 38aa 1e-08 in ref transcript
  • RIIalpha, Regulatory subunit portion of type II PKA R-subunit. RIIalpha, Regulatory subunit portion of type II PKA R-subunit. Contains dimerisation interface and binding site for A-kinase-anchoring proteins (AKAPs).
• COG Crp 111aa 4e-12 in ref transcript
  • cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms].
• COG Crp 127aa 5e-11 in ref transcript

ZMYND8

• refseq_PRKCBP1.F1 refseq_PRKCBP1.R1 197 272
• NCBIGene 36.3 23613
• Alternative 3-prime, size difference: 75
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_183047

• cd Bromo_RACK7 99aa 1e-49 in ref transcript
  • Bromodomain, RACK7_like subfamily. RACK7 (also called human protein kinase C-binding protein) was identified as a potential tumor suppressor genes, it shares domain architecture with BS69/ZMYND11; both have been implicated in the regulation of cellular proliferation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
• cd BS69_related 81aa 4e-35 in ref transcript
  • The PWWP domain is part of BS69 protein, a nuclear protein that specifically binds adenoviral E1A and Epstein-Barr viral EBNA2 proteins, suppressing their transactivation functions. BS69 is a multi-domain protein, containing bromo, PHD, PWWP, and MYND domains. The specific role of the PWWP domain within BS69 is not clearly identified, but BS69 functions in chromatin remodeling, consistent with other PWWP-containing proteins. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
• smart BROMO 101aa 3e-15 in ref transcript
  • bromo domain.
• pfam PWWP 62aa 5e-08 in ref transcript
  • PWWP domain. The PWWP domain is named after a conserved Pro-Trp-Trp-Pro motif. The function of the domain is currently unknown.
• pfam PHD 41aa 2e-07 in ref transcript
  • PHD-finger. PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
• pfam zf-MYND 35aa 4e-05 in ref transcript
  • MYND finger.
• COG COG5076 127aa 8e-07 in ref transcript
  • Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription].

ZMYND8

• refseq_PRKCBP1.F3 refseq_PRKCBP1.R3 180 264
• NCBIGene 36.3 23613
• Single exon skipping, size difference: 84
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_183047

• cd Bromo_RACK7 99aa 1e-49 in ref transcript
  • Bromodomain, RACK7_like subfamily. RACK7 (also called human protein kinase C-binding protein) was identified as a potential tumor suppressor genes, it shares domain architecture with BS69/ZMYND11; both have been implicated in the regulation of cellular proliferation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
• cd BS69_related 81aa 4e-35 in ref transcript
  • The PWWP domain is part of BS69 protein, a nuclear protein that specifically binds adenoviral E1A and Epstein-Barr viral EBNA2 proteins, suppressing their transactivation functions. BS69 is a multi-domain protein, containing bromo, PHD, PWWP, and MYND domains. The specific role of the PWWP domain within BS69 is not clearly identified, but BS69 functions in chromatin remodeling, consistent with other PWWP-containing proteins. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
• smart BROMO 101aa 3e-15 in ref transcript
  • bromo domain.
• pfam PWWP 62aa 5e-08 in ref transcript
  • PWWP domain. The PWWP domain is named after a conserved Pro-Trp-Trp-Pro motif. The function of the domain is currently unknown.
• pfam PHD 41aa 2e-07 in ref transcript
  • PHD-finger. PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
• pfam zf-MYND 35aa 4e-05 in ref transcript
  • MYND finger.
• COG COG5076 127aa 8e-07 in ref transcript
  • Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription].

PRMT1

• refseq_PRMT1.F1 refseq_PRMT1.R1 131 250
• NCBIGene 36.3 3276
• Exon skipping and alternative 3-prime or 5-prime, size difference: 119
• Inclusion in the protein causing a frameshift, Inclusion in the protein causing a new stop codon
• Reference transcript: NM_001536

• Changed! cd AdoMet_MTases 101aa 6e-06 in ref transcript
  • S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.).
• Changed! pfam PrmA 59aa 2e-05 in ref transcript
  • Ribosomal protein L11 methyltransferase (PrmA). This family consists of several Ribosomal protein L11 methyltransferase (EC:2.1.1.-) sequences.
• Changed! PRK prmA 77aa 5e-06 in ref transcript
  • ribosomal protein L11 methyltransferase; Reviewed.

PRMT2

• refseq_PRMT2.F2 refseq_PRMT2.R2 123 232
• NCBIGene 36.3 3275
• Single exon skipping, size difference: 109
• Exclusion in 5'UTR
• Reference transcript: NM_206962

• cd SH3 50aa 2e-08 in ref transcript
  • Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
• cd AdoMet_MTases 101aa 3e-07 in ref transcript
  • S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.).
• smart SH3 54aa 2e-10 in ref transcript
  • Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.
• pfam MTS 83aa 3e-06 in ref transcript
  • Methyltransferase small domain. This domain is found in ribosomal RNA small subunit methyltransferase C as well as other methyltransferases.
• COG COG4076 131aa 4e-07 in ref transcript
  • Predicted RNA methylase [General function prediction only].

PRMT5

• refseq_PRMT5.F2 refseq_PRMT5.R2 260 345
• NCBIGene 36.3 10419
• Alternative 5-prime, size difference: 85
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_006109

• Changed! cd AdoMet_MTases 71aa 4e-04 in ref transcript
  • S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.).
• Changed! pfam PRMT5 439aa 0.0 in ref transcript
  • PRMT5 arginine-N-methyltransferase. The human homologue of yeast Skb1 (Shk1 kinase-binding protein 1) is PRMT5, an arginine-N-methyltransferase. These proteins appear to be key mitotic regulators. They play a role in Jak signalling in higher eukaryotes.
• Changed! COG COG4076 168aa 4e-06 in ref transcript
  • Predicted RNA methylase [General function prediction only].

PRO1853

• refseq_PRO1853.F2 refseq_PRO1853.R2 229 383
• NCBIGene 36.2 55471
• Alternative 5-prime, size difference: 154
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_144736

• Changed! pfam DUF185 247aa 5e-33 in ref transcript
  • Uncharacterized ACR, COG1565. This family contains several uncharacterised proteins. One member has been described as an ATP synthase beta subunit transcription termination factor rho protein.
• Changed! COG COG1565 357aa 4e-61 in ref transcript
  • Uncharacterized conserved protein [Function unknown].
• Changed! pfam DUF185 57aa 1e-07 in modified transcript
• Changed! COG COG1565 106aa 3e-27 in modified transcript

PRPF40B

• refseq_PRPF40B.F2 refseq_PRPF40B.R2 102 123
• NCBIGene 36.3 25766
• Alternative 3-prime, size difference: 21
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001031698

• cd WW 30aa 3e-05 in ref transcript
  • Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
• cd WW 26aa 2e-04 in ref transcript
• pfam WW 30aa 4e-06 in ref transcript
  • WW domain. The WW domain is a protein module with two highly conserved tryptophans that binds proline-rich peptide motifs in vitro.
• smart WW 26aa 5e-05 in ref transcript
  • Domain with 2 conserved Trp (W) residues. Also known as the WWP or rsp5 domain. Binds proline-rich polypeptides.
• smart FF 49aa 5e-05 in ref transcript
  • Contains two conserved F residues. A novel motif that often accompanies WW domains. Often contains two conserved Phe (F) residues.
• smart FF 49aa 6e-04 in ref transcript
• Changed! COG PRP40 280aa 2e-18 in ref transcript
  • Splicing factor [RNA processing and modification].
• COG PRP40 91aa 7e-17 in ref transcript
• Changed! COG PRP40 299aa 1e-19 in modified transcript

PRR13

• refseq_PRR13.F1 refseq_PRR13.R1 249 399
• NCBIGene 36.3 54458
• Alternative 3-prime, size difference: 150
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_018457

PRR5

• refseq_PRR5.F2 refseq_PRR5.R2 231 348
• NCBIGene 36.3 55615
• Single exon skipping, size difference: 117
• Exclusion of the protein initiation site
• Reference transcript: NM_015366

• Changed! pfam HbrB 132aa 6e-40 in ref transcript
  • HbrB-like. HbrB is involved hyphal growth and polarity.
• Changed! pfam HbrB 71aa 4e-22 in modified transcript

PRRX1

• refseq_PRRX1.F1 refseq_PRRX1.R1 161 233
• NCBIGene 36.3 5396
• Single exon skipping, size difference: 72
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_022716

• cd homeodomain 55aa 2e-14 in ref transcript
  • Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
• pfam Homeobox 53aa 3e-20 in ref transcript
  • Homeobox domain.
• COG COG5576 81aa 2e-08 in ref transcript
  • Homeodomain-containing transcription factor [Transcription].

PRSS21

• refseq_PRSS21.F1 refseq_PRSS21.R1 112 154
• NCBIGene 36.3 10942
• Alternative 5-prime, size difference: 42
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_006799

• Changed! cd Tryp_SPc 242aa 3e-66 in ref transcript
  • Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
• Changed! smart Tryp_SPc 241aa 7e-71 in ref transcript
  • Trypsin-like serine protease. Many of these are synthesised as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. A few, however, are active as single chain molecules, and others are inactive due to substitutions of the catalytic triad residues.
• Changed! COG COG5640 255aa 7e-23 in ref transcript
  • Secreted trypsin-like serine protease [Posttranslational modification, protein turnover, chaperones].
• Changed! cd Tryp_SPc 228aa 4e-57 in modified transcript
• Changed! smart Tryp_SPc 227aa 5e-61 in modified transcript
• Changed! COG COG5640 241aa 3e-20 in modified transcript

PSMA3

• refseq_PSMA3.F1 refseq_PSMA3.R1 111 132
• NCBIGene 36.3 5684
• Alternative 3-prime, size difference: 21
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_002788

• Changed! cd proteasome_alpha_type_3 213aa 1e-109 in ref transcript
  • proteasome_alpha_type_3. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.
• Changed! pfam Proteasome 187aa 2e-47 in ref transcript
  • Proteasome A-type and B-type.
• pfam Proteasome_A_N 23aa 8e-09 in ref transcript
  • Proteasome subunit A N-terminal signature. This domain is conserved in the A subunits of the proteasome complex proteins.
• Changed! PRK PRK03996 234aa 1e-44 in ref transcript
  • proteasome subunit alpha; Provisional.
• Changed! cd proteasome_alpha_type_3 206aa 1e-106 in modified transcript
• Changed! pfam Proteasome 180aa 3e-44 in modified transcript
• Changed! PRK PRK03996 227aa 4e-44 in modified transcript

PSMA8

• refseq_PSMA8.F1 refseq_PSMA8.R1 100 118
• NCBIGene 36.3 143471
• Alternative 3-prime, size difference: 18
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_144662

• Changed! cd proteasome_alpha_type_7 215aa 1e-102 in ref transcript
  • proteasome_alpha_type_7. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.
• Changed! TIGR arc_protsome_A 233aa 6e-67 in ref transcript
  • This protein family describes the archaeal proteasome alpha subunit, homologous to both the beta subunit and to the alpha and beta subunits of eukaryotic proteasome subunits. This family is universal in the first 29 complete archaeal genomes but occasionally is duplicated.
• Changed! PRK PRK03996 233aa 5e-71 in ref transcript
  • proteasome subunit alpha; Provisional.
• Changed! cd proteasome_alpha_type_7 209aa 1e-104 in modified transcript
• Changed! TIGR arc_protsome_A 227aa 6e-69 in modified transcript
• Changed! PRK PRK03996 227aa 5e-73 in modified transcript

PSMC3IP

• refseq_PSMC3IP.F1 refseq_PSMC3IP.R1 145 181
• NCBIGene 36.3 29893
• Alternative 3-prime, size difference: 36
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_016556

• cd Fur_like 58aa 0.003 in ref transcript
  • Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions. For example, PerR, a metal-dependent sensor of hydrogen peroxide. PerR regulates DNA-binding activity through metal-based protein oxidation, and co-ordinates Mn2+ or Fe2+ at its regulatory site. Fur family proteins contain an N-terminal winged-helix DNA-binding domain followed by a dimerization domain; this CD spans both those domains.
• Changed! pfam TBPIP 167aa 9e-56 in ref transcript
  • Tat binding protein 1(TBP-1)-interacting protein (TBPIP). This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation.
• Changed! pfam TBPIP 155aa 3e-50 in modified transcript

PSMC4

• refseq_PSMC4.F1 refseq_PSMC4.R1 111 204
• NCBIGene 36.3 5704
• Alternative 3-prime, size difference: 93
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_006503

• cd AAA 168aa 2e-16 in ref transcript
  • The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.
• Changed! TIGR 26Sp45 347aa 1e-103 in ref transcript
  • Many proteins may score above the trusted cutoff because an internal.
• Changed! COG RPT1 383aa 1e-137 in ref transcript
  • ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones].
• Changed! TIGR 26Sp45 348aa 1e-104 in modified transcript
• Changed! COG RPT1 350aa 1e-135 in modified transcript

PSMD10

• refseq_PSMD10.F1 refseq_PSMD10.R1 194 273
• NCBIGene 36.3 5716
• Alternative 5-prime, size difference: 79
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_002814

• Changed! cd ANK 124aa 2e-30 in ref transcript
  • ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats.
• pfam Ank 33aa 6e-06 in ref transcript
  • Ankyrin repeat. There's no clear separation between noise and signal on the HMM search Ankyrin repeats generally consist of a beta, alpha, alpha, beta order of secondary structures. The repeats associate to form a higher order structure.
• pfam Ank 31aa 2e-05 in ref transcript
• pfam Ank 31aa 3e-05 in ref transcript
• Changed! TIGR trp 153aa 2e-04 in ref transcript
  • after chronic exposure to capsaicin. (McCleskey and Gold, 1999).
• Changed! COG Arp 156aa 1e-17 in ref transcript
  • FOG: Ankyrin repeat [General function prediction only].
• Changed! PTZ PTZ00322 66aa 6e-08 in ref transcript
  • 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase; Provisional.
• Changed! cd ANK 115aa 1e-27 in modified transcript
• Changed! TIGR trp 103aa 1e-04 in modified transcript
• Changed! COG Arp 137aa 8e-16 in modified transcript

PSME3

• refseq_PSME3.F2 refseq_PSME3.R2 156 195
• NCBIGene 36.3 10197
• Alternative 3-prime, size difference: 39
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_176863

• Changed! pfam PA28_beta 163aa 1e-68 in ref transcript
  • Proteasome activator pa28 beta subunit. PA28 activator complex (also known as 11s regulator of 20S proteasome) is a ring shaped hexameric structure of alternating alpha and beta subunits. This family represents the beta subunit. The activator complex binds to the 20S proteasome ana simulates peptidase activity in and ATP-independent manner.
• pfam PA28_alpha 58aa 6e-20 in ref transcript
  • Proteasome activator pa28 alpha subunit. PA28 activator complex (also known as 11s regulator of 20S proteasome) is a ring shaped hexameric structure of alternating alpha and beta subunits. This family represents the alpha subunit. The activator complex binds to the 20S proteasome ana simulates peptidase activity in and ATP-independent manner.
• Changed! pfam PA28_beta 150aa 1e-70 in modified transcript

PSMF1

• refseq_PSMF1.F2 refseq_PSMF1.R2 119 202
• NCBIGene 36.2 9491
• Single exon skipping, size difference: 83
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_178578

• Changed! pfam PI31_Prot_Reg 86aa 4e-04 in ref transcript
  • PI31 proteasome regulator. PI31 is a cellular regulator of proteasome formation and of proteasome-mediated antigen processing.

OLA1

• refseq_PTD004.F1 refseq_PTD004.R1 199 300
• NCBIGene 36.3 29789
• Single exon skipping, size difference: 101
• Exclusion of the protein initiation site
• Reference transcript: NM_013341

• Changed! cd YchF 279aa 1e-124 in ref transcript
  • YchF subfamily. YchF is a member of the Obg family, which includes four other subfamilies of GTPases: Obg, DRG, Ygr210, and NOG1. Obg is an essential gene that is involved in DNA replication in C. crescentus and Streptomyces griseus and is associated with the ribosome. Several members of the family, including YchF, possess the TGS domain related to the RNA-binding proteins. Experimental data and genomic analysis suggest that YchF may be part of a nucleoprotein complex and may function as a GTP-dependent translational factor.
• cd TGS_YchF_C 83aa 2e-46 in ref transcript
  • TGS_YchF_C: This subfamily represents TGS domain-containing YchF GTP-binding protein, a universally conserved GTPase whose function is unknown. The N-terminal domain of the YchF protein belongs to the Obg-like family of GTPases, and some members of the family contain a C-terminal TGS domain. TGS is a small domain of about 50 amino acid residues with a predominantly beta-sheet structure. There is no direct information on the function of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role.
• Changed! TIGR TIGR00092 366aa 8e-92 in ref transcript
  • This predicted GTP-binding protein is found in a single copy in every complete bacterial genome, and is found in Eukaryotes. A more distantly related protein, separated from this model, is found in the archaea. It is known to bind GTP and double-stranded nucleic acid. It is suggested to belong to a nucleoprotein complex and act as a translation factor.
• Changed! PTZ PTZ00258 373aa 1e-169 in ref transcript
  • GTP-binding protein; Provisional.
• Changed! cd YchF 141aa 1e-40 in modified transcript
• Changed! TIGR TIGR00092 226aa 8e-51 in modified transcript
• Changed! PTZ PTZ00258 228aa 9e-90 in modified transcript

PTER

• refseq_PTER.F2 refseq_PTER.R2 235 290
• NCBIGene 36.3 9317
• Mutually exclusive exon skipping, size difference: 55
• Inclusion in 5'UTR, Exclusion in 5'UTR
• Reference transcript: NM_030664

• cd PTE 326aa 2e-97 in ref transcript
  • Phosphotriesterase (PTE) catalyzes the hydrolysis of organophosphate nerve agents, including the chemical warfare agents VX, soman, and sarin as well as the insecticide paraoxon. PTE exists as a homodimer with one active site per monomer. The active site is located next to a binuclear metal center, at the C-terminal end of a TIM alpha- beta barrel motif. The native enzyme contains two zinc ions at the active site however these can be replaced with other metals such as cobalt, cadmium, nickel or manganese and the enzyme remains active.
• pfam PTE 333aa 1e-119 in ref transcript
  • Phosphotriesterase family.
• COG Php 345aa 3e-53 in ref transcript
  • Predicted metal-dependent hydrolase with the TIM-barrel fold [General function prediction only].

PTGER3

• refseq_PTGER3.F1 refseq_PTGER3.R1 129 156
• NCBIGene 36.3 5733
• Single exon skipping, size difference: 27
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_198712

• pfam 7tm_1 252aa 3e-10 in ref transcript
  • 7 transmembrane receptor (rhodopsin family). This family contains, amongst other G-protein-coupled receptors (GCPRs), members of the opsin family, which have been considered to be typical members of the rhodopsin superfamily. They share several motifs, mainly the seven transmembrane helices, GCPRs of the rhodopsin superfamily. All opsins bind a chromophore, such as 11-cis-retinal. The function of most opsins other than the photoisomerases is split into two steps: light absorption and G-protein activation. Photoisomerases, on the other hand, are not coupled to G-proteins - they are thought to generate and supply the chromophore that is used by visual opsins.

PTGES2

• refseq_PTGES2.F2 refseq_PTGES2.R2 309 402
• NCBIGene 36.3 80142
• Single exon skipping, size difference: 93
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_025072

• Changed! cd GST_C_mPGES2 149aa 8e-60 in ref transcript
  • GST_C family; microsomal Prostaglandin E synthase Type 2 (mPGES2) subfamily; mPGES2 is a membrane-anchored dimeric protein containing a CXXC motif which catalyzes the isomerization of PGH2 to PGE2. Unlike cytosolic PGE synthase (cPGES) and microsomal PGES Type 1 (mPGES1), mPGES2 does not require glutathione (GSH) for its activity, although its catalytic rate is increased two- to four-fold in the presence of DTT, GSH, or other thiol compounds. PGE2 is widely distributed in various tissues and is implicated in the sleep/wake cycle, relaxation/contraction of smooth muscle, excretion of sodium ions, maintenance of body temperature, and mediation of inflammation. mPGES2 contains an N-terminal hydrophobic domain which is membrane associated and a C-terminal soluble domain with a GST-like structure. The C-terminus contains two structural domains a N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain. The GST active site is located in a cleft between the two domains.
• Changed! cd GST_N_mPGES2 75aa 8e-33 in ref transcript
  • GST_N family; microsomal Prostaglandin E synthase Type 2 (mPGES2) subfamily; mPGES2 is a membrane-anchored dimeric protein containing a CXXC motif which catalyzes the isomerization of PGH2 to PGE2. Unlike cytosolic PGE synthase (cPGES) and microsomal PGES Type 1 (mPGES1), mPGES2 does not require glutathione (GSH) for its activity, although its catalytic rate is increased two- to four-fold in the presence of DTT, GSH or other thiol compounds. PGE2 is widely distributed in various tissues and is implicated in the sleep/wake cycle, relaxation/contraction of smooth muscle, excretion of sodium ions, maintenance of body temperature and mediation of inflammation. mPGES2 contains an N-terminal hydrophobic domain which is membrane associated, and a C-terminal soluble domain with a GST-like structure.
• pfam Glutaredoxin 50aa 5e-08 in ref transcript
  • Glutaredoxin.
• Changed! COG Gst 140aa 5e-04 in ref transcript
  • Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones].
• Changed! cd GST_N_mPGES2 57aa 4e-24 in modified transcript
• Changed! COG GrxC 58aa 6e-04 in modified transcript
  • Glutaredoxin and related proteins [Posttranslational modification, protein turnover, chaperones].

PTGFR

• refseq_PTGFR.F2 refseq_PTGFR.R2 335 406
• NCBIGene 36.3 5737
• Single exon skipping, size difference: 71
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_000959

• Changed! pfam 7tm_1 201aa 1e-12 in ref transcript
  • 7 transmembrane receptor (rhodopsin family). This family contains, amongst other G-protein-coupled receptors (GCPRs), members of the opsin family, which have been considered to be typical members of the rhodopsin superfamily. They share several motifs, mainly the seven transmembrane helices, GCPRs of the rhodopsin superfamily. All opsins bind a chromophore, such as 11-cis-retinal. The function of most opsins other than the photoisomerases is split into two steps: light absorption and G-protein activation. Photoisomerases, on the other hand, are not coupled to G-proteins - they are thought to generate and supply the chromophore that is used by visual opsins.
• Changed! pfam 7tm_1 193aa 5e-10 in modified transcript

PTK2B

• refseq_PTK2B.F1 refseq_PTK2B.R1 159 285
• NCBIGene 36.3 2185
• Single exon skipping, size difference: 126
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_173174

• cd PTKc_FAK 270aa 1e-146 in ref transcript
  • Catalytic Domain of the Protein Tyrosine Kinase, Focal Adhesion Kinase. Protein Tyrosine Kinase (PTK) family; Focal Adhesion kinase (FAK); catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. FAK is a cytoplasmic (or nonreceptor) tyr kinase that contains an autophosphorylation site and a FERM domain at the N-terminus, a central tyr kinase domain, proline-rich regions, and a C-terminal FAT (focal adhesion targeting) domain. FAK activity is dependent on integrin-mediated cell adhesion, which facilitates N-terminal autophosphorylation. Full activation is achieved by the phosphorylation of its two adjacent A-loop tyrosines. FAK is important in mediating signaling initiated at sites of cell adhesions and at growth factor receptors. Through diverse molecular interactions, FAK functions as a biosensor or integrator to control cell motility. It is a key regulator of cell survival, proliferation, migration and invasion, and thus plays an important role in the development and progression of cancer. Src binds to autophosphorylated FAK forming the FAK-Src dual kinase complex, which is activated in a wide variety of tumor cells and generates signals promoting growth and metastasis. FAK is being developed as a target for cancer therapy.
• pfam Pkinase_Tyr 233aa 5e-98 in ref transcript
  • Protein tyrosine kinase.
• pfam Focal_AT 139aa 6e-59 in ref transcript
  • Focal adhesion targeting region. Focal adhesion kinase (FAK) is a tyrosine kinase found in focal adhesions, intracellular signaling complexes that are formed following engagement of the extracellular matrix by integrins. The C-terminal 'focal adhesion targeting' (FAT) region is necessary and sufficient for localising FAK to focal adhesions. The crystal structure of FAT shows it forms a four-helix bundle that resembles those found in two other proteins involved in cell adhesion, alpha-catenin and vinculin. The binding of FAT to the focal adhesion protein, paxillin, requires the integrity of the helical bundle, whereas binding to another focal adhesion protein, talin, does not.
• smart B41 227aa 2e-31 in ref transcript
  • Band 4.1 homologues. Also known as ezrin/radixin/moesin (ERM) protein domains. Present in myosins, ezrin, radixin, moesin, protein tyrosine phosphatases. Plasma membrane-binding domain. These proteins play structural and regulatory roles in the assembly and stabilization of specialized plasmamembrane domains. Some PDZ domain containing proteins bind one or more of this family. Now includes JAKs.
• COG SPS1 229aa 2e-16 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].

PTK2B

• refseq_PTK2B.F3 refseq_PTK2B.R3 102 262
• NCBIGene 36.3 2185
• Single exon skipping, size difference: 160
• Exclusion in 5'UTR
• Reference transcript: NM_173174

• cd PTKc_FAK 270aa 1e-146 in ref transcript
  • Catalytic Domain of the Protein Tyrosine Kinase, Focal Adhesion Kinase. Protein Tyrosine Kinase (PTK) family; Focal Adhesion kinase (FAK); catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. FAK is a cytoplasmic (or nonreceptor) tyr kinase that contains an autophosphorylation site and a FERM domain at the N-terminus, a central tyr kinase domain, proline-rich regions, and a C-terminal FAT (focal adhesion targeting) domain. FAK activity is dependent on integrin-mediated cell adhesion, which facilitates N-terminal autophosphorylation. Full activation is achieved by the phosphorylation of its two adjacent A-loop tyrosines. FAK is important in mediating signaling initiated at sites of cell adhesions and at growth factor receptors. Through diverse molecular interactions, FAK functions as a biosensor or integrator to control cell motility. It is a key regulator of cell survival, proliferation, migration and invasion, and thus plays an important role in the development and progression of cancer. Src binds to autophosphorylated FAK forming the FAK-Src dual kinase complex, which is activated in a wide variety of tumor cells and generates signals promoting growth and metastasis. FAK is being developed as a target for cancer therapy.
• pfam Pkinase_Tyr 233aa 5e-98 in ref transcript
  • Protein tyrosine kinase.
• pfam Focal_AT 139aa 6e-59 in ref transcript
  • Focal adhesion targeting region. Focal adhesion kinase (FAK) is a tyrosine kinase found in focal adhesions, intracellular signaling complexes that are formed following engagement of the extracellular matrix by integrins. The C-terminal 'focal adhesion targeting' (FAT) region is necessary and sufficient for localising FAK to focal adhesions. The crystal structure of FAT shows it forms a four-helix bundle that resembles those found in two other proteins involved in cell adhesion, alpha-catenin and vinculin. The binding of FAT to the focal adhesion protein, paxillin, requires the integrity of the helical bundle, whereas binding to another focal adhesion protein, talin, does not.
• smart B41 227aa 2e-31 in ref transcript
  • Band 4.1 homologues. Also known as ezrin/radixin/moesin (ERM) protein domains. Present in myosins, ezrin, radixin, moesin, protein tyrosine phosphatases. Plasma membrane-binding domain. These proteins play structural and regulatory roles in the assembly and stabilization of specialized plasmamembrane domains. Some PDZ domain containing proteins bind one or more of this family. Now includes JAKs.
• COG SPS1 229aa 2e-16 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].

PTK7

• refseq_PTK7.F1 refseq_PTK7.R1 181 301
• NCBIGene 36.3 5754
• Single exon skipping, size difference: 120
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_002821

• cd PTK_CCK4 274aa 1e-148 in ref transcript
  • Catalytic Domain of the Protein Tyrosine Kinase, Colon Carcinoma Kinase 4. Protein Tyrosine Kinase (PTK) family; Colon carcinoma kinase 4 (CCK4); pseudokinase domain. The PTKc (catalytic domain) family, to which this subfamily belongs, includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. CCK4, also called protein tyrosine kinase 7 (PTK7), is an orphan receptor tyr kinase (RTK) containing an extracellular region with seven immunoglobulin domains, a transmembrane segment, and an intracellular inactive pseudokinase domain. Studies in mice reveal that CCK4 is essential for neural development. Mouse embryos containing a truncated CCK4 die perinatally and display craniorachischisis, a severe form of neural tube defect. The mechanism of action of the CCK4 pseudokinase is still unknown. Other pseudokinases such as HER3 rely on the activity of partner RTKs.
• cd IGcam 85aa 5e-16 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• cd IGcam 86aa 1e-13 in ref transcript
• Changed! cd IGcam 85aa 2e-12 in ref transcript
• cd IGcam 87aa 3e-10 in ref transcript
• cd IGcam 79aa 6e-10 in ref transcript
• cd IGcam 78aa 8e-06 in ref transcript
• cd IGcam 81aa 3e-04 in ref transcript
• smart TyrKc 261aa 1e-98 in ref transcript
  • Tyrosine kinase, catalytic domain. Phosphotransferases. Tyrosine-specific kinase subfamily.
• Changed! pfam I-set 86aa 9e-12 in ref transcript
  • Immunoglobulin I-set domain.
• pfam I-set 77aa 1e-11 in ref transcript
• pfam I-set 87aa 2e-11 in ref transcript
• pfam I-set 92aa 5e-10 in ref transcript
• smart IGc2 59aa 1e-07 in ref transcript
  • Immunoglobulin C-2 Type.
• smart IG_like 71aa 1e-06 in ref transcript
  • Immunoglobulin like. IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
• smart IGc2 61aa 3e-06 in ref transcript
• COG SPS1 265aa 6e-19 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].

PTK7

• refseq_PTK7.F4 refseq_PTK7.R4 197 365
• NCBIGene 36.3 5754
• Exon skipping and alternative 3-prime or 5-prime, size difference: 168
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_002821

• cd PTK_CCK4 274aa 1e-148 in ref transcript
  • Catalytic Domain of the Protein Tyrosine Kinase, Colon Carcinoma Kinase 4. Protein Tyrosine Kinase (PTK) family; Colon carcinoma kinase 4 (CCK4); pseudokinase domain. The PTKc (catalytic domain) family, to which this subfamily belongs, includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. CCK4, also called protein tyrosine kinase 7 (PTK7), is an orphan receptor tyr kinase (RTK) containing an extracellular region with seven immunoglobulin domains, a transmembrane segment, and an intracellular inactive pseudokinase domain. Studies in mice reveal that CCK4 is essential for neural development. Mouse embryos containing a truncated CCK4 die perinatally and display craniorachischisis, a severe form of neural tube defect. The mechanism of action of the CCK4 pseudokinase is still unknown. Other pseudokinases such as HER3 rely on the activity of partner RTKs.
• cd IGcam 85aa 5e-16 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• cd IGcam 86aa 1e-13 in ref transcript
• cd IGcam 85aa 2e-12 in ref transcript
• Changed! cd IGcam 87aa 3e-10 in ref transcript
• cd IGcam 79aa 6e-10 in ref transcript
• cd IGcam 78aa 8e-06 in ref transcript
• cd IGcam 81aa 3e-04 in ref transcript
• smart TyrKc 261aa 1e-98 in ref transcript
  • Tyrosine kinase, catalytic domain. Phosphotransferases. Tyrosine-specific kinase subfamily.
• pfam I-set 86aa 9e-12 in ref transcript
  • Immunoglobulin I-set domain.
• Changed! pfam I-set 77aa 1e-11 in ref transcript
• pfam I-set 87aa 2e-11 in ref transcript
• pfam I-set 92aa 5e-10 in ref transcript
• smart IGc2 59aa 1e-07 in ref transcript
  • Immunoglobulin C-2 Type.
• smart IG_like 71aa 1e-06 in ref transcript
  • Immunoglobulin like. IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
• smart IGc2 61aa 3e-06 in ref transcript
• COG SPS1 265aa 6e-19 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].

PTK9

• refseq_PTK9.F1 refseq_PTK9.R1 109 499
• NCBIGene 36.2 5756
• Alternative 5-prime, size difference: 390
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_002822

• Changed! cd ADF 134aa 2e-23 in ref transcript
  • Actin depolymerisation factor/cofilin -like domains; present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments.
• Changed! cd ADF 131aa 8e-23 in ref transcript
• Changed! smart ADF 133aa 3e-28 in ref transcript
  • Actin depolymerisation factor/cofilin -like domains. Severs actin filaments and binds to actin monomers.
• Changed! smart ADF 128aa 3e-26 in ref transcript

PTP4A2

• refseq_PTP4A2.F1 refseq_PTP4A2.R1 156 362
• NCBIGene 36.3 8073
• Multiple exon skipping, size difference: 206
• Exclusion in the protein causing a frameshift, Exclusion in the protein (no frameshift)
• Reference transcript: NM_080391

• Changed! cd DSPc 116aa 4e-08 in ref transcript
  • Dual specificity phosphatases (DSP); Ser/Thr and Tyr protein phosphatases. Structurally similar to tyrosine-specific phosphatases but with a shallower active site cleft and a distinctive active site signature motif, HCxxGxxR. Characterized as VHR- or Cdc25-like.
• Changed! smart PTPc_motif 86aa 7e-10 in ref transcript
  • Protein tyrosine phosphatase, catalytic domain motif.
• Changed! PTZ PTZ00242 149aa 1e-53 in ref transcript
  • protein tyrosine phosphatase; Provisional.
• Changed! PTZ PTZ00242 59aa 3e-13 in modified transcript

PTP4A3

• refseq_PTP4A3.F2 refseq_PTP4A3.R2 221 296
• NCBIGene 36.3 11156
• Single exon skipping, size difference: 75
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_032611

• Changed! cd DSPc 104aa 2e-07 in ref transcript
  • Dual specificity phosphatases (DSP); Ser/Thr and Tyr protein phosphatases. Structurally similar to tyrosine-specific phosphatases but with a shallower active site cleft and a distinctive active site signature motif, HCxxGxxR. Characterized as VHR- or Cdc25-like.
• Changed! pfam Y_phosphatase 134aa 8e-11 in ref transcript
  • Protein-tyrosine phosphatase.
• Changed! PTZ PTZ00242 151aa 9e-53 in ref transcript
  • protein tyrosine phosphatase; Provisional.
• Changed! cd PTPc 69aa 0.001 in modified transcript
  • Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active.
• Changed! pfam Y_phosphatase 95aa 4e-04 in modified transcript
• Changed! PTZ PTZ00242 126aa 1e-37 in modified transcript

PTPN2

• refseq_PTPN2.F1 refseq_PTPN2.R1 260 362
• NCBIGene 36.3 5771
• Single exon skipping, size difference: 102
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_080422

• cd PTPc 230aa 1e-78 in ref transcript
  • Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active.
• smart PTPc 270aa 2e-88 in ref transcript
  • Protein tyrosine phosphatase, catalytic domain.
• COG PTP2 235aa 1e-41 in ref transcript
  • Protein tyrosine phosphatase [Signal transduction mechanisms].

PTPN5

• refseq_PTPN5.F1 refseq_PTPN5.R1 238 283
• NCBIGene 36.3 84867
• Alternative 3-prime, size difference: 45
• Inclusion in 5'UTR
• Reference transcript: NM_032781

• cd PTPc 229aa 3e-76 in ref transcript
  • Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active.
• smart PTPc 254aa 2e-84 in ref transcript
  • Protein tyrosine phosphatase, catalytic domain.
• COG PTP2 237aa 8e-35 in ref transcript
  • Protein tyrosine phosphatase [Signal transduction mechanisms].

PTPN5

• refseq_PTPN5.F4 refseq_PTPN5.R4 280 376
• NCBIGene 36.3 84867
• Alternative 3-prime, size difference: 96
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_032781

• cd PTPc 229aa 3e-76 in ref transcript
  • Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active.
• smart PTPc 254aa 2e-84 in ref transcript
  • Protein tyrosine phosphatase, catalytic domain.
• COG PTP2 237aa 8e-35 in ref transcript
  • Protein tyrosine phosphatase [Signal transduction mechanisms].

PTPRA

• refseq_PTPRA.F1 refseq_PTPRA.R1 146 173
• NCBIGene 36.3 5786
• Single exon skipping, size difference: 27
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_002836

• cd PTPc 231aa 3e-89 in ref transcript
  • Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active.
• cd PTPc 231aa 5e-85 in ref transcript
• smart PTPc 259aa 1e-97 in ref transcript
  • Protein tyrosine phosphatase, catalytic domain.
• smart PTPc 261aa 1e-93 in ref transcript
• COG PTP2 231aa 2e-43 in ref transcript
  • Protein tyrosine phosphatase [Signal transduction mechanisms].
• COG PTP2 241aa 3e-43 in ref transcript

PTPRC

• refseq_PTPRC.F1 refseq_PTPRC.R1 200 344
• NCBIGene 36.3 5788
• Single exon skipping, size difference: 144
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_002838

• cd PTPc 232aa 2e-86 in ref transcript
  • Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active.
• cd PTPc 256aa 2e-71 in ref transcript
• cd FN3 81aa 2e-06 in ref transcript
  • Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.
• cd FN3 71aa 0.009 in ref transcript
• smart PTPc 260aa 1e-93 in ref transcript
  • Protein tyrosine phosphatase, catalytic domain.
• smart PTPc 283aa 9e-81 in ref transcript
• pfam fn3 71aa 7e-04 in ref transcript
  • Fibronectin type III domain.
• pfam fn3 81aa 0.003 in ref transcript
• Changed! pfam Herpes_BLLF1 136aa 0.003 in ref transcript
  • Herpes virus major outer envelope glycoprotein (BLLF1). This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo.
• COG PTP2 250aa 3e-42 in ref transcript
  • Protein tyrosine phosphatase [Signal transduction mechanisms].
• COG PTP2 265aa 4e-30 in ref transcript
• Changed! smart FN3 76aa 0.002 in modified transcript
  • Fibronectin type 3 domain. One of three types of internal repeat within the plasma protein, fibronectin. The tenth fibronectin type III repeat contains a RGD cell recognition sequence in a flexible loop between 2 strands. Type III modules are present in both extracellular and intracellular proteins.
• Changed! pfam Herpes_BLLF1 124aa 0.006 in modified transcript

PTPRD

• refseq_PTPRD.F2 refseq_PTPRD.R2 136 163
• NCBIGene 36.3 5789
• Multiple exon skipping, size difference: 27
• Exclusion in the protein (no frameshift), Exclusion in the protein (no frameshift)
• Reference transcript: NM_002839

• cd PTPc 230aa 5e-92 in ref transcript
  • Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active.
• cd PTPc 231aa 8e-90 in ref transcript
• cd FN3 92aa 3e-13 in ref transcript
  • Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.
• cd FN3 90aa 7e-13 in ref transcript
• Changed! cd IGcam 88aa 2e-12 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• cd IGcam 91aa 4e-12 in ref transcript
• cd FN3 95aa 8e-12 in ref transcript
• cd FN3 93aa 2e-11 in ref transcript
• cd FN3 89aa 3e-11 in ref transcript
• cd FN3 107aa 4e-09 in ref transcript
• cd FN3 82aa 2e-06 in ref transcript
• cd IGcam 78aa 1e-05 in ref transcript
• smart PTPc 256aa 1e-101 in ref transcript
  • Protein tyrosine phosphatase, catalytic domain.
• smart PTPc 260aa 1e-100 in ref transcript
• pfam I-set 92aa 5e-16 in ref transcript
  • Immunoglobulin I-set domain.
• pfam fn3 85aa 8e-15 in ref transcript
  • Fibronectin type III domain.
• pfam fn3 88aa 2e-13 in ref transcript
• pfam fn3 83aa 2e-13 in ref transcript
• smart FN3 79aa 3e-12 in ref transcript
  • Fibronectin type 3 domain. One of three types of internal repeat within the plasma protein, fibronectin. The tenth fibronectin type III repeat contains a RGD cell recognition sequence in a flexible loop between 2 strands. Type III modules are present in both extracellular and intracellular proteins.
• Changed! smart IGc2 74aa 7e-11 in ref transcript
  • Immunoglobulin C-2 Type.
• smart FN3 83aa 2e-10 in ref transcript
• pfam fn3 100aa 5e-10 in ref transcript
• smart IG_like 79aa 7e-08 in ref transcript
  • Immunoglobulin like. IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
• smart FN3 81aa 4e-05 in ref transcript
• COG PTP2 268aa 1e-48 in ref transcript
  • Protein tyrosine phosphatase [Signal transduction mechanisms].
• COG PTP2 281aa 9e-45 in ref transcript
• Changed! cd IGcam 79aa 4e-13 in modified transcript
• Changed! smart IGc2 65aa 4e-11 in modified transcript

PTPRD

• refseq_PTPRD.F3 refseq_PTPRD.R4 211 250
• NCBIGene 36.3 5789
• Single exon skipping, size difference: 12
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_002839

• cd PTPc 230aa 5e-92 in ref transcript
  • Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active.
• cd PTPc 231aa 8e-90 in ref transcript
• cd FN3 92aa 3e-13 in ref transcript
  • Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.
• cd FN3 90aa 7e-13 in ref transcript
• cd IGcam 88aa 2e-12 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• cd IGcam 91aa 4e-12 in ref transcript
• cd FN3 95aa 8e-12 in ref transcript
• cd FN3 93aa 2e-11 in ref transcript
• cd FN3 89aa 3e-11 in ref transcript
• cd FN3 107aa 4e-09 in ref transcript
• cd FN3 82aa 2e-06 in ref transcript
• Changed! cd IGcam 78aa 1e-05 in ref transcript
• smart PTPc 256aa 1e-101 in ref transcript
  • Protein tyrosine phosphatase, catalytic domain.
• smart PTPc 260aa 1e-100 in ref transcript
• pfam I-set 92aa 5e-16 in ref transcript
  • Immunoglobulin I-set domain.
• pfam fn3 85aa 8e-15 in ref transcript
  • Fibronectin type III domain.
• pfam fn3 88aa 2e-13 in ref transcript
• pfam fn3 83aa 2e-13 in ref transcript
• smart FN3 79aa 3e-12 in ref transcript
  • Fibronectin type 3 domain. One of three types of internal repeat within the plasma protein, fibronectin. The tenth fibronectin type III repeat contains a RGD cell recognition sequence in a flexible loop between 2 strands. Type III modules are present in both extracellular and intracellular proteins.
• smart IGc2 74aa 7e-11 in ref transcript
  • Immunoglobulin C-2 Type.
• smart FN3 83aa 2e-10 in ref transcript
• pfam fn3 100aa 5e-10 in ref transcript
• Changed! smart IG_like 79aa 7e-08 in ref transcript
  • Immunoglobulin like. IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
• smart FN3 81aa 4e-05 in ref transcript
• COG PTP2 268aa 1e-48 in ref transcript
  • Protein tyrosine phosphatase [Signal transduction mechanisms].
• COG PTP2 281aa 9e-45 in ref transcript
• Changed! cd IGcam 83aa 6e-06 in modified transcript
• Changed! pfam I-set 84aa 6e-08 in modified transcript

PTPRD

• refseq_PTPRD.F4 refseq_PTPRD.R5 138 165
• NCBIGene 36.3 5789
• Single exon skipping, size difference: 27
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_002839

• cd PTPc 230aa 5e-92 in ref transcript
  • Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active.
• cd PTPc 231aa 8e-90 in ref transcript
• cd FN3 92aa 3e-13 in ref transcript
  • Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.
• cd FN3 90aa 7e-13 in ref transcript
• cd IGcam 88aa 2e-12 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• cd IGcam 91aa 4e-12 in ref transcript
• cd FN3 95aa 8e-12 in ref transcript
• cd FN3 93aa 2e-11 in ref transcript
• cd FN3 89aa 3e-11 in ref transcript
• Changed! cd FN3 107aa 4e-09 in ref transcript
• cd FN3 82aa 2e-06 in ref transcript
• cd IGcam 78aa 1e-05 in ref transcript
• smart PTPc 256aa 1e-101 in ref transcript
  • Protein tyrosine phosphatase, catalytic domain.
• smart PTPc 260aa 1e-100 in ref transcript
• pfam I-set 92aa 5e-16 in ref transcript
  • Immunoglobulin I-set domain.
• pfam fn3 85aa 8e-15 in ref transcript
  • Fibronectin type III domain.
• pfam fn3 88aa 2e-13 in ref transcript
• pfam fn3 83aa 2e-13 in ref transcript
• smart FN3 79aa 3e-12 in ref transcript
  • Fibronectin type 3 domain. One of three types of internal repeat within the plasma protein, fibronectin. The tenth fibronectin type III repeat contains a RGD cell recognition sequence in a flexible loop between 2 strands. Type III modules are present in both extracellular and intracellular proteins.
• smart IGc2 74aa 7e-11 in ref transcript
  • Immunoglobulin C-2 Type.
• smart FN3 83aa 2e-10 in ref transcript
• Changed! pfam fn3 100aa 5e-10 in ref transcript
• smart IG_like 79aa 7e-08 in ref transcript
  • Immunoglobulin like. IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
• smart FN3 81aa 4e-05 in ref transcript
• COG PTP2 268aa 1e-48 in ref transcript
  • Protein tyrosine phosphatase [Signal transduction mechanisms].
• COG PTP2 281aa 9e-45 in ref transcript
• Changed! cd FN3 98aa 6e-09 in modified transcript
• Changed! pfam fn3 91aa 5e-09 in modified transcript

PTPRF

• refseq_PTPRF.F1 refseq_PTPRF.R1 123 150
• NCBIGene 36.3 5792
• Single exon skipping, size difference: 27
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_002840

• cd PTPc 230aa 2e-94 in ref transcript
  • Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active.
• cd PTPc 231aa 4e-89 in ref transcript
• cd IGcam 79aa 7e-13 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• cd FN3 93aa 2e-12 in ref transcript
  • Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.
• cd FN3 89aa 1e-11 in ref transcript
• cd IGcam 90aa 2e-11 in ref transcript
• cd FN3 95aa 5e-10 in ref transcript
• cd FN3 82aa 3e-09 in ref transcript
• cd FN3 90aa 3e-09 in ref transcript
• cd FN3 90aa 1e-08 in ref transcript
• cd IGcam 83aa 2e-08 in ref transcript
• Changed! cd FN3 107aa 0.001 in ref transcript
• smart PTPc 256aa 1e-105 in ref transcript
  • Protein tyrosine phosphatase, catalytic domain.
• smart PTPc 256aa 4e-97 in ref transcript
• pfam I-set 92aa 9e-18 in ref transcript
  • Immunoglobulin I-set domain.
• smart FN3 79aa 3e-13 in ref transcript
  • Fibronectin type 3 domain. One of three types of internal repeat within the plasma protein, fibronectin. The tenth fibronectin type III repeat contains a RGD cell recognition sequence in a flexible loop between 2 strands. Type III modules are present in both extracellular and intracellular proteins.
• pfam fn3 88aa 3e-11 in ref transcript
  • Fibronectin type III domain.
• smart FN3 83aa 7e-11 in ref transcript
• pfam I-set 84aa 1e-10 in ref transcript
• smart IGc2 65aa 1e-10 in ref transcript
  • Immunoglobulin C-2 Type.
• pfam fn3 83aa 3e-10 in ref transcript
• pfam fn3 70aa 3e-07 in ref transcript
• pfam fn3 83aa 7e-07 in ref transcript
• COG PTP2 272aa 1e-49 in ref transcript
  • Protein tyrosine phosphatase [Signal transduction mechanisms].
• COG PTP2 264aa 5e-47 in ref transcript
• Changed! cd FN3 98aa 4e-04 in modified transcript

PTPRN2

• refseq_PTPRN2.F1 refseq_PTPRN2.R1 258 309
• NCBIGene 36.3 5799
• Single exon skipping, size difference: 51
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_002847

• cd PTPc 233aa 1e-79 in ref transcript
  • Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active.
• smart PTPc 260aa 6e-93 in ref transcript
  • Protein tyrosine phosphatase, catalytic domain.
• COG PTP2 275aa 7e-40 in ref transcript
  • Protein tyrosine phosphatase [Signal transduction mechanisms].

PTPRN2

• refseq_PTPRN2.F4 refseq_PTPRN2.R4 324 411
• NCBIGene 36.3 5799
• Single exon skipping, size difference: 87
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_002847

• cd PTPc 233aa 1e-79 in ref transcript
  • Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active.
• smart PTPc 260aa 6e-93 in ref transcript
  • Protein tyrosine phosphatase, catalytic domain.
• COG PTP2 275aa 7e-40 in ref transcript
  • Protein tyrosine phosphatase [Signal transduction mechanisms].

PTPRO

• refseq_PTPRO.F2 refseq_PTPRO.R2 312 396
• NCBIGene 36.3 5800
• Single exon skipping, size difference: 84
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_030667

• cd PTPc 229aa 3e-87 in ref transcript
  • Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active.
• cd FN3 93aa 1e-04 in ref transcript
  • Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.
• cd FN3 83aa 0.005 in ref transcript
• smart PTPc 256aa 1e-97 in ref transcript
  • Protein tyrosine phosphatase, catalytic domain.
• pfam fn3 83aa 8e-05 in ref transcript
  • Fibronectin type III domain.
• pfam fn3 87aa 0.002 in ref transcript
• smart FN3 83aa 0.005 in ref transcript
  • Fibronectin type 3 domain. One of three types of internal repeat within the plasma protein, fibronectin. The tenth fibronectin type III repeat contains a RGD cell recognition sequence in a flexible loop between 2 strands. Type III modules are present in both extracellular and intracellular proteins.
• COG PTP2 234aa 1e-45 in ref transcript
  • Protein tyrosine phosphatase [Signal transduction mechanisms].

PTPRS

• refseq_PTPRS.F2 refseq_PTPRS.R2 135 183
• NCBIGene 36.3 5802
• Single exon skipping, size difference: 48
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_002850

• cd PTPc 230aa 5e-95 in ref transcript
  • Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active.
• cd PTPc 231aa 2e-90 in ref transcript
• cd FN3 90aa 6e-14 in ref transcript
  • Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.
• cd FN3 89aa 2e-12 in ref transcript
• cd IGcam 87aa 4e-12 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• cd FN3 93aa 4e-11 in ref transcript
• cd IGcam 91aa 5e-11 in ref transcript
• cd FN3 90aa 2e-07 in ref transcript
• cd FN3 80aa 2e-07 in ref transcript
• cd FN3 106aa 2e-07 in ref transcript
• cd IGcam 83aa 2e-06 in ref transcript
• cd FN3 83aa 6e-05 in ref transcript
• cd FN3 64aa 0.001 in ref transcript
• smart PTPc 256aa 1e-106 in ref transcript
  • Protein tyrosine phosphatase, catalytic domain.
• smart PTPc 260aa 1e-100 in ref transcript
• pfam I-set 92aa 2e-17 in ref transcript
  • Immunoglobulin I-set domain.
• smart FN3 79aa 1e-12 in ref transcript
  • Fibronectin type 3 domain. One of three types of internal repeat within the plasma protein, fibronectin. The tenth fibronectin type III repeat contains a RGD cell recognition sequence in a flexible loop between 2 strands. Type III modules are present in both extracellular and intracellular proteins.
• smart FN3 80aa 2e-12 in ref transcript
• smart FN3 83aa 5e-11 in ref transcript
• smart IGc2 74aa 1e-10 in ref transcript
  • Immunoglobulin C-2 Type.
• pfam fn3 80aa 7e-09 in ref transcript
  • Fibronectin type III domain.
• smart IG_like 79aa 7e-09 in ref transcript
  • Immunoglobulin like. IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
• pfam fn3 91aa 4e-08 in ref transcript
• pfam fn3 99aa 2e-07 in ref transcript
• smart FN3 79aa 6e-05 in ref transcript
• smart FN3 62aa 3e-04 in ref transcript
• COG PTP2 268aa 6e-51 in ref transcript
  • Protein tyrosine phosphatase [Signal transduction mechanisms].
• COG PTP2 266aa 2e-48 in ref transcript

PTPRS

• refseq_PTPRS.F3 refseq_PTPRS.R3 136 163
• NCBIGene 36.3 5802
• Multiple exon skipping, size difference: 27
• Exclusion in the protein (no frameshift), Exclusion in the protein (no frameshift)
• Reference transcript: NM_002850

• cd PTPc 230aa 5e-95 in ref transcript
  • Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active.
• cd PTPc 231aa 2e-90 in ref transcript
• cd FN3 90aa 6e-14 in ref transcript
  • Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.
• cd FN3 89aa 2e-12 in ref transcript
• Changed! cd IGcam 87aa 4e-12 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• cd FN3 93aa 4e-11 in ref transcript
• cd IGcam 91aa 5e-11 in ref transcript
• cd FN3 90aa 2e-07 in ref transcript
• cd FN3 80aa 2e-07 in ref transcript
• cd FN3 106aa 2e-07 in ref transcript
• cd IGcam 83aa 2e-06 in ref transcript
• cd FN3 83aa 6e-05 in ref transcript
• cd FN3 64aa 0.001 in ref transcript
• smart PTPc 256aa 1e-106 in ref transcript
  • Protein tyrosine phosphatase, catalytic domain.
• smart PTPc 260aa 1e-100 in ref transcript
• pfam I-set 92aa 2e-17 in ref transcript
  • Immunoglobulin I-set domain.
• smart FN3 79aa 1e-12 in ref transcript
  • Fibronectin type 3 domain. One of three types of internal repeat within the plasma protein, fibronectin. The tenth fibronectin type III repeat contains a RGD cell recognition sequence in a flexible loop between 2 strands. Type III modules are present in both extracellular and intracellular proteins.
• smart FN3 80aa 2e-12 in ref transcript
• smart FN3 83aa 5e-11 in ref transcript
• Changed! smart IGc2 74aa 1e-10 in ref transcript
  • Immunoglobulin C-2 Type.
• pfam fn3 80aa 7e-09 in ref transcript
  • Fibronectin type III domain.
• smart IG_like 79aa 7e-09 in ref transcript
  • Immunoglobulin like. IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
• pfam fn3 91aa 4e-08 in ref transcript
• pfam fn3 99aa 2e-07 in ref transcript
• smart FN3 79aa 6e-05 in ref transcript
• smart FN3 62aa 3e-04 in ref transcript
• COG PTP2 268aa 6e-51 in ref transcript
  • Protein tyrosine phosphatase [Signal transduction mechanisms].
• COG PTP2 266aa 2e-48 in ref transcript
• Changed! cd IGcam 78aa 1e-12 in modified transcript
• Changed! smart IGc2 65aa 6e-11 in modified transcript

PTPRS

• refseq_PTPRS.F6 refseq_PTPRS.R6 150 177
• NCBIGene 36.3 5802
• Single exon skipping, size difference: 27
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_002850

• cd PTPc 230aa 5e-95 in ref transcript
  • Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active.
• cd PTPc 231aa 2e-90 in ref transcript
• cd FN3 90aa 6e-14 in ref transcript
  • Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.
• cd FN3 89aa 2e-12 in ref transcript
• cd IGcam 87aa 4e-12 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• cd FN3 93aa 4e-11 in ref transcript
• cd IGcam 91aa 5e-11 in ref transcript
• cd FN3 90aa 2e-07 in ref transcript
• cd FN3 80aa 2e-07 in ref transcript
• Changed! cd FN3 106aa 2e-07 in ref transcript
• cd IGcam 83aa 2e-06 in ref transcript
• cd FN3 83aa 6e-05 in ref transcript
• cd FN3 64aa 0.001 in ref transcript
• smart PTPc 256aa 1e-106 in ref transcript
  • Protein tyrosine phosphatase, catalytic domain.
• smart PTPc 260aa 1e-100 in ref transcript
• pfam I-set 92aa 2e-17 in ref transcript
  • Immunoglobulin I-set domain.
• smart FN3 79aa 1e-12 in ref transcript
  • Fibronectin type 3 domain. One of three types of internal repeat within the plasma protein, fibronectin. The tenth fibronectin type III repeat contains a RGD cell recognition sequence in a flexible loop between 2 strands. Type III modules are present in both extracellular and intracellular proteins.
• smart FN3 80aa 2e-12 in ref transcript
• smart FN3 83aa 5e-11 in ref transcript
• smart IGc2 74aa 1e-10 in ref transcript
  • Immunoglobulin C-2 Type.
• pfam fn3 80aa 7e-09 in ref transcript
  • Fibronectin type III domain.
• smart IG_like 79aa 7e-09 in ref transcript
  • Immunoglobulin like. IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
• pfam fn3 91aa 4e-08 in ref transcript
• Changed! pfam fn3 99aa 2e-07 in ref transcript
• smart FN3 79aa 6e-05 in ref transcript
• smart FN3 62aa 3e-04 in ref transcript
• COG PTP2 268aa 6e-51 in ref transcript
  • Protein tyrosine phosphatase [Signal transduction mechanisms].
• COG PTP2 266aa 2e-48 in ref transcript
• Changed! cd FN3 97aa 1e-07 in modified transcript
• Changed! smart FN3 87aa 5e-07 in modified transcript

PTPRT

• refseq_PTPRT.F1 refseq_PTPRT.R1 228 285
• NCBIGene 36.3 11122
• Single exon skipping, size difference: 57
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_133170

• cd PTPc 228aa 6e-92 in ref transcript
  • Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active.
• cd PTPc 233aa 1e-69 in ref transcript
• cd MAM 158aa 5e-35 in ref transcript
  • Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region.
• cd FN3 83aa 3e-07 in ref transcript
  • Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.
• cd FN3 91aa 0.005 in ref transcript
• smart PTPc 255aa 1e-102 in ref transcript
  • Protein tyrosine phosphatase, catalytic domain.
• smart PTPc 263aa 4e-76 in ref transcript
• smart MAM 161aa 1e-47 in ref transcript
  • Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others). Likely to have an adhesive function. Mutations in the meprin MAM domain affect noncovalent associations within meprin oligomers. In receptor tyrosine phosphatase mu-like molecules the MAM domain is important for homophilic cell-cell interactions.
• pfam fn3 76aa 2e-07 in ref transcript
  • Fibronectin type III domain.
• pfam fn3 72aa 8e-04 in ref transcript
• COG PTP2 240aa 1e-46 in ref transcript
  • Protein tyrosine phosphatase [Signal transduction mechanisms].
• COG PTP2 284aa 3e-27 in ref transcript

PTPRU

• refseq_PTPRU.F1 refseq_PTPRU.R1 128 158
• NCBIGene 36.3 10076
• Single exon skipping, size difference: 30
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_005704

• cd PTPc 221aa 6e-83 in ref transcript
  • Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active.
• cd PTPc 234aa 6e-67 in ref transcript
• cd MAM 160aa 9e-41 in ref transcript
  • Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region.
• cd FN3 102aa 6e-09 in ref transcript
  • Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.
• cd FN3 96aa 2e-04 in ref transcript
• pfam Y_phosphatase 222aa 1e-91 in ref transcript
  • Protein-tyrosine phosphatase.
• smart PTPc 264aa 2e-72 in ref transcript
  • Protein tyrosine phosphatase, catalytic domain.
• smart MAM 165aa 3e-48 in ref transcript
  • Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others). Likely to have an adhesive function. Mutations in the meprin MAM domain affect noncovalent associations within meprin oligomers. In receptor tyrosine phosphatase mu-like molecules the MAM domain is important for homophilic cell-cell interactions.
• pfam fn3 94aa 2e-09 in ref transcript
  • Fibronectin type III domain.
• pfam fn3 72aa 3e-04 in ref transcript
• smart FN3 86aa 0.002 in ref transcript
  • Fibronectin type 3 domain. One of three types of internal repeat within the plasma protein, fibronectin. The tenth fibronectin type III repeat contains a RGD cell recognition sequence in a flexible loop between 2 strands. Type III modules are present in both extracellular and intracellular proteins.
• COG PTP2 219aa 3e-38 in ref transcript
  • Protein tyrosine phosphatase [Signal transduction mechanisms].
• COG PTP2 289aa 2e-22 in ref transcript

PTPRU

• refseq_PTPRU.F2 refseq_PTPRU.R2 101 119
• NCBIGene 36.3 10076
• Single exon skipping, size difference: 18
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_005704

• Changed! cd PTPc 221aa 6e-83 in ref transcript
  • Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active.
• cd PTPc 234aa 6e-67 in ref transcript
• cd MAM 160aa 9e-41 in ref transcript
  • Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region.
• cd FN3 102aa 6e-09 in ref transcript
  • Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.
• cd FN3 96aa 2e-04 in ref transcript
• Changed! pfam Y_phosphatase 222aa 1e-91 in ref transcript
  • Protein-tyrosine phosphatase.
• smart PTPc 264aa 2e-72 in ref transcript
  • Protein tyrosine phosphatase, catalytic domain.
• smart MAM 165aa 3e-48 in ref transcript
  • Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others). Likely to have an adhesive function. Mutations in the meprin MAM domain affect noncovalent associations within meprin oligomers. In receptor tyrosine phosphatase mu-like molecules the MAM domain is important for homophilic cell-cell interactions.
• pfam fn3 94aa 2e-09 in ref transcript
  • Fibronectin type III domain.
• pfam fn3 72aa 3e-04 in ref transcript
• smart FN3 86aa 0.002 in ref transcript
  • Fibronectin type 3 domain. One of three types of internal repeat within the plasma protein, fibronectin. The tenth fibronectin type III repeat contains a RGD cell recognition sequence in a flexible loop between 2 strands. Type III modules are present in both extracellular and intracellular proteins.
• Changed! COG PTP2 219aa 3e-38 in ref transcript
  • Protein tyrosine phosphatase [Signal transduction mechanisms].
• COG PTP2 289aa 2e-22 in ref transcript
• Changed! cd PTPc 227aa 7e-81 in modified transcript
• Changed! pfam Y_phosphatase 228aa 1e-89 in modified transcript
• Changed! COG PTP2 225aa 4e-38 in modified transcript

PXMP4

• refseq_PXMP4.F2 refseq_PXMP4.R2 195 394
• NCBIGene 36.3 11264
• Single exon skipping, size difference: 199
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_007238

• Changed! pfam Pmp24 171aa 4e-68 in ref transcript
  • Peroxisomal membrane protein 24. Peroxisomes are single membrane bound organelles, present in practically all eukaryotic cells, and involved in a variety of metabolic pathways; the deduced protein is extremely basic, a characteristic of many other peroxisomal intrinsic membrane proteins. They carry two short stretches of hydrophobic residues shown to be necessary for the correct targeting of these proteins. A sequence with these characteristics is found in human PMP24 (amino acid residues 16-30). However, in the absence of experimental data, the involvement of this domain in the targeting of PMP24 remains to be proved. PMP24 was known as Pmp27.
• Changed! pfam Pmp24 32aa 9e-15 in modified transcript

PYCARD

• refseq_PYCARD.F1 refseq_PYCARD.R1 272 329
• NCBIGene 36.3 29108
• Single exon skipping, size difference: 57
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_013258

• pfam CARD 84aa 6e-18 in ref transcript
  • Caspase recruitment domain. Motif contained in proteins involved in apoptotic signaling. Predicted to possess a DEATH (pfam00531) domain-like fold.
• pfam PAAD_DAPIN 84aa 2e-12 in ref transcript
  • PAAD/DAPIN/Pyrin domain. This domain is predicted to contain 6 alpha helices and to have the same fold as the pfam00531 domain. This similarity may mean that this is a protein-protein interaction domain.

PYHIN1

• refseq_PYHIN1.F1 refseq_PYHIN1.R1 227 352
• NCBIGene 36.3 149628
• Single exon skipping, size difference: 125
• Exclusion of the stop codon
• Reference transcript: NM_152501

• pfam HIN 159aa 3e-51 in ref transcript
  • HIN-200/IF120x domain. This domain has no know function. It is found in one or two copies per protein, and is found associated with the PAAD/DAPIN domain pfam02758.
• pfam PAAD_DAPIN 79aa 6e-17 in ref transcript
  • PAAD/DAPIN/Pyrin domain. This domain is predicted to contain 6 alpha helices and to have the same fold as the pfam00531 domain. This similarity may mean that this is a protein-protein interaction domain.

QRICH1

• refseq_QRICH1.F2 refseq_QRICH1.R2 337 397
• NCBIGene 36.3 54870
• Single exon skipping, size difference: 60
• Exclusion in 5'UTR
• Reference transcript: NM_017730

RAB27A

• refseq_RAB27A.F2 refseq_RAB27A.R2 177 266
• NCBIGene 36.3 5873
• Single exon skipping, size difference: 89
• Exclusion in 5'UTR
• Reference transcript: NM_183234

• cd Rab27A 180aa 1e-105 in ref transcript
  • Rab27a subfamily. The Rab27a subfamily consists of Rab27a and its highly homologous isoform, Rab27b. Unlike most Rab proteins whose functions remain poorly defined, Rab27a has many known functions. Rab27a has multiple effector proteins, and depending on which effector it binds, Rab27a has different functions as well as tissue distribution and/or cellular localization. Putative functions have been assigned to Rab27a when associated with the effector proteins Slp1, Slp2, Slp3, Slp4, Slp5, DmSlp, rabphilin, Dm/Ce-rabphilin, Slac2-a, Slac2-b, Slac2-c, Noc2, JFC1, and Munc13-4. Rab27a has been associated with several human diseases, including hemophagocytic syndrome (Griscelli syndrome or GS), Hermansky-Pudlak syndrome, and choroidermia. In the case of GS, a rare, autosomal recessive disease, a Rab27a mutation is directly responsible for the disorder. When Rab27a is localized to the secretory granules of pancreatic beta cells, it is believed to mediate glucose-stimulated insulin secretion, making it a potential target for diabetes therapy. When bound to JFC1 in prostate cells, Rab27a is believed to regulate the exocytosis of prostate- specific markers. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.
• smart RAB 175aa 1e-66 in ref transcript
  • Rab subfamily of small GTPases. Rab GTPases are implicated in vesicle trafficking.
• COG COG1100 187aa 2e-24 in ref transcript
  • GTPase SAR1 and related small G proteins [General function prediction only].

RAB28

• refseq_RAB28.F2 refseq_RAB28.R2 291 386
• NCBIGene 36.3 9364
• Single exon skipping, size difference: 95
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_001017979

• Changed! cd Rab28 209aa 1e-106 in ref transcript
  • Rab28 subfamily. First identified in maize, Rab28 has been shown to be a late embryogenesis-abundant (Lea) protein that is regulated by the plant hormone abcisic acid (ABA). In Arabidopsis, Rab28 is expressed during embryo development and is generally restricted to provascular tissues in mature embryos. Unlike maize Rab28, it is not ABA-inducible. Characterization of the human Rab28 homolog revealed two isoforms, which differ by a 95-base pair insertion, producing an alternative sequence for the 30 amino acids at the C-terminus. The two human isoforms are presumbly the result of alternative splicing. Since they differ at the C-terminus but not in the GTP-binding region, they are predicted to be targeted to different cellular locations. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.
• smart RAB 166aa 6e-38 in ref transcript
  • Rab subfamily of small GTPases. Rab GTPases are implicated in vesicle trafficking.
• Changed! COG COG1100 132aa 6e-20 in ref transcript
  • GTPase SAR1 and related small G proteins [General function prediction only].
• Changed! cd Rab28 205aa 1e-98 in modified transcript
• Changed! COG COG1100 195aa 5e-20 in modified transcript

RAB37

• refseq_RAB37.F1 refseq_RAB37.R1 110 467
• NCBIGene 36.2 326624
• Alternative 5-prime and 3-prime, size difference: 357
• Exclusion in 3'UTR, Exclusion in 3'UTR
• Reference transcript: NM_001006637

• cd Rab26 190aa 1e-104 in ref transcript
  • Rab26 subfamily. First identified in rat pancreatic acinar cells, Rab26 is believed to play a role in recruiting mature granules to the plasma membrane upon beta-adrenergic stimulation. Rab26 belongs to the Rab functional group III, which are considered key regulators of intracellular vesicle transport during exocytosis. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.
• smart RAB 162aa 8e-74 in ref transcript
  • Rab subfamily of small GTPases. Rab GTPases are implicated in vesicle trafficking.
• PTZ PTZ00099 133aa 7e-31 in ref transcript
  • rab6; Provisional.

RAB3IP

• refseq_RAB3IP.F1 refseq_RAB3IP.R1 108 208
• NCBIGene 36.3 117177
• Single exon skipping, size difference: 100
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_175623

• pfam Sec2p 125aa 7e-37 in ref transcript
  • GDP/GTP exchange factor Sec2p. In Saccharomyces cerevisiae, Sec2p is a GDP/GTP exchange factor for Sec4p, which is required for vesicular transport at the post-Golgi stage of yeast secretion.
• COG Smc 87aa 4e-04 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].

RAB5C

• refseq_RAB5C.F1 refseq_RAB5C.R1 257 374
• NCBIGene 36.3 5878
• Single exon skipping, size difference: 117
• Exclusion in 5'UTR
• Reference transcript: NM_201434

• cd Rab5_related 163aa 4e-95 in ref transcript
  • Rab5-related subfamily. This subfamily includes Rab5 and Rab22 of mammals, Ypt51/Ypt52/Ypt53 of yeast, and RabF of plants. The members of this subfamily are involved in endocytosis and endocytic-sorting pathways. In mammals, Rab5 GTPases localize to early endosomes and regulate fusion of clathrin-coated vesicles to early endosomes and fusion between early endosomes. In yeast, Ypt51p family members similarly regulate membrane trafficking through prevacuolar compartments. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.
• pfam Ras 162aa 2e-71 in ref transcript
  • Ras family. Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU, arf and myosin_head. See pfam00009 pfam00025, pfam00063. As regards Rab GTPases, these are important regulators of vesicle formation, motility and fusion. They share a fold in common with all Ras GTPases: this is a six-stranded beta-sheet surrounded by five alpha-helices.
• COG COG1100 196aa 4e-32 in ref transcript
  • GTPase SAR1 and related small G proteins [General function prediction only].

ERC1

• refseq_RAB6IP2.F1 refseq_RAB6IP2.R1 189 321
• NCBIGene 36.3 23085
• Single exon skipping, size difference: 132
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_178040

• Changed! pfam Cast 829aa 1e-148 in ref transcript
  • RIM-binding protein of the cytomatrix active zone. This is a family of proteins that form part of the CAZ (cytomatrix at the active zone) complex which is involved in determining the site of synaptic vesicle fusion. The C-terminus is a PDZ-binding motif that binds directly to RIM (a small G protein Rab-3A effector). The family also contains four coiled-coil domains.
• pfam RBD-FIP 41aa 1e-07 in ref transcript
  • FIP domain. The FIP domain is the Rab11-binding domain (RBD) at the C-terminus of a family of Rab11-interacting proteins (FIPs). The Rab proteins constitute the largest family of small GTPases (>60 members in mammals). Among them Rab11 is a well characterised regulator of endocytic and recycling pathways. Rab11 associates with a broad range of post-Golgi organelles, including recycling endosomes.
• COG Smc 340aa 3e-09 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].
• Changed! COG Smc 318aa 3e-08 in ref transcript
• COG Smc 298aa 5e-06 in ref transcript
• Changed! pfam Cast 785aa 1e-151 in modified transcript
• Changed! COG Smc 328aa 7e-05 in modified transcript

ERC1

• refseq_RAB6IP2.F3 refseq_RAB6IP2.R3 125 290
• NCBIGene 36.3 23085
• Alternative 5-prime, size difference: 165
• Inclusion in 5'UTR
• Reference transcript: NM_178040

• pfam Cast 829aa 1e-148 in ref transcript
  • RIM-binding protein of the cytomatrix active zone. This is a family of proteins that form part of the CAZ (cytomatrix at the active zone) complex which is involved in determining the site of synaptic vesicle fusion. The C-terminus is a PDZ-binding motif that binds directly to RIM (a small G protein Rab-3A effector). The family also contains four coiled-coil domains.
• pfam RBD-FIP 41aa 1e-07 in ref transcript
  • FIP domain. The FIP domain is the Rab11-binding domain (RBD) at the C-terminus of a family of Rab11-interacting proteins (FIPs). The Rab proteins constitute the largest family of small GTPases (>60 members in mammals). Among them Rab11 is a well characterised regulator of endocytic and recycling pathways. Rab11 associates with a broad range of post-Golgi organelles, including recycling endosomes.
• COG Smc 340aa 3e-09 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].
• COG Smc 318aa 3e-08 in ref transcript
• COG Smc 298aa 5e-06 in ref transcript

ERC1

• refseq_RAB6IP2.F5 refseq_RAB6IP2.R5 242 326
• NCBIGene 36.3 23085
• Single exon skipping, size difference: 84
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_178040

• Changed! pfam Cast 829aa 1e-148 in ref transcript
  • RIM-binding protein of the cytomatrix active zone. This is a family of proteins that form part of the CAZ (cytomatrix at the active zone) complex which is involved in determining the site of synaptic vesicle fusion. The C-terminus is a PDZ-binding motif that binds directly to RIM (a small G protein Rab-3A effector). The family also contains four coiled-coil domains.
• pfam RBD-FIP 41aa 1e-07 in ref transcript
  • FIP domain. The FIP domain is the Rab11-binding domain (RBD) at the C-terminus of a family of Rab11-interacting proteins (FIPs). The Rab proteins constitute the largest family of small GTPases (>60 members in mammals). Among them Rab11 is a well characterised regulator of endocytic and recycling pathways. Rab11 associates with a broad range of post-Golgi organelles, including recycling endosomes.
• Changed! COG Smc 340aa 3e-09 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].
• COG Smc 318aa 3e-08 in ref transcript
• Changed! COG Smc 298aa 5e-06 in ref transcript
• Changed! pfam Cast 801aa 1e-154 in modified transcript
• Changed! COG Smc 365aa 7e-07 in modified transcript
• Changed! COG COG2433 126aa 0.004 in modified transcript
  • Uncharacterized conserved protein [Function unknown].

ERC1

• refseq_RAB6IP2.F6 refseq_RAB6IP2.R6 225 290
• NCBIGene 36.3 23085
• Single exon skipping, size difference: 65
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_178040

• pfam Cast 829aa 1e-148 in ref transcript
  • RIM-binding protein of the cytomatrix active zone. This is a family of proteins that form part of the CAZ (cytomatrix at the active zone) complex which is involved in determining the site of synaptic vesicle fusion. The C-terminus is a PDZ-binding motif that binds directly to RIM (a small G protein Rab-3A effector). The family also contains four coiled-coil domains.
• Changed! pfam RBD-FIP 41aa 1e-07 in ref transcript
  • FIP domain. The FIP domain is the Rab11-binding domain (RBD) at the C-terminus of a family of Rab11-interacting proteins (FIPs). The Rab proteins constitute the largest family of small GTPases (>60 members in mammals). Among them Rab11 is a well characterised regulator of endocytic and recycling pathways. Rab11 associates with a broad range of post-Golgi organelles, including recycling endosomes.
• COG Smc 340aa 3e-09 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].
• COG Smc 318aa 3e-08 in ref transcript
• COG Smc 298aa 5e-06 in ref transcript

RAD50

• refseq_RAD50.F1 refseq_RAD50.R1 104 169
• NCBIGene 36.3 10111
• Alternative 5-prime, size difference: 65
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_005732

• Changed! cd ABC_Rad50 150aa 4e-33 in ref transcript
  • The catalytic domains of Rad50 are similar to the ATP-binding cassette of ABC transporters, but are not associated with membrane-spanning domains. The conserved ATP-binding motifs common to Rad50 and the ABC transporter family include the Walker A and Walker B motifs, the Q loop, a histidine residue in the switch region, a D-loop, and a conserved LSGG sequence. This conserved sequence, LSGG, is the most specific and characteristic motif of this family and is thus known as the ABC signature sequence.
• Changed! cd ABC_Rad50 165aa 1e-27 in ref transcript
• Changed! TIGR rad50 1311aa 0.0 in ref transcript
  • This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
• Changed! COG SbcC 676aa 8e-18 in ref transcript
  • ATPase involved in DNA repair [DNA replication, recombination, and repair].
• Changed! COG SbcC 870aa 5e-14 in ref transcript
• Changed! cd ABC_Rad50 98aa 2e-27 in modified transcript
• Changed! TIGR rad50 99aa 8e-53 in modified transcript
• Changed! COG SbcC 98aa 5e-12 in modified transcript

RALY

• refseq_RALY.F2 refseq_RALY.R2 170 218
• NCBIGene 36.3 22913
• Single exon skipping, size difference: 48
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_016732

• cd RRM 67aa 3e-11 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• smart RRM_2 67aa 7e-11 in ref transcript
  • RNA recognition motif.
• COG COG0724 95aa 1e-04 in ref transcript
  • RNA-binding proteins (RRM domain) [General function prediction only].

RANBP3

• refseq_RANBP3.F2 refseq_RANBP3.R2 179 383
• NCBIGene 36.3 8498
• Single exon skipping, size difference: 204
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_007322

• cd RanBD 125aa 3e-26 in ref transcript
  • Ran-binding domain; This domain of approximately 150 residues shares structural similarity to the PH domain, but lacks detectable sequence similarity. Ran is a Ras-like nuclear small GTPase, which regulates receptor-mediated transport between the nucleus and the cytoplasm. RanGTP hydrolysis is stimulated by RanGAP together with the Ran-binding domain containing acessory proteins RanBP1 and RanBP2. These accessory proteins stabilize the active GTP-bound form of Ran . The Ran-binding domain is found in multiple copies in Nuclear pore complex proteins.
• smart RanBD 111aa 3e-15 in ref transcript
  • Ran-binding domain. Domain of apporximately 150 residues that stabilises the GTP-bound form of Ran (the Ras-like nuclear small GTPase).
• COG YRB1 71aa 1e-04 in ref transcript
  • Ran GTPase-activating protein (Ran-binding protein) [Intracellular trafficking and secretion].

RAPH1

• refseq_RAPH1.F1 refseq_RAPH1.R1 200 356
• NCBIGene 36.3 65059
• Multiple exon skipping, size difference: 156
• Inclusion in the protein (no stop codon or frameshift), Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_213589

• cd PH_Apbb1ip 113aa 1e-54 in ref transcript
  • Apbb1ip (Amyloid beta (A4) Precursor protein-Binding, family B, member 1 Interacting Protein) pleckstrin homology (PH) domain. Apbb1ip consists of a Ras-associated domain and a PH domain. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
• cd GRB7_RA 82aa 6e-22 in ref transcript
  • Grb7_RA The RA (RAS-associated like) domain of Grb7. Grb7 is an adaptor molecule that mediates signal transduction from multiple cell surface receptors to various downstream signaling pathways. Grb7 and its related family members Grb10 and Grb14 share a conserved domain architecture that includes an amino-terminal proline-rich region, a central segment termed the GM region (for Grb and Mig) which includes the RA, PIR, and PH domains, and a carboxyl-terminal SH2 domain. Grb7/10/14 family proteins are phosphorylated on serine/threonine as well as tyrosine residues and are mainly localized to the cytoplasm.
• smart PH 109aa 5e-10 in ref transcript
  • Pleckstrin homology domain. Domain commonly found in eukaryotic signalling proteins. The domain family possesses multiple functions including the abilities to bind inositol phosphates, and various proteins. PH domains have been found to possess inserted domains (such as in PLC gamma, syntrophins) and to be inserted within other domains. Mutations in Brutons tyrosine kinase (Btk) within its PH domain cause X-linked agammaglobulinaemia (XLA) in patients. Point mutations cluster into the positively charged end of the molecule around the predicted binding site for phosphatidylinositol lipids.
• smart RA 85aa 5e-10 in ref transcript
  • Ras association (RalGDS/AF-6) domain. RasGTP effectors (in cases of AF6, canoe and RalGDS); putative RasGTP effectors in other cases. Kalhammer et al. have shown that not all RA domains bind RasGTP. Predicted structure similar to that determined, and that of the RasGTP-binding domain of Raf kinase. Predicted RA domains in PLC210 and nore1 found to bind RasGTP. Included outliers (Grb7, Grb14, adenylyl cyclases etc.).

RAPSN

• refseq_RAPSN.F1 refseq_RAPSN.R1 151 328
• NCBIGene 36.3 5913
• Multiple exon skipping, size difference: 177
• Exclusion in the protein (no frameshift), Exclusion in the protein (no frameshift)
• Reference transcript: NM_005055

• cd TPR 112aa 9e-07 in ref transcript
  • Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here.
• pfam Rapsyn_N 80aa 2e-31 in ref transcript
  • Rapsyn N-terminal myristoylation and linker region. Neuromuscular junction formation relies upon the clustering of acetylcholine receptors and other proteins in the muscle membrane. Rapsyn is a peripheral membrane protein that is selectively concentrated at the neuromuscular junction and is essential for the formation of synaptic acetylcholine receptor aggregates. Acetylcholine receptors fail to aggregate beneath nerve terminals in mice where rapsyn has been knocked out. The N-terminal six amino acids of rapsyn are its myristoylation site, and myristoylation is necessary for the targeting of the protein to the membrane.
• COG COG5540 41aa 1e-04 in ref transcript
  • RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones].

RASA1

• refseq_RASA1.F1 refseq_RASA1.R1 118 183
• NCBIGene 36.3 5921
• Alternative 5-prime, size difference: 65
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_002890

• Changed! cd RasGAP_p120GAP 315aa 1e-166 in ref transcript
  • p120GAP is a negative regulator of Ras that stimulates hydrolysis of bound GTP to GDP. Once the Ras regulator p120GAP, a member of the GAP protein family, is recruited to the membrane, it is transiently immobilized to interact with Ras-GTP. The down regulation of Ras by p120GAP is a critical step in the regulation of many cellular processes, which is disrupted in approximately 30% of human cancers. p120GAP contains SH2, SH3, PH, calcium- and lipid-binding domains, suggesting its involvement in a complex network of cellular interactions in vivo.
• Changed! cd PH_RasGAP_CG5898 80aa 2e-20 in ref transcript
  • RAS GTPase-activating protein (GAP) CG5898 Pleckstrin homology (PH) domain. This protein has a domain architecture of SH2-SH3-SH2-PH-C2-Ras_GAP. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinsases, regulators of G-proteins, endocytotic GTPAses, adaptors, a well as cytoskeletal associated molecules and in lipid associated enzymes.
• Changed! cd SH2 91aa 5e-16 in ref transcript
  • Src homology 2 domains; Signal transduction, involved in recognition of phosphorylated tyrosine (pTyr). SH2 domains typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites.
• Changed! cd SH2 80aa 4e-15 in ref transcript
• Changed! cd C2 98aa 1e-09 in ref transcript
  • Protein kinase C conserved region 2 (CalB); Ca2+-binding motif present in phospholipases, protein kinases C, and synaptotagmins (among others). Some do not appear to contain Ca2+-binding sites. Particular C2s appear to bind phospholipids, inositol polyphosphates,and intracellular proteins. Synaptotagmin and PLC C2s are permuted in sequence with respect to N- and C-terminal beta strands.
• Changed! cd SH3 44aa 6e-04 in ref transcript
  • Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
• Changed! smart RasGAP 347aa 1e-107 in ref transcript
  • GTPase-activator protein for Ras-like GTPases. All alpha-helical domain that accelerates the GTPase activity of Ras, thereby "switching" it into an "off" position. Improved domain limits from structure.
• Changed! pfam SH2 76aa 8e-23 in ref transcript
  • SH2 domain.
• Changed! pfam SH2 76aa 2e-20 in ref transcript
• Changed! smart C2 95aa 2e-09 in ref transcript
  • Protein kinase C conserved region 2 (CalB). Ca2+-binding motif present in phospholipases, protein kinases C, and synaptotamins (among others). Some do not appear to contain Ca2+-binding sites. Particular C2s appear to bind phospholipids, inositol polyphosphates, and intracellular proteins. Unusual occurrence in perforin. Synaptotagmin and PLC C2s are permuted in sequence with respect to N- and C-terminal beta strands. SMART detects C2 domains using one or both of two profiles.
• Changed! smart PH 84aa 4e-09 in ref transcript
  • Pleckstrin homology domain. Domain commonly found in eukaryotic signalling proteins. The domain family possesses multiple functions including the abilities to bind inositol phosphates, and various proteins. PH domains have been found to possess inserted domains (such as in PLC gamma, syntrophins) and to be inserted within other domains. Mutations in Brutons tyrosine kinase (Btk) within its PH domain cause X-linked agammaglobulinaemia (XLA) in patients. Point mutations cluster into the positively charged end of the molecule around the predicted binding site for phosphatidylinositol lipids.
• Changed! pfam SH3_1 53aa 2e-06 in ref transcript
  • SH3 domain. SH3 (Src homology 3) domains are often indicative of a protein involved in signal transduction related to cytoskeletal organisation. First described in the Src cytoplasmic tyrosine kinase. The structure is a partly opened beta barrel.
• Changed! COG IQG1 291aa 7e-04 in ref transcript
  • Protein involved in regulation of cellular morphogenesis/cytokinesis [Cell division and chromosome partitioning / Signal transduction mechanisms].
• Changed! COG COG5038 99aa 0.003 in ref transcript
  • Ca2+-dependent lipid-binding protein, contains C2 domain [General function prediction only].

RASGEF1C

• refseq_RASGEF1C.F1 refseq_RASGEF1C.R1 171 209
• NCBIGene 36.2 255426
• Single exon skipping, size difference: 38
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_175062

• Changed! cd RasGEF 243aa 4e-48 in ref transcript
  • Guanine nucleotide exchange factor for Ras-like small GTPases. Small GTP-binding proteins of the Ras superfamily function as molecular switches in fundamental events such as signal transduction, cytoskeleton dynamics and intracellular trafficking. Guanine-nucleotide-exchange factors (GEFs) positively regulate these GTP-binding proteins in response to a variety of signals. GEFs catalyze the dissociation of GDP from the inactive GTP-binding proteins. GTP can then bind and induce structural changes that allow interaction with effectors.
• cd REM 109aa 4e-11 in ref transcript
  • Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal domain (RasGef_N), also called REM domain (Ras exchanger motif). This domain is common in nucleotide exchange factors for Ras-like small GTPases and is typically found immediately N-terminal to the RasGef (Cdc25-like) domain. REM contacts the GTPase and is assumed to participate in the catalytic activity of the exchange factor. Proteins with the REM domain include Sos1 and Sos2, which relay signals from tyrosine-kinase mediated signalling to Ras, RasGRP1-4, RasGRF1,2, CNrasGEF, and RAP-specific nucleotide exchange factors, to name a few.
• Changed! smart RasGEF 248aa 2e-53 in ref transcript
  • Guanine nucleotide exchange factor for Ras-like small GTPases.
• pfam RasGEF_N 89aa 4e-07 in ref transcript
  • Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif. A subset of guanine nucleotide exchange factor for Ras-like small GTPases appear to possess this motif/domain N-terminal to the RasGef (Cdc25-like) domain.
• Changed! cd RasGEF 147aa 1e-36 in modified transcript
• Changed! smart RasGEF 147aa 3e-39 in modified transcript

RASGRP2

• refseq_RASGRP2.F2 refseq_RASGRP2.R2 257 363
• NCBIGene 36.2 10235
• Single exon skipping, size difference: 106
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_005825

• Changed! cd RasGEF 234aa 1e-62 in ref transcript
  • Guanine nucleotide exchange factor for Ras-like small GTPases. Small GTP-binding proteins of the Ras superfamily function as molecular switches in fundamental events such as signal transduction, cytoskeleton dynamics and intracellular trafficking. Guanine-nucleotide-exchange factors (GEFs) positively regulate these GTP-binding proteins in response to a variety of signals. GEFs catalyze the dissociation of GDP from the inactive GTP-binding proteins. GTP can then bind and induce structural changes that allow interaction with effectors.
• Changed! cd REM 112aa 2e-15 in ref transcript
  • Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal domain (RasGef_N), also called REM domain (Ras exchanger motif). This domain is common in nucleotide exchange factors for Ras-like small GTPases and is typically found immediately N-terminal to the RasGef (Cdc25-like) domain. REM contacts the GTPase and is assumed to participate in the catalytic activity of the exchange factor. Proteins with the REM domain include Sos1 and Sos2, which relay signals from tyrosine-kinase mediated signalling to Ras, RasGRP1-4, RasGRF1,2, CNrasGEF, and RAP-specific nucleotide exchange factors, to name a few.
• Changed! cd C1 50aa 4e-11 in ref transcript
  • Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
• Changed! cd EFh 52aa 1e-05 in ref transcript
  • EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers.
• Changed! smart RasGEF 234aa 8e-69 in ref transcript
  • Guanine nucleotide exchange factor for Ras-like small GTPases.
• Changed! smart RasGEFN 115aa 2e-20 in ref transcript
  • Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif. A subset of guanine nucleotide exchange factor for Ras-like small GTPases appear to possess this domain N-terminal to the RasGef (Cdc25-like) domain. The recent crystal structureof Sos shows that this domain is alpha-helical and plays a "purely structural role" (Nature 394, 337-343).
• Changed! pfam C1_1 51aa 4e-10 in ref transcript
  • Phorbol esters/diacylglycerol binding domain (C1 domain). This domain is also known as the Protein kinase C conserved region 1 (C1) domain.
• Changed! PRK PRK12309 60aa 1e-04 in ref transcript
  • transaldolase/EF-hand domain-containing protein; Provisional.

RASSF5

• refseq_RASSF5.F1 refseq_RASSF5.R1 262 378
• NCBIGene 36.3 83593
• Single exon skipping, size difference: 116
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_182663

• Changed! cd RASSF1_RA 94aa 5e-35 in ref transcript
  • RASSF1 (also known as RASSF3 and NORE1) is a tumour suppressor protein with a C-terminal Ras-associating (RA) domain that binds Ras. RASSF1 also binds the proapoptotic protein kinase MST1 and is thus thought to regulate the proapoptotic signalling pathway. RASSF1 also associates with microtubule-associated proteins like MAP1B and regulates tubulin polymerization. RASSF1 also binds CDC20 and regulates mitosis by inhibiting the anaphase-promoting complex and preventing degradation of cyclin A and cyclin B until the spindle checkpoint becomes fully operational.
• cd C1 38aa 9e-05 in ref transcript
  • Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
• Changed! smart RA 92aa 3e-14 in ref transcript
  • Ras association (RalGDS/AF-6) domain. RasGTP effectors (in cases of AF6, canoe and RalGDS); putative RasGTP effectors in other cases. Kalhammer et al. have shown that not all RA domains bind RasGTP. Predicted structure similar to that determined, and that of the RasGTP-binding domain of Raf kinase. Predicted RA domains in PLC210 and nore1 found to bind RasGTP. Included outliers (Grb7, Grb14, adenylyl cyclases etc.).
• pfam C1_1 38aa 4e-05 in ref transcript
  • Phorbol esters/diacylglycerol binding domain (C1 domain). This domain is also known as the Protein kinase C conserved region 1 (C1) domain.
• Changed! cd RASSF1_RA 59aa 7e-20 in modified transcript
• Changed! smart RA 56aa 4e-07 in modified transcript

RBBP6

• refseq_RBBP6.F2 refseq_RBBP6.R2 207 309
• NCBIGene 36.3 5930
• Single exon skipping, size difference: 102
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_006910

• cd RING 44aa 6e-08 in ref transcript
  • RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H).
• pfam DWNN 73aa 7e-28 in ref transcript
  • DWNN domain. DWNN is a ubiquitin like domain found at the N terminus of the RBBP6 family of splicing-associated proteins. The DWNN domain is independently expressed in higher vertebrates so it may function as a novel ubiquitin-like modifier of other proteins.
• smart RING 41aa 2e-08 in ref transcript
  • Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s).
• smart ZnF_C2HC 16aa 0.005 in ref transcript
  • zinc finger.
• COG COG5222 321aa 9e-40 in ref transcript
  • Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only].

RBBP8

• refseq_RBBP8.F1 refseq_RBBP8.R1 145 226
• NCBIGene 36.3 5932
• Alternative 5-prime, size difference: 81
• Inclusion in 5'UTR
• Reference transcript: NM_203291

• pfam CtIP_N 120aa 6e-48 in ref transcript
  • Tumour-suppressor protein CtIP N-terminal domain. CtIP is predominantly a nuclear protein that complexes with both BRCA1 and the BRCA1-associated RING domain protein (BARD1). At the protein level, CtIP expression varies with cell cycle progression in a pattern identical to that of BRCA1. Thus, the steady-state levels of CtIP polypeptides, which remain low in resting cells and G1 cycling cells, increase dramatically as Dividing cells traverse the G1/S boundary. CtIP can potentially modulate the functions ascribed to BRCA1 in transcriptional regulation, DNA repair, and/or cell cycle checkpoint control. This N-terminal domain carries a coiled-coil region and is essential for homodimerisation of the protein. The C-terminal domain is family CtIP_C and carries functionally important CxxC and RHR motifs, absence of which lead cells to grow slowly and show hypersensitivity to genotoxins.
• pfam SAE2 88aa 5e-14 in ref transcript
  • DNA repair protein SAE2/CtIP. SAE2 is a protein involved in repairing meiotic and mitotic double-strand breaks in DNA. It has been shown to negatively regulate DNA damage checkpoint signalling. SAE2 is homologous to the CtIP proteins in mammals.
• PRK PRK12704 130aa 0.003 in ref transcript
  • phosphodiesterase; Provisional.

RBBP8

• refseq_RBBP8.F3 refseq_RBBP8.R3 100 197
• NCBIGene 36.3 5932
• Single exon skipping, size difference: 97
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_002894

• pfam CtIP_N 120aa 6e-48 in ref transcript
  • Tumour-suppressor protein CtIP N-terminal domain. CtIP is predominantly a nuclear protein that complexes with both BRCA1 and the BRCA1-associated RING domain protein (BARD1). At the protein level, CtIP expression varies with cell cycle progression in a pattern identical to that of BRCA1. Thus, the steady-state levels of CtIP polypeptides, which remain low in resting cells and G1 cycling cells, increase dramatically as Dividing cells traverse the G1/S boundary. CtIP can potentially modulate the functions ascribed to BRCA1 in transcriptional regulation, DNA repair, and/or cell cycle checkpoint control. This N-terminal domain carries a coiled-coil region and is essential for homodimerisation of the protein. The C-terminal domain is family CtIP_C and carries functionally important CxxC and RHR motifs, absence of which lead cells to grow slowly and show hypersensitivity to genotoxins.
• Changed! pfam SAE2 88aa 5e-14 in ref transcript
  • DNA repair protein SAE2/CtIP. SAE2 is a protein involved in repairing meiotic and mitotic double-strand breaks in DNA. It has been shown to negatively regulate DNA damage checkpoint signalling. SAE2 is homologous to the CtIP proteins in mammals.
• PRK PRK12704 130aa 0.003 in ref transcript
  • phosphodiesterase; Provisional.

RBCK1

• refseq_RBCK1.F1 refseq_RBCK1.R1 127 272
• NCBIGene 36.3 10616
• Single exon skipping, size difference: 145
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_031229

• Changed! cd Hoil1_N 75aa 4e-35 in ref transcript
  • HOIL1_N HOIL-1 (heme-oxidized IRP2 ubiquitin ligase-1) is an E3 ubiquitin-protein ligase that recognizes heme-oxidized IRP2 (iron regulatory protein2) and is thought to affect the turnover of oxidatively damaged proteins. Hoil-1 has an amino-terminal ubiquitin-like domain as well as an RBR signature consisting of two RING finger domains separated by an IBR/DRIL domain.

RBM10

• refseq_RBM10.F1 refseq_RBM10.R1 152 383
• NCBIGene 36.3 8241
• Single exon skipping, size difference: 231
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_005676

• Changed! cd RRM 76aa 9e-09 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• cd RRM 81aa 1e-04 in ref transcript
• pfam G-patch 44aa 3e-13 in ref transcript
  • G-patch domain. This domain is found in a number of RNA binding proteins, and is also found in proteins that contain RNA binding domains. This suggests that this domain may have an RNA binding function. This domain has seven highly conserved glycines.
• Changed! smart RRM 67aa 5e-09 in ref transcript
  • RNA recognition motif.
• smart ZnF_RBZ 25aa 2e-07 in ref transcript
  • Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
• Changed! TIGR ELAV_HUD_SF 199aa 1e-04 in ref transcript
  • These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
• smart RRM 77aa 3e-04 in ref transcript
• Changed! COG COG0724 104aa 0.002 in ref transcript
  • RNA-binding proteins (RRM domain) [General function prediction only].
• Changed! cd RRM 72aa 2e-05 in modified transcript
• Changed! smart RRM 46aa 2e-06 in modified transcript

RBM3

• refseq_RBM3.F2 refseq_RBM3.R2 120 389
• NCBIGene 36.2 5935
• Single exon skipping, size difference: 269
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_006743

• Changed! cd RRM 75aa 5e-21 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• Changed! smart RRM 71aa 2e-20 in ref transcript
  • RNA recognition motif.
• Changed! COG COG0724 79aa 1e-11 in ref transcript
  • RNA-binding proteins (RRM domain) [General function prediction only].
• Changed! cd RRM 68aa 1e-18 in modified transcript
• Changed! smart RRM 65aa 4e-18 in modified transcript
• Changed! COG COG0724 74aa 5e-13 in modified transcript

RBM38

• refseq_RBM38.F1 refseq_RBM38.R1 132 187
• NCBIGene 36.3 55544
• Single exon skipping, size difference: 55
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_017495

• cd RRM 74aa 6e-17 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• smart RRM 70aa 3e-18 in ref transcript
  • RNA recognition motif.
• COG COG0724 91aa 1e-14 in ref transcript
  • RNA-binding proteins (RRM domain) [General function prediction only].

RBM39

• refseq_RBM39.F2 refseq_RBM39.R2 149 222
• NCBIGene 36.2 9584
• Single exon skipping, size difference: 73
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_184234

• Changed! cd RRM 73aa 1e-20 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• Changed! cd RRM 73aa 3e-09 in ref transcript
• Changed! TIGR SF-CC1 427aa 1e-152 in ref transcript
  • A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed.
• Changed! COG COG0724 99aa 9e-15 in ref transcript
  • RNA-binding proteins (RRM domain) [General function prediction only].

RBM39

• refseq_RBM39.F3 refseq_RBM39.R3 119 191
• NCBIGene 36.2 9584
• Single exon skipping, size difference: 72
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_184234

• Changed! cd RRM 73aa 1e-20 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• Changed! cd RRM 73aa 3e-09 in ref transcript
• Changed! TIGR SF-CC1 427aa 1e-152 in ref transcript
  • A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed.
• Changed! COG COG0724 99aa 9e-15 in ref transcript
  • RNA-binding proteins (RRM domain) [General function prediction only].

RBM39

• refseq_RBM39.F5 refseq_RBM39.R5 101 119
• NCBIGene 36.3 9584
• Alternative 3-prime, size difference: 18
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_184234

• cd RRM 73aa 1e-20 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• cd RRM 73aa 3e-09 in ref transcript
• Changed! TIGR SF-CC1 427aa 1e-152 in ref transcript
  • A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed.
• COG COG0724 99aa 9e-15 in ref transcript
  • RNA-binding proteins (RRM domain) [General function prediction only].
• Changed! TIGR SF-CC1 421aa 1e-150 in modified transcript

RBM9

• refseq_RBM9.F1 refseq_RBM9.R1 206 258
• NCBIGene 36.3 23543
• Single exon skipping, size difference: 40
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_001082578

• cd RRM 72aa 2e-20 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• smart RRM_2 72aa 2e-20 in ref transcript
  • RNA recognition motif.
• COG COG0724 86aa 3e-12 in ref transcript
  • RNA-binding proteins (RRM domain) [General function prediction only].

RBM9

• refseq_RBM9.F3 refseq_RBM9.R3 105 145
• NCBIGene 36.3 23543
• Single exon skipping, size difference: 40
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_001082578

• cd RRM 72aa 2e-20 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• smart RRM_2 72aa 2e-20 in ref transcript
  • RNA recognition motif.
• COG COG0724 86aa 3e-12 in ref transcript
  • RNA-binding proteins (RRM domain) [General function prediction only].

RBMS1

• refseq_RBMS1.F1 refseq_RBMS1.R1 189 299
• NCBIGene 36.3 5937
• Single exon skipping, size difference: 110
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_016836

• Changed! cd RRM 66aa 8e-14 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• Changed! cd RRM 51aa 1e-11 in ref transcript
• Changed! TIGR ELAV_HUD_SF 182aa 5e-22 in ref transcript
  • These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
• Changed! COG COG0724 175aa 3e-08 in ref transcript
  • RNA-binding proteins (RRM domain) [General function prediction only].
• Changed! COG COG0724 113aa 1e-07 in ref transcript

RBMS1

• refseq_RBMS1.F3 refseq_RBMS1.R3 100 148
• NCBIGene 36.3 5937
• Single exon skipping, size difference: 48
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_016836

• cd RRM 66aa 8e-14 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• cd RRM 51aa 1e-11 in ref transcript
• TIGR ELAV_HUD_SF 182aa 5e-22 in ref transcript
  • These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
• Changed! COG COG0724 175aa 3e-08 in ref transcript
  • RNA-binding proteins (RRM domain) [General function prediction only].
• COG COG0724 113aa 1e-07 in ref transcript
• Changed! COG COG0724 187aa 2e-08 in modified transcript

RBMS3

• refseq_RBMS3.F2 refseq_RBMS3.R2 112 160
• NCBIGene 36.3 27303
• Single exon skipping, size difference: 48
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001003793

• cd RRM 66aa 5e-14 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• cd RRM 51aa 7e-12 in ref transcript
• TIGR ELAV_HUD_SF 166aa 9e-23 in ref transcript
  • These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
• COG COG0724 143aa 2e-08 in ref transcript
  • RNA-binding proteins (RRM domain) [General function prediction only].
• Changed! COG COG0724 119aa 7e-07 in modified transcript

RBMS3

• refseq_RBMS3.F4 refseq_RBMS3.R4 111 162
• NCBIGene 36.3 27303
• Single exon skipping, size difference: 51
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001003793

• cd RRM 66aa 5e-14 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• cd RRM 51aa 7e-12 in ref transcript
• TIGR ELAV_HUD_SF 166aa 9e-23 in ref transcript
  • These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
• COG COG0724 143aa 2e-08 in ref transcript
  • RNA-binding proteins (RRM domain) [General function prediction only].
• Changed! TIGR PABP-1234 333aa 1e-18 in modified transcript
  • There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, and of unknown tissue range.
• Changed! COG COG0724 119aa 6e-07 in modified transcript

RBPMS

• refseq_RBPMS.F1 refseq_RBPMS.R1 144 230
• NCBIGene 36.3 11030
• Single exon skipping, size difference: 86
• Exclusion of the stop codon
• Reference transcript: NM_001008711

• cd RRM 74aa 1e-08 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• pfam RRM_1 62aa 9e-09 in ref transcript
  • RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain). The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have a N terminus rrm which is included in the seed. There is a second region towards the C terminus that has some features of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.

RBPMS

• refseq_RBPMS.F2 refseq_RBPMS.R2 149 355
• NCBIGene 36.3 11030
• Single exon skipping, size difference: 206
• Inclusion in 3'UTR
• Reference transcript: NM_001008711

• cd RRM 74aa 1e-08 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• pfam RRM_1 62aa 9e-09 in ref transcript
  • RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain). The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have a N terminus rrm which is included in the seed. There is a second region towards the C terminus that has some features of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.

RBPJ

• refseq_RBPSUH.F1 refseq_RBPSUH.R1 124 240
• NCBIGene 36.3 3516
• Single exon skipping, size difference: 116
• Exclusion of the protein initiation site
• Reference transcript: NM_005349

• cd IPT_RBP-Jkappa 89aa 2e-45 in ref transcript
  • IPT domain of the recombination signal Jkappa binding protein (RBP-Jkappa). RBP-J kappa, was initially considered to be involved in V(D)J recombination because of its DNA binding specificity and structural similarity to site-specific recombinases known as the integrase family. Further studies indicated that RBP-J kappa functions as a repressor of transcription, via destabilization of the general transcription factor IID and recruitment of histone deacetylase complexes.
• pfam Beta-trefoil 150aa 4e-68 in ref transcript
  • Beta-trefoil. Members of this family of DNA binding domains adopt a beta-trefoil fold, that is, a capped beta-barrel with internal pseudo threefold symmetry. In the DNA-binding protein LAG-1, it also is the site of mutually exclusive interactions with NotchIC (and the viral protein EBNA2) and corepressors (SMRT/N-Cor and CIR).
• pfam LAG1-DNAbind 132aa 3e-55 in ref transcript
  • LAG1, DNA binding. Members of this family are found in various eukaryotic hypothetical proteins and in the DNA-binding protein LAG-1. They adopt a beta sandwich structure, with nine strands in two beta-sheets, in a Greek-key topology, and allow for DNA binding.
• pfam TIG 81aa 1e-07 in ref transcript
  • IPT/TIG domain. This family consists of a domain that has an immunoglobulin like fold. These domains are found in cell surface receptors such as Met and Ron as well as in intracellular transcription factors where it is involved in DNA binding. CAUTION: This family does not currently recognise a significant number of members.

RBPJ

• refseq_RBPSUH.F3 refseq_RBPSUH.R1 144 327
• NCBIGene 36.3 3516
• Single exon skipping, size difference: 183
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_015874

• Changed! cd IPT_RBP-Jkappa 89aa 2e-45 in ref transcript
  • IPT domain of the recombination signal Jkappa binding protein (RBP-Jkappa). RBP-J kappa, was initially considered to be involved in V(D)J recombination because of its DNA binding specificity and structural similarity to site-specific recombinases known as the integrase family. Further studies indicated that RBP-J kappa functions as a repressor of transcription, via destabilization of the general transcription factor IID and recruitment of histone deacetylase complexes.
• Changed! pfam Beta-trefoil 150aa 3e-68 in ref transcript
  • Beta-trefoil. Members of this family of DNA binding domains adopt a beta-trefoil fold, that is, a capped beta-barrel with internal pseudo threefold symmetry. In the DNA-binding protein LAG-1, it also is the site of mutually exclusive interactions with NotchIC (and the viral protein EBNA2) and corepressors (SMRT/N-Cor and CIR).
• Changed! pfam LAG1-DNAbind 132aa 3e-55 in ref transcript
  • LAG1, DNA binding. Members of this family are found in various eukaryotic hypothetical proteins and in the DNA-binding protein LAG-1. They adopt a beta sandwich structure, with nine strands in two beta-sheets, in a Greek-key topology, and allow for DNA binding.
• Changed! pfam TIG 81aa 2e-07 in ref transcript
  • IPT/TIG domain. This family consists of a domain that has an immunoglobulin like fold. These domains are found in cell surface receptors such as Met and Ron as well as in intracellular transcription factors where it is involved in DNA binding. CAUTION: This family does not currently recognise a significant number of members.

RCCD1

• refseq_RCCD1.F1 refseq_RCCD1.R1 324 408
• NCBIGene 36.3 91433
• Single exon skipping, size difference: 84
• Exclusion in 5'UTR
• Reference transcript: NM_033544

• COG ATS1 181aa 1e-12 in ref transcript
  • Alpha-tubulin suppressor and related RCC1 domain-containing proteins [Cell division and chromosome partitioning / Cytoskeleton].

RECQL5

• refseq_RECQL5.F2 refseq_RECQL5.R2 197 278
• NCBIGene 36.2 9400
• Alternative 3-prime, size difference: 81
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_004259

• cd HELICc 117aa 4e-20 in ref transcript
  • Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process.
• Changed! cd DEXDc 125aa 3e-09 in ref transcript
  • DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
• Changed! TIGR recQ 397aa 2e-92 in ref transcript
  • The ATP-dependent DNA helicase RecQ of E. coli is about 600 residues long. This model represents bacterial proteins with a high degree of similarity in domain architecture and in primary sequence to E. coli RecQ. The model excludes eukaryotic and archaeal proteins with RecQ-like regions, as well as more distantly related bacterial helicases related to RecQ.
• pfam RecQ5 205aa 7e-87 in ref transcript
  • RecQ helicase protein-like 5 (RecQ5). This family represents a conserved region approximately 200 residues long within eukaryotic RecQ helicase protein-like 5 (RecQ5). The RecQ helicases have been implicated in DNA repair and recombination, and RecQ5 may have an important role in DNA metabolism.
• Changed! COG RecQ 396aa 4e-96 in ref transcript
  • Superfamily II DNA helicase [DNA replication, recombination, and repair].
• Changed! cd DEXDc 149aa 1e-16 in modified transcript
• Changed! TIGR recQ 424aa 1e-109 in modified transcript
• Changed! COG RecQ 423aa 1e-112 in modified transcript
• Changed! PRK PRK07003 150aa 0.010 in modified transcript
  • DNA polymerase III subunits gamma and tau; Validated.

RFC2

• refseq_RFC2.F1 refseq_RFC2.R1 181 283
• NCBIGene 36.3 5982
• Single exon skipping, size difference: 102
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_181471

• Changed! cd AAA 135aa 1e-18 in ref transcript
  • The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.
• pfam Rep_fac_C 89aa 2e-24 in ref transcript
  • Replication factor C. This family includes several subunits of DNA replication factor C.
• Changed! TIGR dnaX_nterm 278aa 6e-21 in ref transcript
  • This model represents the well-conserved first ~ 365 amino acids of the translation of the dnaX gene. The full-length product of the dnaX gene in the model bacterium E. coli is the DNA polymerase III tau subunit. A translational frameshift leads to early termination and a truncated protein subunit gamma, about 1/3 shorter than tau and present in roughly equal amounts. This frameshift mechanism is not necessarily universal for species with DNA polymerase III but appears conserved in the exterme thermophile Thermus thermophilis.
• Changed! PRK rfc 310aa 3e-99 in ref transcript
  • replication factor C small subunit; Reviewed.
• Changed! cd AAA 101aa 3e-08 in modified transcript
• Changed! TIGR dnaX_nterm 244aa 2e-12 in modified transcript
• Changed! PRK rfc 276aa 1e-81 in modified transcript

RFC3

• refseq_RFC3.F2 refseq_RFC3.R2 139 172
• NCBIGene 36.2 5983
• Alternative 3-prime, size difference: 33
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_002915

• cd AAA 159aa 3e-08 in ref transcript
  • The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.
• pfam RFC-E_C 95aa 2e-42 in ref transcript
  • Clamp-loader complex subunit E C-terminus. This is the C-terminal domain of RFC-E, one of the five RFC proteins of the clamp loader complex (replication factor-C, RFC) which binds to the DNA sliding clamp (proliferating cell nuclear antigen, PCNA). The five modules of RFC assemble into a right-handed spiral, which results in only three of the five RFC subunits (RFC-A, RFC-B and RFC-C) making contact with PCNA, leaving a wedge-shaped gap between RFC-E and the PCNA clamp-loader complex. The C-terminal is vital for the correct orientation of RFC-E with respect to RFC-A.
• Changed! TIGR holB 169aa 1e-08 in ref transcript
  • At position 126-127 of the seed alignment, this family lacks the HM motif of gamma/tau; at 132 it has a near-invariant A vs. an invariant F in gamma/tau.
• Changed! TIGR dnaX_nterm 173aa 0.003 in ref transcript
  • This model represents the well-conserved first ~ 365 amino acids of the translation of the dnaX gene. The full-length product of the dnaX gene in the model bacterium E. coli is the DNA polymerase III tau subunit. A translational frameshift leads to early termination and a truncated protein subunit gamma, about 1/3 shorter than tau and present in roughly equal amounts. This frameshift mechanism is not necessarily universal for species with DNA polymerase III but appears conserved in the exterme thermophile Thermus thermophilis.
• Changed! PRK PRK12402 337aa 1e-40 in ref transcript
  • replication factor C small subunit 2; Reviewed.
• Changed! TIGR holB 168aa 3e-08 in modified transcript
• Changed! PRK PRK12402 326aa 4e-38 in modified transcript

RFC5

• refseq_RFC5.F1 refseq_RFC5.R1 106 470
• NCBIGene 36.3 5985
• Single exon skipping, size difference: 364
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_007370

• Changed! cd AAA 142aa 5e-16 in ref transcript
  • The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.
• Changed! TIGR dnaX_nterm 267aa 2e-26 in ref transcript
  • This model represents the well-conserved first ~ 365 amino acids of the translation of the dnaX gene. The full-length product of the dnaX gene in the model bacterium E. coli is the DNA polymerase III tau subunit. A translational frameshift leads to early termination and a truncated protein subunit gamma, about 1/3 shorter than tau and present in roughly equal amounts. This frameshift mechanism is not necessarily universal for species with DNA polymerase III but appears conserved in the exterme thermophile Thermus thermophilis.
• Changed! PRK rfc 313aa 4e-92 in ref transcript
  • replication factor C small subunit; Reviewed.

TRIM13

• refseq_RFP2.F1 refseq_RFP2.R1 106 220
• NCBIGene 36.3 10206
• Single exon skipping, size difference: 114
• Exclusion of the protein initiation site
• Reference transcript: NM_001007278

• cd RING 53aa 1e-06 in ref transcript
  • RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H).
• smart RING 48aa 2e-07 in ref transcript
  • Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s).
• pfam zf-B_box 42aa 2e-06 in ref transcript
  • B-box zinc finger.
• COG COG5222 84aa 0.002 in ref transcript
  • Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only].

RFWD2

• refseq_RFWD2.F1 refseq_RFWD2.R1 266 338
• NCBIGene 36.3 64326
• Single exon skipping, size difference: 60
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_022457

• cd WD40 307aa 6e-33 in ref transcript
  • WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.
• cd RING 42aa 6e-06 in ref transcript
  • RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H).
• smart RING 38aa 2e-07 in ref transcript
  • Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s).
• pfam WD40 40aa 0.003 in ref transcript
  • WD domain, G-beta repeat.
• COG COG2319 284aa 8e-17 in ref transcript
  • FOG: WD40 repeat [General function prediction only].
• COG PEX10 41aa 4e-04 in ref transcript
  • RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones].

RFWD2

• refseq_RFWD2.F2 refseq_RFWD2.R2 321 381
• NCBIGene 36.3 64326
• Single exon skipping, size difference: 60
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_022457

• cd WD40 307aa 6e-33 in ref transcript
  • WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.
• cd RING 42aa 6e-06 in ref transcript
  • RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H).
• smart RING 38aa 2e-07 in ref transcript
  • Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s).
• pfam WD40 40aa 0.003 in ref transcript
  • WD domain, G-beta repeat.
• COG COG2319 284aa 8e-17 in ref transcript
  • FOG: WD40 repeat [General function prediction only].
• COG PEX10 41aa 4e-04 in ref transcript
  • RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones].

RFX2

• refseq_RFX2.F1 refseq_RFX2.R1 282 357
• NCBIGene 36.3 5990
• Single exon skipping, size difference: 75
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000635

• pfam RFX1_trans_act 156aa 1e-28 in ref transcript
  • RFX1 transcription activation region. The RFX family is a family of winged-helix DNA binding proteins. RFX1 is a regulatory factor essential for expression of MHC class II genes. This region is to found N terminal to the RFX DNA binding region (pfam02257) in some mammalian RFX proteins, and is thought to activate transcription when associated with DNA. Deletion analysis has identified the region 233-351 in human RFX1 as being required for maximal activation.
• Changed! pfam RFX_DNA_binding 65aa 1e-20 in ref transcript
  • RFX DNA-binding domain. RFX is a regulatory factor which binds to the X box of MHC class II genes and is essential for their expression. The DNA-binding domain of RFX is the central domain of the protein and binds ssDNA as either a monomer or homodimer.
• Changed! pfam RFX_DNA_binding 83aa 2e-23 in modified transcript

RFXANK

• refseq_RFXANK.F1 refseq_RFXANK.R1 126 192
• NCBIGene 36.3 8625
• Single exon skipping, size difference: 66
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_003721

• cd ANK 125aa 3e-24 in ref transcript
  • ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats.
• pfam Ank 28aa 6e-04 in ref transcript
  • Ankyrin repeat. There's no clear separation between noise and signal on the HMM search Ankyrin repeats generally consist of a beta, alpha, alpha, beta order of secondary structures. The repeats associate to form a higher order structure.
• pfam Ank 29aa 8e-04 in ref transcript
• Changed! COG Arp 192aa 7e-13 in ref transcript
  • FOG: Ankyrin repeat [General function prediction only].
• Changed! COG Arp 145aa 2e-12 in modified transcript

RFXANK

• refseq_RFXANK.F4 refseq_RFXANK.R3 175 244
• NCBIGene 36.3 8625
• Single exon skipping, size difference: 66
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_003721

• cd ANK 125aa 3e-24 in ref transcript
  • ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats.
• pfam Ank 28aa 6e-04 in ref transcript
  • Ankyrin repeat. There's no clear separation between noise and signal on the HMM search Ankyrin repeats generally consist of a beta, alpha, alpha, beta order of secondary structures. The repeats associate to form a higher order structure.
• pfam Ank 29aa 8e-04 in ref transcript
• Changed! COG Arp 192aa 7e-13 in ref transcript
  • FOG: Ankyrin repeat [General function prediction only].
• Changed! COG Arp 145aa 2e-12 in modified transcript

RGMB

• refseq_RGMB.F1 refseq_RGMB.R1 132 377
• NCBIGene 36.3 285704
• Alternative 3-prime, size difference: 245
• Inclusion in 5'UTR
• Reference transcript: NM_001012761

• pfam RGM_C 214aa 5e-97 in ref transcript
  • Repulsive guidance molecule (RGM) C-terminus. This family consists of several mammalian and one bird sequence from Gallus gallus (Chicken). This family represents the C-terminal region of several sequences but in others it represents the full protein. All of the mammalian proteins are hypothetical and have no known function but the member from chicken is annotated as being a repulsive guidance molecule (RGM). RGM is a GPI-linked axon guidance molecule of the retinotectal system. RGM is repulsive for a subset of axons, those from the temporal half of the retina. Temporal retinal axons invade the anterior optic tectum in a superficial layer, and encounter RGM expressed in a gradient with increasing concentration along the anterior-posterior axis. Temporal axons are able to receive posterior-dependent information by sensing gradients or concentrations of guidance cues. Thus, RGM is likely to provide positional information for temporal axons invading the optic tectum in the stratum opticum.
• pfam RGM_N 176aa 5e-50 in ref transcript
  • Repulsive guidance molecule (RGM) N-terminus. This family consists of the N-terminal region of several mammalian and one bird sequence from Gallus gallus (Chicken). All of the mammalian proteins are hypothetical and have no known function but the member from chicken is annotated as being a repulsive guidance molecule (RGM). RGM is a GPI-linked axon guidance molecule of the retinotectal system. RGM is repulsive for a subset of axons, those from the temporal half of the retina. Temporal retinal axons invade the anterior optic tectum in a superficial layer, and encounter RGM expressed in a gradient with increasing concentration along the anterior-posterior axis. Temporal axons are able to receive posterior-dependent information by sensing gradients or concentrations of guidance cues. Thus, RGM is likely to provide positional information for temporal axons invading the optic tectum in the stratum opticum.

RGNEF

• refseq_RGNEF.F1 refseq_RGNEF.R1 228 360
• NCBIGene 36.2 64283
• Single exon skipping, size difference: 132
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: XM_932949

• cd RhoGEF 193aa 4e-34 in ref transcript
  • Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.
• cd C1 46aa 4e-06 in ref transcript
  • Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
• smart RhoGEF 190aa 1e-39 in ref transcript
  • Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases. Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains. Improved coverage.
• smart C1 46aa 3e-06 in ref transcript
  • Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
• COG ROM1 267aa 3e-05 in ref transcript
  • RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms].

RGR

• refseq_RGR.F2 refseq_RGR.R2 280 394
• NCBIGene 36.3 5995
• Single exon skipping, size difference: 114
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_002921

• Changed! pfam 7tm_1 229aa 7e-11 in ref transcript
  • 7 transmembrane receptor (rhodopsin family). This family contains, amongst other G-protein-coupled receptors (GCPRs), members of the opsin family, which have been considered to be typical members of the rhodopsin superfamily. They share several motifs, mainly the seven transmembrane helices, GCPRs of the rhodopsin superfamily. All opsins bind a chromophore, such as 11-cis-retinal. The function of most opsins other than the photoisomerases is split into two steps: light absorption and G-protein activation. Photoisomerases, on the other hand, are not coupled to G-proteins - they are thought to generate and supply the chromophore that is used by visual opsins.
• Changed! pfam 7tm_1 170aa 6e-10 in modified transcript

RGS13

• refseq_RGS13.F1 refseq_RGS13.R1 117 157
• NCBIGene 36.3 6003
• Single exon skipping, size difference: 40
• Exclusion in 5'UTR
• Reference transcript: NM_002927

• pfam RGS 116aa 2e-35 in ref transcript
  • Regulator of G protein signaling domain. RGS family members are GTPase-activating proteins for heterotrimeric G-protein alpha-subunits.

RHBDF2

• refseq_RHBDF2.F1 refseq_RHBDF2.R1 192 279
• NCBIGene 36.3 79651
• Alternative 3-prime, size difference: 87
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_024599

• pfam Rhomboid 124aa 4e-24 in ref transcript
  • Rhomboid family. This family contains integral membrane proteins that are related to Drosophila rhomboid protein. Members of this family are found in bacteria and eukaryotes. Rhomboid promotes the cleavage of the membrane-anchored TGF-alpha-like growth factor Spitz, allowing it to activate the Drosophila EGF receptor. Analysis has shown that Rhomboid-1 is an intramembrane serine protease (EC:3.4.21.105). Parasite-encoded rhomboid enzymes are also important for invasion of host cells by Toxoplasma and the malaria parasite.
• COG GlpG 133aa 8e-14 in ref transcript
  • Uncharacterized membrane protein (homolog of Drosophila rhomboid) [General function prediction only].

RHCE

• refseq_RHCE.F1 refseq_RHCE.R1 179 259
• NCBIGene 36.3 6006
• Single exon skipping, size difference: 80
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_020485

• Changed! pfam Ammonium_transp 360aa 2e-48 in ref transcript
  • Ammonium Transporter Family.
• COG AmtB 104aa 1e-04 in ref transcript
  • Ammonia permease [Inorganic ion transport and metabolism].
• Changed! pfam Ammonium_transp 329aa 9e-49 in modified transcript

RHCE

• refseq_RHCE.F3 refseq_RHCE.R3 147 281
• NCBIGene 36.3 6006
• Single exon skipping, size difference: 134
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_020485

• Changed! pfam Ammonium_transp 360aa 2e-48 in ref transcript
  • Ammonium Transporter Family.
• Changed! COG AmtB 104aa 1e-04 in ref transcript
  • Ammonia permease [Inorganic ion transport and metabolism].
• Changed! pfam Ammonium_transp 293aa 1e-48 in modified transcript
• Changed! COG AmtB 108aa 2e-05 in modified transcript

RHCE

• refseq_RHCE.F5 refseq_RHCE.R5 105 420
• NCBIGene 36.3 6006
• Multiple exon skipping, size difference: 315
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_020485

• Changed! pfam Ammonium_transp 360aa 2e-48 in ref transcript
  • Ammonium Transporter Family.
• Changed! COG AmtB 104aa 1e-04 in ref transcript
  • Ammonia permease [Inorganic ion transport and metabolism].
• Changed! pfam Ammonium_transp 150aa 4e-13 in modified transcript
• Changed! pfam Ammonium_transp 110aa 4e-07 in modified transcript

RHOT1

• refseq_RHOT1.F1 refseq_RHOT1.R1 111 207
• NCBIGene 36.3 55288
• Single exon skipping, size difference: 96
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001033568

• cd Miro1 165aa 8e-74 in ref transcript
  • Miro1 subfamily. Miro (mitochondrial Rho) proteins have tandem GTP-binding domains separated by a linker region containing putative calcium-binding EF hand motifs. Genes encoding Miro-like proteins were found in several eukaryotic organisms. This CD represents the N-terminal GTPase domain of Miro proteins. These atypical Rho GTPases have roles in mitochondrial homeostasis and apoptosis. Most Rho proteins contain a lipid modification site at the C-terminus; however, Miro is one of few Rho subfamilies that lack this feature.
• Changed! cd Miro2 166aa 8e-71 in ref transcript
  • Miro2 subfamily. Miro (mitochondrial Rho) proteins have tandem GTP-binding domains separated by a linker region containing putative calcium-binding EF hand motifs. Genes encoding Miro-like proteins were found in several eukaryotic organisms. This CD represents the putative GTPase domain in the C terminus of Miro proteins. These atypical Rho GTPases have roles in mitochondrial homeostasis and apoptosis. Most Rho proteins contain a lipid modification site at the C-terminus; however, Miro is one of few Rho subfamilies that lack this feature.
• pfam EF_assoc_2 89aa 2e-38 in ref transcript
  • EF hand associated. This region predominantly appears near EF-hands (pfam00036) in GTP-binding proteins. It is found in all three eukaryotic kingdoms.
• pfam EF_assoc_1 75aa 1e-23 in ref transcript
  • EF hand associated. This region typically appears on the C-terminus of EF hands in GTP-binding proteins such as Arht/Rhot (may be involved in mitochondrial homeostasis and apoptosis). The EF hand associated region is found in yeast, vertebrates and plants.
• smart RHO 163aa 5e-15 in ref transcript
  • Rho (Ras homology) subfamily of Ras-like small GTPases. Members of this subfamily of Ras-like small GTPases include Cdc42 and Rac, as well as Rho isoforms.
• pfam Miro 111aa 2e-11 in ref transcript
  • Miro-like protein. Mitochondrial Rho proteins (Miro-1 and Miro-2), are atypical Rho GTPases. They have a unique domain organisation, with tandem GTP-binding domains and two EF hand domains (pfam00036), that may bind calcium. They are also larger than classical small GTPases. It has been proposed that they are involved in mitochondrial homeostasis and apoptosis.
• COG COG1100 173aa 5e-15 in ref transcript
  • GTPase SAR1 and related small G proteins [General function prediction only].
• Changed! cd Miro2 167aa 1e-71 in modified transcript

RHOT1

• refseq_RHOT1.F2 refseq_RHOT1.R2 276 400
• NCBIGene 36.2 55288
• Single exon skipping, size difference: 124
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_001033568

• Changed! cd Miro1 165aa 8e-74 in ref transcript
  • Miro1 subfamily. Miro (mitochondrial Rho) proteins have tandem GTP-binding domains separated by a linker region containing putative calcium-binding EF hand motifs. Genes encoding Miro-like proteins were found in several eukaryotic organisms. This CD represents the N-terminal GTPase domain of Miro proteins. These atypical Rho GTPases have roles in mitochondrial homeostasis and apoptosis. Most Rho proteins contain a lipid modification site at the C-terminus; however, Miro is one of few Rho subfamilies that lack this feature.
• Changed! cd Miro2 166aa 8e-71 in ref transcript
  • Miro2 subfamily. Miro (mitochondrial Rho) proteins have tandem GTP-binding domains separated by a linker region containing putative calcium-binding EF hand motifs. Genes encoding Miro-like proteins were found in several eukaryotic organisms. This CD represents the putative GTPase domain in the C terminus of Miro proteins. These atypical Rho GTPases have roles in mitochondrial homeostasis and apoptosis. Most Rho proteins contain a lipid modification site at the C-terminus; however, Miro is one of few Rho subfamilies that lack this feature.
• Changed! pfam EF_assoc_2 89aa 2e-38 in ref transcript
  • EF hand associated. This region predominantly appears near EF-hands (pfam00036) in GTP-binding proteins. It is found in all three eukaryotic kingdoms.
• Changed! pfam EF_assoc_1 75aa 1e-23 in ref transcript
  • EF hand associated. This region typically appears on the C-terminus of EF hands in GTP-binding proteins such as Arht/Rhot (may be involved in mitochondrial homeostasis and apoptosis). The EF hand associated region is found in yeast, vertebrates and plants.
• Changed! smart RHO 163aa 5e-15 in ref transcript
  • Rho (Ras homology) subfamily of Ras-like small GTPases. Members of this subfamily of Ras-like small GTPases include Cdc42 and Rac, as well as Rho isoforms.
• Changed! pfam Miro 111aa 2e-11 in ref transcript
  • Miro-like protein. Mitochondrial Rho proteins (Miro-1 and Miro-2), are atypical Rho GTPases. They have a unique domain organisation, with tandem GTP-binding domains and two EF hand domains (pfam00036), that may bind calcium. They are also larger than classical small GTPases. It has been proposed that they are involved in mitochondrial homeostasis and apoptosis.
• Changed! COG COG1100 173aa 5e-15 in ref transcript
  • GTPase SAR1 and related small G proteins [General function prediction only].
• Changed! cd Miro1 29aa 6e-08 in modified transcript
• Changed! pfam Miro 27aa 0.007 in modified transcript

RIPK5

• refseq_RIPK5.F1 refseq_RIPK5.R1 114 249
• NCBIGene 36.3 25778
• Single exon skipping, size difference: 135
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_015375

• Changed! cd S_TKc 245aa 2e-37 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• Changed! pfam Pkinase 245aa 2e-38 in ref transcript
  • Protein kinase domain.
• Changed! COG SPS1 245aa 1e-20 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].
• Changed! cd S_TKc 200aa 2e-27 in modified transcript
• Changed! pfam Pkinase 168aa 2e-27 in modified transcript
• Changed! COG SPS1 176aa 2e-15 in modified transcript

RNASE4

• refseq_RNASE4.F2 refseq_RNASE4.R2 278 382
• NCBIGene 36.2 6038
• Single exon skipping, size difference: 104
• Exclusion of the stop codon
• Reference transcript: NM_194430

RNF12

• refseq_RNF12.F2 refseq_RNF12.R2 231 291
• NCBIGene 36.3 51132
• Single exon skipping, size difference: 60
• Exclusion in 5'UTR
• Reference transcript: NM_183353

• cd RING 46aa 1e-10 in ref transcript
  • RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H).
• smart RING 41aa 6e-09 in ref transcript
  • Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s).
• COG COG5540 75aa 2e-09 in ref transcript
  • RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones].

RNF121

• refseq_RNF121.F1 refseq_RNF121.R1 105 368
• NCBIGene 36.3 55298
• Multiple exon skipping, size difference: 263
• Exclusion in the protein causing a frameshift, Exclusion in the protein (no frameshift)
• Reference transcript: NM_018320

• Changed! cd RING 54aa 7e-04 in ref transcript
  • RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H).
• Changed! smart RING 50aa 0.001 in ref transcript
  • Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s).
• Changed! COG HRD1 58aa 7e-06 in ref transcript
  • HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones].

RNF121

• refseq_RNF121.F3 refseq_RNF121.R3 161 199
• NCBIGene 36.3 55298
• Single exon skipping, size difference: 38
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_018320

• Changed! cd RING 54aa 7e-04 in ref transcript
  • RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H).
• Changed! smart RING 50aa 0.001 in ref transcript
  • Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s).
• Changed! COG HRD1 58aa 7e-06 in ref transcript
  • HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones].

RNF13

• refseq_RNF13.F2 refseq_RNF13.R2 184 286
• NCBIGene 36.3 11342
• Single exon skipping, size difference: 102
• Exclusion in 5'UTR
• Reference transcript: NM_007282

• cd PA_C_RZF_like 158aa 8e-50 in ref transcript
  • PA_C-RZF_ like: Protease-associated (PA) domain C_RZF-like. This group includes various PA domain-containing proteins similar to C-RZF (chicken embryo RING zinc finger) protein. These proteins contain a C3H2C3 RING finger. C-RZF is expressed in embryo cells and is restricted mainly to brain and heart, it is localized to both the nucleus and endosomes. Additional C3H2C3 RING finger proteins belonging to this group, include Arabidopsis ReMembR-H2 protein and mouse sperizin. ReMembR-H2 is likely to be an integral membrane protein, and to traffic through the endosomal pathway. Sperizin is expressed in haploid germ cells and localized in the cytoplasm, it may participate in spermatogenesis. The significance of the PA domain to these proteins has not been ascertained. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate.
• cd RING 46aa 1e-10 in ref transcript
  • RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H).
• pfam PA 92aa 2e-11 in ref transcript
  • PA domain. The PA (Protease associated) domain is found as an insert domain in diverse proteases. The PA domain is also found in a plant vacuolar sorting receptor and members of the RZF family. It has been suggested that this domain forms a lid-like structure that covers the active site in active proteases, and is involved in protein recognition in vacuolar sorting receptors.
• smart RING 42aa 7e-09 in ref transcript
  • Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s).
• COG COG5540 253aa 1e-11 in ref transcript
  • RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones].

RNF135

• refseq_RNF135.F1 refseq_RNF135.R1 120 283
• NCBIGene 36.3 84282
• Single exon skipping, size difference: 163
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_032322

• cd RING 44aa 5e-06 in ref transcript
  • RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H).
• Changed! smart SPRY 109aa 6e-15 in ref transcript
  • Domain in SPla and the RYanodine Receptor. Domain of unknown function. Distant homologues are domains in butyrophilin/marenostrin/pyrin homologues.
• Changed! smart RING 42aa 1e-05 in ref transcript
  • Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s).
• Changed! smart PRY 51aa 0.006 in ref transcript
  • associated with SPRY domains.
• Changed! COG PEX10 49aa 4e-04 in ref transcript
  • RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones].
• Changed! TIGR rad18 73aa 8e-06 in modified transcript
  • This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
• Changed! COG RAD18 69aa 1e-04 in modified transcript
  • RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms].

RNF138

• refseq_RNF138.F1 refseq_RNF138.R1 128 410
• NCBIGene 36.3 51444
• Multiple exon skipping, size difference: 282
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_016271

• Changed! cd RING 44aa 2e-06 in ref transcript
  • RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H).
• Changed! smart RING 40aa 9e-05 in ref transcript
  • Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s).
• Changed! COG COG5222 40aa 2e-05 in ref transcript
  • Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only].

RNF14

• refseq_RNF14.F1 refseq_RNF14.R1 176 350
• NCBIGene 36.3 9604
• Single exon skipping, size difference: 174
• Exclusion in 5'UTR
• Reference transcript: NM_004290

• pfam RWD 130aa 3e-14 in ref transcript
  • RWD domain. This domain was identified in WD40 repeat proteins and Ring finger domain proteins. The function of this domain is unknown. GCN2 is the alpha-subunit of the only translation initiation factor (eIF2 alpha) kinase that appears in all eukaryotes. Its function requires an interaction with GCN1 via the domain at its N-terminus, which is termed the RWD domain after three major RWD-containing proteins: RING finger-containing proteins, WD-repeat-containing proteins, and yeast DEAD (DEXD)-like helicases. The structure forms an alpha + beta sandwich fold consisting of two layers: a four-stranded antiparallel beta-sheet, and three side-by-side alpha-helices.
• pfam IBR 62aa 4e-12 in ref transcript
  • IBR domain. The IBR (In Between Ring fingers) domain is often found to occur between pairs of ring fingers (pfam00097). This domain has also been called the C6HC domain and DRIL (for double RING finger linked) domain. Proteins that contain two Ring fingers and an IBR domain (these proteins are also termed RBR family proteins) are thought to exist in all eukaryotic organisms. RBR family members play roles in protein quality control and can indirectly regulate transcription. Evidence suggests that RBR proteins are often parts of cullin-containing ubiquitin ligase complexes. The ubiquitin ligase Parkin is an RBR family protein whose mutations are involved in forms of familial Parkinson's disease.

RNF14

• refseq_RNF14.F4 refseq_RNF14.R4 217 369
• NCBIGene 36.3 9604
• Single exon skipping, size difference: 152
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_183399

• Changed! pfam RWD 130aa 3e-14 in ref transcript
  • RWD domain. This domain was identified in WD40 repeat proteins and Ring finger domain proteins. The function of this domain is unknown. GCN2 is the alpha-subunit of the only translation initiation factor (eIF2 alpha) kinase that appears in all eukaryotes. Its function requires an interaction with GCN1 via the domain at its N-terminus, which is termed the RWD domain after three major RWD-containing proteins: RING finger-containing proteins, WD-repeat-containing proteins, and yeast DEAD (DEXD)-like helicases. The structure forms an alpha + beta sandwich fold consisting of two layers: a four-stranded antiparallel beta-sheet, and three side-by-side alpha-helices.
• Changed! pfam IBR 62aa 4e-12 in ref transcript
  • IBR domain. The IBR (In Between Ring fingers) domain is often found to occur between pairs of ring fingers (pfam00097). This domain has also been called the C6HC domain and DRIL (for double RING finger linked) domain. Proteins that contain two Ring fingers and an IBR domain (these proteins are also termed RBR family proteins) are thought to exist in all eukaryotic organisms. RBR family members play roles in protein quality control and can indirectly regulate transcription. Evidence suggests that RBR proteins are often parts of cullin-containing ubiquitin ligase complexes. The ubiquitin ligase Parkin is an RBR family protein whose mutations are involved in forms of familial Parkinson's disease.
• Changed! pfam RWD 45aa 0.002 in modified transcript

RNF34

• refseq_RNF34.F2 refseq_RNF34.R2 135 201
• NCBIGene 36.3 80196
• Single exon skipping, size difference: 66
• Exclusion of the protein initiation site
• Reference transcript: NM_194271

RNF38

• refseq_RNF38.F2 refseq_RNF38.R2 227 377
• NCBIGene 36.3 152006
• Single exon skipping, size difference: 150
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_022781

• cd RING 44aa 6e-07 in ref transcript
  • RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H).
• smart RING 41aa 3e-06 in ref transcript
  • Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s).
• COG COG5540 42aa 7e-10 in ref transcript
  • RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones].

RNF38

• refseq_RNF38.F4 refseq_RNF38.R3 252 402
• NCBIGene 36.3 152006
• Single exon skipping, size difference: 150
• Exclusion in 5'UTR
• Reference transcript: NM_194328

• cd RING 44aa 8e-07 in ref transcript
  • RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H).
• smart RING 41aa 4e-06 in ref transcript
  • Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s).
• COG COG5540 42aa 5e-10 in ref transcript
  • RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones].

RNF41

• refseq_RNF41.F2 refseq_RNF41.R2 221 364
• NCBIGene 36.3 10193
• Single exon skipping, size difference: 143
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_194359

• Changed! cd RING 43aa 7e-06 in ref transcript
  • RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H).
• Changed! pfam USP8_interact 179aa 8e-86 in ref transcript
  • USP8 interacting. This domain interacts with the UBP deubiquitinating enzyme USP8.
• Changed! smart RING 38aa 4e-05 in ref transcript
  • Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s).
• Changed! COG COG5219 44aa 0.002 in ref transcript
  • Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only].

RNF41

• refseq_RNF41.F3 refseq_RNF41.R3 189 332
• NCBIGene 36.3 10193
• Alternative 5-prime, size difference: 143
• Exclusion in 5'UTR
• Reference transcript: NM_005785

• cd RING 43aa 7e-06 in ref transcript
  • RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H).
• pfam USP8_interact 179aa 8e-86 in ref transcript
  • USP8 interacting. This domain interacts with the UBP deubiquitinating enzyme USP8.
• smart RING 38aa 4e-05 in ref transcript
  • Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s).
• COG COG5219 44aa 0.002 in ref transcript
  • Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only].

RNF8

• refseq_RNF8.F2 refseq_RNF8.R2 190 395
• NCBIGene 36.3 9025
• Single exon skipping, size difference: 205
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_003958

• cd FHA 95aa 2e-11 in ref transcript
  • Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins localize to the nucleus, where they participate in establishing or maintaining cell cycle checkpoints, DNA repair, or transcriptional regulation. Members of the FHA family include: Dun1, Rad53, Cds1, Mek1, KAPP(kinase-associated protein phosphatase),and Ki-67 (a human nuclear protein related to cell proliferation).
• Changed! cd RING 43aa 5e-08 in ref transcript
  • RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H).
• pfam FHA 72aa 3e-12 in ref transcript
  • FHA domain. The FHA (Forkhead-associated) domain is a phosphopeptide binding motif.
• Changed! smart RING 38aa 7e-08 in ref transcript
  • Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s).
• COG COG1716 104aa 5e-06 in ref transcript
  • FOG: FHA domain [Signal transduction mechanisms].
• Changed! COG RAD18 47aa 5e-06 in ref transcript
  • RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms].

RNH1

• refseq_RNH1.F2 refseq_RNH1.R2 186 254
• NCBIGene 36.3 6050
• Alternative 3-prime, size difference: 68
• Inclusion in 5'UTR
• Reference transcript: NM_203386

• cd LRR_RI 320aa 6e-76 in ref transcript
  • Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1).
• smart LRR_RI 28aa 0.009 in ref transcript
  • Leucine rich repeat, ribonuclease inhibitor type.

RNH1

• refseq_RNH1.F3 refseq_RNH1.R1 163 231
• NCBIGene 36.3 6050
• Alternative 3-prime, size difference: 68
• Inclusion in 5'UTR
• Reference transcript: NM_203384

• cd LRR_RI 320aa 6e-76 in ref transcript
  • Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1).
• smart LRR_RI 28aa 0.009 in ref transcript
  • Leucine rich repeat, ribonuclease inhibitor type.

RNH1

• refseq_RNH1.F6 refseq_RNH1.R3 124 297
• NCBIGene 36.3 6050
• Single exon skipping, size difference: 173
• Exclusion in 5'UTR
• Reference transcript: NM_203387

• cd LRR_RI 320aa 6e-76 in ref transcript
  • Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1).
• smart LRR_RI 28aa 0.009 in ref transcript
  • Leucine rich repeat, ribonuclease inhibitor type.

RP11-564C4.2

• refseq_RP11-564C4.2.F1 refseq_RP11-564C4.2.R1 102 121
• NCBIGene 36.2 653308
• Alternative 5-prime, size difference: 19
• Exclusion in 5'UTR
• Reference transcript: XM_933039

• pfam Ceramidase_alk 134aa 5e-45 in ref transcript
  • Neutral/alkaline non-lysosomal ceramidase. This family represents a group of neutral/alkaline ceramidases found in both bacteria and eukaryotes.

RP11-564C4.2

• refseq_RP11-564C4.2.F1 refseq_RP11-564C4.2.R3 269 324
• NCBIGene 36.2 653308
• Alternative 3-prime, size difference: 74
• Inclusion in the protein causing a new stop codon
• Reference transcript: XM_933039

• Changed! pfam Ceramidase_alk 134aa 5e-45 in ref transcript
  • Neutral/alkaline non-lysosomal ceramidase. This family represents a group of neutral/alkaline ceramidases found in both bacteria and eukaryotes.

RPAIN

• refseq_RPAIN.F1 refseq_RPAIN.R1 153 217
• NCBIGene 36.2 84268
• Single exon skipping, size difference: 64
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_001033002

RPE

• refseq_RPE.F1 refseq_RPE.R1 171 251
• NCBIGene 36.3 6120
• Single exon skipping, size difference: 80
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_199229

• Changed! cd RPE 209aa 3e-84 in ref transcript
  • Ribulose-5-phosphate 3-epimerase (RPE). This enzyme catalyses the interconversion of D-ribulose 5-phosphate (Ru5P) into D-xylulose 5-phosphate, as part of the Calvin cycle (reductive pentose phosphate pathway) in chloroplasts and in the oxidative pentose phosphate pathway. In the Calvin cycle Ru5P is phosphorylated by phosphoribulose kinase to ribulose-1,5-bisphosphate, which in turn is used by RubisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase) to incorporate CO2 as the central step in carbohydrate synthesis.
• Changed! pfam Ribul_P_3_epim 199aa 5e-62 in ref transcript
  • Ribulose-phosphate 3 epimerase family. This enzyme catalyses the conversion of D-ribulose 5-phosphate into D-xylulose 5-phosphate.
• Changed! PTZ PTZ00170 210aa 1e-82 in ref transcript
  • D-ribulose-5-phosphate 3-epimerase; Provisional.
• Changed! cd RPE 37aa 2e-12 in modified transcript
• Changed! pfam Ribul_P_3_epim 37aa 3e-09 in modified transcript
• Changed! PRK PRK05581 37aa 1e-11 in modified transcript
  • ribulose-phosphate 3-epimerase; Validated.

RPE

• refseq_RPE.F3 refseq_RPE.R3 192 246
• NCBIGene 36.3 6120
• Single exon skipping, size difference: 54
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_199229

• Changed! cd RPE 209aa 3e-84 in ref transcript
  • Ribulose-5-phosphate 3-epimerase (RPE). This enzyme catalyses the interconversion of D-ribulose 5-phosphate (Ru5P) into D-xylulose 5-phosphate, as part of the Calvin cycle (reductive pentose phosphate pathway) in chloroplasts and in the oxidative pentose phosphate pathway. In the Calvin cycle Ru5P is phosphorylated by phosphoribulose kinase to ribulose-1,5-bisphosphate, which in turn is used by RubisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase) to incorporate CO2 as the central step in carbohydrate synthesis.
• Changed! pfam Ribul_P_3_epim 199aa 5e-62 in ref transcript
  • Ribulose-phosphate 3 epimerase family. This enzyme catalyses the conversion of D-ribulose 5-phosphate into D-xylulose 5-phosphate.
• Changed! PTZ PTZ00170 210aa 1e-82 in ref transcript
  • D-ribulose-5-phosphate 3-epimerase; Provisional.
• Changed! cd RPE 227aa 7e-82 in modified transcript
• Changed! TIGR rpe 226aa 1e-59 in modified transcript
  • This family consists of Ribulose-phosphate 3-epimerase, also known as pentose-5-phosphate 3-epimerase (PPE). PPE converts D-ribulose 5-phosphate into D-xylulose 5-phosphate in Calvin's reductive pentose phosphate cycle. It has been found in a wide range of bacteria, archebacteria, fungi and plants.
• Changed! PTZ PTZ00170 228aa 8e-80 in modified transcript

RPL17

• refseq_RPL17.F1 refseq_RPL17.R1 111 360
• NCBIGene 36.3 6139
• Alternative 3-prime, size difference: 249
• Inclusion in 5'UTR
• Reference transcript: NM_001035006

• cd Ribosomal_L22 136aa 1e-26 in ref transcript
  • Ribosomal protein L22/L17e. L22 (L17 in eukaryotes) is a core protein of the large ribosomal subunit. It is the only ribosomal protein that interacts with all six domains of 23S rRNA, and is one of the proteins important for directing the proper folding and stabilizing the conformation of 23S rRNA. L22 is the largest protein contributor to the surface of the polypeptide exit channel, the tunnel through which the polypeptide product passes. L22 is also one of six proteins located at the putative translocon binding site on the exterior surface of the ribosome.
• TIGR L22_arch 150aa 6e-67 in ref transcript
  • This model describes the ribosomal protein of the eukaryotic cytosol and of the Archaea, variously designated as L17, L22, and L23. The corresponding bacterial homolog, described by a separate model, is designated L22.
• PTZ PTZ00178 163aa 2e-73 in ref transcript
  • 60S ribosomal protein L22/L17e; Provisional.

RPL3

• refseq_RPL3.F1 refseq_RPL3.R1 186 333
• NCBIGene 36.3 6122
• Alternative 5-prime and 3-prime, size difference: 147
• Exclusion in the protein (no frameshift), Exclusion in the protein (no frameshift)
• Reference transcript: NM_000967

• Changed! TIGR L3_arch 367aa 3e-73 in ref transcript
  • This model describes exclusively the archaeal class of ribosomal protein L3. A separate model (TIGR03625) describes the bacterial/organelle form, and both belong to pfam00297. Eukaryotic proteins are excluded from this model.
• Changed! PTZ PTZ00103 401aa 0.0 in ref transcript
  • 60S ribosomal protein L3; Provisional.
• Changed! TIGR L3_arch 318aa 1e-66 in modified transcript
• Changed! PTZ PTZ00103 352aa 1e-165 in modified transcript

RPL32

• refseq_RPL32.F1 refseq_RPL32.R1 156 255
• NCBIGene 36.3 6161
• Alternative 3-prime, size difference: 99
• Inclusion in 5'UTR
• Reference transcript: NM_000994

• cd Ribosomal_L32_L32e 105aa 8e-43 in ref transcript
  • Ribosomal_L32_L32e: L32 is a protein from the large subunit that contains a surface-exposed globular domain and a finger-like projection that extends into the RNA core to stabilize the tertiary structure. L32 does not appear to play a role in forming the A (aminacyl), P (peptidyl) or E (exit) sites of the ribosome, but does interact with 23S rRNA, which has a "kink-turn" secondary structure motif. L32 is overexpressed in human prostate cancer and has been identified as a stably expressed housekeeping gene in macrophages of human chronic obstructive pulmonary disease (COPD) patients. In Schizosaccharomyces pombe, L32 has also been suggested to play a role as a transcriptional regulator in the nucleus. Found in archaea and eukaryotes, this protein is known as L32 in eukaryotes and L32e in archaea.
• pfam Ribosomal_L32e 106aa 3e-42 in ref transcript
  • Ribosomal protein L32. This family includes ribosomal protein L32 from eukaryotes and archaebacteria.
• PTZ PTZ00159 133aa 7e-47 in ref transcript
  • 60S ribosomal protein L32; Provisional.

RPL38

• refseq_RPL38.F1 refseq_RPL38.R1 133 168
• NCBIGene 36.3 6169
• Alternative 5-prime, size difference: 35
• Exclusion in 5'UTR
• Reference transcript: NM_000999

• pfam Ribosomal_L38e 68aa 3e-14 in ref transcript
  • Ribosomal L38e protein family.
• PTZ PTZ00181 62aa 1e-05 in ref transcript
  • 60S ribosomal protein L38; Provisional.

RPL6

• refseq_RPL6.F1 refseq_RPL6.R1 219 395
• NCBIGene 36.3 6128
• Alternative 5-prime, size difference: 176
• Exclusion in 5'UTR
• Reference transcript: NM_001024662

• pfam Ribosomal_L6e 108aa 6e-39 in ref transcript
  • Ribosomal protein L6e.
• pfam Ribosomal_L6e_N 32aa 3e-07 in ref transcript
  • Ribosomal protein L6, N-terminal domain.
• COG RPL14A 109aa 1e-06 in ref transcript
  • Ribosomal protein L14E/L6E/L27E [Translation, ribosomal structure and biogenesis].

RPLP0

• refseq_RPLP0.F2 refseq_RPLP0.R2 150 210
• NCBIGene 36.3 6175
• Alternative 3-prime, size difference: 60
• Inclusion in 5'UTR
• Reference transcript: NM_001002

• cd Ribosomal_P0_L10e 175aa 1e-69 in ref transcript
  • Ribosomal protein L10 family, P0 and L10e subfamily; composed of eukaryotic 60S ribosomal protein P0 and the archaeal P0 homolog, L10e. P0 or L10e forms a tight complex with multiple copies of the small acidic protein L12(e). This complex forms a stalk structure on the large subunit of the ribosome. The stalk is known to contain the binding site for elongation factors G and Tu (EF-G and EF-Tu, respectively); however, there is disagreement as to whether or not L10 is involved in forming the binding site. The stalk is believed to be associated with GTPase activities in protein synthesis. In a neuroblastoma cell line, L10 has been shown to interact with the SH3 domain of Src and to activate the binding of the Nck1 adaptor protein with skeletal proteins such as the Wiskott-Aldrich Syndrome Protein (WASP) and the WASP-interacting protein (WIP). These eukaryotic and archaeal P0 sequences have an additional C-terminal domain homologous with acidic proteins P1 and P2.
• pfam Ribosomal_L10 103aa 2e-32 in ref transcript
  • Ribosomal protein L10.
• PTZ PTZ00135 269aa 4e-82 in ref transcript
  • ribosomal phosphoprotein P0; Provisional.

RPLP1

• refseq_RPLP1.F1 refseq_RPLP1.R1 189 264
• NCBIGene 36.3 6176
• Single exon skipping, size difference: 75
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001003

• Changed! cd Ribosomal_P1 108aa 7e-24 in ref transcript
  • Ribosomal protein P1. This subfamily represents the eukaryotic large ribosomal protein P1. Eukaryotic P1 and P2 are functionally equivalent to the bacterial protein L7/L12, but are not homologous to L7/L12. P1 is located in the L12 stalk, with proteins P2, P0, L11, and 28S rRNA. P1 and P2 are the only proteins in the ribosome to occur as multimers, always appearing as sets of heterodimers. Recent data indicate that eukaryotes have four copies (two heterodimers), while most archaeal species contain six copies of L12p (three homodimers) and bacteria may have four or six copies (two or three homodimers), depending on the species. Experiments using S. cerevisiae P1 and P2 indicate that P1 proteins are positioned more internally with limited reactivity in the C-terminal domains, while P2 proteins seem to be more externally located and are more likely to interact with other cellular components. In lower eukaryotes, P1 and P2 are further subdivided into P1A, P1B, P2A, and P2B, which form P1A/P2B and P1B/P2A heterodimers. Some plant species have a third P-protein, called P3, which is not homologous to P1 and P2. In humans, P1 and P2 are strongly autoimmunogenic. They play a significant role in the etiology and pathogenesis of systemic lupus erythema (SLE). In addition, the ribosome-inactivating protein trichosanthin (TCS) interacts with human P0, P1, and P2, with its primary binding site located in the C-terminal region of P2. TCS inactivates the ribosome by depurinating a specific adenine in the sarcin-ricin loop of 28S rRNA.
• Changed! pfam Ribosomal_60s 92aa 8e-07 in ref transcript
  • 60s Acidic ribosomal protein. This family includes archaebacterial L12, eukaryotic P0, P1 and P2.
• Changed! COG RPP1A 53aa 2e-05 in ref transcript
  • Ribosomal protein L12E/L44/L45/RPP1/RPP2 [Translation, ribosomal structure and biogenesis].
• Changed! cd Ribosomal_P1 83aa 4e-07 in modified transcript

RPS6KA4

• refseq_RPS6KA4.F1 refseq_RPS6KA4.R1 100 118
• NCBIGene 36.3 8986
• Alternative 3-prime, size difference: 18
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_003942

• cd STKc_MSK2_N 333aa 1e-178 in ref transcript
  • STKc_MSK2_N: Serine/Threonine Kinases (STKs), Mitogen and stress-activated kinase (MSK) subfamily, MSK2, N-terminal catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The MSK subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. MSKs contain an N-terminal kinase domain (NTD) from the AGC family and a C-terminal kinase domain (CTD) from the CAMK family, similar to 90 kDa ribosomal protein S6 kinases (RSKs). MSKs are activated by two major signaling cascades, the Ras-MAPK and p38 stress kinase pathways, which trigger phosphorylation in the activation loop (A-loop) of the CTD of MSK. The active CTD phosphorylates the hydrophobic motif (HM) of NTD, which facilitates the phosphorylation of the A-loop and activates the NTD, which in turn phosphorylates downstream targets. MSK2 and MSK1 play nonredundant roles in activating histone H3 kinases, which play pivotal roles in compaction of the chromatin fiber. MSK2 is the required H3 kinase in response to stress stimuli and activation of the p38 MAPK pathway. MSK2 also plays a role in the pathogenesis of psoriasis.
• cd S_TKc 258aa 2e-57 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• smart S_TKc 259aa 5e-77 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• smart S_TKc 254aa 3e-62 in ref transcript
• smart S_TK_X 61aa 2e-08 in ref transcript
  • Extension to Ser/Thr-type protein kinases.
• PTZ PTZ00263 300aa 2e-74 in ref transcript
  • protein kinase A catalytic subunit; Provisional.
• PTZ PTZ00263 255aa 1e-30 in ref transcript

RPS6KB2

• refseq_RPS6KB2.F2 refseq_RPS6KB2.R2 122 144
• NCBIGene 36.2 6199
• Alternative 5-prime, size difference: 22
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_003952

• Changed! cd STKc_p70S6K 323aa 0.0 in ref transcript
  • STKc_p70S6K: Serine/Threonine Kinases (STKs), 70 kDa ribosomal protein S6 kinase (p70S6K) subfamily, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The p70S6K subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. p70S6K (or S6K) contains only one catalytic kinase domain, unlike p90 ribosomal S6 kinases (RSKs). It acts as a downstream effector of the STK mTOR (mammalian Target of Rapamycin) and plays a role in the regulation of the translation machinery during protein synthesis. p70S6K also plays a pivotal role in regulating cell size and glucose homeostasis. Its targets include S6, the translation initiation factor eIF3, and the insulin receptor substrate IRS-1, among others. Mammals contain two isoforms of p70S6K, named S6K1 and S6K2 (or S6K-beta).
• Changed! smart S_TKc 252aa 2e-84 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• Changed! smart S_TK_X 63aa 2e-15 in ref transcript
  • Extension to Ser/Thr-type protein kinases.
• Changed! PTZ PTZ00263 321aa 3e-81 in ref transcript
  • protein kinase A catalytic subunit; Provisional.
• Changed! cd STKc_p70S6K 190aa 1e-109 in modified transcript
• Changed! smart S_TKc 183aa 1e-65 in modified transcript
• Changed! PTZ PTZ00263 193aa 8e-54 in modified transcript

RRAGB

• refseq_RRAGB.F1 refseq_RRAGB.R1 110 194
• NCBIGene 36.3 10325
• Single exon skipping, size difference: 84
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_016656

• Changed! cd Ras_like_GTPase 180aa 8e-09 in ref transcript
  • Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulate initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions.
• pfam Gtr1_RagA 199aa 6e-74 in ref transcript
  • Gtr1/RagA G protein conserved region. GTR1 was first identified in Saccharomyces cerevisiae as a suppressor of a mutation in RCC1. Biochemical analysis revealed that Gtr1 is in fact a G protein of the Ras family. The RagA/B proteins are the human homologues of Gtr1. Included in this family is the human Rag C, a novel protein that has been shown to interact with RagA/B.
• Changed! pfam Ras 178aa 2e-05 in ref transcript
  • Ras family. Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU, arf and myosin_head. See pfam00009 pfam00025, pfam00063. As regards Rab GTPases, these are important regulators of vesicle formation, motility and fusion. They share a fold in common with all Ras GTPases: this is a six-stranded beta-sheet surrounded by five alpha-helices.
• Changed! cd Ras_like_GTPase 152aa 6e-11 in modified transcript
• Changed! pfam Ras 150aa 7e-07 in modified transcript
• Changed! COG COG1100 145aa 2e-06 in modified transcript
  • GTPase SAR1 and related small G proteins [General function prediction only].

RREB1

• refseq_RREB1.F1 refseq_RREB1.R1 161 326
• NCBIGene 36.3 6239
• Single exon skipping, size difference: 165
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001003699

RSPO4

• refseq_RSPO4.F1 refseq_RSPO4.R1 314 500
• NCBIGene 36.3 343637
• Single exon skipping, size difference: 186
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001029871

• Changed! smart FU 41aa 0.006 in modified transcript
  • Furin-like repeats.

RSU1

• refseq_RSU1.F2 refseq_RSU1.R2 133 245
• NCBIGene 36.3 6251
• Single exon skipping, size difference: 112
• Exclusion of the protein initiation site
• Reference transcript: NM_012425

• Changed! cd LRR_RI 154aa 0.002 in ref transcript
  • Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1).
• Changed! COG COG4886 181aa 2e-09 in ref transcript
  • Leucine-rich repeat (LRR) protein [Function unknown].
• Changed! cd LRR_RI 114aa 3e-04 in modified transcript
• Changed! COG COG4886 147aa 2e-10 in modified transcript

RTEL1

• refseq_RTEL1.F1 refseq_RTEL1.R1 231 401
• NCBIGene 36.3 51750
• Alternative 5-prime, size difference: 170
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_032957

• pfam DEAD_2 162aa 1e-61 in ref transcript
  • DEAD_2. This represents a conserved region within a number of RAD3-like DNA-binding helicases that are seemingly ubiquitous - members include proteins of eukaryotic, bacterial and archaeal origin. RAD3 is involved in nucleotide excision repair, and forms part of the transcription factor TFIIH in yeast.
• TIGR rad3 292aa 4e-60 in ref transcript
  • All proteins in this family for which funcitons are known are DNA-DNA helicases that funciton in the initiation of transcription and nucleotide excision repair as part of the TFIIH complex. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
• COG DinG 737aa 1e-53 in ref transcript
  • Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair].

RTN3

• refseq_RTN3.F2 refseq_RTN3.R2 308 367
• NCBIGene 36.3 10313
• Single exon skipping, size difference: 59
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_201428

• Changed! pfam Reticulon 171aa 8e-41 in ref transcript
  • Reticulon. Reticulon, also know as neuroendocrine-specific protein (NSP), is a protein of unknown function which associates with the endoplasmic reticulum. This family represents the C-terminal domain of the three reticulon isoforms and their homologues.
• Changed! pfam Reticulon 157aa 4e-36 in modified transcript

SGSM1

• refseq_RUTBC2.F2 refseq_RUTBC2.R2 100 283
• NCBIGene 36.3 129049
• Single exon skipping, size difference: 183
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001039948

• smart TBC 145aa 2e-30 in ref transcript
  • Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs. Widespread domain present in Gyp6 and Gyp7, thereby giving rise to the notion that it performs a GTP-activator activity on Rab-like GTPases.
• pfam RUN 146aa 5e-21 in ref transcript
  • RUN domain. This domain is present in several proteins that are linked to the functions of GTPases in the Rap and Rab families. They could hence play important roles in multiple Ras-like GTPase signalling pathways. The domain is comprises six conserved regions, which in some proteins have considerable insertions between them. The domain core is thought to take up a predominantly alpha fold, with basic amino acids in regions A and D possibly playing a functional role in interactions with Ras GTPases.
• COG COG5210 212aa 2e-18 in ref transcript
  • GTPase-activating protein [General function prediction only].

RWDD1

• refseq_RWDD1.F1 refseq_RWDD1.R1 102 230
• NCBIGene 36.3 51389
• Single exon skipping, size difference: 128
• Exclusion in 5'UTR
• Reference transcript: NM_016104

SAA1

• refseq_SAA1.F1 refseq_SAA1.R1 162 309
• NCBIGene 36.3 6288
• Alternative 5-prime, size difference: 147
• Exclusion in 5'UTR
• Reference transcript: NM_000331

• pfam SAA 103aa 2e-47 in ref transcript
  • Serum amyloid A protein.

SAR1B

• refseq_SAR1B.F1 refseq_SAR1B.R1 113 232
• NCBIGene 36.3 51128
• Single exon skipping, size difference: 119
• Exclusion in 5'UTR
• Reference transcript: NM_001033503

• cd Sar1 195aa 3e-98 in ref transcript
  • Sar1 subfamily. Sar1 is an essential component of COPII vesicle coats involved in export of cargo from the ER. The GTPase activity of Sar1 functions as a molecular switch to control protein-protein and protein-lipid interactions that direct vesicle budding from the ER. Activation of the GDP to the GTP-bound form of Sar1 involves the membrane-associated guanine nucleotide exchange factor (GEF) Sec12. Sar1 is unlike all Ras superfamily GTPases that use either myristoyl or prenyl groups to direct membrane association and function, in that Sar1 lacks such modification. Instead, Sar1 contains a unique nine-amino-acid N-terminal extension. This extension contains an evolutionarily conserved cluster of bulky hydrophobic amino acids, referred to as the Sar1-N-terminal activation recruitment (STAR) motif. The STAR motif mediates the recruitment of Sar1 to ER membranes and facilitates its interaction with mammalian Sec12 GEF leading to activation.
• smart SAR 193aa 5e-75 in ref transcript
  • Sar1p-like members of the Ras-family of small GTPases. Yeast SAR1 is an essential gene required for transport of secretory proteins from the endoplasmic reticulum to the Golgi apparatus.
• PTZ PTZ00133 191aa 3e-23 in ref transcript
  • ADP-ribosylation factor; Provisional.

SC4MOL

• refseq_SC4MOL.F1 refseq_SC4MOL.R1 123 409
• NCBIGene 36.3 6307
• Single exon skipping, size difference: 286
• Exclusion of the protein initiation site
• Reference transcript: NM_006745

• pfam FA_hydroxylase 113aa 3e-18 in ref transcript
  • Fatty acid hydroxylase superfamily. This superfamily includes fatty acid and carotene hydroxylases and sterol desaturases. Beta-carotene hydroxylase is involved in zeaxanthin synthesis by hydroxylating beta-carotene, but the enzyme may be involved in other pathways. This family includes C-5 sterol desaturase and C-4 sterol methyl oxidase. Members of this family are involved in cholesterol biosynthesis and biosynthesis a plant cuticular wax. These enzymes contain two copies of a HXHH motif. Members of this family are integral membrane proteins.
• Changed! COG ERG3 234aa 6e-24 in ref transcript
  • Sterol desaturase [Lipid metabolism].
• Changed! COG ERG3 143aa 1e-20 in modified transcript

SCAMP1

• refseq_SCAMP1.F1 refseq_SCAMP1.R1 200 360
• NCBIGene 36.2 9522
• Single exon skipping, size difference: 160
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_004866

• Changed! pfam SCAMP 128aa 4e-47 in ref transcript
  • SCAMP family. In vertebrates, secretory carrier membrane proteins (SCAMPs) 1-3 constitute a family of putative membrane-trafficking proteins composed of cytoplasmic N-terminal sequences with NPF repeats, four central transmembrane regions (TMRs), and a cytoplasmic tail. SCAMPs probably function in endocytosis by recruiting EH-domain proteins to the N-terminal NPF repeats but may have additional functions mediated by their other sequences.
• Changed! pfam SCAMP 42aa 6e-20 in modified transcript

SCAMP3

• refseq_SCAMP3.F2 refseq_SCAMP3.R2 139 217
• NCBIGene 36.3 10067
• Single exon skipping, size difference: 78
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_005698

• pfam SCAMP 178aa 1e-50 in ref transcript
  • SCAMP family. In vertebrates, secretory carrier membrane proteins (SCAMPs) 1-3 constitute a family of putative membrane-trafficking proteins composed of cytoplasmic N-terminal sequences with NPF repeats, four central transmembrane regions (TMRs), and a cytoplasmic tail. SCAMPs probably function in endocytosis by recruiting EH-domain proteins to the N-terminal NPF repeats but may have additional functions mediated by their other sequences.

SCARF1

• refseq_SCARF1.F1 refseq_SCARF1.R1 171 208
• NCBIGene 36.3 8578
• Alternative 3-prime, size difference: 37
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_003693

SCEL

• refseq_SCEL.F1 refseq_SCEL.R1 337 397
• NCBIGene 36.3 8796
• Single exon skipping, size difference: 60
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_144777

• smart LIM 39aa 7e-04 in ref transcript
  • Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.

SCFD1

• refseq_SCFD1.F1 refseq_SCFD1.R1 109 180
• NCBIGene 36.3 23256
• Single exon skipping, size difference: 71
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_016106

• Changed! pfam Sec1 594aa 1e-167 in ref transcript
  • Sec1 family.
• Changed! COG SEC1 628aa 2e-79 in ref transcript
  • Proteins involved in synaptic transmission and general secretion, Sec1 family [Intracellular trafficking and secretion].

SCMH1

• refseq_SCMH1.F1 refseq_SCMH1.R1 221 287
• NCBIGene 36.3 22955
• Single exon skipping, size difference: 66
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001031694

• cd SAM 65aa 2e-08 in ref transcript
  • Sterile alpha motif.; Widespread domain in signalling and nuclear proteins. In EPH-related tyrosine kinases, appears to mediate cell-cell initiated signal transduction via the binding of SH2-containing proteins to a conserved tyrosine that is phosphorylated. In many cases mediates homodimerization.
• smart MBT 96aa 7e-35 in ref transcript
  • Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2. Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2. These proteins are involved in transcriptional regulation.
• smart MBT 99aa 1e-31 in ref transcript
• pfam SAM_1 64aa 7e-12 in ref transcript
  • SAM domain (Sterile alpha motif). It has been suggested that SAM is an evolutionarily conserved protein binding domain that is involved in the regulation of numerous developmental processes in diverse eukaryotes. The SAM domain can potentially function as a protein interaction module through its ability to homo- and heterooligomerise with other SAM domains.

SCMH1

• refseq_SCMH1.F3 refseq_SCMH1.R3 148 362
• NCBIGene 36.3 22955
• Multiple exon skipping, size difference: 214
• Exclusion of the protein initiation site, Exclusion in the protein causing a frameshift
• Reference transcript: NM_001031694

• cd SAM 65aa 2e-08 in ref transcript
  • Sterile alpha motif.; Widespread domain in signalling and nuclear proteins. In EPH-related tyrosine kinases, appears to mediate cell-cell initiated signal transduction via the binding of SH2-containing proteins to a conserved tyrosine that is phosphorylated. In many cases mediates homodimerization.
• Changed! smart MBT 96aa 7e-35 in ref transcript
  • Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2. Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2. These proteins are involved in transcriptional regulation.
• smart MBT 99aa 1e-31 in ref transcript
• pfam SAM_1 64aa 7e-12 in ref transcript
  • SAM domain (Sterile alpha motif). It has been suggested that SAM is an evolutionarily conserved protein binding domain that is involved in the regulation of numerous developmental processes in diverse eukaryotes. The SAM domain can potentially function as a protein interaction module through its ability to homo- and heterooligomerise with other SAM domains.
• Changed! smart MBT 79aa 8e-27 in modified transcript

SCML1

• refseq_SCML1.F2 refseq_SCML1.R2 151 303
• NCBIGene 36.3 6322
• Exon skipping and alternative 3-prime or 5-prime, size difference: 152
• Exclusion of the protein initiation site, Exclusion in the protein (no frameshift)
• Reference transcript: NM_006746

• cd SAM 66aa 8e-08 in ref transcript
  • Sterile alpha motif.; Widespread domain in signalling and nuclear proteins. In EPH-related tyrosine kinases, appears to mediate cell-cell initiated signal transduction via the binding of SH2-containing proteins to a conserved tyrosine that is phosphorylated. In many cases mediates homodimerization.
• pfam SAM_1 65aa 1e-10 in ref transcript
  • SAM domain (Sterile alpha motif). It has been suggested that SAM is an evolutionarily conserved protein binding domain that is involved in the regulation of numerous developmental processes in diverse eukaryotes. The SAM domain can potentially function as a protein interaction module through its ability to homo- and heterooligomerise with other SAM domains.

SCML1

• refseq_SCML1.F3 refseq_SCML1.R1 137 218
• NCBIGene 36.3 6322
• Exon skipping and alternative 3-prime or 5-prime, size difference: 81
• Inclusion in the protein (no stop codon or frameshift), Exclusion in the protein (no frameshift)
• Reference transcript: NM_001037540

• cd SAM 66aa 9e-08 in ref transcript
  • Sterile alpha motif.; Widespread domain in signalling and nuclear proteins. In EPH-related tyrosine kinases, appears to mediate cell-cell initiated signal transduction via the binding of SH2-containing proteins to a conserved tyrosine that is phosphorylated. In many cases mediates homodimerization.
• pfam SAM_1 65aa 1e-10 in ref transcript
  • SAM domain (Sterile alpha motif). It has been suggested that SAM is an evolutionarily conserved protein binding domain that is involved in the regulation of numerous developmental processes in diverse eukaryotes. The SAM domain can potentially function as a protein interaction module through its ability to homo- and heterooligomerise with other SAM domains.

SCNM1

• refseq_SCNM1.F2 refseq_SCNM1.R2 106 155
• NCBIGene 36.2 79005
• Alternative 5-prime, size difference: 49
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_024041

SCP2

• refseq_SCP2.F1 refseq_SCP2.R1 101 233
• NCBIGene 36.3 6342
• Single exon skipping, size difference: 132
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_002979

• Changed! cd nondecarbox_cond_enzymes 387aa 1e-153 in ref transcript
  • nondecarboxylating condensing enzymes; In general, thiolases catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. There are 2 functional different classes: thiolase-I (3-ketoacyl-CoA thiolase) and thiolase-II (acetoacetyl-CoA thiolase). Thiolase-I can cleave longer fatty acid molecules and plays an important role in the beta-oxidative degradation of fatty acids. Thiolase-II has a high substrate specificity. Although it can cleave acetoacyl-CoA, its main function is the synthesis of acetoacyl-CoA from two molecules of acetyl-CoA, which gives it importance in several biosynthetic pathways.
• Changed! TIGR AcCoA-C-Actrans 364aa 4e-26 in ref transcript
  • This model represents a large family of enzymes which catalyze the thiolysis of a linear fatty acid CoA (or acetoacetyl-CoA) using a second CoA molecule to produce acetyl-CoA and a CoA-ester product two carbons shorter (or, alternatively, the condensation of two molecules of acetyl-CoA to produce acetoacetyl-CoA and CoA). This enzyme is also known as "thiolase", "3-ketoacyl-CoA thiolase", "beta-ketothiolase" and "Fatty oxidation complex beta subunit". When catalyzing the degradative reaction on fatty acids the corresponding EC number is 2.3.1.16. The condensation reaction corresponds to 2.3.1.9. Note that the enzymes which catalyze the condensation are generally not involved in fatty acid biosynthesis, which is carried out by a decarboxylating condensation of acetyl and malonyl esters of acyl carrier proteins. Rather, this activity may produce acetoacetyl-CoA for pathways such as IPP biosynthesis in the absence of sufficient fatty acid oxidation.
• pfam SCP2 88aa 7e-20 in ref transcript
  • SCP-2 sterol transfer family. This domain is involved in binding sterols. It is found in the SCP2 protein, as well as the C terminus of the enzyme estradiol 17 beta-dehydrogenase EC:1.1.1.62. The UNC-24 protein contains an SPFH domain pfam01145.
• Changed! PRK PRK08256 393aa 0.0 in ref transcript
  • lipid-transfer protein; Provisional.
• COG COG3154 66aa 2e-07 in ref transcript
  • Putative lipid carrier protein [Lipid metabolism].
• Changed! cd nondecarbox_cond_enzymes 343aa 1e-129 in modified transcript
• Changed! TIGR AcCoA-C-Actrans 177aa 5e-17 in modified transcript
• Changed! PRK PRK08256 349aa 1e-168 in modified transcript

SCP2

• refseq_SCP2.F3 refseq_SCP2.R3 118 248
• NCBIGene 36.3 6342
• Single exon skipping, size difference: 130
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_002979

• cd nondecarbox_cond_enzymes 387aa 1e-153 in ref transcript
  • nondecarboxylating condensing enzymes; In general, thiolases catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. There are 2 functional different classes: thiolase-I (3-ketoacyl-CoA thiolase) and thiolase-II (acetoacetyl-CoA thiolase). Thiolase-I can cleave longer fatty acid molecules and plays an important role in the beta-oxidative degradation of fatty acids. Thiolase-II has a high substrate specificity. Although it can cleave acetoacyl-CoA, its main function is the synthesis of acetoacyl-CoA from two molecules of acetyl-CoA, which gives it importance in several biosynthetic pathways.
• TIGR AcCoA-C-Actrans 364aa 4e-26 in ref transcript
  • This model represents a large family of enzymes which catalyze the thiolysis of a linear fatty acid CoA (or acetoacetyl-CoA) using a second CoA molecule to produce acetyl-CoA and a CoA-ester product two carbons shorter (or, alternatively, the condensation of two molecules of acetyl-CoA to produce acetoacetyl-CoA and CoA). This enzyme is also known as "thiolase", "3-ketoacyl-CoA thiolase", "beta-ketothiolase" and "Fatty oxidation complex beta subunit". When catalyzing the degradative reaction on fatty acids the corresponding EC number is 2.3.1.16. The condensation reaction corresponds to 2.3.1.9. Note that the enzymes which catalyze the condensation are generally not involved in fatty acid biosynthesis, which is carried out by a decarboxylating condensation of acetyl and malonyl esters of acyl carrier proteins. Rather, this activity may produce acetoacetyl-CoA for pathways such as IPP biosynthesis in the absence of sufficient fatty acid oxidation.
• Changed! pfam SCP2 88aa 7e-20 in ref transcript
  • SCP-2 sterol transfer family. This domain is involved in binding sterols. It is found in the SCP2 protein, as well as the C terminus of the enzyme estradiol 17 beta-dehydrogenase EC:1.1.1.62. The UNC-24 protein contains an SPFH domain pfam01145.
• PRK PRK08256 393aa 0.0 in ref transcript
  • lipid-transfer protein; Provisional.
• Changed! COG COG3154 66aa 2e-07 in ref transcript
  • Putative lipid carrier protein [Lipid metabolism].

SCRIB

• refseq_SCRIB.F1 refseq_SCRIB.R1 199 274
• NCBIGene 36.3 23513
• Single exon skipping, size difference: 75
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_182706

• cd PDZ_signaling 89aa 1e-16 in ref transcript
  • PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of PDZ domains an N-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in proteases.
• cd PDZ_signaling 88aa 4e-14 in ref transcript
• cd PDZ_signaling 60aa 6e-12 in ref transcript
• cd PDZ_signaling 92aa 3e-07 in ref transcript
• cd LRR_RI 223aa 1e-05 in ref transcript
  • Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1).
• smart PDZ 90aa 6e-19 in ref transcript
  • Domain present in PSD-95, Dlg, and ZO-1/2. Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities.
• smart PDZ 91aa 3e-16 in ref transcript
• smart PDZ 66aa 3e-14 in ref transcript
• TIGR degP_htrA_DO 172aa 2e-08 in ref transcript
  • This family consists of a set proteins various designated DegP, heat shock protein HtrA, and protease DO. The ortholog in Pseudomonas aeruginosa is designated MucD and is found in an operon that controls mucoid phenotype. This family also includes the DegQ (HhoA) paralog in E. coli which can rescue a DegP mutant, but not the smaller DegS paralog, which cannot. Members of this family are located in the periplasm and have separable functions as both protease and chaperone. Members have a trypsin domain and two copies of a PDZ domain. This protein protects bacteria from thermal and other stresses and may be important for the survival of bacterial pathogens.// The chaperone function is dominant at low temperatures, whereas the proteolytic activity is turned on at elevated temperatures.
• smart PDZ 94aa 6e-06 in ref transcript
• COG COG4886 200aa 4e-27 in ref transcript
  • Leucine-rich repeat (LRR) protein [Function unknown].
• COG COG4886 270aa 1e-21 in ref transcript
• COG Prc 68aa 2e-07 in ref transcript
  • Periplasmic protease [Cell envelope biogenesis, outer membrane].
• COG Prc 47aa 2e-04 in ref transcript

SCYL3

• refseq_SCYL3.F1 refseq_SCYL3.R1 236 398
• NCBIGene 36.3 57147
• Single exon skipping, size difference: 162
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_181093

• cd S_TKc 211aa 5e-08 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• pfam Pkinase 220aa 2e-07 in ref transcript
  • Protein kinase domain.

SDCCAG3

• refseq_SDCCAG3.F1 refseq_SDCCAG3.R1 209 278
• NCBIGene 36.3 10807
• Single exon skipping, size difference: 69
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001039707

• pfam SMC_N 162aa 4e-06 in ref transcript
  • RecF/RecN/SMC N terminal domain. This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.

SDF4

• refseq_SDF4.F2 refseq_SDF4.R2 198 314
• NCBIGene 36.3 51150
• Alternative 3-prime, size difference: 116
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_016176

• cd EFh 61aa 0.002 in ref transcript
  • EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers.
• Changed! cd EFh 54aa 0.003 in ref transcript
• Changed! COG FRQ1 89aa 0.009 in modified transcript
  • Ca2+-binding protein (EF-Hand superfamily) [Signal transduction mechanisms / Cytoskeleton / Cell division and chromosome partitioning / General function prediction only].

SDHC

• refseq_SDHC.F1 refseq_SDHC.R1 116 218
• NCBIGene 36.3 6391
• Single exon skipping, size difference: 102
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_003001

• Changed! cd SQR_TypeC_SdhC 119aa 5e-24 in ref transcript
  • Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase C (SdhC) subunit; composed of bacterial SdhC and eukaryotic large cytochrome b binding (CybL) proteins. SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol. Members of this family reduce high potential quinones such as ubiquinone. SQR is also called succinate dehydrogenase or Complex II, and is part of the citric acid cycle and the aerobic respiratory chain. SQR is composed of a flavoprotein catalytic subunit, an iron-sulfur protein and one or two hydrophobic transmembrane subunits. Proteins in this subfamily are classified as Type C SQRs because they contain two transmembrane subunits and one heme group. The heme and quinone binding sites reside in the transmembrane subunits. The SdhC or CybL protein is one of the two transmembrane subunits of bacterial and eukaryotic SQRs. The two-electron oxidation of succinate in the flavoprotein active site is coupled to the two-electron reduction of quinone in the membrane anchor subunits via electron transport through FAD and three iron-sulfur centers. The reversible reduction of quinone is an essential feature of respiration, allowing transfer of electrons between respiratory complexes.
• Changed! pfam Sdh_cyt 105aa 2e-22 in ref transcript
  • Succinate dehydrogenase cytochrome b subunit.
• Changed! COG SdhC 103aa 7e-12 in ref transcript
  • Succinate dehydrogenase/fumarate reductase, cytochrome b subunit [Energy production and conversion].
• Changed! cd SQR_TypeC_SdhC 116aa 3e-18 in modified transcript
• Changed! pfam Sdh_cyt 100aa 4e-16 in modified transcript
• Changed! COG SdhC 101aa 2e-07 in modified transcript

SDHC

• refseq_SDHC.F4 refseq_SDHC.R4 214 378
• NCBIGene 36.3 6391
• Single exon skipping, size difference: 164
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_003001

• Changed! cd SQR_TypeC_SdhC 119aa 5e-24 in ref transcript
  • Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase C (SdhC) subunit; composed of bacterial SdhC and eukaryotic large cytochrome b binding (CybL) proteins. SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol. Members of this family reduce high potential quinones such as ubiquinone. SQR is also called succinate dehydrogenase or Complex II, and is part of the citric acid cycle and the aerobic respiratory chain. SQR is composed of a flavoprotein catalytic subunit, an iron-sulfur protein and one or two hydrophobic transmembrane subunits. Proteins in this subfamily are classified as Type C SQRs because they contain two transmembrane subunits and one heme group. The heme and quinone binding sites reside in the transmembrane subunits. The SdhC or CybL protein is one of the two transmembrane subunits of bacterial and eukaryotic SQRs. The two-electron oxidation of succinate in the flavoprotein active site is coupled to the two-electron reduction of quinone in the membrane anchor subunits via electron transport through FAD and three iron-sulfur centers. The reversible reduction of quinone is an essential feature of respiration, allowing transfer of electrons between respiratory complexes.
• Changed! pfam Sdh_cyt 105aa 2e-22 in ref transcript
  • Succinate dehydrogenase cytochrome b subunit.
• Changed! COG SdhC 103aa 7e-12 in ref transcript
  • Succinate dehydrogenase/fumarate reductase, cytochrome b subunit [Energy production and conversion].
• Changed! cd SQR_TypeC_SdhC 30aa 4e-08 in modified transcript
• Changed! pfam Sdh_cyt 31aa 3e-08 in modified transcript
• Changed! COG SdhC 29aa 5e-04 in modified transcript

SEC13L1

• refseq_SEC13L1.F2 refseq_SEC13L1.R2 154 188
• NCBIGene 36.2 6396
• Single exon skipping, size difference: 34
• Exclusion of the protein initiation site
• Reference transcript: NM_030673

• cd WD40 280aa 3e-23 in ref transcript
  • WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.
• smart WD40 38aa 0.001 in ref transcript
  • WD40 repeats. Note that these repeats are permuted with respect to the structural repeats (blades) of the beta propeller domain.
• pfam WD40 42aa 0.002 in ref transcript
  • WD domain, G-beta repeat.
• COG COG2319 296aa 1e-16 in ref transcript
  • FOG: WD40 repeat [General function prediction only].

SEC23B

• refseq_SEC23B.F1 refseq_SEC23B.R1 102 120
• NCBIGene 36.3 10483
• Alternative 5-prime, size difference: 18
• Exclusion in 5'UTR
• Reference transcript: NM_032985

• cd Sec23-like 265aa 1e-125 in ref transcript
  • Sec23-like: Protein and membrane traffic in eukaryotes is mediated by at least in part by the budding and fusion of intracellular transport vesicles that selectively carry cargo proteins and lipids from donor to acceptor organelles. The two main classes of vesicular carriers within the endocytic and the biosynthetic pathways are COP- and clathrin-coated vesicles. Formation of COPII vesicles requires the ordered assembly of the coat built from several cytosolic components GTPase Sar1, complexes of Sec23-Sec24 and Sec13-Sec31. The process is initiated by the conversion of GDP to GTP by the GTPase Sar1 which then recruits the heterodimeric complex of Sec23 and Sec24. This heterodimeric complex generates the pre-budding complex. The final step leading to membrane deformation and budding of COPII-coated vesicles is carried by the heterodimeric complex Sec13-Sec31. The members of this CD belong to the Sec23-like family. Sec 23 is very similar to Sec24. The Sec23 and Sec24 polypeptides fold into five distinct domains: a beta-barrel, a zinc finger, a vWA or trunk, an all helical region and a carboxy Gelsolin domain. The members of this subgroup lack the consensus MIDAS motif but have the overall Para-Rossmann type fold that is characteristic of this superfamily.
• pfam Sec23_trunk 267aa 5e-81 in ref transcript
  • Sec23/Sec24 trunk domain. COPII-coated vesicles carry proteins from the endoplasmic reticulum to the Golgi complex. This vesicular transport can be reconstituted by using three cytosolic components containing five proteins: the small GTPase Sar1p, the Sec23p/24p complex, and the Sec13p/Sec31p complex. This domain is known as the trunk domain and has an alpha/beta vWA fold and forms the dimer interface.
• pfam Sec23_helical 101aa 3e-36 in ref transcript
  • Sec23/Sec24 helical domain. COPII-coated vesicles carry proteins from the endoplasmic reticulum to the Golgi complex. This vesicular transport can be reconstituted by using three cytosolic components containing five proteins: the small GTPase Sar1p, the Sec23p/24p complex, and the Sec13p/Sec31p complex. This domain is composed of five alpha helices.
• pfam Sec23_BS 104aa 1e-23 in ref transcript
  • Sec23/Sec24 beta-sandwich domain.
• pfam zf-Sec23_Sec24 42aa 2e-13 in ref transcript
  • Sec23/Sec24 zinc finger. COPII-coated vesicles carry proteins from the endoplasmic reticulum to the Golgi complex. This vesicular transport can be reconstituted by using three cytosolic components containing five proteins: the small GTPase Sar1p, the Sec23p/24p complex, and the Sec13p/Sec31p complex. This domain is found to be zinc binding domain.
• pfam Gelsolin 87aa 1e-11 in ref transcript
  • Gelsolin repeat.
• COG SEC23 758aa 0.0 in ref transcript
  • Vesicle coat complex COPII, subunit SEC23 [Intracellular trafficking and secretion].

SEC24C

• refseq_SEC24C.F1 refseq_SEC24C.R1 236 323
• NCBIGene 36.3 9632
• Single exon skipping, size difference: 87
• Exclusion in 5'UTR
• Reference transcript: NM_004922

• cd Sec24-like 245aa 3e-93 in ref transcript
  • Sec24-like: Protein and membrane traffic in eukaryotes is mediated by at least in part by the budding and fusion of intracellular transport vesicles that selectively carry cargo proteins and lipids from donor to acceptor organelles. The two main classes of vesicular carriers within the endocytic and the biosynthetic pathways are COP- and clathrin-coated vesicles. Formation of COPII vesicles requires the ordered assembly of the coat built from several cytosolic components GTPase Sar1, complexes of Sec23-Sec24 and Sec13-Sec31. The process is initiated by the conversion of GDP to GTP by the GTPase Sar1 which then recruits the heterodimeric complex of Sec23 and Sec24. This heterodimeric complex generates the pre-budding complex. The final step leading to membrane deformation and budding of COPII-coated vesicles is carried by the heterodimeric complex Sec13-Sec31. The members of this CD belong to the Sec23-like family. Sec 24 is very similar to Sec23. The Sec23 and Sec24 polypeptides fold into five distinct domains: a beta-barrel, a zinc finger, a vWA or trunk, an all helical region and a carboxy Gelsolin domain. The members of this subgroup carry a partial MIDAS motif and have the overall Para-Rossmann type fold that is characteristic of this superfamily.
• pfam Sec23_trunk 245aa 4e-96 in ref transcript
  • Sec23/Sec24 trunk domain. COPII-coated vesicles carry proteins from the endoplasmic reticulum to the Golgi complex. This vesicular transport can be reconstituted by using three cytosolic components containing five proteins: the small GTPase Sar1p, the Sec23p/24p complex, and the Sec13p/Sec31p complex. This domain is known as the trunk domain and has an alpha/beta vWA fold and forms the dimer interface.
• pfam Sec23_helical 104aa 3e-29 in ref transcript
  • Sec23/Sec24 helical domain. COPII-coated vesicles carry proteins from the endoplasmic reticulum to the Golgi complex. This vesicular transport can be reconstituted by using three cytosolic components containing five proteins: the small GTPase Sar1p, the Sec23p/24p complex, and the Sec13p/Sec31p complex. This domain is composed of five alpha helices.
• pfam Sec23_BS 84aa 2e-25 in ref transcript
  • Sec23/Sec24 beta-sandwich domain.
• pfam zf-Sec23_Sec24 40aa 7e-15 in ref transcript
  • Sec23/Sec24 zinc finger. COPII-coated vesicles carry proteins from the endoplasmic reticulum to the Golgi complex. This vesicular transport can be reconstituted by using three cytosolic components containing five proteins: the small GTPase Sar1p, the Sec23p/24p complex, and the Sec13p/Sec31p complex. This domain is found to be zinc binding domain.
• pfam Gelsolin 31aa 7e-05 in ref transcript
  • Gelsolin repeat.
• pfam PAT1 173aa 1e-04 in ref transcript
  • Topoisomerase II-associated protein PAT1. Members of this family are necessary for accurate chromosome transmission during cell division.
• COG COG5028 910aa 1e-132 in ref transcript
  • Vesicle coat complex COPII, subunit SEC24/subunit SFB2/subunit SFB3 [Intracellular trafficking and secretion].

SEC31A

• refseq_SEC31L1.F1 refseq_SEC31L1.R1 118 235
• NCBIGene 36.3 22872
• Multiple exon skipping, size difference: 117
• Exclusion in the protein (no frameshift), Exclusion in the protein (no frameshift)
• Reference transcript: NM_001077207

• cd WD40 244aa 4e-22 in ref transcript
  • WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.
• COG COG2319 306aa 6e-15 in ref transcript
  • FOG: WD40 repeat [General function prediction only].

SEMA6D

• refseq_SEMA6D.F1 refseq_SEMA6D.R1 106 145
• NCBIGene 36.3 80031
• Alternative 3-prime, size difference: 39
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_153618

• pfam Sema 418aa 1e-121 in ref transcript
  • Sema domain. The Sema domain occurs in semaphorins, which are a large family of secreted and transmembrane proteins, some of which function as repellent signals during axon guidance. Sema domains also occur in the hepatocyte growth factor receptor and the human Plexin-A3 precursor.
• Changed! pfam PSI 45aa 7e-07 in ref transcript
  • Plexin repeat. A cysteine rich repeat found in several different extracellular receptors. The function of the repeat is unknown. Three copies of the repeat are found Plexin. Two copies of the repeat are found in mahogany protein. A related Caenorhabditis elegans protein contains four copies of the repeat. The Met receptor contains a single copy of the repeat. The Pfam alignment shows 6 conserved cysteine residues that may form three conserved disulphide bridges, whereas shows 8 conserved cysteines. The pattern of conservation suggests that cysteines 5 and 7 (that are not absolutely conserved) form a disulphide bridge (Personal observation. A Bateman).
• pfam DUF1043 111aa 0.007 in ref transcript
  • Protein of unknown function (DUF1043). This family consists of several hypothetical bacterial proteins of unknown function.
• Changed! pfam PSI 35aa 1e-05 in modified transcript

SEMA6D

• refseq_SEMA6D.F3 refseq_SEMA6D.R3 220 388
• NCBIGene 36.3 80031
• Single exon skipping, size difference: 168
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_153618

• pfam Sema 418aa 1e-121 in ref transcript
  • Sema domain. The Sema domain occurs in semaphorins, which are a large family of secreted and transmembrane proteins, some of which function as repellent signals during axon guidance. Sema domains also occur in the hepatocyte growth factor receptor and the human Plexin-A3 precursor.
• pfam PSI 45aa 7e-07 in ref transcript
  • Plexin repeat. A cysteine rich repeat found in several different extracellular receptors. The function of the repeat is unknown. Three copies of the repeat are found Plexin. Two copies of the repeat are found in mahogany protein. A related Caenorhabditis elegans protein contains four copies of the repeat. The Met receptor contains a single copy of the repeat. The Pfam alignment shows 6 conserved cysteine residues that may form three conserved disulphide bridges, whereas shows 8 conserved cysteines. The pattern of conservation suggests that cysteines 5 and 7 (that are not absolutely conserved) form a disulphide bridge (Personal observation. A Bateman).
• pfam DUF1043 111aa 0.007 in ref transcript
  • Protein of unknown function (DUF1043). This family consists of several hypothetical bacterial proteins of unknown function.

SEP15

• refseq_SEP15.F1 refseq_SEP15.R1 160 210
• NCBIGene 36.3 9403
• Single exon skipping, size difference: 50
• Exclusion in 3'UTR
• Reference transcript: NM_004261

SEPN1

• refseq_SEPN1.F1 refseq_SEPN1.R1 115 217
• NCBIGene 36.3 57190
• Single exon skipping, size difference: 102
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_206926

SEPT10

• refseq_SEPT10.F1 refseq_SEPT10.R1 320 389
• NCBIGene 36.3 151011
• Single exon skipping, size difference: 69
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_144710

• cd CDC_Septin 269aa 1e-112 in ref transcript
  • CDC/Septin. Septins are a conserved family of GTP-binding proteins associated with diverse processes in dividing and non-dividing cells. They were first discovered in the budding yeast S. cerevisiae as a set of genes (CDC3, CDC10, CDC11 and CDC12) required for normal bud morphology. Septins are also present in metazoan cells, where they are required for cytokinesis in some systems, and implicated in a variety of other processes involving organization of the cell cortex and exocytosis. In humans, 12 septin genes generate dozens of polypeptides, many of which comprise heterooligomeric complexes. Since septin mutants are commonly defective in cytokinesis and formation of the neck formation of the neck filaments/septin rings, septins have been considered to be the primary constituents of the neck filaments. Septins belong to the GTPase superfamily for their conserved GTPase motifs and enzymatic activities.
• pfam Septin 268aa 8e-90 in ref transcript
  • Septin. Members of this family include CDC3, CDC10, CDC11 and CDC12/Septin. Members of this family bind GTP. As regards the septins, these are polypeptides of 30-65kDa with three characteristic GTPase motifs (G-1, G-3 and G-4) that are similar to those of the Ras family. The G-4 motif is strictly conserved with a unique septin consensus of AKAD. Most septins are thought to have at least one coiled-coil region, which in some cases is necessary for intermolecular interactions that allow septins to polymerise to form rod-shaped complexes. In turn, these are arranged into tandem arrays to form filaments. They are multifunctional proteins, with roles in cytokinesis, sporulation, germ cell development, exocytosis and apoptosis.
• COG CDC3 354aa 1e-81 in ref transcript
  • Septin family protein [Cell division and chromosome partitioning / Cytoskeleton].

SEPT2

• refseq_SEPT2.F2 refseq_SEPT2.R2 219 320
• NCBIGene 36.3 4735
• Single exon skipping, size difference: 101
• Exclusion in 5'UTR
• Reference transcript: NM_001008491

• cd CDC_Septin 275aa 1e-127 in ref transcript
  • CDC/Septin. Septins are a conserved family of GTP-binding proteins associated with diverse processes in dividing and non-dividing cells. They were first discovered in the budding yeast S. cerevisiae as a set of genes (CDC3, CDC10, CDC11 and CDC12) required for normal bud morphology. Septins are also present in metazoan cells, where they are required for cytokinesis in some systems, and implicated in a variety of other processes involving organization of the cell cortex and exocytosis. In humans, 12 septin genes generate dozens of polypeptides, many of which comprise heterooligomeric complexes. Since septin mutants are commonly defective in cytokinesis and formation of the neck formation of the neck filaments/septin rings, septins have been considered to be the primary constituents of the neck filaments. Septins belong to the GTPase superfamily for their conserved GTPase motifs and enzymatic activities.
• pfam Septin 280aa 1e-139 in ref transcript
  • Septin. Members of this family include CDC3, CDC10, CDC11 and CDC12/Septin. Members of this family bind GTP. As regards the septins, these are polypeptides of 30-65kDa with three characteristic GTPase motifs (G-1, G-3 and G-4) that are similar to those of the Ras family. The G-4 motif is strictly conserved with a unique septin consensus of AKAD. Most septins are thought to have at least one coiled-coil region, which in some cases is necessary for intermolecular interactions that allow septins to polymerise to form rod-shaped complexes. In turn, these are arranged into tandem arrays to form filaments. They are multifunctional proteins, with roles in cytokinesis, sporulation, germ cell development, exocytosis and apoptosis.
• COG CDC3 312aa 1e-92 in ref transcript
  • Septin family protein [Cell division and chromosome partitioning / Cytoskeleton].

SEPT2

• refseq_SEPT2.F3 refseq_SEPT2.R1 128 213
• NCBIGene 36.3 4735
• Single exon skipping, size difference: 85
• Exclusion in 5'UTR
• Reference transcript: NM_001008492

• cd CDC_Septin 275aa 1e-127 in ref transcript
  • CDC/Septin. Septins are a conserved family of GTP-binding proteins associated with diverse processes in dividing and non-dividing cells. They were first discovered in the budding yeast S. cerevisiae as a set of genes (CDC3, CDC10, CDC11 and CDC12) required for normal bud morphology. Septins are also present in metazoan cells, where they are required for cytokinesis in some systems, and implicated in a variety of other processes involving organization of the cell cortex and exocytosis. In humans, 12 septin genes generate dozens of polypeptides, many of which comprise heterooligomeric complexes. Since septin mutants are commonly defective in cytokinesis and formation of the neck formation of the neck filaments/septin rings, septins have been considered to be the primary constituents of the neck filaments. Septins belong to the GTPase superfamily for their conserved GTPase motifs and enzymatic activities.
• pfam Septin 280aa 1e-139 in ref transcript
  • Septin. Members of this family include CDC3, CDC10, CDC11 and CDC12/Septin. Members of this family bind GTP. As regards the septins, these are polypeptides of 30-65kDa with three characteristic GTPase motifs (G-1, G-3 and G-4) that are similar to those of the Ras family. The G-4 motif is strictly conserved with a unique septin consensus of AKAD. Most septins are thought to have at least one coiled-coil region, which in some cases is necessary for intermolecular interactions that allow septins to polymerise to form rod-shaped complexes. In turn, these are arranged into tandem arrays to form filaments. They are multifunctional proteins, with roles in cytokinesis, sporulation, germ cell development, exocytosis and apoptosis.
• COG CDC3 312aa 1e-92 in ref transcript
  • Septin family protein [Cell division and chromosome partitioning / Cytoskeleton].

SEPT6

• refseq_SEPT6.F1 refseq_SEPT6.R1 253 298
• NCBIGene 36.3 23157
• Single exon skipping, size difference: 45
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_145802

• cd CDC_Septin 269aa 1e-117 in ref transcript
  • CDC/Septin. Septins are a conserved family of GTP-binding proteins associated with diverse processes in dividing and non-dividing cells. They were first discovered in the budding yeast S. cerevisiae as a set of genes (CDC3, CDC10, CDC11 and CDC12) required for normal bud morphology. Septins are also present in metazoan cells, where they are required for cytokinesis in some systems, and implicated in a variety of other processes involving organization of the cell cortex and exocytosis. In humans, 12 septin genes generate dozens of polypeptides, many of which comprise heterooligomeric complexes. Since septin mutants are commonly defective in cytokinesis and formation of the neck formation of the neck filaments/septin rings, septins have been considered to be the primary constituents of the neck filaments. Septins belong to the GTPase superfamily for their conserved GTPase motifs and enzymatic activities.
• pfam Septin 270aa 2e-88 in ref transcript
  • Septin. Members of this family include CDC3, CDC10, CDC11 and CDC12/Septin. Members of this family bind GTP. As regards the septins, these are polypeptides of 30-65kDa with three characteristic GTPase motifs (G-1, G-3 and G-4) that are similar to those of the Ras family. The G-4 motif is strictly conserved with a unique septin consensus of AKAD. Most septins are thought to have at least one coiled-coil region, which in some cases is necessary for intermolecular interactions that allow septins to polymerise to form rod-shaped complexes. In turn, these are arranged into tandem arrays to form filaments. They are multifunctional proteins, with roles in cytokinesis, sporulation, germ cell development, exocytosis and apoptosis.
• COG CDC3 322aa 5e-77 in ref transcript
  • Septin family protein [Cell division and chromosome partitioning / Cytoskeleton].

SERBP1

• refseq_SERBP1.F1 refseq_SERBP1.R1 100 118
• NCBIGene 36.3 26135
• Alternative 3-prime, size difference: 18
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001018067

• Changed! pfam HABP4_PAI-RBP1 125aa 2e-16 in ref transcript
  • Hyaluronan / mRNA binding family. This family includes the HABP4 family of hyaluronan-binding proteins, and the PAI-1 mRNA-binding protein, PAI-RBP1. HABP4 has been observed to bind hyaluronan (a glucosaminoglycan), but it is not known whether this is its primary role in vivo. It has also been observed to bind RNA, but with a lower affinity than that for hyaluronan. PAI-1 mRNA-binding protein specifically binds the mRNA of type-1 plasminogen activator inhibitor (PAI-1), and is thought to be involved in regulation of mRNA stability. However, in both cases, the sequence motifs predicted to be important for ligand binding are not conserved throughout the family, so it is not known whether members of this family share a common function.
• Changed! pfam HABP4_PAI-RBP1 119aa 5e-18 in modified transcript

SERPINA1

• refseq_SERPINA1.F1 refseq_SERPINA1.R1 100 414
• NCBIGene 36.3 5265
• Multiple exon skipping, size difference: 314
• Exclusion in 5'UTR, Exclusion in 5'UTR
• Reference transcript: NM_001002236

• cd alpha-1-antitrypsin_like 358aa 1e-154 in ref transcript
  • alpha-1-antitrypsin_like. This family contains a variety of different members of clade A of the serpin superfamily. They include the classical serine proteinase inhibitors, alpha-1-antitrypsin and alpha-1-antichymotrypsin, protein C inhibitor, kallistatin, and noninhibitory serpins, like corticosteroid and thyroxin binding globulins. In general, SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia.
• pfam Serpin 373aa 1e-158 in ref transcript
  • Serpin (serine protease inhibitor). Structure is a multi-domain fold containing a bundle of helices and a beta sandwich.
• COG COG4826 359aa 2e-52 in ref transcript
  • Serine protease inhibitor [Posttranslational modification, protein turnover, chaperones].

SETD4

• refseq_SETD4.F1 refseq_SETD4.R1 113 207
• NCBIGene 36.2 54093
• Single exon skipping, size difference: 94
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_017438

• Changed! pfam Rubis-subs-bind 119aa 2e-21 in ref transcript
  • Rubisco LSMT substrate-binding. Members of this family adopt a multihelical structure, with an irregular array of long and short alpha-helices. They allow binding of the protein to substrate, such as the N-terminal tails of histones H3 and H4 and the large subunit of the Rubisco holoenzyme complex.

SETD4

• refseq_SETD4.F3 refseq_SETD4.R3 150 199
• NCBIGene 36.2 54093
• Alternative 3-prime, size difference: 49
• Inclusion in 5'UTR
• Reference transcript: NM_017438

• pfam Rubis-subs-bind 119aa 2e-21 in ref transcript
  • Rubisco LSMT substrate-binding. Members of this family adopt a multihelical structure, with an irregular array of long and short alpha-helices. They allow binding of the protein to substrate, such as the N-terminal tails of histones H3 and H4 and the large subunit of the Rubisco holoenzyme complex.

SETD5

• refseq_SETD5.F2 refseq_SETD5.R2 181 220
• NCBIGene 36.2 55209
• Single exon skipping, size difference: 39
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: XM_931455

• pfam SET 102aa 4e-21 in ref transcript
  • SET domain. SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure.
• COG COG2940 100aa 7e-05 in ref transcript
  • Proteins containing SET domain [General function prediction only].

SETD5

• refseq_SETD5.F3 refseq_SETD5.R3 263 320
• NCBIGene 36.2 55209
• Single exon skipping, size difference: 57
• Exclusion in the protein (no frameshift)
• Reference transcript: XM_931455

• pfam SET 102aa 4e-21 in ref transcript
  • SET domain. SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure.
• COG COG2940 100aa 7e-05 in ref transcript
  • Proteins containing SET domain [General function prediction only].

SETD5

• refseq_SETD5.F5 refseq_SETD5.R5 148 373
• NCBIGene 36.2 55209
• Single exon skipping, size difference: 225
• Inclusion in the protein causing a new stop codon
• Reference transcript: XM_931455

• Changed! pfam SET 102aa 4e-21 in ref transcript
  • SET domain. SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure.
• Changed! COG COG2940 100aa 7e-05 in ref transcript
  • Proteins containing SET domain [General function prediction only].

SEZ6L2

• refseq_SEZ6L2.F1 refseq_SEZ6L2.R1 221 260
• NCBIGene 36.3 26470
• Single exon skipping, size difference: 39
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_201575

• cd CUB 91aa 6e-11 in ref transcript
  • CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.
• cd CUB 69aa 7e-11 in ref transcript
• cd CCP 57aa 4e-09 in ref transcript
  • Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR); The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function.
• cd CUB 113aa 3e-08 in ref transcript
• cd CCP 59aa 3e-08 in ref transcript
• cd CCP 60aa 2e-07 in ref transcript
• cd CCP 56aa 2e-06 in ref transcript
• pfam CUB 91aa 2e-08 in ref transcript
  • CUB domain.
• smart CCP 56aa 3e-08 in ref transcript
  • Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR). The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. A missense mutation in seventh CCP domain causes deficiency of the b subunit of factor XIII.
• smart CCP 56aa 5e-08 in ref transcript
• pfam Sushi 58aa 1e-07 in ref transcript
  • Sushi domain (SCR repeat).
• smart CCP 60aa 3e-07 in ref transcript
• smart CUB 59aa 3e-06 in ref transcript
  • Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. This domain is found mostly among developmentally-regulated proteins. Spermadhesins contain only this domain.
• smart CUB 102aa 5e-04 in ref transcript
• pfam Sushi 57aa 0.003 in ref transcript

SF3A1

• refseq_SF3A1.F1 refseq_SF3A1.R1 121 316
• NCBIGene 36.3 10291
• Alternative 5-prime and 3-prime, size difference: 195
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_005877

• cd SF3a120_C 76aa 4e-32 in ref transcript
  • SF3a120_C Mammalian splicing factor SF3a consists of three subunits of 60, 66, and 120 kDa and functions early during pre-mRNA splicing by converting the U2 snRNP to its active form. The 120kDa subunit (SF3a120) has a carboxy-terminal ubiquitin-like domain and two SWAP (suppressor-of-white-apricot) domains, referred to collectively as the SURP module, at its amino-terminus.
• smart SWAP 54aa 4e-21 in ref transcript
  • Suppressor-of-White-APricot splicing regulator. domain present in regulators which are responsible for pre-mRNA splicing processes.
• Changed! smart SWAP 54aa 3e-17 in ref transcript
• pfam ubiquitin 67aa 1e-11 in ref transcript
  • Ubiquitin family. This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue), Nedd8, Elongin B, Rub1, and Parkin. A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites.
• PTZ PTZ00044 69aa 0.002 in ref transcript
  • ubiquitin; Provisional.
• Changed! smart SWAP 47aa 4e-14 in modified transcript

SFI1

• refseq_SFI1.F1 refseq_SFI1.R1 253 346
• NCBIGene 36.3 9814
• Single exon skipping, size difference: 93
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001007467

• Changed! pfam Sfi1 551aa 3e-05 in ref transcript
  • Sfi1 spindle body protein. This is a family of fungal spindle pole body proteins that play a role in spindle body duplication. They contain binding sites for calmodulin-like proteins called centrins which are present in microtubule-organising centres.
• Changed! pfam Sfi1 568aa 3e-07 in modified transcript

SFMBT1

• refseq_SFMBT1.F1 refseq_SFMBT1.R1 205 324
• NCBIGene 36.3 51460
• Single exon skipping, size difference: 119
• Exclusion in 5'UTR
• Reference transcript: NM_001005158

• cd SAM 63aa 3e-07 in ref transcript
  • Sterile alpha motif.; Widespread domain in signalling and nuclear proteins. In EPH-related tyrosine kinases, appears to mediate cell-cell initiated signal transduction via the binding of SH2-containing proteins to a conserved tyrosine that is phosphorylated. In many cases mediates homodimerization.
• smart MBT 98aa 1e-30 in ref transcript
  • Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2. Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2. These proteins are involved in transcriptional regulation.
• smart MBT 94aa 4e-28 in ref transcript
• smart MBT 91aa 2e-23 in ref transcript
• smart MBT 102aa 1e-21 in ref transcript
• smart SAM 65aa 7e-06 in ref transcript
  • Sterile alpha motif. Widespread domain in signalling and nuclear proteins. In EPH-related tyrosine kinases, appears to mediate cell-cell initiated signal transduction via the binding of SH2-containing proteins to a conserved tyrosine that is phosphorylated. In many cases mediates homodimerisation.

SFRS5

• refseq_SFRS5.F1 refseq_SFRS5.R1 228 357
• NCBIGene 36.3 6430
• Alternative 5-prime, size difference: 129
• Exclusion in 5'UTR
• Reference transcript: NM_001039465

• cd RRM 67aa 6e-12 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• cd RRM 68aa 3e-08 in ref transcript
• pfam RRM_1 63aa 4e-12 in ref transcript
  • RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain). The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have a N terminus rrm which is included in the seed. There is a second region towards the C terminus that has some features of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.
• smart RRM_2 68aa 8e-09 in ref transcript
  • RNA recognition motif.
• TIGR PABP-1234 168aa 3e-07 in ref transcript
  • There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, and of unknown tissue range.
• COG COG0724 72aa 2e-06 in ref transcript
  • RNA-binding proteins (RRM domain) [General function prediction only].
• COG COG0724 69aa 0.001 in ref transcript

SFXN4

• refseq_SFXN4.F2 refseq_SFXN4.R2 271 392
• NCBIGene 36.2 119559
• Single exon skipping, size difference: 121
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_213649

• Changed! TIGR mtc 298aa 2e-27 in ref transcript
  • The MTC family consists of a limited number of homologues, all from eukaryotes. A single member of the family has been functionally characterized, the tricarboxylate carrier from rat liver mitochondria. The rat liver mitochondrial tricarboxylate carrier has been reported to transport citrate, cis-aconitate, threo-D-isocitrate, D- and L-tartrate, malate, succinate and phosphoenolpyruvate. It presumably functions by a proton symport mechanism.
• Changed! TIGR mtc 271aa 2e-25 in modified transcript

SFXN4

• refseq_SFXN4.F3 refseq_SFXN4.R3 103 130
• NCBIGene 36.2 119559
• Single exon skipping, size difference: 27
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_213649

• Changed! TIGR mtc 298aa 2e-27 in ref transcript
  • The MTC family consists of a limited number of homologues, all from eukaryotes. A single member of the family has been functionally characterized, the tricarboxylate carrier from rat liver mitochondria. The rat liver mitochondrial tricarboxylate carrier has been reported to transport citrate, cis-aconitate, threo-D-isocitrate, D- and L-tartrate, malate, succinate and phosphoenolpyruvate. It presumably functions by a proton symport mechanism.
• Changed! TIGR mtc 289aa 1e-26 in modified transcript

SGK3

• refseq_SGK3.F2 refseq_SGK3.R2 162 258
• NCBIGene 36.3 23678
• Single exon skipping, size difference: 96
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001033578

• Changed! cd STKc_SGK3 325aa 0.0 in ref transcript
  • STKc_SGK3: Serine/Threonine Kinases (STKs), Serum- and Glucocorticoid-induced Kinase (SGK) subfamily, SGK3 isoform, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The SGK subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. There are three isoforms of SGK, named SGK1, SGK2, and SGK3 (also called cytokine-independent survival kinase CISK). SGK3 is expressed in most tissues and is most abundant in the embryo and adult heart and spleen. It was originally discovered in a screen for antiapoptotic genes. It phosphorylates and inhibits the proapoptotic proteins, Bad and FKHRL1. SGK3 also regulates many transporters, ion channels, and receptors. It plays a critical role in hair follicle morphogenesis and hair cycling.
• cd PX_CISK 109aa 9e-53 in ref transcript
  • The phosphoinositide binding Phox Homology Domain of Cytokine-Independent Survival Kinase. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Cytokine-independent survival kinase (CISK), also called Serum- and Glucocorticoid-induced Kinase 3 (SGK3), plays a role in cell growth and survival. It is expressed in most tissues and is most abundant in the embryo and adult heart and spleen. It was originally discovered in a screen for antiapoptotic genes. It phosphorylates and inhibits the proapoptotic proteins, Bad and FKHRL1. CISK/SGK3 also regulates many transporters, ion channels, and receptors. It plays a critical role in hair follicle morphogenesis and hair cycling. N-terminal to a catalytic kinase domain, CISK contains a PX domain which binds highly phosphorylated PIs, directs membrane localization, and regulates the enzyme's activity.
• Changed! smart S_TKc 248aa 7e-79 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• pfam PX 104aa 7e-19 in ref transcript
  • PX domain. PX domains bind to phosphoinositides.
• smart S_TK_X 67aa 9e-10 in ref transcript
  • Extension to Ser/Thr-type protein kinases.
• Changed! PTZ PTZ00263 293aa 9e-76 in ref transcript
  • protein kinase A catalytic subunit; Provisional.
• COG COG5391 113aa 1e-08 in ref transcript
  • Phox homology (PX) domain protein [Intracellular trafficking and secretion / General function prediction only].
• Changed! cd STKc_SGK3 293aa 1e-158 in modified transcript
• Changed! smart S_TKc 216aa 3e-58 in modified transcript
• Changed! PTZ PTZ00263 261aa 2e-57 in modified transcript

SH3BP5

• refseq_SH3BP5.F1 refseq_SH3BP5.R1 134 202
• NCBIGene 36.3 9467
• Alternative 3-prime, size difference: 68
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_004844

• Changed! pfam SH3BP5 233aa 3e-82 in ref transcript
  • SH3 domain-binding protein 5 (SH3BP5). This family consists of several eukaryotic SH3 domain-binding protein 5 or c-Jun N-terminal kinase (JNK)-interacting proteins (SH3BP5 or Sab). Sab binds to and serves as a substrate for JNK in vitro, and has been found to interact with the Src homology 3 (SH3) domain of Bruton's tyrosine kinase (Btk). Inspection of the sequence of Sab reveals the presence of two putative mitogen-activated protein kinase interaction motifs (KIMs) similar to that found in the JNK docking domain of the c-Jun transcription factor, and four potential serine-proline JNK phosphorylation sites in the C-terminal half of the molecule.
• Changed! PRK PRK10929 193aa 0.008 in ref transcript
  • hypothetical protein; Provisional.
• Changed! pfam SH3BP5 27aa 9e-05 in modified transcript

SHANK2

• refseq_SHANK2.F1 refseq_SHANK2.R1 100 121
• NCBIGene 36.3 22941
• Single exon skipping, size difference: 21
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_012309

• cd SAM 62aa 2e-16 in ref transcript
  • Sterile alpha motif.; Widespread domain in signalling and nuclear proteins. In EPH-related tyrosine kinases, appears to mediate cell-cell initiated signal transduction via the binding of SH2-containing proteins to a conserved tyrosine that is phosphorylated. In many cases mediates homodimerization.
• cd PDZ_signaling 94aa 3e-15 in ref transcript
  • PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of PDZ domains an N-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in proteases.
• pfam SAM_1 61aa 1e-18 in ref transcript
  • SAM domain (Sterile alpha motif). It has been suggested that SAM is an evolutionarily conserved protein binding domain that is involved in the regulation of numerous developmental processes in diverse eukaryotes. The SAM domain can potentially function as a protein interaction module through its ability to homo- and heterooligomerise with other SAM domains.
• smart PDZ 95aa 8e-13 in ref transcript
  • Domain present in PSD-95, Dlg, and ZO-1/2. Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities.

SHOX2

• refseq_SHOX2.F2 refseq_SHOX2.R2 186 222
• NCBIGene 36.3 6474
• Alternative 3-prime, size difference: 36
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_006884

• cd homeodomain 59aa 2e-15 in ref transcript
  • Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
• pfam Homeobox 57aa 8e-22 in ref transcript
  • Homeobox domain.
• COG COG5576 60aa 1e-09 in ref transcript
  • Homeodomain-containing transcription factor [Transcription].

PUF60

• refseq_SIAHBP1.F1 refseq_SIAHBP1.R1 138 189
• NCBIGene 36.3 22827
• Single exon skipping, size difference: 51
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_078480

• cd RRM 75aa 3e-17 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• cd RRM 75aa 1e-15 in ref transcript
• cd RRM 74aa 3e-05 in ref transcript
• Changed! TIGR half-pint 295aa 1e-132 in ref transcript
  • In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.
• TIGR half-pint 127aa 2e-59 in ref transcript
• TIGR half-pint 56aa 7e-13 in ref transcript
• Changed! COG COG0724 258aa 1e-16 in ref transcript
  • RNA-binding proteins (RRM domain) [General function prediction only].
• Changed! TIGR half-pint 278aa 1e-130 in modified transcript
• Changed! COG COG0724 160aa 3e-15 in modified transcript

SIGLEC6

• refseq_SIGLEC6.F1 refseq_SIGLEC6.R1 130 306
• NCBIGene 36.3 946
• Multiple exon skipping, size difference: 176
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_001245

• cd IGcam 80aa 8e-05 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• pfam I-set 83aa 8e-08 in ref transcript
  • Immunoglobulin I-set domain.
• pfam V-set 105aa 3e-07 in ref transcript
  • Immunoglobulin V-set domain. This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.
• pfam C2-set_2 74aa 0.003 in ref transcript
  • CD80-like C2-set immunoglobulin domain. These domains belong to the immunoglobulin superfamily.

SIGLEC6

• refseq_SIGLEC6.F4 refseq_SIGLEC6.R4 228 276
• NCBIGene 36.3 946
• Single exon skipping, size difference: 48
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001245

• cd IGcam 80aa 8e-05 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• pfam I-set 83aa 8e-08 in ref transcript
  • Immunoglobulin I-set domain.
• pfam V-set 105aa 3e-07 in ref transcript
  • Immunoglobulin V-set domain. This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.
• pfam C2-set_2 74aa 0.003 in ref transcript
  • CD80-like C2-set immunoglobulin domain. These domains belong to the immunoglobulin superfamily.

SIGLEC7

• refseq_SIGLEC7.F1 refseq_SIGLEC7.R1 206 485
• NCBIGene 36.3 27036
• Single exon skipping, size difference: 279
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_014385

• cd IGcam 74aa 1e-04 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• smart IG_like 78aa 2e-08 in ref transcript
  • Immunoglobulin like. IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
• pfam V-set 99aa 1e-07 in ref transcript
  • Immunoglobulin V-set domain. This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.
• Changed! pfam C2-set_2 74aa 7e-05 in ref transcript
  • CD80-like C2-set immunoglobulin domain. These domains belong to the immunoglobulin superfamily.

SIL1

• refseq_SIL1.F1 refseq_SIL1.R1 151 239
• NCBIGene 36.3 64374
• Single exon skipping, size difference: 88
• Exclusion in 5'UTR
• Reference transcript: NM_001037633

SIP1

• refseq_SIP1.F1 refseq_SIP1.R1 107 166
• NCBIGene 36.3 8487
• Single exon skipping, size difference: 59
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_003616

• Changed! pfam SIP1 247aa 5e-97 in ref transcript
  • Survival motor neuron (SMN) interacting protein 1 (SIP1). Survival motor neuron (SMN) interacting protein 1 (SIP1) interacts with SMN protein and plays a crucial role in the biogenesis of spliceosomes. There is evidence that the protein is linked to spinal muscular atrophy (SMA) and amyotrophic lateral sclerosis(ALS) in humans.
• Changed! pfam SIP1 221aa 2e-85 in modified transcript

SIP1

• refseq_SIP1.F3 refseq_SIP1.R3 216 261
• NCBIGene 36.3 8487
• Single exon skipping, size difference: 45
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_003616

• Changed! pfam SIP1 247aa 5e-97 in ref transcript
  • Survival motor neuron (SMN) interacting protein 1 (SIP1). Survival motor neuron (SMN) interacting protein 1 (SIP1) interacts with SMN protein and plays a crucial role in the biogenesis of spliceosomes. There is evidence that the protein is linked to spinal muscular atrophy (SMA) and amyotrophic lateral sclerosis(ALS) in humans.
• Changed! pfam SIP1 232aa 1e-91 in modified transcript

SIRPB2

• refseq_SIRPB2.F1 refseq_SIRPB2.R1 106 400
• NCBIGene 36.2 284759
• Alternative 5-prime, size difference: 294
• Exclusion in the protein (no frameshift)
• Reference transcript: XM_209363

• cd IGcam 84aa 5e-05 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• pfam V-set 107aa 3e-10 in ref transcript
  • Immunoglobulin V-set domain. This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.
• Changed! pfam V-set 113aa 7e-10 in ref transcript

SIRPG

• refseq_SIRPG.F2 refseq_SIRPG.R2 103 436
• NCBIGene 36.3 55423
• Single exon skipping, size difference: 333
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_018556

• Changed! cd IGc 87aa 2e-06 in ref transcript
  • Immunoglobulin domain constant region subfamily; members of the IGc subfamily are components of immunoglobulins, T-cell receptors, CD1 cell surface glycoproteins, secretory glycoproteins A/C, and Major Histocompatibility Complex (MHC) class I/II molecules. In immunoglobulins, each chain is composed of one variable domain (IGv) and one or more constant domains (IGc); these names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. T-cell receptors form heterodimers, pairing two chains (alpha/beta or gamma/delta), each with a IGv and IGc domain. MHCs form heterodimers pairing two chains (alpha/beta or delta/epsilon), each with a MHC and IGc domain. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• cd IGc 89aa 5e-05 in ref transcript
• cd IGv 98aa 7e-05 in ref transcript
  • Immunoglobulin domain variable region (v) subfamily; members of the IGv subfamily are components of immunoglobulins and T-cell receptors. In immunoglobulins, each chain is composed of one variable domain (IGv) and one or more constant domains (IGc); these names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. Within the variable domain, there are regions of even more variability called the hypervariable or complementarity-determining regions (CDRs) which are responsible for antigen binding. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• Changed! pfam V-set 90aa 3e-11 in ref transcript
  • Immunoglobulin V-set domain. This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.
• smart IGc1 73aa 5e-07 in ref transcript
  • Immunoglobulin C-Type.
• Changed! smart IGc1 70aa 9e-06 in ref transcript
• Changed! pfam V-set 103aa 8e-12 in modified transcript

SIRT2

• refseq_SIRT2.F1 refseq_SIRT2.R1 183 230
• NCBIGene 36.3 22933
• Single exon skipping, size difference: 47
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_012237

• Changed! cd SIRT1 255aa 1e-108 in ref transcript
  • SIRT1: Eukaryotic group (class1) which includes human sirtuins SIRT1-3 and yeast Hst1-4; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The nuclear SIRT1 has been shown to target the p53 tumor suppressor protein for deacetylation to suppress DNA damage, and the cytoplasmic SIRT2 homolog has been shown to target alpha-tubulin for deacetylation for the maintenance of cell integrity.
• Changed! pfam SIR2 182aa 3e-69 in ref transcript
  • Sir2 family. This region is characteristic of Silent information regulator 2 (Sir2) proteins, or sirtuins. These are protein deacetylases that depend on nicotine adenine dinucleotide (NAD). They are found in many subcellular locations, including the nucleus, cytoplasm and mitochondria. Eukaryotic forms play in important role in the regulation of transcriptional repression. Moreover, they are involved in microtubule organisation and DNA damage repair processes.
• Changed! COG SIR2 206aa 3e-48 in ref transcript
  • NAD-dependent protein deacetylases, SIR2 family [Transcription].

SIRT3

• refseq_SIRT3.F1 refseq_SIRT3.R1 138 284
• NCBIGene 36.3 23410
• Alternative 5-prime, size difference: 146
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_012239

• Changed! cd SIRT1 236aa 2e-94 in ref transcript
  • SIRT1: Eukaryotic group (class1) which includes human sirtuins SIRT1-3 and yeast Hst1-4; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The nuclear SIRT1 has been shown to target the p53 tumor suppressor protein for deacetylation to suppress DNA damage, and the cytoplasmic SIRT2 homolog has been shown to target alpha-tubulin for deacetylation for the maintenance of cell integrity.
• Changed! pfam SIR2 179aa 3e-56 in ref transcript
  • Sir2 family. This region is characteristic of Silent information regulator 2 (Sir2) proteins, or sirtuins. These are protein deacetylases that depend on nicotine adenine dinucleotide (NAD). They are found in many subcellular locations, including the nucleus, cytoplasm and mitochondria. Eukaryotic forms play in important role in the regulation of transcriptional repression. Moreover, they are involved in microtubule organisation and DNA damage repair processes.
• Changed! COG SIR2 253aa 4e-47 in ref transcript
  • NAD-dependent protein deacetylases, SIR2 family [Transcription].

SIVA1

• refseq_SIVA.F1 refseq_SIVA.R1 118 313
• NCBIGene 36.3 10572
• Single exon skipping, size difference: 195
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_006427

• Changed! pfam Siva 175aa 4e-84 in ref transcript
  • Cd27 binding protein (Siva). Siva binds to the CD27 cytoplasmic tail. It has a DD homology region, a box-B-like ring finger, and a zinc finger-like domain. Overexpression of Siva in various cell lines induces apoptosis, suggesting an important role for Siva in the CD27-transduced apoptotic pathway. Siva-1 binds to and inhibits BCL-X(L)-mediated protection against UV radiation-induced apoptosis. Indeed, the unique amphipathic helical region (SAH) present in Siva-1 is required for its binding to BCL-X(L) and sensitising cells to UV radiation. Natural complexes of Siva-1/BCL-X(L) are detected in HUT78 and murine thymocyte, suggesting a potential role for Siva-1 in regulating T cell homeostasis. This family contains both Siva-1 and the shorter Siva-2 lacking the sequence coded by exon 2. It has been suggested that Siva-2 could regulate the function of Siva-1.
• Changed! pfam Siva 71aa 2e-29 in modified transcript

SKIP

• refseq_SKIP__51763.F1 refseq_SKIP__51763.R1 171 402
• NCBIGene 36.3 51763
• Single exon skipping, size difference: 231
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_016532

• Changed! smart IPPc 314aa 3e-82 in ref transcript
  • Inositol polyphosphate phosphatase, catalytic domain homologues. Mg(2+)-dependent/Li(+)-sensitive enzymes.
• Changed! pfam CALCOCO1 70aa 8e-04 in ref transcript
  • Calcium binding and coiled-coil domain (CALCOCO1) like. Proteins found in this family are similar to the coiled-coil transcriptional coactivator protein coexpressed by Mus musculus (CoCoA/CALCOCO1). This protein binds to a highly conserved N-terminal domain of p160 coactivators, such as GRIP1, and thus enhances transcriptional activation by a number of nuclear receptors. CALCOCO1 has a central coiled-coil region with three leucine zipper motifs, which is required for its interaction with GRIP1 and may regulate the autonomous transcriptional activation activity of the C-terminal region.
• Changed! COG COG5411 277aa 2e-31 in ref transcript
  • Phosphatidylinositol 5-phosphate phosphatase [Signal transduction mechanisms].

SLA2

• refseq_SLA2.F1 refseq_SLA2.R1 149 199
• NCBIGene 36.3 84174
• Alternative 3-prime, size difference: 50
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_032214

• Changed! cd SH2 99aa 2e-18 in ref transcript
  • Src homology 2 domains; Signal transduction, involved in recognition of phosphorylated tyrosine (pTyr). SH2 domains typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites.
• cd SH3 54aa 0.004 in ref transcript
  • Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
• pfam SH2 83aa 1e-17 in ref transcript
  • SH2 domain.
• pfam SH3_1 55aa 3e-05 in ref transcript
  • SH3 domain. SH3 (Src homology 3) domains are often indicative of a protein involved in signal transduction related to cytoskeletal organisation. First described in the Src cytoplasmic tyrosine kinase. The structure is a partly opened beta barrel.
• Changed! cd SH2 85aa 6e-16 in modified transcript

SEPSECS

• refseq_SLA_LP.F2 refseq_SLA_LP.R2 123 278
• NCBIGene 36.3 51091
• Single exon skipping, size difference: 155
• Exclusion of the protein initiation site
• Reference transcript: NM_153825

• cd AAT_like 182aa 5e-04 in ref transcript
  • Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. The major groups in this CD corresponds to Aspartate aminotransferase a, b and c, Tyrosine, Alanine, Aromatic-amino-acid, Glutamine phenylpyruvate, 1-Aminocyclopropane-1-carboxylate synthase, Histidinol-phosphate, gene products of malY and cobC, Valine-pyruvate aminotransferase and Rhizopine catabolism regulatory protein.
• Changed! TIGR selenium_SpcS 398aa 0.0 in ref transcript
  • In the archaea and eukaryotes, the conversion of the mischarged serine to selenocysteine (Sec) on its tRNA is accomplished in two steps. This enzyme, O-phosphoseryl-tRNA(Sec) selenium transferase, acts second, after a phosphophorylation step catalyzed by a homolog of the bacterial SelA protein.
• COG GadB 342aa 3e-16 in ref transcript
  • Glutamate decarboxylase and related PLP-dependent proteins [Amino acid transport and metabolism].
• Changed! TIGR selenium_SpcS 369aa 0.0 in modified transcript

SLC22A1

• refseq_SLC22A1.F1 refseq_SLC22A1.R1 149 262
• NCBIGene 36.3 6580
• Single exon skipping, size difference: 113
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_003057

• cd MFS 166aa 2e-16 in ref transcript
  • The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated.
• Changed! cd MFS 143aa 4e-08 in ref transcript
• Changed! TIGR 2A0119 513aa 1e-180 in ref transcript
• COG AraJ 124aa 5e-09 in ref transcript
  • Arabinose efflux permease [Carbohydrate transport and metabolism].
• Changed! PRK xylE 301aa 3e-07 in ref transcript
  • D-xylose transporter XylE; Provisional.
• Changed! cd MFS 124aa 1e-05 in modified transcript
• Changed! TIGR 2A0119 454aa 1e-166 in modified transcript
• Changed! PRK xylE 241aa 1e-07 in modified transcript

SLC22A12

• refseq_SLC22A12.F2 refseq_SLC22A12.R2 197 352
• NCBIGene 36.3 116085
• Single exon skipping, size difference: 155
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_144585

• Changed! cd MFS 158aa 1e-13 in ref transcript
  • The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated.
• Changed! cd MFS 141aa 0.004 in ref transcript
• Changed! TIGR 2A0119 516aa 1e-103 in ref transcript
• Changed! COG AraJ 93aa 6e-05 in ref transcript
  • Arabinose efflux permease [Carbohydrate transport and metabolism].
• Changed! TIGR 2A0119 159aa 2e-22 in modified transcript

SLC22A17

• refseq_SLC22A17.F1 refseq_SLC22A17.R1 306 360
• NCBIGene 36.3 51310
• Alternative 5-prime, size difference: 54
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_020372

• Changed! cd MFS 75aa 0.004 in ref transcript
  • The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated.
• Changed! TIGR 2A0119 374aa 2e-21 in ref transcript
• Changed! PRK xylE 158aa 4e-06 in ref transcript
  • D-xylose transporter XylE; Provisional.
• Changed! cd MFS 118aa 2e-04 in modified transcript
• Changed! TIGR 2A0119 356aa 1e-23 in modified transcript
• Changed! PRK xylE 213aa 7e-08 in modified transcript

SLC22A6

• refseq_SLC22A6.F1 refseq_SLC22A6.R1 121 253
• NCBIGene 36.3 9356
• Alternative 3-prime, size difference: 132
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_004790

• cd MFS 123aa 6e-14 in ref transcript
  • The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated.
• Changed! cd MFS 171aa 2e-09 in ref transcript
• Changed! TIGR 2A0119 505aa 0.0 in ref transcript
• Changed! PRK xylE 429aa 3e-08 in ref transcript
  • D-xylose transporter XylE; Provisional.
• Changed! cd MFS 122aa 0.003 in modified transcript
• Changed! TIGR 2A0119 461aa 1e-172 in modified transcript
• Changed! COG AraJ 67aa 3e-07 in modified transcript
  • Arabinose efflux permease [Carbohydrate transport and metabolism].
• Changed! PRK PRK03893 128aa 1e-05 in modified transcript
  • putative sialic acid transporter; Provisional.
• Changed! PRK xylE 353aa 5e-05 in modified transcript

SLC22A6

• refseq_SLC22A6.F2 refseq_SLC22A6.R2 149 188
• NCBIGene 36.3 9356
• Alternative 5-prime, size difference: 39
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_004790

• cd MFS 123aa 6e-14 in ref transcript
  • The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated.
• cd MFS 171aa 2e-09 in ref transcript
• TIGR 2A0119 505aa 0.0 in ref transcript
• Changed! PRK xylE 429aa 3e-08 in ref transcript
  • D-xylose transporter XylE; Provisional.
• Changed! PRK xylE 430aa 1e-07 in modified transcript

SLC24A4

• refseq_SLC24A4.F1 refseq_SLC24A4.R1 100 157
• NCBIGene 36.3 123041
• Alternative 5-prime, size difference: 57
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_153646

• TIGR 2A1904 173aa 3e-59 in ref transcript
• TIGR 2A1904 193aa 2e-45 in ref transcript
• COG ECM27 132aa 1e-15 in ref transcript
  • Ca2+/Na+ antiporter [Inorganic ion transport and metabolism].
• COG ECM27 151aa 2e-15 in ref transcript

SLC25A25

• refseq_SLC25A25.F2 refseq_SLC25A25.R2 183 226
• NCBIGene 36.3 114789
• Alternative 5-prime, size difference: 43
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_052901

• Changed! cd EFh 60aa 4e-09 in ref transcript
  • EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers.
• Changed! pfam Mito_carr 93aa 7e-24 in ref transcript
  • Mitochondrial carrier protein.
• Changed! pfam Mito_carr 89aa 2e-23 in ref transcript
• Changed! pfam Mito_carr 92aa 1e-16 in ref transcript
• Changed! PTZ PTZ00169 269aa 1e-29 in ref transcript
  • ADP/ATP transporter on adenylate translocase; Provisional.
• Changed! COG FRQ1 113aa 9e-11 in ref transcript
  • Ca2+-binding protein (EF-Hand superfamily) [Signal transduction mechanisms / Cytoskeleton / Cell division and chromosome partitioning / General function prediction only].

SLC25A26

• refseq_SLC25A26.F1 refseq_SLC25A26.R1 349 434
• NCBIGene 36.2 115286
• Single exon skipping, size difference: 85
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_173471

• Changed! pfam Mito_carr 83aa 4e-11 in ref transcript
  • Mitochondrial carrier protein.
• Changed! pfam Mito_carr 89aa 2e-10 in ref transcript
• Changed! PTZ PTZ00168 168aa 1e-17 in ref transcript
  • mitochondrial carrier protein; Provisional.
• Changed! pfam Mito_carr 61aa 8e-08 in modified transcript
• Changed! PTZ PTZ00168 61aa 4e-06 in modified transcript

SLC25A29

• refseq_SLC25A29.F2 refseq_SLC25A29.R2 246 290
• NCBIGene 36.2 123096
• Single exon skipping, size difference: 44
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_152333

SLC25A3

• refseq_SLC25A3.F1 refseq_SLC25A3.R1 100 391
• NCBIGene 36.2 5250
• Alternative 5-prime, size difference: 291
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_005888

• Changed! pfam Mito_carr 75aa 2e-16 in ref transcript
  • Mitochondrial carrier protein.
• Changed! pfam Mito_carr 83aa 6e-16 in ref transcript
• Changed! pfam Mito_carr 78aa 2e-06 in ref transcript
• Changed! PTZ PTZ00169 259aa 4e-08 in ref transcript
  • ADP/ATP transporter on adenylate translocase; Provisional.

SLC26A1

• refseq_SLC26A1.F2 refseq_SLC26A1.R2 104 319
• NCBIGene 36.3 10861
• Single exon skipping, size difference: 215
• Exclusion in 5'UTR
• Reference transcript: NM_213613

• cd STAS_SulP_like_sulfate_transporter 142aa 1e-14 in ref transcript
  • Sulphate Transporter and Anti-Sigma factor antagonist domain of SulP-like sulfate transporters, plays a role in the function and regulation of the transport activity, proposed general NTP binding function. The SulP family is a large and diverse family of anion transporters, with members from eubacteria, plants, fungi, and mammals. They contain 10 to 14 transmembrane helices which form the catalytic core of the protein and a C-terminal extension, the STAS (Sulphate Transporter and AntiSigma factor antagonist) domain which plays a role in the function and regulation of the transport activity. The STAS domain is found in the C-terminal region of sulphate transporters and bacterial anti-sigma factor antagonists. It has been suggested that this domain may have a general NTP binding function.
• TIGR sulP 629aa 1e-145 in ref transcript
  • (2) SO42- (out) + nHCO3- (in) SO42- (in) + nHCO3- (out).
• COG SUL1 640aa 3e-54 in ref transcript
  • Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism].

SLC26A10

• refseq_SLC26A10.F1 refseq_SLC26A10.R1 305 400
• NCBIGene 36.2 65012
• Single exon skipping, size difference: 107
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_133489

• Changed! cd STAS_SulP_like_sulfate_transporter 123aa 4e-08 in ref transcript
  • Sulphate Transporter and Anti-Sigma factor antagonist domain of SulP-like sulfate transporters, plays a role in the function and regulation of the transport activity, proposed general NTP binding function. The SulP family is a large and diverse family of anion transporters, with members from eubacteria, plants, fungi, and mammals. They contain 10 to 14 transmembrane helices which form the catalytic core of the protein and a C-terminal extension, the STAS (Sulphate Transporter and AntiSigma factor antagonist) domain which plays a role in the function and regulation of the transport activity. The STAS domain is found in the C-terminal region of sulphate transporters and bacterial anti-sigma factor antagonists. It has been suggested that this domain may have a general NTP binding function.
• Changed! TIGR sulP 496aa 2e-49 in ref transcript
  • (2) SO42- (out) + nHCO3- (in) SO42- (in) + nHCO3- (out).
• Changed! COG SUL1 374aa 8e-31 in ref transcript
  • Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism].
• Changed! TIGR sulP 395aa 1e-46 in modified transcript
• Changed! COG SUL1 397aa 1e-29 in modified transcript

SLC26A10

• refseq_SLC26A10.F3 refseq_SLC26A10.R4 155 262
• NCBIGene 36.2 65012
• Single exon skipping, size difference: 107
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_133489

• Changed! cd STAS_SulP_like_sulfate_transporter 123aa 4e-08 in ref transcript
  • Sulphate Transporter and Anti-Sigma factor antagonist domain of SulP-like sulfate transporters, plays a role in the function and regulation of the transport activity, proposed general NTP binding function. The SulP family is a large and diverse family of anion transporters, with members from eubacteria, plants, fungi, and mammals. They contain 10 to 14 transmembrane helices which form the catalytic core of the protein and a C-terminal extension, the STAS (Sulphate Transporter and AntiSigma factor antagonist) domain which plays a role in the function and regulation of the transport activity. The STAS domain is found in the C-terminal region of sulphate transporters and bacterial anti-sigma factor antagonists. It has been suggested that this domain may have a general NTP binding function.
• Changed! TIGR sulP 496aa 2e-49 in ref transcript
  • (2) SO42- (out) + nHCO3- (in) SO42- (in) + nHCO3- (out).
• Changed! COG SUL1 374aa 8e-31 in ref transcript
  • Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism].
• Changed! TIGR sulP 395aa 1e-46 in modified transcript
• Changed! COG SUL1 397aa 1e-29 in modified transcript

SLC26A8

• refseq_SLC26A8.F1 refseq_SLC26A8.R1 101 416
• NCBIGene 36.3 116369
• Multiple exon skipping, size difference: 315
• Exclusion in the protein (no frameshift), Exclusion in the protein (no frameshift)
• Reference transcript: NM_052961

• cd STAS_SulP_like_sulfate_transporter 58aa 1e-08 in ref transcript
  • Sulphate Transporter and Anti-Sigma factor antagonist domain of SulP-like sulfate transporters, plays a role in the function and regulation of the transport activity, proposed general NTP binding function. The SulP family is a large and diverse family of anion transporters, with members from eubacteria, plants, fungi, and mammals. They contain 10 to 14 transmembrane helices which form the catalytic core of the protein and a C-terminal extension, the STAS (Sulphate Transporter and AntiSigma factor antagonist) domain which plays a role in the function and regulation of the transport activity. The STAS domain is found in the C-terminal region of sulphate transporters and bacterial anti-sigma factor antagonists. It has been suggested that this domain may have a general NTP binding function.
• Changed! TIGR sulP 502aa 2e-71 in ref transcript
  • (2) SO42- (out) + nHCO3- (in) SO42- (in) + nHCO3- (out).
• pfam STAS 72aa 2e-06 in ref transcript
  • STAS domain. The STAS (after Sulphate Transporter and AntiSigma factor antagonist) domain is found in the C terminal region of Sulphate transporters and bacterial antisigma factor antagonists. It has been suggested that this domain may have a general NTP binding function.
• Changed! COG SUL1 504aa 3e-53 in ref transcript
  • Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism].
• COG SpoIIAA 61aa 0.009 in ref transcript
  • Anti-anti-sigma regulatory factor (antagonist of anti-sigma factor) [Signal transduction mechanisms].
• Changed! TIGR sulP 288aa 2e-41 in modified transcript
• Changed! TIGR sulP 134aa 4e-14 in modified transcript
• Changed! COG SUL1 399aa 8e-32 in modified transcript

SLC2A11

• refseq_SLC2A11.F1 refseq_SLC2A11.R1 119 230
• NCBIGene 36.3 66035
• Single exon skipping, size difference: 111
• Exclusion of the protein initiation site
• Reference transcript: NM_030807

• cd MFS 119aa 1e-04 in ref transcript
  • The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated.
• cd MFS 181aa 0.002 in ref transcript
• Changed! pfam Sugar_tr 454aa 2e-63 in ref transcript
  • Sugar (and other) transporter.
• PRK xylE 378aa 6e-19 in ref transcript
  • D-xylose transporter XylE; Provisional.
• Changed! pfam Sugar_tr 445aa 3e-62 in modified transcript

SLC30A10

• refseq_SLC30A10.F1 refseq_SLC30A10.R1 104 142
• NCBIGene 36.2 55532
• Alternative 3-prime, size difference: 38
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_018713

• Changed! TIGR CDF 153aa 2e-28 in ref transcript
  • This model describes a broadly distributed family of transporters, a number of which have been shown to transport divalent cations of cobalt, cadmium and/or zinc. The family has six predicted transmembrane domains. Members of the family are variable in length because of variably sized inserts, often containing low-complexity sequence.
• TIGR CDF 94aa 1e-18 in ref transcript
• Changed! COG CzcD 152aa 9e-30 in ref transcript
  • Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism].
• COG CzcD 102aa 5e-23 in ref transcript

SLC30A2

• refseq_SLC30A2.F1 refseq_SLC30A2.R1 143 290
• NCBIGene 36.3 7780
• Single exon skipping, size difference: 147
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001004434

• Changed! TIGR CDF 275aa 2e-69 in ref transcript
  • This model describes a broadly distributed family of transporters, a number of which have been shown to transport divalent cations of cobalt, cadmium and/or zinc. The family has six predicted transmembrane domains. Members of the family are variable in length because of variably sized inserts, often containing low-complexity sequence.
• Changed! COG CzcD 304aa 4e-53 in ref transcript
  • Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism].
• Changed! TIGR CDF 218aa 2e-46 in modified transcript
• Changed! COG CzcD 216aa 2e-32 in modified transcript

SLC37A3

• refseq_SLC37A3.F1 refseq_SLC37A3.R1 101 403
• NCBIGene 36.3 84255
• Multiple exon skipping, size difference: 302
• Exclusion in the protein (no frameshift), Exclusion in the protein (no frameshift), Exclusion in the protein causing a frameshift
• Reference transcript: NM_207113

• cd MFS 144aa 6e-13 in ref transcript
  • The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated.
• Changed! cd MFS 185aa 3e-09 in ref transcript
• Changed! TIGR 2A0104 371aa 3e-24 in ref transcript
• Changed! COG UhpC 466aa 3e-42 in ref transcript
  • Sugar phosphate permease [Carbohydrate transport and metabolism].
• Changed! TIGR 2A0104 258aa 2e-17 in modified transcript
• Changed! COG UhpC 328aa 4e-29 in modified transcript

SLC3A2

• refseq_SLC3A2.F1 refseq_SLC3A2.R1 268 361
• NCBIGene 36.3 6520
• Single exon skipping, size difference: 93
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001012661

• TIGR trehalose_treC 136aa 4e-16 in ref transcript
  • Trehalose is a glucose disaccharide that serves in many biological systems as a compatible solute for protection against hyperosmotic and thermal stress. This family describes trehalose-6-phosphate hydrolase, product of the treC (or treA) gene, which is often found together with a trehalose uptake transporter and a trehalose operon repressor.
• pfam Alpha-amylase 244aa 8e-14 in ref transcript
  • Alpha amylase, catalytic domain. Alpha amylase is classified as family 13 of the glycosyl hydrolases. The structure is an 8 stranded alpha/beta barrel containing the active site, interrupted by a ~70 a.a. calcium-binding domain protruding between beta strand 3 and alpha helix 3, and a carboxyl-terminal Greek key beta-barrel domain.
• TIGR treS_nterm 120aa 3e-08 in ref transcript
  • Trehalose synthase interconverts maltose and alpha, alpha-trehalose by transglucosylation. This is one of at least three mechanisms for biosynthesis of trehalose, an important and widespread compatible solute. However, it is not driven by phosphate activation of sugars and its physiological role may tend toward trehalose degradation. This view is accentuated by numerous examples of fusion to a probable maltokinase domain. The sequence region described by this model is found both as the whole of a trehalose synthase and as the N-terminal region of a larger fusion protein that includes trehalose synthase activity. Several of these fused trehalose synthases have a domain homologous to proteins with maltokinase activity from Actinoplanes missouriensis and Streptomyces coelicolor (PMID:15378530).
• COG AmyA 340aa 3e-18 in ref transcript
  • Glycosidases [Carbohydrate transport and metabolism].

SLC41A3

• refseq_SLC41A3.F1 refseq_SLC41A3.R1 287 395
• NCBIGene 36.3 54946
• Single exon skipping, size difference: 108
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001008485

• Changed! pfam MgtE 136aa 2e-14 in ref transcript
  • Divalent cation transporter. This region is the integral membrane part of the eubacterial MgtE family of magnesium transporters. Related regions are found also in archaebacterial and eukaryotic proteins. All the archaebacterial and eukaryotic examples have two copies of the region. This suggests that the eubacterial examples may act as dimers. Members of this family probably transport Mg2+ or other divalent cations into the cell. The alignment contains two highly conserved aspartates that may be involved in cation binding (Bateman A unpubl.).
• pfam MgtE 132aa 0.007 in ref transcript
• COG COG1824 170aa 1e-05 in ref transcript
  • Permease, similar to cation transporters [Inorganic ion transport and metabolism].
• Changed! COG COG1824 171aa 1e-05 in ref transcript
• Changed! pfam MgtE 65aa 3e-07 in modified transcript
• Changed! COG COG1824 55aa 0.010 in modified transcript

SLC4A3

• refseq_SLC4A3.F1 refseq_SLC4A3.R1 189 270
• NCBIGene 36.3 6508
• Alternative 3-prime, size difference: 81
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_201574

• TIGR ae 910aa 0.0 in ref transcript
  • They preferentially catalyze anion exchange (antiport) reactions, typically acting as HCO3-:Cl- antiporters, but also transporting a range of other inorganic and organic anions. Additionally, renal Na+:HCO3- cotransporters have been found to be members of the AE family. They catalyze the reabsorption of HCO3- in the renal proximal tubule.

SLC4A5

• refseq_SLC4A5.F2 refseq_SLC4A5.R2 229 277
• NCBIGene 36.3 57835
• Single exon skipping, size difference: 48
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_021196

• Changed! TIGR ae 957aa 0.0 in ref transcript
  • They preferentially catalyze anion exchange (antiport) reactions, typically acting as HCO3-:Cl- antiporters, but also transporting a range of other inorganic and organic anions. Additionally, renal Na+:HCO3- cotransporters have been found to be members of the AE family. They catalyze the reabsorption of HCO3- in the renal proximal tubule.
• Changed! TIGR ae 941aa 0.0 in modified transcript

SLC6A20

• refseq_SLC6A20.F1 refseq_SLC6A20.R1 243 354
• NCBIGene 36.3 54716
• Single exon skipping, size difference: 111
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_020208

• Changed! pfam SNF 576aa 1e-123 in ref transcript
  • Sodium:neurotransmitter symporter family.
• Changed! COG COG0733 300aa 3e-35 in ref transcript
  • Na+-dependent transporters of the SNF family [General function prediction only].
• COG COG0733 164aa 6e-08 in ref transcript
• Changed! pfam SNF 539aa 1e-102 in modified transcript
• Changed! COG COG0733 117aa 2e-20 in modified transcript
• Changed! COG COG0733 68aa 2e-07 in modified transcript

SLC6A9

• refseq_SLC6A9.F2 refseq_SLC6A9.R2 241 403
• NCBIGene 36.3 6536
• Single exon skipping, size difference: 162
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_201649

• pfam SNF 551aa 0.0 in ref transcript
  • Sodium:neurotransmitter symporter family.
• COG COG0733 495aa 1e-55 in ref transcript
  • Na+-dependent transporters of the SNF family [General function prediction only].

SMARCA1

• refseq_SMARCA1.F1 refseq_SMARCA1.R1 157 220
• NCBIGene 36.2 6594
• Alternative 5-prime and 3-prime, size difference: 63
• Exclusion in the protein (no frameshift), Exclusion in the protein (no frameshift)
• Reference transcript: NM_003069

• cd HELICc 144aa 1e-21 in ref transcript
  • Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process.
• Changed! cd DEXDc 140aa 4e-19 in ref transcript
  • DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
• cd SANT 40aa 6e-04 in ref transcript
  • 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
• Changed! pfam SNF2_N 271aa 1e-108 in ref transcript
  • SNF2 family N-terminal domain. This domain is found in proteins involved in a variety of processes including transcription regulation (e.g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as well as a variety of other proteins with little functional information (e.g., lodestar, ETL1).
• pfam SLIDE 110aa 4e-42 in ref transcript
  • SLIDE. The SLIDE domain adopts a secondary structure comprising a main core of three alpha-helices. It has a role in DNA binding, contacting DNA target sites similar to c-Myb (pfam00249) repeats or homeodomains.
• pfam HAND 81aa 3e-26 in ref transcript
  • HAND. The HAND domain adopts a secondary structure consisting of four alpha helices, three of which (H2, H3, H4) form an L-like configuration. Helix H2 runs antiparallel to helices H3 and H4, packing closely against helix H4, whilst helix H1 reposes in the concave surface formed by these three helices and runs perpendicular to them. The domain confers DNA and nucleosome binding properties to the protein.
• smart HELICc 97aa 1e-18 in ref transcript
  • helicase superfamily c-terminal domain.
• smart SANT 42aa 9e-05 in ref transcript
  • SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
• Changed! COG HepA 493aa 3e-86 in ref transcript
  • Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair].
• Changed! cd DEXDc 116aa 1e-12 in modified transcript
• Changed! pfam SNF2_N 250aa 2e-93 in modified transcript
• Changed! COG HepA 472aa 3e-76 in modified transcript

SMARCA2

• refseq_SMARCA2.F1 refseq_SMARCA2.R1 238 292
• NCBIGene 36.3 6595
• Single exon skipping, size difference: 54
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_003070

• Changed! cd Bromo_SNF2L2 125aa 6e-47 in ref transcript
  • Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2 is a global transcriptional activator, which cooperates with nuclear hormone receptors to boost transcriptional activation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
• cd HELICc 133aa 2e-20 in ref transcript
  • Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process.
• cd DEXDc 140aa 3e-18 in ref transcript
  • DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
• pfam SNF2_N 286aa 3e-95 in ref transcript
  • SNF2 family N-terminal domain. This domain is found in proteins involved in a variety of processes including transcription regulation (e.g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as well as a variety of other proteins with little functional information (e.g., lodestar, ETL1).
• Changed! smart BROMO 126aa 8e-24 in ref transcript
  • bromo domain.
• pfam Helicase_C 81aa 5e-18 in ref transcript
  • Helicase conserved C-terminal domain. The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.
• smart HSA 58aa 5e-13 in ref transcript
  • domain in helicases and associated with SANT domains.
• pfam BRK 45aa 4e-12 in ref transcript
  • BRK domain. The function of this domain is unknown. It is often found associated with helicases and transcription factors.
• pfam QLQ 37aa 4e-10 in ref transcript
  • QLQ. The QLQ domain is named after the conserved Gln, Leu, Gln motif. The QLQ domain is found at the N-terminus of SWI2/SNF2 protein, which has been shown to be involved in protein-protein interactions. This domain has thus been postulated to be involved in mediating protein interactions.
• COG HepA 502aa 2e-82 in ref transcript
  • Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair].
• Changed! COG COG5076 91aa 4e-12 in ref transcript
  • Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription].
• Changed! cd Bromo_SNF2L2 107aa 3e-50 in modified transcript
• Changed! smart BROMO 108aa 4e-26 in modified transcript
• Changed! COG COG5076 122aa 6e-14 in modified transcript

SMARCB1

• refseq_SMARCB1.F2 refseq_SMARCB1.R2 133 160
• NCBIGene 36.3 6598
• Alternative 5-prime, size difference: 27
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_003073

• pfam SNF5 219aa 5e-93 in ref transcript
  • SNF5 / SMARCB1 / INI1. SNF5 is a component of the yeast SWI/SNF complex, which is an ATP-dependent nucleosome-remodelling complex that regulates the transcription of a subset of yeast genes. SNF5 is a key component of all SWI/SNF-class complexes characterised so far. This family consists of the conserved region of SNF5, including a direct repeat motif. SNF5 is essential for the assembly promoter targeting and chromatin remodelling activity of the SWI-SNF complex. SNF5 is also known as SMARCB1, for SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily b, member 1, and also INI1 for integrase interactor 1. Loss-of function mutations in SNF5 are thought to contribute to oncogenesis in malignant rhabdoid tumours (MRTs).

SMARCC2

• refseq_SMARCC2.F1 refseq_SMARCC2.R1 137 230
• NCBIGene 36.3 6601
• Single exon skipping, size difference: 93
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_003075

• pfam SWIRM 85aa 3e-29 in ref transcript
  • SWIRM domain. This SWIRM domain is a small alpha-helical domain of about 85 amino acid residues found in chromosomal proteins. It contains a helix-turn helix motif and binds to DNA.
• smart CHROMO 36aa 0.001 in ref transcript
  • Chromatin organization modifier domain.
• Changed! COG RSC8 193aa 2e-49 in ref transcript
  • RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription].
• Changed! COG RSC8 114aa 4e-17 in ref transcript
• COG RSC8 42aa 3e-04 in ref transcript
• COG MDN1 173aa 0.007 in ref transcript
  • AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only].
• Changed! COG RSC8 381aa 2e-67 in modified transcript

SMARCC2

• refseq_SMARCC2.F3 refseq_SMARCC2.R3 112 457
• NCBIGene 36.3 6601
• Alternative 5-prime, size difference: 345
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_003075

• pfam SWIRM 85aa 3e-29 in ref transcript
  • SWIRM domain. This SWIRM domain is a small alpha-helical domain of about 85 amino acid residues found in chromosomal proteins. It contains a helix-turn helix motif and binds to DNA.
• smart CHROMO 36aa 0.001 in ref transcript
  • Chromatin organization modifier domain.
• COG RSC8 193aa 2e-49 in ref transcript
  • RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription].
• COG RSC8 114aa 4e-17 in ref transcript
• COG RSC8 42aa 3e-04 in ref transcript
• COG MDN1 173aa 0.007 in ref transcript
  • AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only].

SMARCD1

• refseq_SMARCD1.F1 refseq_SMARCD1.R1 199 322
• NCBIGene 36.3 6602
• Single exon skipping, size difference: 123
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_003076

• smart SWIB 77aa 3e-24 in ref transcript
  • SWI complex, BAF60b domains.
• Changed! pfam Bindin 60aa 0.009 in ref transcript
  • Bindin.
• COG COG5531 204aa 4e-15 in ref transcript
  • SWIB-domain-containing proteins implicated in chromatin remodeling [Chromatin structure and dynamics].

SMC4

• refseq_SMC4.F2 refseq_SMC4.R2 220 295
• NCBIGene 36.2 10051
• Alternative 3-prime, size difference: 75
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001002800

• cd ABC_SMC4_euk 160aa 1e-51 in ref transcript
  • Eukaryotic SMC4 proteins; SMC proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (formerly known as Rad18).
• cd ABC_SMC4_euk 95aa 9e-51 in ref transcript
• pfam SMC_N 1192aa 0.0 in ref transcript
  • RecF/RecN/SMC N terminal domain. This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.
• COG Smc 1201aa 1e-123 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].

SMG7

• refseq_SMG7.F1 refseq_SMG7.R1 256 394
• NCBIGene 36.3 9887
• Alternative 5-prime, size difference: 138
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_173156

• cd TPR 79aa 0.003 in ref transcript
  • Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here.
• pfam EST1 119aa 6e-25 in ref transcript
  • Telomerase activating protein Est1. Est1 is a protein which recruits or activates telomerase at the site of polymerisation.

SMG7

• refseq_SMG7.F3 refseq_SMG7.R3 101 133
• NCBIGene 36.3 9887
• Single exon skipping, size difference: 32
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_173156

• Changed! cd TPR 79aa 0.003 in ref transcript
  • Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here.
• Changed! pfam EST1 119aa 6e-25 in ref transcript
  • Telomerase activating protein Est1. Est1 is a protein which recruits or activates telomerase at the site of polymerisation.

SMN2

• refseq_SMN2.F1 refseq_SMN2.R1 132 186
• NCBIGene 36.3 6607
• Single exon skipping, size difference: 54
• Exclusion of the stop codon
• Reference transcript: NM_017411

• cd TUDOR 48aa 2e-08 in ref transcript
  • Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal.
• pfam SMN 166aa 3e-40 in ref transcript
  • Survival motor neuron protein (SMN). This family consists of several eukaryotic survival motor neuron (SMN) proteins. The Survival of Motor Neurons (SMN) protein, the product of the spinal muscular atrophy-determining gene, is part of a large macromolecular complex (SMN complex) that functions in the assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs). The SMN complex functions as a specificity factor essential for the efficient assembly of Sm proteins on U snRNAs and likely protects cells from illicit, and potentially deleterious, non-specific binding of Sm proteins to RNAs.
• Changed! pfam SMN 35aa 2e-11 in ref transcript
• Changed! pfam SMN 27aa 2e-08 in modified transcript

SMOX

• refseq_SMOX.F1 refseq_SMOX.R1 263 353
• NCBIGene 36.3 54498
• Single exon skipping, size difference: 90
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_175839

• Changed! pfam Amino_oxidase 500aa 1e-53 in ref transcript
  • Flavin containing amine oxidoreductase. This family consists of various amine oxidases, including maze polyamine oxidase (PAO) and various flavin containing monoamine oxidases (MAO). The aligned region includes the flavin binding site of these enzymes. The family also contains phytoene dehydrogenases and related enzymes. In vertebrates MAO plays an important role regulating the intracellular levels of amines via there oxidation; these include various neurotransmitters, neurotoxins and trace amines. In lower eukaryotes such as aspergillus and in bacteria the main role of amine oxidases is to provide a source of ammonium. PAOs in plants, bacteria and protozoa oxidase spermidine and spermine to an aminobutyral, diaminopropane and hydrogen peroxide and are involved in the catabolism of polyamines. Other members of this family include tryptophan 2-monooxygenase, putrescine oxidase, corticosteroid binding proteins and antibacterial glycoproteins.
• Changed! COG COG1231 241aa 1e-08 in ref transcript
  • Monoamine oxidase [Amino acid transport and metabolism].
• COG COG1233 72aa 3e-04 in ref transcript
  • Phytoene dehydrogenase and related proteins [Secondary metabolites biosynthesis, transport, and catabolism].
• Changed! pfam Amino_oxidase 530aa 9e-51 in modified transcript
• Changed! COG COG1231 181aa 5e-06 in modified transcript

SMPD1

• refseq_SMPD1.F2 refseq_SMPD1.R2 217 349
• NCBIGene 36.3 6609
• Exon skipping and alternative 3-prime or 5-prime, size difference: 132
• Inclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_000543

• smart SapB 74aa 1e-06 in ref transcript
  • Saposin (B) Domains. Present in multiple copies in prosaposin and in pulmonary surfactant-associated protein B. In plant aspartic proteinases, a saposin domain is circularly permuted. This causes the prediction algorithm to predict two such domains, where only one is truly present.
• Changed! pfam Metallophos 97aa 0.006 in ref transcript
  • Calcineurin-like phosphoesterase. This family includes a diverse range of phosphoesterases, including protein phosphoserine phosphatases, nucleotidases, sphingomyelin phosphodiesterases and 2'-3' cAMP phosphodiesterases as well as nucleases such as bacterial SbcD or yeast MRE11. The most conserved regions in this superfamily centre around the metal chelating residues.
• COG COG0535 101aa 0.003 in ref transcript
  • Predicted Fe-S oxidoreductases [General function prediction only].
• Changed! pfam Metallophos 151aa 1e-06 in modified transcript

SMPD4

• refseq_SMPD4.F1 refseq_SMPD4.R1 118 256
• NCBIGene 36.2 55627
• Alternative 3-prime, size difference: 138
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_017751

SMPD4

• refseq_SMPD4.F4 refseq_SMPD4.R4 300 387
• NCBIGene 36.3 55627
• Single exon skipping, size difference: 87
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_017951

SMTN

• refseq_SMTN.F2 refseq_SMTN.R2 186 282
• NCBIGene 36.3 6525
• Alternative 5-prime, size difference: 96
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_134270

• Changed! cd CH 128aa 1e-19 in ref transcript
  • Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav).
• Changed! pfam CH 128aa 6e-23 in ref transcript
  • Calponin homology (CH) domain. The CH domain is found in both cytoskeletal proteins and signal transduction proteins. The CH domain is involved in actin binding in some members of the family. However in calponins there is evidence that the CH domain is not involved in its actin binding activity. Most proteins have two copies of the CH domain, however some proteins such as calponin have only a single copy.
• Changed! COG SAC6 92aa 1e-12 in ref transcript
  • Ca2+-binding actin-bundling protein fimbrin/plastin (EF-Hand superfamily) [Cytoskeleton].
• Changed! cd CH 101aa 9e-21 in modified transcript
• Changed! pfam CH 101aa 9e-24 in modified transcript
• Changed! COG SAC6 102aa 2e-14 in modified transcript

SMURF1

• refseq_SMURF1.F2 refseq_SMURF1.R2 270 348
• NCBIGene 36.3 57154
• Single exon skipping, size difference: 78
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_020429

• cd HECTc 356aa 1e-129 in ref transcript
  • HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ubiquitin molecules to the end of growing ubiquitin chains.
• cd C2 105aa 8e-12 in ref transcript
  • Protein kinase C conserved region 2 (CalB); Ca2+-binding motif present in phospholipases, protein kinases C, and synaptotagmins (among others). Some do not appear to contain Ca2+-binding sites. Particular C2s appear to bind phospholipids, inositol polyphosphates,and intracellular proteins. Synaptotagmin and PLC C2s are permuted in sequence with respect to N- and C-terminal beta strands.
• cd WW 30aa 2e-06 in ref transcript
  • Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
• cd WW 31aa 1e-04 in ref transcript
• pfam HECT 306aa 1e-125 in ref transcript
  • HECT-domain (ubiquitin-transferase). The name HECT comes from Homologous to the E6-AP Carboxyl Terminus.
• pfam C2 85aa 7e-15 in ref transcript
  • C2 domain.
• smart WW 32aa 7e-08 in ref transcript
  • Domain with 2 conserved Trp (W) residues. Also known as the WWP or rsp5 domain. Binds proline-rich polypeptides.
• smart WW 32aa 1e-05 in ref transcript
• Changed! COG HUL4 530aa 1e-133 in ref transcript
  • Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones].
• Changed! COG COG5038 89aa 0.001 in ref transcript
  • Ca2+-dependent lipid-binding protein, contains C2 domain [General function prediction only].
• Changed! COG HUL4 504aa 1e-133 in modified transcript
• Changed! COG HUL4 301aa 3e-04 in modified transcript

SNAP23

• refseq_SNAP23.F1 refseq_SNAP23.R1 188 347
• NCBIGene 36.3 8773
• Single exon skipping, size difference: 159
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_003825

• cd t_SNARE 60aa 3e-07 in ref transcript
  • Soluble NSF (N-ethylmaleimide-sensitive fusion protein)-Attachment protein (SNAP) REceptor domain; these alpha-helical motifs form twisted and parallel heterotetrameric helix bundles; the core complex contains one helix from a protein that is anchored in the vesicle membrane (synaptobrevin), one helix from a protein of the target membrane (syntaxin), and two helices from another protein anchored in the target membrane (SNAP-25); their interaction forms a core which is composed of a polar zero layer, a flanking leucine-zipper layer acts as a water tight shield to isolate ionic interactions in the zero layer from the surrounding solvent.
• Changed! cd t_SNARE 59aa 0.006 in ref transcript
• pfam SNARE 58aa 5e-09 in ref transcript
  • SNARE domain. Most if not all vesicular membrane fusion events in eukaryotic cells are believed to be mediated by a conserved fusion machinery, the SNARE [soluble N-ethylmaleimide-sensitive factor (NSF) attachment protein (SNAP) receptors] machinery. The SNARE domain is thought to act as a protein-protein interaction module in the assembly of a SNARE protein complex.
• Changed! pfam SNAP-25 62aa 2e-08 in ref transcript
  • SNAP-25 family. SNAP-25 (synaptosome-associated protein 25 kDa) proteins are components of SNARE complexes. Members of this family contain a cluster of cysteine residues that can be palmitoylated for membrane attachment.
• smart t_SNARE 66aa 2e-05 in ref transcript
  • Helical region found in SNAREs. All alpha-helical motifs that form twisted and parallel four-helix bundles in target soluble N-ethylmaleimide-sensitive factor (NSF) attachment protein (SNAP) receptor proteins. This motif found in "Q-SNAREs".

SNCA

• refseq_SNCA.F2 refseq_SNCA.R2 283 367
• NCBIGene 36.3 6622
• Single exon skipping, size difference: 84
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000345

• Changed! pfam Synuclein 132aa 8e-26 in ref transcript
  • Synuclein. There are three types of synucleins in humans, these are called alpha, beta and gamma. Alpha synuclein has been found mutated in families with autosomal dominant Parkinson's disease. A peptide of alpha synuclein has also been found in amyloid plaques in Alzheimer's patients.
• Changed! pfam Synuclein 107aa 1e-17 in modified transcript

SNCB

• refseq_SNCB.F1 refseq_SNCB.R1 204 361
• NCBIGene 36.3 6620
• Single exon skipping, size difference: 157
• Exclusion in 5'UTR
• Reference transcript: NM_001001502

• pfam Synuclein 92aa 8e-26 in ref transcript
  • Synuclein. There are three types of synucleins in humans, these are called alpha, beta and gamma. Alpha synuclein has been found mutated in families with autosomal dominant Parkinson's disease. A peptide of alpha synuclein has also been found in amyloid plaques in Alzheimer's patients.

SNRP70

• refseq_SNRP70.F2 refseq_SNRP70.R2 109 181
• NCBIGene 36.2 6625
• Single exon skipping, size difference: 72
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_003089

• Changed! cd RRM 74aa 5e-17 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• Changed! smart RRM 71aa 2e-16 in ref transcript
  • RNA recognition motif.
• Changed! COG COG0724 91aa 1e-10 in ref transcript
  • RNA-binding proteins (RRM domain) [General function prediction only].
• Changed! cd RRM 53aa 3e-12 in modified transcript
• Changed! smart RRM 51aa 1e-11 in modified transcript
• Changed! COG COG0724 68aa 8e-08 in modified transcript

SNRPB

• refseq_SNRPB.F1 refseq_SNRPB.R1 160 306
• NCBIGene 36.3 6628
• Alternative 3-prime, size difference: 146
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_198216

• cd Sm_B 79aa 2e-40 in ref transcript
  • The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit B heterodimerizes with subunit D3 and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
• smart Sm 76aa 2e-16 in ref transcript
  • snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing.
• COG LSM1 82aa 3e-08 in ref transcript
  • Small nuclear ribonucleoprotein (snRNP) homolog [Transcription].

SNRPB2

• refseq_SNRPB2.F1 refseq_SNRPB2.R1 169 269
• NCBIGene 36.3 6629
• Alternative 5-prime, size difference: 100
• Exclusion in 5'UTR
• Reference transcript: NM_003092

• cd RRM 76aa 2e-11 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• cd RRM 60aa 5e-08 in ref transcript
• smart RRM_2 75aa 3e-11 in ref transcript
  • RNA recognition motif.
• pfam RRM_1 60aa 3e-10 in ref transcript
  • RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain). The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have a N terminus rrm which is included in the seed. There is a second region towards the C terminus that has some features of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.
• COG COG0724 95aa 5e-07 in ref transcript
  • RNA-binding proteins (RRM domain) [General function prediction only].
• COG COG0724 89aa 0.002 in ref transcript

SNRPD2

• refseq_SNRPD2.F1 refseq_SNRPD2.R1 157 272
• NCBIGene 36.3 6633
• Single exon skipping, size difference: 115
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_004597

• Changed! cd Sm_D2 88aa 2e-35 in ref transcript
  • The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D2 heterodimerizes with subunit D1 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing D2, D3, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
• Changed! smart Sm 72aa 1e-10 in ref transcript
  • snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing.
• Changed! COG LSM1 82aa 2e-07 in ref transcript
  • Small nuclear ribonucleoprotein (snRNP) homolog [Transcription].

SNX1

• refseq_SNX1.F1 refseq_SNX1.R1 301 496
• NCBIGene 36.3 6642
• Multiple exon skipping, size difference: 195
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_003099

• Changed! cd PX_SNX1 123aa 3e-64 in ref transcript
  • The phosphoinositide binding Phox Homology domain of Sorting Nexin 1. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. SNX1 is both membrane associated and a cytosolic protein that exists as a tetramer in protein complexes. It can associate reversibly with membranes of the endosomal compartment, thereby coating these vesicles. SNX1 is a component of the retromer complex, a membrane coat multimeric complex required for endosomal retrieval of lysosomal hydrolase receptors to the Golgi. The retromer consists of a cargo-recognition subcomplex and a subcomplex formed by a dimer of sorting nexins (SNX1 and/or SNX2), which ensures efficient cargo sorting by facilitating proper membrane localization of the cargo-recognition subcomplex. SNX1 contains a Bin/Amphiphysin/Rvs (BAR) domain C-terminal to the PX domain. The PX domain of SNX1 specifically binds phosphatidylinositol-3-phosphate (PI3P) and PI(3,5)P2, while the BAR domain detects membrane curvature. Both domains help determine the specific membrane-targeting of SNX1, which is localized to a microdomain in early endosomes where it regulates cation-independent mannose-6-phosphate receptor retrieval to the trans Golgi network.
• pfam Vps5 234aa 6e-81 in ref transcript
  • Vps5 C terminal like. Vps5 is a sorting nexin that functions in membrane trafficking. This is the C terminal dimerisation domain.
• Changed! smart PX 118aa 8e-24 in ref transcript
  • PhoX homologous domain, present in p47phox and p40phox. Eukaryotic domain of unknown function present in phox proteins, PLD isoforms, a PI3K isoform.
• Changed! pfam Sorting_nexin 122aa 1e-22 in ref transcript
  • Sorting nexin, N-terminal domain. These proteins bins to the cytoplasmic domain of plasma membrane receptors. and are involved in endocytic protein trafficking. The N-terminal domain appears to be specific to sorting nexins 1 and 2.
• Changed! COG COG5391 355aa 7e-08 in ref transcript
  • Phox homology (PX) domain protein [Intracellular trafficking and secretion / General function prediction only].
• Changed! cd PX_SNX1 113aa 2e-59 in modified transcript
• Changed! smart PX 111aa 5e-21 in modified transcript
• Changed! pfam Sorting_nexin 81aa 3e-14 in modified transcript
• Changed! COG COG5391 392aa 9e-09 in modified transcript

SNX1

• refseq_SNX1.F2 refseq_SNX1.R2 189 333
• NCBIGene 36.3 6642
• Single exon skipping, size difference: 144
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_003099

• cd PX_SNX1 123aa 3e-64 in ref transcript
  • The phosphoinositide binding Phox Homology domain of Sorting Nexin 1. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. SNX1 is both membrane associated and a cytosolic protein that exists as a tetramer in protein complexes. It can associate reversibly with membranes of the endosomal compartment, thereby coating these vesicles. SNX1 is a component of the retromer complex, a membrane coat multimeric complex required for endosomal retrieval of lysosomal hydrolase receptors to the Golgi. The retromer consists of a cargo-recognition subcomplex and a subcomplex formed by a dimer of sorting nexins (SNX1 and/or SNX2), which ensures efficient cargo sorting by facilitating proper membrane localization of the cargo-recognition subcomplex. SNX1 contains a Bin/Amphiphysin/Rvs (BAR) domain C-terminal to the PX domain. The PX domain of SNX1 specifically binds phosphatidylinositol-3-phosphate (PI3P) and PI(3,5)P2, while the BAR domain detects membrane curvature. Both domains help determine the specific membrane-targeting of SNX1, which is localized to a microdomain in early endosomes where it regulates cation-independent mannose-6-phosphate receptor retrieval to the trans Golgi network.
• Changed! pfam Vps5 234aa 6e-81 in ref transcript
  • Vps5 C terminal like. Vps5 is a sorting nexin that functions in membrane trafficking. This is the C terminal dimerisation domain.
• smart PX 118aa 8e-24 in ref transcript
  • PhoX homologous domain, present in p47phox and p40phox. Eukaryotic domain of unknown function present in phox proteins, PLD isoforms, a PI3K isoform.
• pfam Sorting_nexin 122aa 1e-22 in ref transcript
  • Sorting nexin, N-terminal domain. These proteins bins to the cytoplasmic domain of plasma membrane receptors. and are involved in endocytic protein trafficking. The N-terminal domain appears to be specific to sorting nexins 1 and 2.
• Changed! COG COG5391 355aa 7e-08 in ref transcript
  • Phox homology (PX) domain protein [Intracellular trafficking and secretion / General function prediction only].
• Changed! pfam Vps5 186aa 2e-56 in modified transcript
• Changed! COG COG5391 109aa 8e-07 in modified transcript

SNX11

• refseq_SNX11.F1 refseq_SNX11.R1 114 174
• NCBIGene 36.3 29916
• Single exon skipping, size difference: 60
• Exclusion in 5'UTR
• Reference transcript: NM_152244

• cd PX_SNX10 92aa 7e-37 in ref transcript
  • The phosphoinositide binding Phox Homology domain of Sorting Nexin 10. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. Some SNXs are localized in early endosome structures such as clathrin-coated pits, while others are located in late structures of the endocytic pathway. SNX10 may be involved in the regulation of endosome homeostasis. Its expression induces the formation of giant vacuoles in mammalian cells.
• pfam PX 91aa 2e-20 in ref transcript
  • PX domain. PX domains bind to phosphoinositides.
• COG COG5391 93aa 3e-09 in ref transcript
  • Phox homology (PX) domain protein [Intracellular trafficking and secretion / General function prediction only].

SNX14

• refseq_SNX14.F1 refseq_SNX14.R1 136 163
• NCBIGene 36.3 57231
• Single exon skipping, size difference: 27
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_153816

• cd PX_SNX14 123aa 3e-50 in ref transcript
  • The phosphoinositide binding Phox Homology domain of Sorting Nexin 14. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. SNX14 may be involved in recruiting other proteins to the membrane via protein-protein and protein-ligand interaction. It is expressed in the embryonic nervous system of mice, and is co-expressed in the motoneurons and the anterior pituary with Islet-1. SNX14 shows a similar domain architecture as SNX13, containing an N-terminal PXA domain, a regulator of G protein signaling (RGS) domain, a PX domain, and a C-terminal domain that is conserved in some SNXs.
• pfam Nexin_C 106aa 5e-25 in ref transcript
  • Sorting nexin C terminal. This region is found a the C terminal of proteins belonging to the sorting nexin family. It is found on proteins which also contain pfam00787.
• smart PXA 156aa 6e-22 in ref transcript
  • Domain associated with PX domains. unpubl. observations.
• pfam PX 105aa 2e-17 in ref transcript
  • PX domain. PX domains bind to phosphoinositides.
• smart RGS 128aa 2e-07 in ref transcript
  • Regulator of G protein signalling domain. RGS family members are GTPase-activating proteins for heterotrimeric G-protein alpha-subunits.
• COG COG5391 140aa 0.002 in ref transcript
  • Phox homology (PX) domain protein [Intracellular trafficking and secretion / General function prediction only].

SNX15

• refseq_SNX15.F1 refseq_SNX15.R1 141 399
• NCBIGene 36.3 29907
• Single exon skipping, size difference: 258
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_013306

• cd PX_SNX15 118aa 9e-51 in ref transcript
  • The phosphoinositide binding Phox Homology domain of Sorting Nexin 15. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. SNX15 contains an N-terminal PX domain and a C-terminal Microtubule Interacting and Trafficking (MIT) domain. It plays a role in protein trafficking processes in the endocytic pathway and the trans-Golgi network. The PX domain of SNX15 interacts with the PDGF receptor and is responsible for the membrane association of the protein.
• Changed! cd MIT_SNX15 75aa 1e-19 in ref transcript
  • MIT: domain contained within Microtubule Interacting and Trafficking molecules. This MIT domain sub-family is found in sorting nexin 15 and related proteins. The molecular function of the MIT domain is unclear.
• Changed! smart MIT 77aa 4e-18 in ref transcript
  • Microtubule Interacting and Trafficking molecule domain.
• pfam PX 112aa 2e-12 in ref transcript
  • PX domain. PX domains bind to phosphoinositides.
• Changed! cd MIT_SNX15 74aa 2e-10 in modified transcript
• Changed! smart MIT 74aa 9e-09 in modified transcript

SNX16

• refseq_SNX16.F2 refseq_SNX16.R2 269 356
• NCBIGene 36.3 64089
• Single exon skipping, size difference: 87
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_152836

• Changed! cd PX_SNX16 110aa 2e-57 in ref transcript
  • The phosphoinositide binding Phox Homology domain of Sorting Nexin 16. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. SNX16 contains a central PX domain followed by a coiled-coil region. SNX16 is localized in early and recycling endosomes through the binding of its PX domain to phosphatidylinositol-3-phosphate (PI3P). It plays a role in epidermal growth factor (EGF) signaling by regulating EGF receptor membrane trafficking.
• Changed! pfam PX 89aa 3e-16 in ref transcript
  • PX domain. PX domains bind to phosphoinositides.
• Changed! COG COG5391 148aa 7e-05 in ref transcript
  • Phox homology (PX) domain protein [Intracellular trafficking and secretion / General function prediction only].
• Changed! cd PX_SNX16 81aa 3e-36 in modified transcript
• Changed! pfam PX 57aa 3e-07 in modified transcript

SNX7

• refseq_SNX7.F2 refseq_SNX7.R2 222 375
• NCBIGene 36.3 51375
• Single exon skipping, size difference: 153
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_015976

• cd PX_SNX7 116aa 2e-62 in ref transcript
  • The phosphoinositide binding Phox Homology domain of Sorting Nexin 7. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. Some SNXs are localized in early endosome structures such as clathrin-coated pits, while others are located in late structures of the endocytic pathway. SNX7 harbors a Bin/Amphiphysin/Rvs (BAR) domain, which detects membrane curvature, C-terminal to the PX domain, similar to the sorting nexins SNX1-2, SNX4-6, SNX8, SNX30, and SNX32. Both domains have been shown to determine the specific membrane-targeting of SNX1. The specific function of SNX7 has yet to be elucidated.
• pfam PX 114aa 1e-21 in ref transcript
  • PX domain. PX domains bind to phosphoinositides.
• Changed! COG COG5391 374aa 2e-12 in ref transcript
  • Phox homology (PX) domain protein [Intracellular trafficking and secretion / General function prediction only].
• Changed! COG COG5391 236aa 5e-12 in modified transcript

SNX7

• refseq_SNX7.F3 refseq_SNX7.R3 283 403
• NCBIGene 36.3 51375
• Single exon skipping, size difference: 120
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_015976

• Changed! cd PX_SNX7 116aa 2e-62 in ref transcript
  • The phosphoinositide binding Phox Homology domain of Sorting Nexin 7. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. Some SNXs are localized in early endosome structures such as clathrin-coated pits, while others are located in late structures of the endocytic pathway. SNX7 harbors a Bin/Amphiphysin/Rvs (BAR) domain, which detects membrane curvature, C-terminal to the PX domain, similar to the sorting nexins SNX1-2, SNX4-6, SNX8, SNX30, and SNX32. Both domains have been shown to determine the specific membrane-targeting of SNX1. The specific function of SNX7 has yet to be elucidated.
• Changed! pfam PX 114aa 1e-21 in ref transcript
  • PX domain. PX domains bind to phosphoinositides.
• Changed! COG COG5391 374aa 2e-12 in ref transcript
  • Phox homology (PX) domain protein [Intracellular trafficking and secretion / General function prediction only].

SOCS4

• refseq_SOCS4.F1 refseq_SOCS4.R1 236 365
• NCBIGene 36.3 122809
• Single exon skipping, size difference: 129
• Exclusion in 5'UTR
• Reference transcript: NM_199421

• cd SOCS_SOCS4 56aa 8e-27 in ref transcript
  • SOCS (suppressors of cytokine signaling) box of SOCS4-like proteins. Together with CIS1, the CIS/SOCS family of proteins is characterized by the presence of a C-terminal SOCS box and a central SH2 domain. The general function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions.
• cd SH2 96aa 1e-11 in ref transcript
  • Src homology 2 domains; Signal transduction, involved in recognition of phosphorylated tyrosine (pTyr). SH2 domains typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites.
• smart SH2 85aa 2e-14 in ref transcript
  • Src homology 2 domains. Src homology 2 domains bind phosphotyrosine-containing polypeptides via 2 surface pockets. Specificity is provided via interaction with residues that are distinct from the phosphotyrosine. Only a single occurrence of a SH2 domain has been found in S. cerevisiae.
• smart SOCS 40aa 9e-09 in ref transcript
  • suppressors of cytokine signalling. suppressors of cytokine signalling.

SORBS1

• refseq_SORBS1.F1 refseq_SORBS1.R1 182 389
• NCBIGene 36.3 10580
• Alternative 3-prime, size difference: 207
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001034954

• cd SH3 54aa 3e-12 in ref transcript
  • Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
• cd SH3 52aa 8e-11 in ref transcript
• cd SH3 52aa 6e-10 in ref transcript
• smart SH3 59aa 4e-13 in ref transcript
  • Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.
• smart SH3 53aa 3e-12 in ref transcript
• smart SH3 59aa 7e-11 in ref transcript
• pfam Sorb 41aa 4e-10 in ref transcript
  • Sorbin homologous domain.

SORBS1

• refseq_SORBS1.F4 refseq_SORBS1.R4 195 363
• NCBIGene 36.3 10580
• Single exon skipping, size difference: 168
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001034954

• cd SH3 54aa 3e-12 in ref transcript
  • Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
• cd SH3 52aa 8e-11 in ref transcript
• cd SH3 52aa 6e-10 in ref transcript
• smart SH3 59aa 4e-13 in ref transcript
  • Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.
• smart SH3 53aa 3e-12 in ref transcript
• smart SH3 59aa 7e-11 in ref transcript
• pfam Sorb 41aa 4e-10 in ref transcript
  • Sorbin homologous domain.

SORBS1

• refseq_SORBS1.F6 refseq_SORBS1.R6 189 285
• NCBIGene 36.3 10580
• Single exon skipping, size difference: 96
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001034954

• cd SH3 54aa 3e-12 in ref transcript
  • Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
• cd SH3 52aa 8e-11 in ref transcript
• cd SH3 52aa 6e-10 in ref transcript
• smart SH3 59aa 4e-13 in ref transcript
  • Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.
• smart SH3 53aa 3e-12 in ref transcript
• smart SH3 59aa 7e-11 in ref transcript
• pfam Sorb 41aa 4e-10 in ref transcript
  • Sorbin homologous domain.

SORBS1

• refseq_SORBS1.F7 refseq_SORBS1.R7 130 157
• NCBIGene 36.3 10580
• Single exon skipping, size difference: 27
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001034954

• cd SH3 54aa 3e-12 in ref transcript
  • Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
• cd SH3 52aa 8e-11 in ref transcript
• cd SH3 52aa 6e-10 in ref transcript
• smart SH3 59aa 4e-13 in ref transcript
  • Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.
• smart SH3 53aa 3e-12 in ref transcript
• smart SH3 59aa 7e-11 in ref transcript
• pfam Sorb 41aa 4e-10 in ref transcript
  • Sorbin homologous domain.

SORBS2

• refseq_SORBS2.F1 refseq_SORBS2.R1 204 273
• NCBIGene 36.3 8470
• Alternative 3-prime, size difference: 69
• Exclusion in 5'UTR
• Reference transcript: NM_021069

• cd SH3 52aa 8e-14 in ref transcript
  • Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
• cd SH3 54aa 9e-12 in ref transcript
• cd SH3 54aa 3e-11 in ref transcript
• pfam Sorb 50aa 9e-21 in ref transcript
  • Sorbin homologous domain.
• smart SH3 53aa 5e-16 in ref transcript
  • Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.
• smart SH3 59aa 2e-12 in ref transcript
• smart SH3 59aa 2e-12 in ref transcript

SORBS2

• refseq_SORBS2.F2 refseq_SORBS2.R2 217 358
• NCBIGene 36.3 8470
• Multiple exon skipping, size difference: 141
• Inclusion in the protein (no stop codon or frameshift), Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_021069

• cd SH3 52aa 8e-14 in ref transcript
  • Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
• cd SH3 54aa 9e-12 in ref transcript
• cd SH3 54aa 3e-11 in ref transcript
• pfam Sorb 50aa 9e-21 in ref transcript
  • Sorbin homologous domain.
• smart SH3 53aa 5e-16 in ref transcript
  • Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.
• smart SH3 59aa 2e-12 in ref transcript
• smart SH3 59aa 2e-12 in ref transcript

SORCS1

• refseq_SORCS1.F1 refseq_SORCS1.R1 268 377
• NCBIGene 36.3 114815
• Exon skipping and alternative 3-prime or 5-prime, size difference: 109
• Inclusion in the protein causing a new stop codon, Exclusion in the protein causing a frameshift
• Reference transcript: NM_001013031

• smart VPS10 598aa 0.0 in ref transcript
  • VPS10 domain.
• pfam PKD 80aa 8e-06 in ref transcript
  • PKD domain. This domain was first identified in the Polycystic kidney disease protein PKD1. This domain has been predicted to contain an Ig-like fold.

SOX6

• refseq_SOX6.F1 refseq_SOX6.R1 227 269
• NCBIGene 36.3 55553
• Alternative 5-prime, size difference: 42
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_033326

• cd SOX-TCF_HMG-box 64aa 1e-24 in ref transcript
  • SOX-TCF_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and vertebrates, and transcription factor-like proteins, TCF-1, -3, -4, and LEF-1. They appear to bind the minor groove of the A/T C A A A G/C-motif.
• smart HMG 64aa 5e-16 in ref transcript
  • high mobility group.
• COG NHP6B 52aa 2e-06 in ref transcript
  • Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics].

SOX6

• refseq_SOX6.F4 refseq_SOX6.R4 137 260
• NCBIGene 36.3 55553
• Single exon skipping, size difference: 123
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_033326

• cd SOX-TCF_HMG-box 64aa 1e-24 in ref transcript
  • SOX-TCF_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and vertebrates, and transcription factor-like proteins, TCF-1, -3, -4, and LEF-1. They appear to bind the minor groove of the A/T C A A A G/C-motif.
• smart HMG 64aa 5e-16 in ref transcript
  • high mobility group.
• COG NHP6B 52aa 2e-06 in ref transcript
  • Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics].

SOX6

• refseq_SOX6.F5 refseq_SOX6.R5 185 245
• NCBIGene 36.3 55553
• Alternative 3-prime, size difference: 60
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_033326

• cd SOX-TCF_HMG-box 64aa 1e-24 in ref transcript
  • SOX-TCF_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and vertebrates, and transcription factor-like proteins, TCF-1, -3, -4, and LEF-1. They appear to bind the minor groove of the A/T C A A A G/C-motif.
• smart HMG 64aa 5e-16 in ref transcript
  • high mobility group.
• COG NHP6B 52aa 2e-06 in ref transcript
  • Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics].

SP110

• refseq_SP110.F2 refseq_SP110.R2 295 367
• NCBIGene 36.3 3431
• Single exon skipping, size difference: 72
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_080424

• Changed! cd Bromo_SP100C_like 101aa 8e-39 in ref transcript
  • Bromodomain, SP100C_like subfamily. The SP100C protein is a splice variant of SP100, a major component of PML-SP100 nuclear bodies (NBs), which are poorly understood. It is covalently modified by SUMO-1 and may play a role in processes at the chromatin level. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
• pfam SAND 82aa 7e-29 in ref transcript
  • SAND domain. The DNA binding activity of two proteins has been mapped to the SAND domain. The conserved KDWK motif is necessary for DNA binding, and it appears to be important for dimerisation.
• pfam Sp100 101aa 3e-26 in ref transcript
  • Sp100 domain. The function of this domain is unknown. It is about 105 amino acid residues in length and is predicted to be predominantly alpha helical. This domain is usually found at the amino terminus of protein that contain a SAND domain pfam01342.
• Changed! smart BROMO 98aa 5e-09 in ref transcript
  • bromo domain.
• Changed! cd Bromo_SP100C_like 110aa 2e-38 in modified transcript
• Changed! smart BROMO 74aa 1e-06 in modified transcript

SPAST

• refseq_SPAST.F1 refseq_SPAST.R1 231 327
• NCBIGene 36.3 6683
• Single exon skipping, size difference: 96
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_014946

• cd MIT_spastin 80aa 2e-22 in ref transcript
  • MIT: domain contained within Microtubule Interacting and Trafficking molecules. This MIT domain sub-family is found in the AAA protein spastin, a probable ATPase involved in the assembly or function of nuclear protein complexes; spastins might also be involved in microtubule dynamics. The molecular function of the MIT domain is unclear.
• cd AAA 164aa 5e-21 in ref transcript
  • The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.
• pfam AAA 186aa 3e-50 in ref transcript
  • ATPase family associated with various cellular activities (AAA). AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes.
• smart MIT 78aa 3e-13 in ref transcript
  • Microtubule Interacting and Trafficking molecule domain.
• pfam Mg_chelatase 54aa 3e-05 in ref transcript
  • Magnesium chelatase, subunit ChlI. Magnesium-chelatase is a three-component enzyme that catalyses the insertion of Mg2+ into protoporphyrin IX. This is the first unique step in the synthesis of (bacterio)chlorophyll. Due to this, it is thought that Mg-chelatase has an important role in channelling inter- mediates into the (bacterio)chlorophyll branch in response to conditions suitable for photosynthetic growth. ChlI and BchD have molecular weight between 38-42 kDa.
• COG SpoVK 268aa 7e-60 in ref transcript
  • ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones].

SPATA7

• refseq_SPATA7.F1 refseq_SPATA7.R1 110 206
• NCBIGene 36.3 55812
• Single exon skipping, size difference: 96
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_018418

SPHK1

• refseq_SPHK1.F1 refseq_SPHK1.R1 107 470
• NCBIGene 36.3 8877
• Alternative 5-prime, size difference: 363
• Exclusion of the protein initiation site
• Reference transcript: NM_182965

• pfam DAGK_cat 104aa 1e-19 in ref transcript
  • Diacylglycerol kinase catalytic domain. Diacylglycerol (DAG) is a second messenger that acts as a protein kinase C activator. The catalytic domain is assumed from the finding of bacterial homologues. YegS is the Escherichia coli protein in this family whose crystal structure reveals an active site in the inter-domain cleft formed by four conserved sequence motifs, revealing a novel metal-binding site. The residues of this site are conserved across the family.
• COG LCB5 333aa 4e-18 in ref transcript
  • Sphingosine kinase and enzymes related to eukaryotic diacylglycerol kinase [Lipid metabolism / General function prediction only].

SPHK1

• refseq_SPHK1.F3 refseq_SPHK1.R3 164 206
• NCBIGene 36.3 8877
• Alternative 3-prime, size difference: 42
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_182965

• pfam DAGK_cat 104aa 1e-19 in ref transcript
  • Diacylglycerol kinase catalytic domain. Diacylglycerol (DAG) is a second messenger that acts as a protein kinase C activator. The catalytic domain is assumed from the finding of bacterial homologues. YegS is the Escherichia coli protein in this family whose crystal structure reveals an active site in the inter-domain cleft formed by four conserved sequence motifs, revealing a novel metal-binding site. The residues of this site are conserved across the family.
• COG LCB5 333aa 4e-18 in ref transcript
  • Sphingosine kinase and enzymes related to eukaryotic diacylglycerol kinase [Lipid metabolism / General function prediction only].

SPINT1

• refseq_SPINT1.F1 refseq_SPINT1.R1 192 240
• NCBIGene 36.3 6692
• Alternative 5-prime, size difference: 48
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_181642

• cd KU 52aa 8e-12 in ref transcript
  • BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
• cd KU 54aa 1e-11 in ref transcript
• cd LDLa 35aa 7e-06 in ref transcript
  • Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure.
• pfam MANEC 92aa 3e-31 in ref transcript
  • MANEC domain. This region of similarity, comprising 8 conserved cysteines, is found in the N-terminal region of several membrane-associated and extracellular proteins. Although formerly called MANSC (for motif at N terminus with seven cysteines) it has now been renamed by MANEC (motif at N terminus with eight cysteines) by Richard Mitter and Stephen Fitzgerald after the discovery of an eighth conserved cysteine. It is postulated that this domain may play a role in the formation of protein complexes involving various protease activators and inhibitors.
• pfam Kunitz_BPTI 53aa 3e-14 in ref transcript
  • Kunitz/Bovine pancreatic trypsin inhibitor domain. Indicative of a protease inhibitor, usually a serine protease inhibitor. Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure. Certain family members are similar to the tick anticoagulant peptide (TAP). This is a highly selective inhibitor of factor Xa in the blood coagulation pathways. TAP molecules are highly dipolar, and are arranged to form a twisted two- stranded antiparallel beta-sheet followed by an alpha helix.
• pfam Kunitz_BPTI 52aa 4e-13 in ref transcript
• smart LDLa 33aa 3e-06 in ref transcript
  • Low-density lipoprotein receptor domain class A. Cysteine-rich repeat in the low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. The N-terminal type A repeats in LDL receptor bind the lipoproteins. Other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement. Mutations in the LDL receptor gene cause familial hypercholesterolemia.

SPO11

• refseq_SPO11.F2 refseq_SPO11.R2 263 377
• NCBIGene 36.3 23626
• Single exon skipping, size difference: 114
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_012444

• cd TOPRIM_TopoIIB_SPO 163aa 2e-53 in ref transcript
  • TOPRIM_TopoIIB_SPO: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in the type IIB family of DNA topoisomerases and Spo11. This subgroup contains proteins similar to Sulfolobus shibatae topoisomerase VI (TopoVI) and Saccharomyces cerevisiae meiotic recombination factor: Spo11. Type II DNA topoisomerases catalyze the ATP-dependent transport of one DNA duplex through another, in the process generating transient double strand breaks via covalent attachments to both DNA strands at the 5' positions. TopoVI enzymes are heterotetramers found in archaea and plants. Spo11 plays a role in generating the double strand breaks that initiate homologous recombination during meiosis. S. shibatae TopoVI relaxes both positive and negative supercoils, and in addition has a strong decatenase activity. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD. For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
• pfam SPO11_like 42aa 3e-19 in ref transcript
  • SPO11 homologue.
• pfam TP6A_N 68aa 7e-19 in ref transcript
  • Type IIB DNA topoisomerase. Type II DNA topoisomerases are ubiquitous enzymes that catalyse the ATP-dependent transport of one DNA duplex through a second DNA segment via a transient double-strand break. Type II DNA topoisomerases are now subdivided into two sub-families, type IIA and IIB DNA topoisomerases. TP6A_N is present in type IIB topoisomerase and is thought to be involved in DNA binding owing to its sequence similarity to Escherichia coli catabolite activator protein (CAP).
• Changed! PRK PRK04342 354aa 4e-65 in ref transcript
  • DNA topoisomerase VI subunit A; Provisional.
• Changed! PRK PRK04342 291aa 2e-63 in modified transcript

SPOP

• refseq_SPOP.F1 refseq_SPOP.R1 118 240
• NCBIGene 36.3 8405
• Single exon skipping, size difference: 122
• Exclusion in 5'UTR
• Reference transcript: NM_001007226

• cd MATH_SPOP 139aa 8e-70 in ref transcript
  • Speckle-type POZ protein (SPOP) family, MATH domain; composed of proteins with similarity to human SPOP. SPOP was isolated as a novel antigen recognized by serum from a scleroderma patient, whose overexpression in COS cells results in a discrete speckled pattern in the nuclei. It contains an N-terminal MATH domain and a C-terminal BTB (also called POZ) domain. Together with Cul3, SPOP constitutes an ubiquitin E3 ligase which is able to ubiquitinate the PcG protein BMI1, the variant histone macroH2A1 and the death domain-associated protein Daxx. Therefore, SPOP may be involved in the regulation of these proteins and may play a role in transcriptional regulation, apoptosis and X-chromosome inactivation. Cul3 binds to the BTB domain of SPOP whereas Daxx and the macroH2A1 nonhistone region have been shown to bind to the MATH domain. Both MATH and BTB domains are necessary for the nuclear speckled accumulation of SPOP. There are many proteins, mostly uncharacterized, containing both MATH and BTB domains from C. elegans and plants which are excluded from this family.
• pfam BTB 108aa 3e-21 in ref transcript
  • BTB/POZ domain. The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN.
• smart MATH 102aa 8e-10 in ref transcript
  • meprin and TRAF homology.

SPOP

• refseq_SPOP.F2 refseq_SPOP.R2 121 172
• NCBIGene 36.3 8405
• Single exon skipping, size difference: 51
• Exclusion in 5'UTR
• Reference transcript: NM_001007230

• cd MATH_SPOP 139aa 8e-70 in ref transcript
  • Speckle-type POZ protein (SPOP) family, MATH domain; composed of proteins with similarity to human SPOP. SPOP was isolated as a novel antigen recognized by serum from a scleroderma patient, whose overexpression in COS cells results in a discrete speckled pattern in the nuclei. It contains an N-terminal MATH domain and a C-terminal BTB (also called POZ) domain. Together with Cul3, SPOP constitutes an ubiquitin E3 ligase which is able to ubiquitinate the PcG protein BMI1, the variant histone macroH2A1 and the death domain-associated protein Daxx. Therefore, SPOP may be involved in the regulation of these proteins and may play a role in transcriptional regulation, apoptosis and X-chromosome inactivation. Cul3 binds to the BTB domain of SPOP whereas Daxx and the macroH2A1 nonhistone region have been shown to bind to the MATH domain. Both MATH and BTB domains are necessary for the nuclear speckled accumulation of SPOP. There are many proteins, mostly uncharacterized, containing both MATH and BTB domains from C. elegans and plants which are excluded from this family.
• pfam BTB 108aa 3e-21 in ref transcript
  • BTB/POZ domain. The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN.
• smart MATH 102aa 8e-10 in ref transcript
  • meprin and TRAF homology.

SREBF1

• refseq_SREBF1.F1 refseq_SREBF1.R1 182 272
• NCBIGene 36.3 6720
• Single exon skipping, size difference: 90
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001005291

• cd HLH 58aa 9e-12 in ref transcript
  • Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins.
• pfam HLH 51aa 2e-12 in ref transcript
  • Helix-loop-helix DNA-binding domain.

SS18

• refseq_SS18.F1 refseq_SS18.R1 115 208
• NCBIGene 36.3 6760
• Single exon skipping, size difference: 93
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001007559

• pfam SSXT 66aa 4e-20 in ref transcript
  • SSXT protein (N-terminal region). The SSXT or SS18 protein is involved in synovial sarcoma in humans. A SYT-SSX fusion gene resulting from the chromosomal translocation t(X;18) (p11;q11) is characteristic of synovial sarcomas. This translocation fuses the SSXT (SYT) gene from chromosome 18 to either of two homologous genes at Xp11, SSX1 or SSX2.

SSBP3

• refseq_SSBP3.F1 refseq_SSBP3.R1 126 207
• NCBIGene 36.3 23648
• Single exon skipping, size difference: 81
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_145716

• pfam SSDP 144aa 2e-06 in ref transcript
  • Single-stranded DNA binding protein, SSDP. This is a family of eukaryotic single-stranded DNA binding proteins with specificity to a pyrimidine-rich element found in the promoter region of the alpha2(I) collagen gene.

SSBP4

• refseq_SSBP4.F1 refseq_SSBP4.R1 100 166
• NCBIGene 36.3 170463
• Single exon skipping, size difference: 66
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_032627

• pfam SSDP 149aa 7e-15 in ref transcript
  • Single-stranded DNA binding protein, SSDP. This is a family of eukaryotic single-stranded DNA binding proteins with specificity to a pyrimidine-rich element found in the promoter region of the alpha2(I) collagen gene.
• Changed! pfam PAT1 157aa 3e-07 in ref transcript
  • Topoisomerase II-associated protein PAT1. Members of this family are necessary for accurate chromosome transmission during cell division.
• Changed! PRK PRK07764 149aa 1e-04 in ref transcript
  • DNA polymerase III subunits gamma and tau; Validated.
• Changed! PRK PRK07764 137aa 5e-04 in modified transcript

SSH3

• refseq_SSH3.F1 refseq_SSH3.R1 246 344
• NCBIGene 36.2 54961
• Alternative 3-prime, size difference: 98
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_017857

• cd DSPc 136aa 2e-37 in ref transcript
  • Dual specificity phosphatases (DSP); Ser/Thr and Tyr protein phosphatases. Structurally similar to tyrosine-specific phosphatases but with a shallower active site cleft and a distinctive active site signature motif, HCxxGxxR. Characterized as VHR- or Cdc25-like.
• smart DSPc 135aa 3e-36 in ref transcript
  • Dual specificity phosphatase, catalytic domain.
• pfam DEK_C 54aa 4e-12 in ref transcript
  • DEK C terminal domain. DEK is a chromatin associated protein that is linked with cancers and autoimmune disease. This domain is found at the C terminal of DEK and is of clinical importance since it can reverse the characteristic abnormal DNA-mutagen sensitivity in fibroblasts from ataxia-telangiectasia (A-T) patients. The structure of this domain shows it to be homologous to the E2F/DP transcription factor family. This domain is also found in chitin synthase proteins, and in protein phosphatases.
• PRK PRK12361 131aa 7e-12 in ref transcript
  • hypothetical protein; Provisional.

SSX4

• refseq_SSX4B.F1 refseq_SSX4B.R1 121 257
• NCBIGene 36.3 6759
• Single exon skipping, size difference: 136
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_005636

• Changed! pfam SSXRD 34aa 2e-08 in ref transcript
  • SSXRD motif. SSX1 can repress transcription, and this has been attributed to a putative Kruppel associated box (KRAB) repression domain at the N-terminus. However, from the analysis of these deletion constructs further repression activity was found at the C-terminus of SSX1. Which has been called the SSXRD (SSX Repression Domain). The potent repression exerted by full-length SSX1 appears to localise to this region.
• smart KRAB 60aa 1e-05 in ref transcript
  • krueppel associated box.

ST3GAL3

• refseq_ST3GAL3.F1 refseq_ST3GAL3.R1 107 401
• NCBIGene 36.3 6487
• Multiple exon skipping, size difference: 294
• Exclusion in the protein (no frameshift), Exclusion in the protein (no frameshift)
• Reference transcript: NM_174963

• Changed! pfam Glyco_transf_29 218aa 4e-38 in ref transcript
  • Glycosyltransferase family 29 (sialyltransferase). Members of this family belong to glycosyltransferase family 29.
• Changed! pfam Glyco_transf_29 85aa 4e-19 in modified transcript

ST3GAL3

• refseq_ST3GAL3.F3 refseq_ST3GAL3.R3 134 179
• NCBIGene 36.3 6487
• Alternative 5-prime, size difference: 45
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_174963

• pfam Glyco_transf_29 218aa 4e-38 in ref transcript
  • Glycosyltransferase family 29 (sialyltransferase). Members of this family belong to glycosyltransferase family 29.

ST3GAL3

• refseq_ST3GAL3.F5 refseq_ST3GAL3.R5 109 271
• NCBIGene 36.3 6487
• Single exon skipping, size difference: 162
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_174963

• pfam Glyco_transf_29 218aa 4e-38 in ref transcript
  • Glycosyltransferase family 29 (sialyltransferase). Members of this family belong to glycosyltransferase family 29.

ST6GALNAC4

• refseq_ST6GALNAC4.F1 refseq_ST6GALNAC4.R1 137 224
• NCBIGene 36.3 27090
• Single exon skipping, size difference: 87
• Exclusion of the protein initiation site
• Reference transcript: NM_175039

• Changed! pfam Glyco_transf_29 273aa 2e-69 in ref transcript
  • Glycosyltransferase family 29 (sialyltransferase). Members of this family belong to glycosyltransferase family 29.
• Changed! pfam Glyco_transf_29 201aa 3e-61 in modified transcript

ST7

• refseq_ST7.F1 refseq_ST7.R1 197 266
• NCBIGene 36.3 7982
• Single exon skipping, size difference: 69
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_021908

• Changed! pfam ST7 535aa 0.0 in ref transcript
  • ST7 protein. The ST7 (for suppression of tumorigenicity 7) protein is thought to be a tumour suppressor gene. The molecular function of this protein is uncertain.
• Changed! pfam ST7 512aa 0.0 in modified transcript

ST7L

• refseq_ST7L.F1 refseq_ST7L.R1 166 259
• NCBIGene 36.3 54879
• Single exon skipping, size difference: 93
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_017744

• Changed! pfam ST7 502aa 0.0 in ref transcript
  • ST7 protein. The ST7 (for suppression of tumorigenicity 7) protein is thought to be a tumour suppressor gene. The molecular function of this protein is uncertain.
• Changed! pfam ST7 471aa 0.0 in modified transcript

ST7L

• refseq_ST7L.F2 refseq_ST7L.R2 101 152
• NCBIGene 36.3 54879
• Alternative 3-prime, size difference: 51
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_017744

• Changed! pfam ST7 502aa 0.0 in ref transcript
  • ST7 protein. The ST7 (for suppression of tumorigenicity 7) protein is thought to be a tumour suppressor gene. The molecular function of this protein is uncertain.
• Changed! pfam ST7 485aa 0.0 in modified transcript

STAP2

• refseq_STAP2.F2 refseq_STAP2.R2 223 361
• NCBIGene 36.3 55620
• Alternative 3-prime, size difference: 138
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_017720

• cd SH2 96aa 8e-05 in ref transcript
  • Src homology 2 domains; Signal transduction, involved in recognition of phosphorylated tyrosine (pTyr). SH2 domains typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites.
• pfam SH2 78aa 0.003 in ref transcript
  • SH2 domain.

STARD5

• refseq_STARD5.F2 refseq_STARD5.R2 108 158
• NCBIGene 36.2 80765
• Single exon skipping, size difference: 50
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_181900

• Changed! cd START 211aa 8e-31 in ref transcript
  • START(STeroidogenic Acute Regulatory (STAR) related lipid Transfer) Domain. These domains are 200-210 amino acid in length and occur in proteins involved in lipid transport (phosphatidylcholine) and metabolism, signal transduction, and transcriptional regulation. The most striking feature of the START domain structure is a predominantly hydrophobic tunnel extending nearly the entire protein and used to binding a single molecule of large lipophilic compounds, like cholesterol.
• Changed! pfam START 206aa 2e-17 in ref transcript
  • START domain.

STATH

• refseq_STATH.F1 refseq_STATH.R1 112 142
• NCBIGene 36.3 6779
• Single exon skipping, size difference: 30
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_003154

• Changed! pfam Statherin 19aa 5e-05 in ref transcript
  • Statherin. Statherin functions biologically to inhibit the nucleation and growth of calcium phosphate minerals. The N-terminus of statherin is highly charge, the glutamic acids of which have been shown to be important in the recognition hydroxyapatite.

STAU1

• refseq_STAU1.F1 refseq_STAU1.R1 101 119
• NCBIGene 36.3 6780
• Alternative 3-prime, size difference: 18
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_017453

• cd DSRM 67aa 1e-12 in ref transcript
  • Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, RNases H1, and dsRNA dependent adenosine deaminases.
• smart DSRM 67aa 3e-14 in ref transcript
  • Double-stranded RNA binding motif.
• Changed! smart DSRM 32aa 0.001 in ref transcript
• PRK rnc 72aa 1e-10 in ref transcript
  • ribonuclease III; Reviewed.

STAU1

• refseq_STAU1.F2 refseq_STAU1.R2 107 396
• NCBIGene 36.3 6780
• Single exon skipping, size difference: 289
• Exclusion of the protein initiation site
• Reference transcript: NM_017453

• cd DSRM 67aa 1e-12 in ref transcript
  • Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, RNases H1, and dsRNA dependent adenosine deaminases.
• smart DSRM 67aa 3e-14 in ref transcript
  • Double-stranded RNA binding motif.
• smart DSRM 32aa 0.001 in ref transcript
• PRK rnc 72aa 1e-10 in ref transcript
  • ribonuclease III; Reviewed.

STRN4

• refseq_STRN4.F1 refseq_STRN4.R1 118 139
• NCBIGene 36.3 29888
• Alternative 3-prime, size difference: 21
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001039877

• cd WD40 306aa 2e-42 in ref transcript
  • WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.
• pfam Striatin 134aa 3e-31 in ref transcript
  • Striatin family. Striatin is an intracellular protein which has a caveolin-binding motif, a coiled-coil structure, a calmodulin-binding site, and a WD (pfam00400) repeat domain. It acts as a scaffold protein and is involved in signalling pathways.
• smart WD40 40aa 1e-08 in ref transcript
  • WD40 repeats. Note that these repeats are permuted with respect to the structural repeats (blades) of the beta propeller domain.
• smart WD40 40aa 1e-06 in ref transcript
• smart WD40 40aa 6e-06 in ref transcript
• COG COG2319 303aa 5e-25 in ref transcript
  • FOG: WD40 repeat [General function prediction only].

STX16

• refseq_STX16.F1 refseq_STX16.R1 112 175
• NCBIGene 36.3 8675
• Exon skipping and alternative 3-prime or 5-prime, size difference: 63
• Exclusion in the protein (no frameshift), Exclusion in the protein (no frameshift)
• Reference transcript: NM_001001433

• cd t_SNARE 47aa 3e-06 in ref transcript
  • Soluble NSF (N-ethylmaleimide-sensitive fusion protein)-Attachment protein (SNAP) REceptor domain; these alpha-helical motifs form twisted and parallel heterotetrameric helix bundles; the core complex contains one helix from a protein that is anchored in the vesicle membrane (synaptobrevin), one helix from a protein of the target membrane (syntaxin), and two helices from another protein anchored in the target membrane (SNAP-25); their interaction forms a core which is composed of a polar zero layer, a flanking leucine-zipper layer acts as a water tight shield to isolate ionic interactions in the zero layer from the surrounding solvent.
• pfam Syntaxin 107aa 6e-13 in ref transcript
  • Syntaxin. Syntaxins are the prototype family of SNARE proteins. They usually consist of three main regions - a C-terminal transmembrane region, a central SNARE domain which is characteristic of and conserved in all syntaxins (pfam05739), and an N-terminal domain that is featured in this entry. This domain varies between syntaxin isoforms; in syntaxin 1A it is found as three alpha-helices with a left-handed twist. It may fold back on the SNARE domain to allow the molecule to adopt a 'closed' configuration that prevents formation of the core fusion complex - it thus has an auto-inhibitory role. The function of syntaxins is determined by their localisation. They are involved in neuronal exocytosis, ER-Golgi transport and Golgi-endosome transport, for example. They also interact with other proteins as well as those involved in SNARE complexes. These include vesicle coat proteins, Rab GTPases, and tethering factors.
• pfam SNARE 52aa 6e-10 in ref transcript
  • SNARE domain. Most if not all vesicular membrane fusion events in eukaryotic cells are believed to be mediated by a conserved fusion machinery, the SNARE [soluble N-ethylmaleimide-sensitive factor (NSF) attachment protein (SNAP) receptors] machinery. The SNARE domain is thought to act as a protein-protein interaction module in the assembly of a SNARE protein complex.
• COG COG5325 227aa 3e-15 in ref transcript
  • t-SNARE complex subunit, syntaxin [Intracellular trafficking and secretion].

STX2

• refseq_STX2.F1 refseq_STX2.R1 192 318
• NCBIGene 36.3 2054
• Single exon skipping, size difference: 126
• Exclusion of the stop codon
• Reference transcript: NM_194356

• cd SynN 152aa 1e-29 in ref transcript
  • Syntaxin N-terminus domain; syntaxins are nervous system-specific proteins implicated in the docking of synaptic vesicles with the presynaptic plasma membrane; they are a family of receptors for intracellular transport vesicles; each target membrane may be identified by a specific member of the syntaxin family; syntaxins contain a moderately well conserved amino-terminal domain, called Habc, whose structure is an antiparallel three-helix bundle; a linker of about 30 amino acids connects this to the carboxy-terminal region, designated H3 (t_SNARE), of the syntaxin cytoplasmic domain; the highly conserved H3 region forms a single, long alpha-helix when it is part of the core SNARE complex and anchors the protein on the cytoplasmic surface of cellular membranes; H3 is not included in defining this domain.
• cd t_SNARE 60aa 2e-07 in ref transcript
  • Soluble NSF (N-ethylmaleimide-sensitive fusion protein)-Attachment protein (SNAP) REceptor domain; these alpha-helical motifs form twisted and parallel heterotetrameric helix bundles; the core complex contains one helix from a protein that is anchored in the vesicle membrane (synaptobrevin), one helix from a protein of the target membrane (syntaxin), and two helices from another protein anchored in the target membrane (SNAP-25); their interaction forms a core which is composed of a polar zero layer, a flanking leucine-zipper layer acts as a water tight shield to isolate ionic interactions in the zero layer from the surrounding solvent.
• smart SynN 119aa 4e-23 in ref transcript
  • Syntaxin N-terminal domain. Three-helix domain that (in Sso1p) slows the rate of its reaction with the SNAP-25 homologue Sec9p.
• pfam SNARE 62aa 6e-13 in ref transcript
  • SNARE domain. Most if not all vesicular membrane fusion events in eukaryotic cells are believed to be mediated by a conserved fusion machinery, the SNARE [soluble N-ethylmaleimide-sensitive factor (NSF) attachment protein (SNAP) receptors] machinery. The SNARE domain is thought to act as a protein-protein interaction module in the assembly of a SNARE protein complex.
• Changed! COG COG5074 234aa 9e-15 in ref transcript
  • t-SNARE complex subunit, syntaxin [Intracellular trafficking and secretion].
• Changed! COG COG5074 235aa 7e-14 in modified transcript

STXBP1

• refseq_STXBP1.F1 refseq_STXBP1.R1 227 353
• NCBIGene 36.3 6812
• Single exon skipping, size difference: 126
• Exclusion of the stop codon
• Reference transcript: NM_003165

• Changed! pfam Sec1 549aa 1e-180 in ref transcript
  • Sec1 family.
• Changed! COG SEC1 543aa 7e-55 in ref transcript
  • Proteins involved in synaptic transmission and general secretion, Sec1 family [Intracellular trafficking and secretion].
• Changed! pfam Sec1 543aa 1e-178 in modified transcript
• Changed! COG SEC1 535aa 2e-53 in modified transcript

SULF2

• refseq_SULF2.F1 refseq_SULF2.R1 159 213
• NCBIGene 36.3 55959
• Single exon skipping, size difference: 54
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_018837

• pfam Sulfatase 352aa 3e-34 in ref transcript
  • Sulfatase.
• COG AslA 353aa 2e-29 in ref transcript
  • Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism].

SULT1A1

• refseq_SULT1A1.F1 refseq_SULT1A1.R1 129 160
• NCBIGene 36.3 6817
• Alternative 3-prime, size difference: 31
• Inclusion in 5'UTR
• Reference transcript: NM_001055

• pfam Sulfotransfer_1 250aa 7e-77 in ref transcript
  • Sulfotransferase domain.

SULT1C2

• refseq_SULT1C1.F1 refseq_SULT1C1.R1 160 193
• NCBIGene 36.3 6819
• Exon skipping and alternative 3-prime or 5-prime, size difference: 33
• Inclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_176825

• Changed! pfam Sulfotransfer_1 261aa 7e-86 in ref transcript
  • Sulfotransferase domain.
• Changed! pfam Sulfotransfer_1 250aa 2e-95 in modified transcript

SUMO1

• refseq_SUMO1.F1 refseq_SUMO1.R1 288 363
• NCBIGene 36.3 7341
• Single exon skipping, size difference: 75
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_003352

• Changed! cd Sumo 87aa 2e-31 in ref transcript
  • Small ubiquitin-related modifier (SUMO) proteins are conjugated to numerous intracellular targets and serve to modulate protein interaction, localization, activity or stability. SUMO (also known as "Smt3" and "sentrin" in other organisms) is linked to several different pathways, including nucleocytoplasmic transport. Attachment of SUMO to targets proteins is stimulated by PIAS (Protein inhibitor of activated STATs) proteins which serve as E3-like ligases.
• pfam ubiquitin 66aa 2e-10 in ref transcript
  • Ubiquitin family. This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue), Nedd8, Elongin B, Rub1, and Parkin. A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites.
• Changed! COG SMT3 96aa 2e-19 in ref transcript
  • Ubiquitin-like protein (sentrin) [Posttranslational modification, protein turnover, chaperones].
• Changed! cd Sumo 71aa 1e-27 in modified transcript
• Changed! COG SMT3 72aa 4e-17 in modified transcript

SUOX

• refseq_SUOX.F1 refseq_SUOX.R1 121 247
• NCBIGene 36.3 6821
• Single exon skipping, size difference: 126
• Exclusion in 5'UTR
• Reference transcript: NM_000456

• cd eukary_SO_Moco 359aa 1e-145 in ref transcript
  • molybdopterin binding domain of sulfite oxidase (SO). SO catalyzes the terminal reaction in the oxidative degradation of the sulfur-containing amino acids cysteine and methionine. Common features of all known members of the sulfite oxidase (SO) family of molybdopterin binding domains are that they contain one single pterin cofactor and part of the coordination of the metal (Mo) is a cysteine ligand of the protein and that they catalyze the transfer of an oxygen to or from a lone pair of electrons on the substrate.
• pfam Mo-co_dimer 127aa 5e-46 in ref transcript
  • Mo-co oxidoreductase dimerisation domain. This domain is found in molybdopterin cofactor (Mo-co) oxidoreductases. It is involved in dimer formation, and has an Ig-fold structure.
• pfam Oxidored_molyb 183aa 1e-32 in ref transcript
  • Oxidoreductase molybdopterin binding domain. This domain is found in a variety of oxidoreductases. This domain binds to a molybdopterin cofactor. Xanthine dehydrogenases, that also bind molybdopterin, have essentially no similarity.
• pfam Cyt-b5 77aa 1e-14 in ref transcript
  • Cytochrome b5-like Heme/Steroid binding domain. This family includes heme binding domains from a diverse range of proteins. This family also includes proteins that bind to steroids. The family includes progesterone receptors. Many members of this subfamily are membrane anchored by an N-terminal transmembrane alpha helix. This family also includes a domain in some chitin synthases. There is no known ligand for this domain in the chitin synthases.
• COG COG2041 237aa 5e-18 in ref transcript
  • Sulfite oxidase and related enzymes [General function prediction only].
• COG CYB5 90aa 2e-05 in ref transcript
  • Cytochrome b involved in lipid metabolism [Energy production and conversion / Lipid metabolism].

SUPT3H

• refseq_SUPT3H.F1 refseq_SUPT3H.R1 243 428
• NCBIGene 36.3 8464
• Multiple exon skipping, size difference: 185
• Exclusion of the protein initiation site, Exclusion in the protein (no frameshift)
• Reference transcript: NM_181356

• Changed! pfam TFIID-18kDa 82aa 5e-18 in ref transcript
  • Transcription initiation factor IID, 18kD subunit. This family includes the Spt3 yeast transcription factors and the 18kD subunit from human transcription initiation factor IID (TFIID-18). Determination of the crystal structure reveals an atypical histone fold.
• Changed! pfam TFIID-18kDa 91aa 2e-22 in modified transcript

SVIL

• refseq_SVIL.F1 refseq_SVIL.R1 160 256
• NCBIGene 36.3 6840
• Single exon skipping, size difference: 96
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_021738

• smart GEL 95aa 5e-17 in ref transcript
  • Gelsolin homology domain. Gelsolin/severin/villin homology domain. Calcium-binding and actin-binding. Both intra- and extracellular domains.
• smart GEL 97aa 7e-11 in ref transcript
• smart VHP 36aa 7e-11 in ref transcript
  • Villin headpiece domain.
• smart GEL 107aa 5e-10 in ref transcript
• smart GEL 96aa 4e-05 in ref transcript
• smart GEL 99aa 0.002 in ref transcript

SYF2

• refseq_SYF2.F1 refseq_SYF2.R1 196 322
• NCBIGene 36.3 25949
• Single exon skipping, size difference: 126
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_015484

• Changed! pfam SYF2 145aa 6e-46 in ref transcript
  • SYF2 splicing factor. Proteins in this family are involved in cell cycle progression and pre-mRNA splicing.
• Changed! pfam SYF2 152aa 4e-49 in modified transcript

SYN3

• refseq_SYN3.F1 refseq_SYN3.R1 109 401
• NCBIGene 36.3 8224
• Single exon skipping, size difference: 292
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_003490

• pfam Synapsin_C 203aa 1e-119 in ref transcript
  • Synapsin, ATP binding domain. Ca dependent ATP binding in this ATP grasp fold. Function unknown.
• pfam Synapsin 105aa 2e-52 in ref transcript
  • Synapsin, N-terminal domain.
• pfam Synapsin_N 29aa 1e-10 in ref transcript
  • Synapsin N-terminal. This highly conserved domain of synapsin proteins has a serine at position 9 or 10 which is a phosphorylation site. The domain appears to be the part of the molecule that binds to calmodulin.
• Changed! COG RimK 227aa 0.001 in ref transcript
  • Glutathione synthase/Ribosomal protein S6 modification enzyme (glutaminyl transferase) [Coenzyme metabolism / Translation, ribosomal structure and biogenesis].
• Changed! COG RimK 138aa 0.002 in modified transcript

SYNE1

• refseq_SYNE1.F2 refseq_SYNE1.R2 104 125
• NCBIGene 36.3 23345
• Single exon skipping, size difference: 21
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_182961

• cd SPEC 211aa 6e-14 in ref transcript
  • Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here.
• Changed! cd CH 107aa 1e-13 in ref transcript
  • Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav).
• cd SPEC 216aa 6e-11 in ref transcript
• cd SPEC 210aa 2e-09 in ref transcript
• cd CH 105aa 8e-09 in ref transcript
• cd SPEC 219aa 1e-07 in ref transcript
• cd SPEC 217aa 4e-07 in ref transcript
• cd SPEC 217aa 7e-07 in ref transcript
• cd SPEC 215aa 8e-07 in ref transcript
• cd SPEC 206aa 2e-05 in ref transcript
• cd SPEC 212aa 3e-05 in ref transcript
• cd SPEC 210aa 7e-05 in ref transcript
• cd SPEC 227aa 8e-05 in ref transcript
• cd SPEC 216aa 1e-04 in ref transcript
• cd SPEC 217aa 3e-04 in ref transcript
• cd SPEC 223aa 7e-04 in ref transcript
• cd SPEC 206aa 0.003 in ref transcript
• cd SPEC 212aa 0.003 in ref transcript
• cd SPEC 208aa 0.004 in ref transcript
• Changed! smart CH 103aa 1e-14 in ref transcript
  • Calponin homology domain. Actin binding domains present in duplicate at the N-termini of spectrin-like proteins (including dystrophin, alpha-actinin). These domains cross-link actin filaments into bundles and networks. A calponin homology domain is predicted in yeasst Cdc24p.
• pfam KASH 60aa 1e-13 in ref transcript
  • Nuclear envelope localisation domain. The KASH (for Klarsicht/ANC-1/Syne-1 homology) or KLS domain is a highly hydrophobic nuclear envelope localisation domain of approximately 60 amino acids comprising an 20-amino-acid transmembrane region and a 30-35-residue C-terminal region that lies between the inner and the outer nuclear membranes.
• pfam CH 104aa 9e-11 in ref transcript
  • Calponin homology (CH) domain. The CH domain is found in both cytoskeletal proteins and signal transduction proteins. The CH domain is involved in actin binding in some members of the family. However in calponins there is evidence that the CH domain is not involved in its actin binding activity. Most proteins have two copies of the CH domain, however some proteins such as calponin have only a single copy.
• pfam SMC_N 808aa 2e-09 in ref transcript
  • RecF/RecN/SMC N terminal domain. This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.
• pfam SMC_N 755aa 2e-06 in ref transcript
• smart SPEC 100aa 2e-06 in ref transcript
  • Spectrin repeats.
• pfam Spectrin 98aa 8e-05 in ref transcript
  • Spectrin repeat. Spectrin repeats are found in several proteins involved in cytoskeletal structure. These include spectrin, alpha-actinin and dystrophin. The sequence repeat used in this family is taken from the structural repeat in reference. The spectrin repeat forms a three helix bundle. The second helix is interrupted by proline in some sequences. The repeats are defined by a characteristic tryptophan (W) residue at position 17 in helix A and a leucine (L) at 2 residues from the carboxyl end of helix C.
• pfam SMC_N 247aa 3e-04 in ref transcript
• pfam SMC_N 199aa 5e-04 in ref transcript
• TIGR SMC_prok_B 254aa 6e-04 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• smart SPEC 103aa 0.001 in ref transcript
• smart SPEC 97aa 0.002 in ref transcript
• pfam SMC_N 247aa 0.003 in ref transcript
• pfam Spectrin 101aa 0.005 in ref transcript
• pfam SMC_N 296aa 0.009 in ref transcript
• Changed! COG SAC6 259aa 3e-20 in ref transcript
  • Ca2+-binding actin-bundling protein fimbrin/plastin (EF-Hand superfamily) [Cytoskeleton].
• COG Smc 854aa 2e-11 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].
• COG Smc 819aa 6e-06 in ref transcript
• COG Smc 303aa 0.002 in ref transcript
• PRK PRK02224 459aa 0.002 in ref transcript
  • chromosome segregation protein; Provisional.
• Changed! cd CH 114aa 1e-11 in modified transcript
• Changed! smart CH 110aa 2e-12 in modified transcript
• Changed! TIGR SMC_prok_B 839aa 0.010 in modified transcript
• Changed! COG SAC6 266aa 3e-18 in modified transcript

SYNE1

• refseq_SYNE1.F3 refseq_SYNE1.R3 251 317
• NCBIGene 36.3 23345
• Alternative 5-prime, size difference: 66
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_182961

• cd SPEC 211aa 6e-14 in ref transcript
  • Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here.
• cd CH 107aa 1e-13 in ref transcript
  • Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav).
• cd SPEC 216aa 6e-11 in ref transcript
• cd SPEC 210aa 2e-09 in ref transcript
• cd CH 105aa 8e-09 in ref transcript
• cd SPEC 219aa 1e-07 in ref transcript
• cd SPEC 217aa 4e-07 in ref transcript
• cd SPEC 217aa 7e-07 in ref transcript
• cd SPEC 215aa 8e-07 in ref transcript
• cd SPEC 206aa 2e-05 in ref transcript
• cd SPEC 212aa 3e-05 in ref transcript
• cd SPEC 210aa 7e-05 in ref transcript
• cd SPEC 227aa 8e-05 in ref transcript
• cd SPEC 216aa 1e-04 in ref transcript
• cd SPEC 217aa 3e-04 in ref transcript
• cd SPEC 223aa 7e-04 in ref transcript
• cd SPEC 206aa 0.003 in ref transcript
• cd SPEC 212aa 0.003 in ref transcript
• cd SPEC 208aa 0.004 in ref transcript
• smart CH 103aa 1e-14 in ref transcript
  • Calponin homology domain. Actin binding domains present in duplicate at the N-termini of spectrin-like proteins (including dystrophin, alpha-actinin). These domains cross-link actin filaments into bundles and networks. A calponin homology domain is predicted in yeasst Cdc24p.
• pfam KASH 60aa 1e-13 in ref transcript
  • Nuclear envelope localisation domain. The KASH (for Klarsicht/ANC-1/Syne-1 homology) or KLS domain is a highly hydrophobic nuclear envelope localisation domain of approximately 60 amino acids comprising an 20-amino-acid transmembrane region and a 30-35-residue C-terminal region that lies between the inner and the outer nuclear membranes.
• pfam CH 104aa 9e-11 in ref transcript
  • Calponin homology (CH) domain. The CH domain is found in both cytoskeletal proteins and signal transduction proteins. The CH domain is involved in actin binding in some members of the family. However in calponins there is evidence that the CH domain is not involved in its actin binding activity. Most proteins have two copies of the CH domain, however some proteins such as calponin have only a single copy.
• pfam SMC_N 808aa 2e-09 in ref transcript
  • RecF/RecN/SMC N terminal domain. This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.
• pfam SMC_N 755aa 2e-06 in ref transcript
• smart SPEC 100aa 2e-06 in ref transcript
  • Spectrin repeats.
• pfam Spectrin 98aa 8e-05 in ref transcript
  • Spectrin repeat. Spectrin repeats are found in several proteins involved in cytoskeletal structure. These include spectrin, alpha-actinin and dystrophin. The sequence repeat used in this family is taken from the structural repeat in reference. The spectrin repeat forms a three helix bundle. The second helix is interrupted by proline in some sequences. The repeats are defined by a characteristic tryptophan (W) residue at position 17 in helix A and a leucine (L) at 2 residues from the carboxyl end of helix C.
• pfam SMC_N 247aa 3e-04 in ref transcript
• pfam SMC_N 199aa 5e-04 in ref transcript
• TIGR SMC_prok_B 254aa 6e-04 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• smart SPEC 103aa 0.001 in ref transcript
• smart SPEC 97aa 0.002 in ref transcript
• pfam SMC_N 247aa 0.003 in ref transcript
• pfam Spectrin 101aa 0.005 in ref transcript
• pfam SMC_N 296aa 0.009 in ref transcript
• COG SAC6 259aa 3e-20 in ref transcript
  • Ca2+-binding actin-bundling protein fimbrin/plastin (EF-Hand superfamily) [Cytoskeleton].
• COG Smc 854aa 2e-11 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].
• Changed! COG Smc 819aa 6e-06 in ref transcript
• COG Smc 303aa 0.002 in ref transcript
• PRK PRK02224 459aa 0.002 in ref transcript
  • chromosome segregation protein; Provisional.
• Changed! TIGR SMC_prok_A 180aa 0.005 in modified transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent.
• Changed! TIGR SMC_prok_B 839aa 0.010 in modified transcript
• Changed! COG Smc 760aa 4e-06 in modified transcript

SYNE1

• refseq_SYNE1.F5 refseq_SYNE1.R5 157 226
• NCBIGene 36.3 23345
• Single exon skipping, size difference: 69
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_182961

• cd SPEC 211aa 6e-14 in ref transcript
  • Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here.
• cd CH 107aa 1e-13 in ref transcript
  • Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav).
• cd SPEC 216aa 6e-11 in ref transcript
• cd SPEC 210aa 2e-09 in ref transcript
• cd CH 105aa 8e-09 in ref transcript
• cd SPEC 219aa 1e-07 in ref transcript
• cd SPEC 217aa 4e-07 in ref transcript
• cd SPEC 217aa 7e-07 in ref transcript
• cd SPEC 215aa 8e-07 in ref transcript
• cd SPEC 206aa 2e-05 in ref transcript
• cd SPEC 212aa 3e-05 in ref transcript
• cd SPEC 210aa 7e-05 in ref transcript
• cd SPEC 227aa 8e-05 in ref transcript
• cd SPEC 216aa 1e-04 in ref transcript
• cd SPEC 217aa 3e-04 in ref transcript
• cd SPEC 223aa 7e-04 in ref transcript
• cd SPEC 206aa 0.003 in ref transcript
• cd SPEC 212aa 0.003 in ref transcript
• cd SPEC 208aa 0.004 in ref transcript
• smart CH 103aa 1e-14 in ref transcript
  • Calponin homology domain. Actin binding domains present in duplicate at the N-termini of spectrin-like proteins (including dystrophin, alpha-actinin). These domains cross-link actin filaments into bundles and networks. A calponin homology domain is predicted in yeasst Cdc24p.
• pfam KASH 60aa 1e-13 in ref transcript
  • Nuclear envelope localisation domain. The KASH (for Klarsicht/ANC-1/Syne-1 homology) or KLS domain is a highly hydrophobic nuclear envelope localisation domain of approximately 60 amino acids comprising an 20-amino-acid transmembrane region and a 30-35-residue C-terminal region that lies between the inner and the outer nuclear membranes.
• pfam CH 104aa 9e-11 in ref transcript
  • Calponin homology (CH) domain. The CH domain is found in both cytoskeletal proteins and signal transduction proteins. The CH domain is involved in actin binding in some members of the family. However in calponins there is evidence that the CH domain is not involved in its actin binding activity. Most proteins have two copies of the CH domain, however some proteins such as calponin have only a single copy.
• pfam SMC_N 808aa 2e-09 in ref transcript
  • RecF/RecN/SMC N terminal domain. This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.
• pfam SMC_N 755aa 2e-06 in ref transcript
• smart SPEC 100aa 2e-06 in ref transcript
  • Spectrin repeats.
• pfam Spectrin 98aa 8e-05 in ref transcript
  • Spectrin repeat. Spectrin repeats are found in several proteins involved in cytoskeletal structure. These include spectrin, alpha-actinin and dystrophin. The sequence repeat used in this family is taken from the structural repeat in reference. The spectrin repeat forms a three helix bundle. The second helix is interrupted by proline in some sequences. The repeats are defined by a characteristic tryptophan (W) residue at position 17 in helix A and a leucine (L) at 2 residues from the carboxyl end of helix C.
• pfam SMC_N 247aa 3e-04 in ref transcript
• pfam SMC_N 199aa 5e-04 in ref transcript
• TIGR SMC_prok_B 254aa 6e-04 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• smart SPEC 103aa 0.001 in ref transcript
• smart SPEC 97aa 0.002 in ref transcript
• pfam SMC_N 247aa 0.003 in ref transcript
• pfam Spectrin 101aa 0.005 in ref transcript
• pfam SMC_N 296aa 0.009 in ref transcript
• COG SAC6 259aa 3e-20 in ref transcript
  • Ca2+-binding actin-bundling protein fimbrin/plastin (EF-Hand superfamily) [Cytoskeleton].
• COG Smc 854aa 2e-11 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].
• COG Smc 819aa 6e-06 in ref transcript
• COG Smc 303aa 0.002 in ref transcript
• PRK PRK02224 459aa 0.002 in ref transcript
  • chromosome segregation protein; Provisional.
• Changed! TIGR SMC_prok_B 839aa 0.010 in modified transcript

SYNE1

• refseq_SYNE1.F8 refseq_SYNE1.R8 236 404
• NCBIGene 36.3 23345
• Single exon skipping, size difference: 168
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_182961

• cd SPEC 211aa 6e-14 in ref transcript
  • Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here.
• cd CH 107aa 1e-13 in ref transcript
  • Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav).
• cd SPEC 216aa 6e-11 in ref transcript
• cd SPEC 210aa 2e-09 in ref transcript
• cd CH 105aa 8e-09 in ref transcript
• Changed! cd SPEC 219aa 1e-07 in ref transcript
• cd SPEC 217aa 4e-07 in ref transcript
• cd SPEC 217aa 7e-07 in ref transcript
• cd SPEC 215aa 8e-07 in ref transcript
• cd SPEC 206aa 2e-05 in ref transcript
• cd SPEC 212aa 3e-05 in ref transcript
• cd SPEC 210aa 7e-05 in ref transcript
• Changed! cd SPEC 227aa 8e-05 in ref transcript
• cd SPEC 216aa 1e-04 in ref transcript
• cd SPEC 217aa 3e-04 in ref transcript
• cd SPEC 223aa 7e-04 in ref transcript
• cd SPEC 206aa 0.003 in ref transcript
• cd SPEC 212aa 0.003 in ref transcript
• cd SPEC 208aa 0.004 in ref transcript
• smart CH 103aa 1e-14 in ref transcript
  • Calponin homology domain. Actin binding domains present in duplicate at the N-termini of spectrin-like proteins (including dystrophin, alpha-actinin). These domains cross-link actin filaments into bundles and networks. A calponin homology domain is predicted in yeasst Cdc24p.
• pfam KASH 60aa 1e-13 in ref transcript
  • Nuclear envelope localisation domain. The KASH (for Klarsicht/ANC-1/Syne-1 homology) or KLS domain is a highly hydrophobic nuclear envelope localisation domain of approximately 60 amino acids comprising an 20-amino-acid transmembrane region and a 30-35-residue C-terminal region that lies between the inner and the outer nuclear membranes.
• pfam CH 104aa 9e-11 in ref transcript
  • Calponin homology (CH) domain. The CH domain is found in both cytoskeletal proteins and signal transduction proteins. The CH domain is involved in actin binding in some members of the family. However in calponins there is evidence that the CH domain is not involved in its actin binding activity. Most proteins have two copies of the CH domain, however some proteins such as calponin have only a single copy.
• pfam SMC_N 808aa 2e-09 in ref transcript
  • RecF/RecN/SMC N terminal domain. This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.
• pfam SMC_N 755aa 2e-06 in ref transcript
• smart SPEC 100aa 2e-06 in ref transcript
  • Spectrin repeats.
• pfam Spectrin 98aa 8e-05 in ref transcript
  • Spectrin repeat. Spectrin repeats are found in several proteins involved in cytoskeletal structure. These include spectrin, alpha-actinin and dystrophin. The sequence repeat used in this family is taken from the structural repeat in reference. The spectrin repeat forms a three helix bundle. The second helix is interrupted by proline in some sequences. The repeats are defined by a characteristic tryptophan (W) residue at position 17 in helix A and a leucine (L) at 2 residues from the carboxyl end of helix C.
• pfam SMC_N 247aa 3e-04 in ref transcript
• pfam SMC_N 199aa 5e-04 in ref transcript
• TIGR SMC_prok_B 254aa 6e-04 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• smart SPEC 103aa 0.001 in ref transcript
• smart SPEC 97aa 0.002 in ref transcript
• pfam SMC_N 247aa 0.003 in ref transcript
• pfam Spectrin 101aa 0.005 in ref transcript
• pfam SMC_N 296aa 0.009 in ref transcript
• COG SAC6 259aa 3e-20 in ref transcript
  • Ca2+-binding actin-bundling protein fimbrin/plastin (EF-Hand superfamily) [Cytoskeleton].
• COG Smc 854aa 2e-11 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].
• COG Smc 819aa 6e-06 in ref transcript
• COG Smc 303aa 0.002 in ref transcript
• PRK PRK02224 459aa 0.002 in ref transcript
  • chromosome segregation protein; Provisional.
• Changed! pfam SMC_N 200aa 0.002 in modified transcript
• Changed! pfam SMC_N 336aa 0.003 in modified transcript
• Changed! TIGR SMC_prok_B 839aa 0.010 in modified transcript
• Changed! COG SbcC 570aa 4e-04 in modified transcript
  • ATPase involved in DNA repair [DNA replication, recombination, and repair].

SYNJ1

• refseq_SYNJ1.F2 refseq_SYNJ1.R2 174 222
• NCBIGene 36.3 8867
• Single exon skipping, size difference: 48
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_003895

• cd RRM 59aa 3e-04 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• pfam Syja_N 289aa 1e-113 in ref transcript
  • SacI homology domain. This Pfam family represents a protein domain which shows homology to the yeast protein SacI. The SacI homology domain is most notably found at the amino terminal of the inositol 5'-phosphatase synaptojanin.
• smart IPPc 344aa 1e-110 in ref transcript
  • Inositol polyphosphate phosphatase, catalytic domain homologues. Mg(2+)-dependent/Li(+)-sensitive enzymes.
• pfam DUF1866 143aa 7e-55 in ref transcript
  • Domain of unknown function (DUF1866). This domain, found in Synaptojanin, has no known function.
• COG COG5329 442aa 4e-80 in ref transcript
  • Phosphoinositide polyphosphatase (Sac family) [Signal transduction mechanisms].
• COG COG5411 362aa 1e-56 in ref transcript
  • Phosphatidylinositol 5-phosphate phosphatase [Signal transduction mechanisms].

SYNJ1

• refseq_SYNJ1.F4 refseq_SYNJ1.R4 136 160
• NCBIGene 36.3 8867
• Single exon skipping, size difference: 24
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_003895

• cd RRM 59aa 3e-04 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• pfam Syja_N 289aa 1e-113 in ref transcript
  • SacI homology domain. This Pfam family represents a protein domain which shows homology to the yeast protein SacI. The SacI homology domain is most notably found at the amino terminal of the inositol 5'-phosphatase synaptojanin.
• smart IPPc 344aa 1e-110 in ref transcript
  • Inositol polyphosphate phosphatase, catalytic domain homologues. Mg(2+)-dependent/Li(+)-sensitive enzymes.
• pfam DUF1866 143aa 7e-55 in ref transcript
  • Domain of unknown function (DUF1866). This domain, found in Synaptojanin, has no known function.
• COG COG5329 442aa 4e-80 in ref transcript
  • Phosphoinositide polyphosphatase (Sac family) [Signal transduction mechanisms].
• Changed! COG COG5411 362aa 1e-56 in ref transcript
  • Phosphatidylinositol 5-phosphate phosphatase [Signal transduction mechanisms].
• Changed! COG COG5411 369aa 5e-58 in modified transcript

SYTL2

• refseq_SYTL2.F1 refseq_SYTL2.R1 203 323
• NCBIGene 36.3 54843
• Single exon skipping, size difference: 120
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_206927

• cd C2_1 127aa 9e-17 in ref transcript
  • Protein kinase C conserved region 2, subgroup 1; C2 Ca2+-binding motif present in phospholipases, protein kinases C, and synaptotagmins (amongst others); some PKCs lack calcium dependence. Particular C2s appear to bind phospholipids, inositol polyphosphates,and intracellular proteins. Two distinct C2 topologies generated by permutation of the sequence with respect to the N- and C-terminal beta strands are seen. In this subgroup, containing synaptotagmins, specific protein kinases C (PKC) subtypes and other proteins, the N-terminal beta strand occupies the position of what is the C-terminal strand in subgroup 2.
• cd C2_1 128aa 4e-15 in ref transcript
• pfam C2 90aa 2e-10 in ref transcript
  • C2 domain.
• pfam C2 88aa 7e-10 in ref transcript

TAC1

• refseq_TAC1.F1 refseq_TAC1.R1 106 151
• NCBIGene 36.3 6863
• Single exon skipping, size difference: 45
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_003182

TAC1

• refseq_TAC1.F2 refseq_TAC1.R2 114 168
• NCBIGene 36.3 6863
• Single exon skipping, size difference: 54
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_003182

TAC3

• refseq_TAC3.F1 refseq_TAC3.R1 127 244
• NCBIGene 36.3 6866
• Single exon skipping, size difference: 117
• Exclusion of the stop codon
• Reference transcript: NM_001006667

• pfam Neurokinin_B 55aa 4e-20 in ref transcript
  • Neurokinin B.

TACC2

• refseq_TACC2.F1 refseq_TACC2.R1 124 214
• NCBIGene 36.3 10579
• Single exon skipping, size difference: 90
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_206862

• pfam TACC 206aa 2e-92 in ref transcript
  • Transforming acidic coiled-coil-containing protein (TACC). This family contains the proteins TACC 1, 2 and 3 the genes for which are found concentrated in the centrosomes of eukaryotic and may play a conserved role in organising centrosomal microtubules. The human TACC proteins have been linked to cancer and TACC2 has been identified as a possible tumour suppressor (AZU-1). The functional homologue (Alp7) in Schizosaccharomyces pombe has been shown to be required for organisation of bipolar spindles.
• COG Smc 200aa 7e-10 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].
• PRK PRK07003 236aa 2e-04 in ref transcript
  • DNA polymerase III subunits gamma and tau; Validated.

TACC2

• refseq_TACC2.F4 refseq_TACC2.R4 123 258
• NCBIGene 36.3 10579
• Single exon skipping, size difference: 135
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_206862

• pfam TACC 206aa 2e-92 in ref transcript
  • Transforming acidic coiled-coil-containing protein (TACC). This family contains the proteins TACC 1, 2 and 3 the genes for which are found concentrated in the centrosomes of eukaryotic and may play a conserved role in organising centrosomal microtubules. The human TACC proteins have been linked to cancer and TACC2 has been identified as a possible tumour suppressor (AZU-1). The functional homologue (Alp7) in Schizosaccharomyces pombe has been shown to be required for organisation of bipolar spindles.
• COG Smc 200aa 7e-10 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].
• PRK PRK07003 236aa 2e-04 in ref transcript
  • DNA polymerase III subunits gamma and tau; Validated.

TAF1

• refseq_TAF1.F2 refseq_TAF1.R2 229 292
• NCBIGene 36.3 6872
• Alternative 3-prime, size difference: 63
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_004606

• cd Bromo_TFIID 113aa 7e-51 in ref transcript
  • Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, a large multi-domain complex, which initiates the assembly of the transcription machinery. TAFII250 contains two bromodomains that specifically bind to acetylated histone H4. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
• cd Bromo_TFIID 89aa 2e-37 in ref transcript
• smart BROMO 108aa 2e-27 in ref transcript
  • bromo domain.
• smart BROMO 96aa 1e-20 in ref transcript
• pfam TBP-binding 61aa 4e-11 in ref transcript
  • TATA box-binding protein binding. Members of this family adopt a structure consisting of three alpha helices and a beta-hairpin. They bind to TATA box-binding protein (TBP), inhibiting TBP interaction with the TATA element, thereby resulting in shutting down of gene transcription.
• COG TAF1 742aa 3e-73 in ref transcript
  • Transcription initiation factor TFIID, subunit TAF1 [Transcription].
• COG COG5076 210aa 1e-16 in ref transcript
  • Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription].

TAF1A

• refseq_TAF1A.F1 refseq_TAF1A.R1 121 291
• NCBIGene 36.3 9015
• Single exon skipping, size difference: 170
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_005681

TAF1C

• refseq_TAF1C.F1 refseq_TAF1C.R1 118 279
• NCBIGene 36.3 9013
• Alternative 3-prime, size difference: 161
• Exclusion of the protein initiation site
• Reference transcript: NM_005679

TAF6

• refseq_TAF6.F1 refseq_TAF6.R1 126 450
• NCBIGene 36.3 6878
• Alternative 5-prime, size difference: 324
• Exclusion in 5'UTR
• Reference transcript: NM_005641

• pfam DUF1546 95aa 7e-35 in ref transcript
  • Protein of unknown function (DUF1546). Associated with pfam02969 in Transcription initiation factor TFIID subunit 6 (TAF6).
• pfam TAF 66aa 1e-25 in ref transcript
  • TATA box binding protein associated factor (TAF). TAF proteins adopt a histone-like fold.
• COG TAF6 400aa 2e-72 in ref transcript
  • Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription].

TAF6

• refseq_TAF6.F3 refseq_TAF6.R3 170 200
• NCBIGene 36.3 6878
• Alternative 5-prime, size difference: 30
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_139315

• pfam DUF1546 95aa 7e-35 in ref transcript
  • Protein of unknown function (DUF1546). Associated with pfam02969 in Transcription initiation factor TFIID subunit 6 (TAF6).
• pfam TAF 66aa 1e-25 in ref transcript
  • TATA box binding protein associated factor (TAF). TAF proteins adopt a histone-like fold.
• COG TAF6 400aa 2e-72 in ref transcript
  • Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription].

TAF6

• refseq_TAF6.F6 refseq_TAF6.R6 149 179
• NCBIGene 36.3 6878
• Alternative 5-prime, size difference: 30
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_139315

• pfam DUF1546 95aa 7e-35 in ref transcript
  • Protein of unknown function (DUF1546). Associated with pfam02969 in Transcription initiation factor TFIID subunit 6 (TAF6).
• Changed! pfam TAF 66aa 1e-25 in ref transcript
  • TATA box binding protein associated factor (TAF). TAF proteins adopt a histone-like fold.
• Changed! COG TAF6 400aa 2e-72 in ref transcript
  • Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription].
• Changed! pfam TAF 56aa 2e-17 in modified transcript
• Changed! COG TAF6 390aa 6e-66 in modified transcript

TAGAP

• refseq_TAGAP.F1 refseq_TAGAP.R1 201 368
• NCBIGene 36.3 117289
• Single exon skipping, size difference: 167
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_054114

• Changed! cd RhoGAP_ARHGAP20 197aa 7e-66 in ref transcript
  • RhoGAP_ARHGAP20: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of ArhGAP20-like proteins. ArhGAP20, also known as KIAA1391 and RA-RhoGAP, contains a RhoGAP, a RA, and a PH domain, and ANXL repeats. ArhGAP20 is activated by Rap1 and induces inactivation of Rho, which in turn leads to neurite outgrowth. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
• Changed! pfam RhoGAP 142aa 5e-31 in ref transcript
  • RhoGAP domain. GTPase activator proteins towards Rho/Rac/Cdc42-like small GTPases.

TAGLN

• refseq_TAGLN.F1 refseq_TAGLN.R1 100 497
• NCBIGene 36.3 6876
• Alternative 5-prime, size difference: 397
• Exclusion in 5'UTR
• Reference transcript: NM_001001522

• cd CH 113aa 5e-16 in ref transcript
  • Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav).
• smart CH 107aa 1e-16 in ref transcript
  • Calponin homology domain. Actin binding domains present in duplicate at the N-termini of spectrin-like proteins (including dystrophin, alpha-actinin). These domains cross-link actin filaments into bundles and networks. A calponin homology domain is predicted in yeasst Cdc24p.
• pfam Calponin 26aa 7e-06 in ref transcript
  • Calponin family repeat.
• COG SCP1 177aa 1e-16 in ref transcript
  • Calponin [Cytoskeleton].

TAGLN3

• refseq_TAGLN3.F1 refseq_TAGLN3.R1 167 341
• NCBIGene 36.3 29114
• Alternative 3-prime, size difference: 174
• Inclusion in 5'UTR
• Reference transcript: NM_001008272

• cd CH 109aa 1e-17 in ref transcript
  • Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav).
• smart CH 106aa 3e-19 in ref transcript
  • Calponin homology domain. Actin binding domains present in duplicate at the N-termini of spectrin-like proteins (including dystrophin, alpha-actinin). These domains cross-link actin filaments into bundles and networks. A calponin homology domain is predicted in yeasst Cdc24p.
• pfam Calponin 25aa 1e-05 in ref transcript
  • Calponin family repeat.
• COG SCP1 176aa 3e-18 in ref transcript
  • Calponin [Cytoskeleton].

TAS1R1

• refseq_TAS1R1.F2 refseq_TAS1R1.R2 103 437
• NCBIGene 36.3 80835
• Multiple exon skipping, size difference: 334
• Exclusion in the protein (no frameshift), Exclusion in the protein causing a frameshift
• Reference transcript: NM_138697

• Changed! cd PBP1_Taste_receptor 455aa 1e-175 in ref transcript
  • Ligand-binding domain of the T1R taste receptor. The T1R is a member of the family C receptors within the G-protein coupled receptor superfamily, which also includes the metabotropic glutamate receptors, GABAb receptors, the calcium-sensing receptor (CaSR), the V2R pheromone receptors, and a small group of uncharacterized orphan receptors.
• Changed! pfam ANF_receptor 384aa 1e-48 in ref transcript
  • Receptor family ligand binding region. This family includes extracellular ligand binding domains of a wide range of receptors. This family also includes the bacterial amino acid binding proteins of known structure.
• Changed! pfam 7tm_3 235aa 8e-34 in ref transcript
  • 7 transmembrane sweet-taste receptor of 3 GCPR. This is a domain of seven transmembrane regions that forms the C-terminus of some subclass 3 G-coupled-protein receptors. It is often associated with a downstream cysteine-rich linker domain, NCD3G pfam07562, which is the human sweet-taste receptor, and the N-terminal domain, ANF_receptor pfam01094. The seven TM regions assemble in such a way as to produce a docking pocket into which such molecules as cyclamate and lactisole have been found to bind and consequently confer the taste of sweetness.
• Changed! pfam NCD3G 54aa 7e-16 in ref transcript
  • Nine Cysteines Domain of family 3 GPCR. This conserved sequence contains several highly-conserved Cys residues that are predicted to form disulphide bridges. It is predicted to lie outside the cell membrane, tethered to the pfam00003 in several receptor proteins.
• Changed! COG LivK 280aa 3e-15 in ref transcript
  • ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism].
• Changed! cd PBP1_Taste_receptor 389aa 1e-147 in modified transcript
• Changed! pfam ANF_receptor 283aa 4e-45 in modified transcript
• Changed! COG LivK 212aa 1e-14 in modified transcript

TAZ

• refseq_TAZ.F1 refseq_TAZ.R1 101 207
• NCBIGene 36.2 6901
• Alternative 5-prime, size difference: 106
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_000116

• Changed! pfam Acyltransferase 175aa 3e-18 in ref transcript
  • Acyltransferase. This family contains acyltransferases involved in phospholipid biosynthesis and other proteins of unknown function. This family also includes tafazzin, the Barth syndrome gene.
• Changed! PRK PRK08633 232aa 4e-06 in ref transcript
  • 2-acyl-glycerophospho-ethanolamine acyltransferase; Validated.
• Changed! pfam Acyltransferase 46aa 0.001 in modified transcript

TAZ

• refseq_TAZ.F2 refseq_TAZ.R2 100 190
• NCBIGene 36.3 6901
• Single exon skipping, size difference: 90
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000116

• Changed! pfam Acyltransferase 175aa 3e-18 in ref transcript
  • Acyltransferase. This family contains acyltransferases involved in phospholipid biosynthesis and other proteins of unknown function. This family also includes tafazzin, the Barth syndrome gene.
• Changed! PRK PRK08633 232aa 4e-06 in ref transcript
  • 2-acyl-glycerophospho-ethanolamine acyltransferase; Validated.
• Changed! pfam Acyltransferase 145aa 5e-21 in modified transcript
• Changed! PRK PRK08633 202aa 7e-09 in modified transcript

TAZ

• refseq_TAZ.F3 refseq_TAZ.R3 128 170
• NCBIGene 36.3 6901
• Single exon skipping, size difference: 42
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000116

• Changed! pfam Acyltransferase 175aa 3e-18 in ref transcript
  • Acyltransferase. This family contains acyltransferases involved in phospholipid biosynthesis and other proteins of unknown function. This family also includes tafazzin, the Barth syndrome gene.
• Changed! PRK PRK08633 232aa 4e-06 in ref transcript
  • 2-acyl-glycerophospho-ethanolamine acyltransferase; Validated.
• Changed! pfam Acyltransferase 141aa 3e-12 in modified transcript
• Changed! PRK PRK08633 218aa 4e-04 in modified transcript

TBC1D9B

• refseq_TBC1D9B.F1 refseq_TBC1D9B.R1 129 180
• NCBIGene 36.3 23061
• Single exon skipping, size difference: 51
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_198868

• pfam TBC 210aa 3e-49 in ref transcript
  • TBC domain. Identification of a TBC domain in GYP6_YEAST and GYP7_YEAST, which are GTPase activator proteins of yeast Ypt6 and Ypt7, imply that these domains are GTPase activator proteins of Rab-like small GTPases.
• pfam GRAM 59aa 4e-16 in ref transcript
  • GRAM domain. The GRAM domain is found in in glucosyltransferases, myotubularins and other putative membrane-associated proteins.
• pfam GRAM 59aa 7e-13 in ref transcript
• COG COG5210 343aa 2e-40 in ref transcript
  • GTPase-activating protein [General function prediction only].

TBCD

• refseq_TBCD.F1 refseq_TBCD.R1 289 340
• NCBIGene 36.2 6904
• Single exon skipping, size difference: 51
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_005993

• COG CIN1 277aa 4e-20 in ref transcript
  • Beta-tubulin folding cofactor D [Posttranslational modification, protein turnover, chaperones / Cytoskeleton].
• COG CIN1 63aa 2e-04 in ref transcript
• Changed! COG CIN1 109aa 0.003 in ref transcript

TBL1Y

• refseq_TBL1Y.F1 refseq_TBL1Y.R1 114 209
• NCBIGene 36.3 90665
• Single exon skipping, size difference: 95
• Exclusion in 5'UTR
• Reference transcript: NM_033284

• cd WD40 307aa 8e-63 in ref transcript
  • WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.
• smart WD40 40aa 1e-07 in ref transcript
  • WD40 repeats. Note that these repeats are permuted with respect to the structural repeats (blades) of the beta propeller domain.
• smart WD40 38aa 2e-07 in ref transcript
• pfam LisH 27aa 2e-06 in ref transcript
  • LisH. The LisH (lis homology) domain mediates protein dimerisation and tetramerisation. The LisH domain is found in Sif2, a component of the Set3 complex which is responsible for repressing meiotic genes. It has been shown that the LisH domain helps mediate interaction with components of the Set3 complex.
• pfam WD40 35aa 1e-04 in ref transcript
  • WD domain, G-beta repeat.
• smart WD40 46aa 2e-04 in ref transcript
• smart WD40 40aa 0.001 in ref transcript
• pfam eIF2A 209aa 0.002 in ref transcript
  • Eukaryotic translation initiation factor eIF2A. This is a family of eukaryotic translation initiation factors.
• COG COG2319 378aa 5e-30 in ref transcript
  • FOG: WD40 repeat [General function prediction only].

TBL1Y

• refseq_TBL1Y.F2 refseq_TBL1Y.R2 134 165
• NCBIGene 36.3 90665
• Single exon skipping, size difference: 31
• Exclusion in 5'UTR
• Reference transcript: NM_033284

• cd WD40 307aa 8e-63 in ref transcript
  • WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.
• smart WD40 40aa 1e-07 in ref transcript
  • WD40 repeats. Note that these repeats are permuted with respect to the structural repeats (blades) of the beta propeller domain.
• smart WD40 38aa 2e-07 in ref transcript
• pfam LisH 27aa 2e-06 in ref transcript
  • LisH. The LisH (lis homology) domain mediates protein dimerisation and tetramerisation. The LisH domain is found in Sif2, a component of the Set3 complex which is responsible for repressing meiotic genes. It has been shown that the LisH domain helps mediate interaction with components of the Set3 complex.
• pfam WD40 35aa 1e-04 in ref transcript
  • WD domain, G-beta repeat.
• smart WD40 46aa 2e-04 in ref transcript
• smart WD40 40aa 0.001 in ref transcript
• pfam eIF2A 209aa 0.002 in ref transcript
  • Eukaryotic translation initiation factor eIF2A. This is a family of eukaryotic translation initiation factors.
• COG COG2319 378aa 5e-30 in ref transcript
  • FOG: WD40 repeat [General function prediction only].

TBRG4

• refseq_TBRG4.F2 refseq_TBRG4.R2 102 432
• NCBIGene 36.3 9238
• Multiple exon skipping, size difference: 330
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_004749

• pfam FAST_1 71aa 3e-17 in ref transcript
  • FAST kinase-like protein, subdomain 1. This family represents a conserved region of eukaryotic Fas-activated serine/threonine (FAST) kinases (EC:2.7.1.-) that contains several conserved leucine residues. FAST kinase is rapidly activated during Fas-mediated apoptosis, when it phosphorylates TIA-1, a nuclear RNA-binding protein that has been implicated as an effector of apoptosis. Note that many family members are hypothetical proteins. This region is often found immediately N-terminal to the FAST kinase-like protein, subdomain 2.
• pfam RAP 58aa 4e-12 in ref transcript
  • RAP domain. This domain is found in various eukaryotic species, particularly in apicomplexans such as Plasmodium falciparum, where it is found in proteins that are important in various parasite-host cell interactions. It is thought to be an RNA-binding domain.
• pfam FAST_2 84aa 3e-11 in ref transcript
  • FAST kinase-like protein, subdomain 2. This family represents a conserved region of eukaryotic Fas-activated serine/threonine (FAST) kinases (EC:2.7.1.-) that contains several conserved leucine residues. FAST kinase is rapidly activated during Fas-mediated apoptosis, when it phosphorylates TIA-1, a nuclear RNA-binding protein that has been implicated as an effector of apoptosis. Note that many family members are hypothetical proteins. This subdomain is often found associated with the FAST kinase-like protein, subdomain 2.

TBRG4

• refseq_TBRG4.F3 refseq_TBRG4.R3 115 136
• NCBIGene 36.3 9238
• Alternative 5-prime, size difference: 21
• Exclusion in 5'UTR
• Reference transcript: NM_004749

• pfam FAST_1 71aa 3e-17 in ref transcript
  • FAST kinase-like protein, subdomain 1. This family represents a conserved region of eukaryotic Fas-activated serine/threonine (FAST) kinases (EC:2.7.1.-) that contains several conserved leucine residues. FAST kinase is rapidly activated during Fas-mediated apoptosis, when it phosphorylates TIA-1, a nuclear RNA-binding protein that has been implicated as an effector of apoptosis. Note that many family members are hypothetical proteins. This region is often found immediately N-terminal to the FAST kinase-like protein, subdomain 2.
• pfam RAP 58aa 4e-12 in ref transcript
  • RAP domain. This domain is found in various eukaryotic species, particularly in apicomplexans such as Plasmodium falciparum, where it is found in proteins that are important in various parasite-host cell interactions. It is thought to be an RNA-binding domain.
• pfam FAST_2 84aa 3e-11 in ref transcript
  • FAST kinase-like protein, subdomain 2. This family represents a conserved region of eukaryotic Fas-activated serine/threonine (FAST) kinases (EC:2.7.1.-) that contains several conserved leucine residues. FAST kinase is rapidly activated during Fas-mediated apoptosis, when it phosphorylates TIA-1, a nuclear RNA-binding protein that has been implicated as an effector of apoptosis. Note that many family members are hypothetical proteins. This subdomain is often found associated with the FAST kinase-like protein, subdomain 2.

TBX5

• refseq_TBX5.F1 refseq_TBX5.R1 166 351
• NCBIGene 36.3 6910
• Single exon skipping, size difference: 185
• Exclusion of the protein initiation site
• Reference transcript: NM_000192

• cd TBOX 189aa 5e-91 in ref transcript
  • T-box DNA binding domain of the T-box family of transcriptional regulators. The T-box family is an ancient group that appears to play a critical role in development in all animal species. These genes were uncovered on the basis of similarity to the DNA binding domain of murine Brachyury (T) gene product, the defining feature of the family. Common features shared by T-box family members are DNA-binding and transcriptional regulatory activity, a role in development and conserved expression patterns, most of the known genes in all species being expressed in mesoderm or mesoderm precursors.
• pfam T-box 183aa 9e-90 in ref transcript
  • T-box. The T-box encodes a 180 amino acid domain that binds to DNA. Genes encoding T-box proteins are found in a wide range of animals, but not in other kingdoms such as plants. Family members are all thought to bind to the DNA consensus sequence TCACACCT. they are found exclusively in the nucleus, and perform DNA-binding and transcriptional activation/repression roles. They are generally required for development of the specific tissues they are expressed in, and mutations in T-box genes are implicated in human conditions such as DiGeorge syndrome and X-linked cleft palate, which feature malformations.

TBXAS1

• refseq_TBXAS1.F1 refseq_TBXAS1.R1 157 320
• NCBIGene 36.3 6916
• Single exon skipping, size difference: 163
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_001061

• Changed! pfam p450 482aa 2e-71 in ref transcript
  • Cytochrome P450. Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyse regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures.
• Changed! COG CypX 478aa 3e-38 in ref transcript
  • Cytochrome P450 [Secondary metabolites biosynthesis, transport, and catabolism].
• Changed! pfam p450 410aa 2e-57 in modified transcript
• Changed! COG CypX 410aa 3e-32 in modified transcript

TCEA1

• refseq_TCEA1.F1 refseq_TCEA1.R1 269 332
• NCBIGene 36.3 6917
• Single exon skipping, size difference: 63
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_006756

• Changed! cd TFIIS_I 77aa 7e-16 in ref transcript
  • N-terminal domain (domain I) of transcription elongation factor S-II (TFIIS); similar to a domain found in elongin A and CRSP70; likely to be involved in transcription; domain I from TFIIS interacts with RNA polymerase II holoenzyme.
• Changed! TIGR TFSII 298aa 4e-89 in ref transcript
  • This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
• COG RPB9 68aa 4e-11 in ref transcript
  • DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription].
• Changed! cd TFIIS_I 56aa 1e-05 in modified transcript
• Changed! TIGR TFSII 277aa 9e-77 in modified transcript

TCEAL8

• refseq_TCEAL8.F1 refseq_TCEAL8.R1 228 301
• NCBIGene 36.3 90843
• Single exon skipping, size difference: 73
• Exclusion in 5'UTR
• Reference transcript: NM_153333

• pfam TFA 111aa 3e-08 in ref transcript
  • Transcription elongation factor A, SII-related family. The function of this family is unclear, but two members from Homo sapiesn are described as transcription elongation factor A, SII-like proteins.

TCERG1

• refseq_TCERG1.F1 refseq_TCERG1.R1 130 193
• NCBIGene 36.3 10915
• Single exon skipping, size difference: 63
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_006706

• cd WW 28aa 2e-04 in ref transcript
  • Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
• cd WW 25aa 0.004 in ref transcript
• cd WW 30aa 0.008 in ref transcript
• pfam FF 52aa 5e-09 in ref transcript
  • FF domain. This domain has been predicted to be involved in protein-protein interaction. This domain was recently shown to bind the hyperphosphorylated C-terminal repeat domain of RNA polymerase II, confirming its role in protein-protein interactions.
• smart FF 54aa 4e-07 in ref transcript
  • Contains two conserved F residues. A novel motif that often accompanies WW domains. Often contains two conserved Phe (F) residues.
• pfam FF 61aa 1e-05 in ref transcript
• smart FF 54aa 1e-05 in ref transcript
• smart WW 28aa 2e-05 in ref transcript
  • Domain with 2 conserved Trp (W) residues. Also known as the WWP or rsp5 domain. Binds proline-rich polypeptides.
• smart FF 56aa 2e-04 in ref transcript
• pfam WW 27aa 5e-04 in ref transcript
  • WW domain. The WW domain is a protein module with two highly conserved tryptophans that binds proline-rich peptide motifs in vitro.
• pfam FF 48aa 6e-04 in ref transcript
• pfam WW 25aa 0.001 in ref transcript
• COG PRP40 350aa 3e-09 in ref transcript
  • Splicing factor [RNA processing and modification].
• COG PRP40 38aa 4e-04 in ref transcript
• COG SbcC 223aa 0.005 in ref transcript
  • ATPase involved in DNA repair [DNA replication, recombination, and repair].

TCF12

• refseq_TCF12.F2 refseq_TCF12.R2 219 291
• NCBIGene 36.3 6938
• Single exon skipping, size difference: 72
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_207037

• cd HLH 61aa 1e-06 in ref transcript
  • Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins.
• smart HLH 54aa 7e-10 in ref transcript
  • helix loop helix domain.

TCF20

• refseq_TCF20.F2 refseq_TCF20.R2 101 229
• NCBIGene 36.3 6942
• Single exon skipping, size difference: 128
• Exclusion of the stop codon
• Reference transcript: NM_005650

TCF7

• refseq_TCF7.F1 refseq_TCF7.R1 100 196
• NCBIGene 36.3 6932
• Exon skipping and alternative 3-prime or 5-prime, size difference: 96
• Inclusion in the protein causing a frameshift, Inclusion in the protein causing a new stop codon
• Reference transcript: NM_003202

• cd SOX-TCF_HMG-box 71aa 9e-24 in ref transcript
  • SOX-TCF_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and vertebrates, and transcription factor-like proteins, TCF-1, -3, -4, and LEF-1. They appear to bind the minor groove of the A/T C A A A G/C-motif.
• pfam CTNNB1_binding 187aa 6e-33 in ref transcript
  • N-terminal CTNNB1 binding. This region tends to appear at the N-terminus of proteins also containing DNA-binding HMG (high mobility group) boxes (pfam00505) and appears to bind the armadillo repeat of CTNNB1 (beta-catenin), forming a stable complex. Signaling by Wnt through TCF/LCF is involved in developmental patterning, induction of neural tissues, cell fate decisions and stem cell differentiation. Isoforms of HMG T-cell factors lacking the N-terminal CTNNB1-binding domain cannot fulfill their role as transcriptional activators in T-cell differentiation.
• pfam HMG_box 68aa 5e-18 in ref transcript
  • HMG (high mobility group) box.
• Changed! PTZ PTZ00199 57aa 4e-04 in ref transcript
  • high mobility group protein; Provisional.
• Changed! COG NHP6B 96aa 2e-04 in modified transcript
  • Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics].

TCL6

• refseq_TCL6.F1 refseq_TCL6.R1 118 254
• NCBIGene 36.3 27004
• Single exon skipping, size difference: 136
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_020554

TCOF1

• refseq_TCOF1.F2 refseq_TCOF1.R2 217 331
• NCBIGene 36.3 6949
• Single exon skipping, size difference: 114
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_001008656

• pfam Treacle 321aa 9e-36 in ref transcript
  • Treacher Collins syndrome protein Treacle.

TCP1

• refseq_TCP1.F1 refseq_TCP1.R1 137 223
• NCBIGene 36.3 6950
• Single exon skipping, size difference: 86
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_030752

• Changed! cd TCP1_alpha 527aa 0.0 in ref transcript
  • TCP-1 (CTT or eukaryotic type II) chaperonin family, alpha subunit. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings. In contrast to bacterial group I chaperonins (GroEL), each ring of the eukaryotic cytosolic chaperonin (CTT) consists of eight different, but homologous subunits. Their common function is to sequester nonnative proteins inside their central cavity and promote folding by using energy derived from ATP hydrolysis. The best studied in vivo substrates of CTT are actin and tubulin.
• Changed! TIGR chap_CCT_alpha 536aa 0.0 in ref transcript
  • Members of this family, all eukaryotic, are part of the group II chaperonin complex called CCT (chaperonin containing TCP-1) or TRiC. The archaeal equivalent group II chaperonin is often called the thermosome. Both are somewhat related to the group I chaperonin of bacterial, GroEL/GroES. This family consists exclusively of the CCT alpha chain (part of a paralogous family) from animals, plants, fungi, and other eukaryotes.
• Changed! COG GroL 533aa 1e-111 in ref transcript
  • Chaperonin GroEL (HSP60 family) [Posttranslational modification, protein turnover, chaperones].

TDP1

• refseq_TDP1.F1 refseq_TDP1.R1 125 348
• NCBIGene 36.3 55775
• Single exon skipping, size difference: 223
• Exclusion in 5'UTR
• Reference transcript: NM_018319

• pfam Tyr-DNA_phospho 422aa 1e-104 in ref transcript
  • Tyrosyl-DNA phosphodiesterase. Covalent intermediates between topoisomerase I and DNA can become dead-end complexes that lead to cell death. Tyrosyl-DNA phosphodiesterase can hydrolyse the bond between topoisomerase I and DNA.

TEAD4

• refseq_TEAD4.F2 refseq_TEAD4.R2 106 235
• NCBIGene 36.3 7004
• Single exon skipping, size difference: 129
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_003213

• Changed! pfam TEA 353aa 1e-130 in ref transcript
  • TEA/ATTS domain family.
• Changed! pfam TEA 310aa 1e-128 in modified transcript

TEAD4

• refseq_TEAD4.F3 refseq_TEAD4.R3 109 364
• NCBIGene 36.3 7004
• Single exon skipping, size difference: 255
• Exclusion of the protein initiation site
• Reference transcript: NM_003213

• Changed! pfam TEA 353aa 1e-130 in ref transcript
  • TEA/ATTS domain family.
• Changed! pfam TEA 270aa 1e-107 in modified transcript

TEPP

• refseq_TEPP.F2 refseq_TEPP.R2 106 187
• NCBIGene 36.3 374739
• Alternative 3-prime, size difference: 81
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_199046

TEX11

• refseq_TEX11.F1 refseq_TEX11.R1 205 327
• NCBIGene 36.3 56159
• Single exon skipping, size difference: 122
• Exclusion of the protein initiation site
• Reference transcript: NM_001003811

• pfam SPO22 257aa 1e-58 in ref transcript
  • Meiosis protein SPO22/ZIP4 like. SPO22/ZIP4 in yeast is a meiosis specific protein involved in sporulation. It has been shown to regulate crossover distribution by promoting synaptonemal complex formation.

TEX14

• refseq_TEX14.F1 refseq_TEX14.R1 123 243
• NCBIGene 36.3 56155
• Single exon skipping, size difference: 120
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_198393

• cd S_TKc 234aa 5e-19 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• cd ANK 109aa 5e-17 in ref transcript
  • ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats.
• pfam Pkinase_Tyr 214aa 9e-23 in ref transcript
  • Protein tyrosine kinase.
• COG SPS1 328aa 1e-08 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].
• COG Arp 141aa 5e-08 in ref transcript
  • FOG: Ankyrin repeat [General function prediction only].

TFEC

• refseq_TFEC.F2 refseq_TFEC.R2 255 342
• NCBIGene 36.3 22797
• Single exon skipping, size difference: 87
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_012252

• cd HLH 61aa 1e-05 in ref transcript
  • Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins.
• Changed! pfam HLH 54aa 3e-04 in ref transcript
  • Helix-loop-helix DNA-binding domain.
• Changed! smart HLH 53aa 2e-04 in modified transcript
  • helix loop helix domain.

TFG

• refseq_TFG.F2 refseq_TFG.R2 171 461
• NCBIGene 36.3 10342
• Alternative 5-prime, size difference: 290
• Exclusion in 5'UTR
• Reference transcript: NM_006070

• cd PB1_TFG 81aa 4e-41 in ref transcript
  • The PB1 domain found in TFG protein, an oncogenic gene product and fusion partner to nerve growth factor tyrosine kinase receptor TrkA and to the tyrosine kinase ALK. The PB1 domain is a modular domain mediating specific protein-protein interaction in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. The PB1 domains of TFG represent a type I/II PB1 domain. The physiological function of TFG remains unknown.
• smart PB1 77aa 5e-16 in ref transcript
  • PB1 domain. Phox and Bem1p domain, present in many eukaryotic cytoplasmic signalling proteins. The domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pairs associate.

TFIP11

• refseq_TFIP11.F2 refseq_TFIP11.R2 267 344
• NCBIGene 36.3 24144
• Single exon skipping, size difference: 77
• Exclusion in 5'UTR
• Reference transcript: NM_001008697

• pfam TFP11 235aa 1e-106 in ref transcript
  • Tuftelin interacting protein 11. This family contains tuftelin interacting protein 11 which has been identified as both a nuclear and cytoplasmic protein, and has been implicated in the secretory pathway. Sip1, a septin interacting protein is also a member of this family. Proteins in this family often contain pfam01595.
• pfam G-patch 45aa 4e-13 in ref transcript
  • G-patch domain. This domain is found in a number of RNA binding proteins, and is also found in proteins that contain RNA binding domains. This suggests that this domain may have an RNA binding function. This domain has seven highly conserved glycines.

TGIF1

• refseq_TGIF.F2 refseq_TGIF.R2 119 303
• NCBIGene 36.3 7050
• Single exon skipping, size difference: 184
• Exclusion of the protein initiation site
• Reference transcript: NM_173208

• cd homeodomain 53aa 0.003 in ref transcript
  • Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
• smart HOX 53aa 0.001 in ref transcript
  • Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes.

TGM5

• refseq_TGM5.F1 refseq_TGM5.R1 142 388
• NCBIGene 36.3 9333
• Single exon skipping, size difference: 246
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_201631

• pfam Transglut_C 97aa 9e-23 in ref transcript
  • Transglutaminase family, C-terminal ig like domain.
• Changed! pfam Transglut_N 117aa 3e-22 in ref transcript
  • Transglutaminase family.
• smart TGc 94aa 4e-20 in ref transcript
  • Transglutaminase/protease-like homologues. Transglutaminases are enzymes that establish covalent links between proteins. A subset of transglutaminase homologues appear to catalyse the reverse reaction, the hydrolysis of peptide bonds. Proteins with this domain are both extracellular and intracellular, and it is likely that the eukaryotic intracellular proteins are involved in signalling events.
• pfam Transglut_C 100aa 4e-16 in ref transcript
• COG COG1305 98aa 3e-04 in ref transcript
  • Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism].
• Changed! pfam Transglut_N 61aa 1e-11 in modified transcript

THADA

• refseq_THADA.F2 refseq_THADA.R2 121 303
• NCBIGene 36.2 63892
• Multiple exon skipping, size difference: 182
• Exclusion in the protein causing a frameshift, Exclusion in the protein (no frameshift)
• Reference transcript: NM_022065

• pfam DUF2428 304aa 3e-68 in ref transcript
  • Putative death-receptor fusion protein (DUF2428). This is a family of proteins conserved from plants to humans. The function is not known. Several members have been annotated as being HEAT repeat-containing proteins while others are designated as death-receptor interacting proteins, but neither of these could be confirmed.
• Changed! COG COG5543 475aa 5e-37 in ref transcript
  • Uncharacterized conserved protein [Function unknown].
• Changed! COG COG5543 239aa 2e-19 in modified transcript

THAP1

• refseq_THAP1.F1 refseq_THAP1.R1 109 305
• NCBIGene 36.3 55145
• Single exon skipping, size difference: 196
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_018105

• Changed! pfam THAP 79aa 2e-16 in ref transcript
  • THAP domain. The THAP domain is a putative DNA-binding domain (DBD) and probably also binds a zinc ion. It features the conserved C2CH architecture (consensus sequence: Cys - 2-4 residues - Cys - 35-50 residues - Cys - 2 residues - His). Other universal features include the location of the domain at the N-termini of proteins, its size of about 90 residues, a C-terminal AVPTIF box and several other conserved residues. Orthologs of the human THAP domain have been identified in other vertebrates and probably worms and flies, but not in other eukaryotes or any prokaryotes.

THEG

• refseq_THEG.F1 refseq_THEG.R1 131 203
• NCBIGene 36.3 51298
• Single exon skipping, size difference: 72
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_016585

THOC5

• refseq_THOC5.F2 refseq_THOC5.R2 108 224
• NCBIGene 36.3 8563
• Single exon skipping, size difference: 116
• Exclusion in 5'UTR
• Reference transcript: NM_001002877

• pfam FimP 358aa 1e-128 in ref transcript
  • Fms-interacting protein. This entry carries part of the crucial 144 N-terminal residues of the FmiP protein, which is essential for the binding of the protein to the cytoplasmic domain of activated Fms-molecules in M-CSF induced haematopoietic differentiation of macrophages. The C-terminus contains a putative nuclear localisation sequence and a leucine zipper which suggest further, as yet unknown, nuclear functions. The level of FMIP expression might form a threshold that determines whether cells differentiate into macrophages or into granulocytes.

THOC5

• refseq_THOC5.F4 refseq_THOC5.R3 197 313
• NCBIGene 36.3 8563
• Single exon skipping, size difference: 116
• Exclusion in 5'UTR
• Reference transcript: NM_001002878

• pfam FimP 358aa 1e-128 in ref transcript
  • Fms-interacting protein. This entry carries part of the crucial 144 N-terminal residues of the FmiP protein, which is essential for the binding of the protein to the cytoplasmic domain of activated Fms-molecules in M-CSF induced haematopoietic differentiation of macrophages. The C-terminus contains a putative nuclear localisation sequence and a leucine zipper which suggest further, as yet unknown, nuclear functions. The level of FMIP expression might form a threshold that determines whether cells differentiate into macrophages or into granulocytes.

THSD1

• refseq_THSD1.F1 refseq_THSD1.R1 228 387
• NCBIGene 36.3 55901
• Single exon skipping, size difference: 159
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_018676

• Changed! smart TSP1 50aa 5e-10 in ref transcript
  • Thrombospondin type 1 repeats. Type 1 repeats in thrombospondin-1 bind and activate TGF-beta.

THSD3

• refseq_THSD3.F2 refseq_THSD3.R2 243 348
• NCBIGene 36.3 145501
• Single exon skipping, size difference: 105
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_199296

• Changed! pfam AMOP 158aa 2e-40 in ref transcript
  • AMOP domain. This domain may have a role in cell adhesion. It is called the AMOP domain after Adhesion associated domain in MUC4 and Other Proteins. This domain is extracellular and contains a number of cysteines that probably form disulphide bridges.
• Changed! smart TSP1 41aa 3e-06 in ref transcript
  • Thrombospondin type 1 repeats. Type 1 repeats in thrombospondin-1 bind and activate TGF-beta.

THSD3

• refseq_THSD3.F3 refseq_THSD3.R3 100 446
• NCBIGene 36.3 145501
• Single exon skipping, size difference: 346
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_199296

• Changed! pfam AMOP 158aa 2e-40 in ref transcript
  • AMOP domain. This domain may have a role in cell adhesion. It is called the AMOP domain after Adhesion associated domain in MUC4 and Other Proteins. This domain is extracellular and contains a number of cysteines that probably form disulphide bridges.
• Changed! smart TSP1 41aa 3e-06 in ref transcript
  • Thrombospondin type 1 repeats. Type 1 repeats in thrombospondin-1 bind and activate TGF-beta.

THYN1

• refseq_THYN1.F1 refseq_THYN1.R1 170 321
• NCBIGene 36.3 29087
• Single exon skipping, size difference: 151
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_014174

• Changed! pfam DUF55 134aa 3e-29 in ref transcript
  • Protein of unknown function DUF55. This family of proteins have no known function.
• Changed! COG COG2947 169aa 3e-46 in ref transcript
  • Uncharacterized conserved protein [Function unknown].
• Changed! pfam DUF55 66aa 4e-16 in modified transcript
• Changed! COG COG2947 105aa 2e-34 in modified transcript

TIAL1

• refseq_TIAL1.F1 refseq_TIAL1.R1 281 332
• NCBIGene 36.3 7073
• Alternative 3-prime, size difference: 51
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001033925

• cd RRM 74aa 2e-19 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• Changed! cd RRM 90aa 2e-16 in ref transcript
• cd RRM 69aa 3e-13 in ref transcript
• Changed! TIGR PABP-1234 275aa 3e-28 in ref transcript
  • There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, and of unknown tissue range.
• Changed! COG COG0724 277aa 2e-20 in ref transcript
  • RNA-binding proteins (RRM domain) [General function prediction only].
• Changed! cd RRM 73aa 3e-18 in modified transcript
• Changed! TIGR PABP-1234 258aa 3e-29 in modified transcript
• Changed! COG COG0724 192aa 3e-20 in modified transcript

TJP1

• refseq_TJP1.F1 refseq_TJP1.R1 145 385
• NCBIGene 36.3 7082
• Single exon skipping, size difference: 240
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_003257

• cd PDZ_signaling 86aa 3e-14 in ref transcript
  • PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of PDZ domains an N-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in proteases.
• cd PDZ_signaling 79aa 1e-10 in ref transcript
• cd PDZ_signaling 78aa 7e-10 in ref transcript
• pfam ZU5 103aa 7e-35 in ref transcript
  • ZU5 domain. Domain present in ZO-1 and Unc5-like netrin receptors Domain of unknown function.
• smart GuKc 176aa 5e-34 in ref transcript
  • Guanylate kinase homologues. Active enzymes catalyze ATP-dependent phosphorylation of GMP to GDP. Structure resembles that of adenylate kinase. So-called membrane-associated guanylate kinase homologues (MAGUKs) do not possess guanylate kinase activities; instead at least some possess protein-binding functions.
• smart PDZ 91aa 4e-14 in ref transcript
  • Domain present in PSD-95, Dlg, and ZO-1/2. Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities.
• smart PDZ 81aa 1e-12 in ref transcript
• pfam PDZ 77aa 3e-12 in ref transcript
  • PDZ domain (Also known as DHR or GLGF). PDZ domains are found in diverse signaling proteins.
• pfam SH3_2 62aa 3e-06 in ref transcript
  • Variant SH3 domain. SH3 (Src homology 3) domains are often indicative of a protein involved in signal transduction related to cytoskeletal organisation. First described in the Src cytoplasmic tyrosine kinase. The structure is a partly opened beta barrel.
• TIGR degP_htrA_DO 214aa 7e-06 in ref transcript
  • This family consists of a set proteins various designated DegP, heat shock protein HtrA, and protease DO. The ortholog in Pseudomonas aeruginosa is designated MucD and is found in an operon that controls mucoid phenotype. This family also includes the DegQ (HhoA) paralog in E. coli which can rescue a DegP mutant, but not the smaller DegS paralog, which cannot. Members of this family are located in the periplasm and have separable functions as both protease and chaperone. Members have a trypsin domain and two copies of a PDZ domain. This protein protects bacteria from thermal and other stresses and may be important for the survival of bacterial pathogens.// The chaperone function is dominant at low temperatures, whereas the proteolytic activity is turned on at elevated temperatures.
• TIGR degP_htrA_DO 131aa 0.004 in ref transcript
• COG Prc 85aa 5e-08 in ref transcript
  • Periplasmic protease [Cell envelope biogenesis, outer membrane].
• COG Prc 60aa 0.006 in ref transcript
• COG Prc 58aa 0.009 in ref transcript

TLR8

• refseq_TLR8.F1 refseq_TLR8.R1 142 279
• NCBIGene 36.2 51311
• Single exon skipping, size difference: 137
• Exclusion of the protein initiation site
• Reference transcript: NM_016610

• cd LRR_RI 214aa 1e-06 in ref transcript
  • Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1).
• pfam TIR 139aa 4e-15 in ref transcript
  • TIR domain. The Toll/interleukin-1 receptor (TIR) homology domain is an intracellular signalling domain found in MyD88, interleukin 1 receptor and the Toll receptor. It contains three highly-conserved regions, and mediates protein-protein interactions between the Toll-like receptors (TLRs) and signal-transduction components. TIR-like motifs are also found in plant proteins thought to be involved in resistance to disease. When activated, TIR domains recruit cytoplasmic adaptor proteins MyD88 and TOLLIP (Toll interacting protein). In turn, these associate with various kinases to set off signalling cascades.
• TIGR PCC 84aa 2e-06 in ref transcript
  • Note: this model is restricted to the amino half because a full-length model is incompatible with the HMM software package.

TM2D2

• refseq_TM2D2.F1 refseq_TM2D2.R1 100 489
• NCBIGene 36.3 83877
• Alternative 3-prime, size difference: 389
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_078473

• Changed! pfam TM2 50aa 2e-11 in ref transcript
  • TM2 domain. This family is composed of a pair of transmembrane alpha helices connected by a short linker. The function of this domain is unknown, however it occurs in a wide range or protein contexts.
• Changed! PHA PHA01886 53aa 9e-04 in ref transcript
  • TM2 domain-containing protein.

TM2D2

• refseq_TM2D2.F3 refseq_TM2D2.R3 172 378
• NCBIGene 36.3 83877
• Alternative 5-prime, size difference: 206
• Exclusion in 5'UTR
• Reference transcript: NM_031940

• pfam TM2 50aa 1e-10 in ref transcript
  • TM2 domain. This family is composed of a pair of transmembrane alpha helices connected by a short linker. The function of this domain is unknown, however it occurs in a wide range or protein contexts.
• PHA PHA01886 53aa 0.001 in ref transcript
  • TM2 domain-containing protein.

TM2D3

• refseq_TM2D3.F1 refseq_TM2D3.R1 101 179
• NCBIGene 36.3 80213
• Single exon skipping, size difference: 78
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_078474

• pfam TM2 50aa 2e-06 in ref transcript
  • TM2 domain. This family is composed of a pair of transmembrane alpha helices connected by a short linker. The function of this domain is unknown, however it occurs in a wide range or protein contexts.

TM6SF2

• refseq_TM6SF2.F1 refseq_TM6SF2.R1 162 287
• NCBIGene 36.2 53345
• Single exon skipping, size difference: 125
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_001001524

TMEM10

• refseq_TMEM10.F1 refseq_TMEM10.R1 105 144
• NCBIGene 36.3 93377
• Single exon skipping, size difference: 39
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_033207

TMEM107

• refseq_TMEM107.F1 refseq_TMEM107.R1 101 119
• NCBIGene 36.3 84314
• Alternative 3-prime, size difference: 18
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_032354

TMEM150

• refseq_TMEM150.F1 refseq_TMEM150.R1 151 219
• NCBIGene 36.3 129303
• Single exon skipping, size difference: 68
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_001031738

• Changed! pfam Frag1 229aa 2e-44 in ref transcript
  • Frag1/DRAM/Sfk1 family. This family includes Frag1, DRAM and Sfk1 proteins. Frag1 (FGF receptor activating protein 1) is a protein that is conserved from fungi to humans. There are four potential iso-prenylation sites throughout the peptide, viz CILW, CIIW and CIGL. Frag1 is a membrane-spanning protein that is ubiquitously expressed in adult tissues suggesting an important cellular function. Dram is a family of proteins conserved from nematodes to humans with six hydrophobic transmembrane regions and an Endoplasmic Reticulum signal peptide. It is a lysosomal protein that induces macro-autophagy as an effector of p53-mediated death, where p53 is the tumour-suppressor gene that is frequently mutated in cancer. Expression of Dram is stress-induced. This region is also part of a family of small plasma membrane proteins, referred to as Sfk1, that may act together with or upstream of Stt4p to generate normal levels of the essential phospholipid PI4P, thus allowing proper localisation of Stt4p to the actin cytoskeleton.
• Changed! pfam Frag1 66aa 2e-07 in modified transcript

TMEM44

• refseq_TMEM44.F1 refseq_TMEM44.R1 108 141
• NCBIGene 36.3 93109
• Single exon skipping, size difference: 33
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_138399

TMEM93

• refseq_TMEM93.F1 refseq_TMEM93.R1 229 342
• NCBIGene 36.3 83460
• Alternative 5-prime, size difference: 113
• Exclusion in 5'UTR
• Reference transcript: NM_001014764

• pfam DUF786 110aa 5e-25 in ref transcript
  • Protein of unknown function (DUF786). This family consists of several eukaryotic proteins of unknown function.

TMEM98

• refseq_TMEM98.F1 refseq_TMEM98.R1 199 275
• NCBIGene 36.3 26022
• Single exon skipping, size difference: 76
• Exclusion in 5'UTR
• Reference transcript: NM_015544

TMPRSS4

• refseq_TMPRSS4.F1 refseq_TMPRSS4.R1 150 293
• NCBIGene 36.2 56649
• Single exon skipping, size difference: 143
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_019894

• Changed! cd Tryp_SPc 228aa 2e-68 in ref transcript
  • Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
• cd LDLa 35aa 0.002 in ref transcript
  • Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure.
• Changed! smart Tryp_SPc 226aa 2e-77 in ref transcript
  • Trypsin-like serine protease. Many of these are synthesised as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. A few, however, are active as single chain molecules, and others are inactive due to substitutions of the catalytic triad residues.
• smart SR 91aa 9e-07 in ref transcript
  • Scavenger receptor Cys-rich. The sea ucrhin egg peptide speract contains 4 repeats of SR domains that contain 6 conserved cysteines. May bind bacterial antigens in the protein MARCO.
• pfam Ldl_recept_a 22aa 0.005 in ref transcript
  • Low-density lipoprotein receptor domain class A.
• Changed! COG COG5640 228aa 8e-26 in ref transcript
  • Secreted trypsin-like serine protease [Posttranslational modification, protein turnover, chaperones].
• Changed! cd Tryp_SPc 132aa 1e-32 in modified transcript
• Changed! smart Tryp_SPc 134aa 1e-36 in modified transcript
• Changed! COG COG5640 133aa 2e-08 in modified transcript

TMUB2

• refseq_TMUB2.F1 refseq_TMUB2.R1 112 401
• NCBIGene 36.2 79089
• Alternative 5-prime, size difference: 289
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_177441

• Changed! cd UBL 63aa 1e-05 in ref transcript
  • UBLs function by remodeling the surface of their target proteins, changing their target's half-life, enzymatic activity, protein-protein interactions, subcellular localization or other properties. At least 10 different ubiquitin-like modifications exist in mammals, and attachment of different ubls to a target leads to different biological consequences. Ubl-conjugation cascades are initiated by activating enzymes, which also coordinate the ubls with their downstream pathways.
• Changed! pfam ubiquitin 51aa 5e-08 in ref transcript
  • Ubiquitin family. This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue), Nedd8, Elongin B, Rub1, and Parkin. A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites.

TNFRSF18

• refseq_TNFRSF18.F1 refseq_TNFRSF18.R1 101 122
• NCBIGene 36.3 8784
• Alternative 5-prime, size difference: 21
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_004195

TNFRSF25

• refseq_TNFRSF25.F1 refseq_TNFRSF25.R1 153 180
• NCBIGene 36.3 8718
• Alternative 5-prime, size difference: 7
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_148965

• Changed! cd TNFR 107aa 4e-13 in ref transcript
  • Tumor necrosis factor receptor (TNFR) domain; superfamily of TNF-like receptor domains. When bound to TNF-like cytokines, TNFRs trigger multiple signal transduction pathways, they are involved in inflammation response, apoptosis, autoimmunity and organogenesis. TNFRs domains are elongated with generally three tandem repeats of cysteine-rich domains (CRDs). They fit in the grooves between protomers within the ligand trimer. Some TNFRs, such as NGFR and HveA, bind ligands with no structural similarity to TNF and do not bind ligand trimers.
• Changed! smart DEATH 85aa 6e-12 in ref transcript
  • DEATH domain, found in proteins involved in cell death (apoptosis). Alpha-helical domain present in a variety of proteins with apoptotic functions. Some (but not all) of these domains form homotypic and heterotypic dimers.
• Changed! cd TNFR 88aa 3e-09 in modified transcript

TNFRSF25

• refseq_TNFRSF25.F1 refseq_TNFRSF25.R5 107 127
• NCBIGene 36.3 8718
• Alternative 3-prime, size difference: 20
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_148965

• Changed! cd TNFR 107aa 4e-13 in ref transcript
  • Tumor necrosis factor receptor (TNFR) domain; superfamily of TNF-like receptor domains. When bound to TNF-like cytokines, TNFRs trigger multiple signal transduction pathways, they are involved in inflammation response, apoptosis, autoimmunity and organogenesis. TNFRs domains are elongated with generally three tandem repeats of cysteine-rich domains (CRDs). They fit in the grooves between protomers within the ligand trimer. Some TNFRs, such as NGFR and HveA, bind ligands with no structural similarity to TNF and do not bind ligand trimers.
• Changed! smart DEATH 85aa 6e-12 in ref transcript
  • DEATH domain, found in proteins involved in cell death (apoptosis). Alpha-helical domain present in a variety of proteins with apoptotic functions. Some (but not all) of these domains form homotypic and heterotypic dimers.
• Changed! cd TNFR 88aa 2e-08 in modified transcript

TNFRSF25

• refseq_TNFRSF25.F4 refseq_TNFRSF25.R4 235 370
• NCBIGene 36.3 8718
• Single exon skipping, size difference: 135
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_148965

• Changed! cd TNFR 107aa 4e-13 in ref transcript
  • Tumor necrosis factor receptor (TNFR) domain; superfamily of TNF-like receptor domains. When bound to TNF-like cytokines, TNFRs trigger multiple signal transduction pathways, they are involved in inflammation response, apoptosis, autoimmunity and organogenesis. TNFRs domains are elongated with generally three tandem repeats of cysteine-rich domains (CRDs). They fit in the grooves between protomers within the ligand trimer. Some TNFRs, such as NGFR and HveA, bind ligands with no structural similarity to TNF and do not bind ligand trimers.
• Changed! smart DEATH 85aa 6e-12 in ref transcript
  • DEATH domain, found in proteins involved in cell death (apoptosis). Alpha-helical domain present in a variety of proteins with apoptotic functions. Some (but not all) of these domains form homotypic and heterotypic dimers.
• Changed! cd TNFR 100aa 0.001 in modified transcript
• Changed! pfam Death 80aa 6e-12 in modified transcript
  • Death domain.

TNFSF13

• refseq_TNFSF13.F2 refseq_TNFSF13.R2 217 265
• NCBIGene 36.3 8741
• Single exon skipping, size difference: 48
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_003808

• Changed! cd TNF 132aa 2e-18 in ref transcript
  • Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT (lymphotoxin-alpha, TNF-beta), CD40 ligand, Apo2L (TRAIL), Fas ligand, and osteoprotegerin (OPG) ligand. These proteins generally have an intracellular N-terminal domain, a short transmembrane segment, an extracellular stalk, and a globular TNF-like extracellular domain of about 150 residues. They initiate apoptosis by binding to related receptors, some of which have intracellular death domains. They generally form homo- or hetero- trimeric complexes.TNF cytokines bind one elongated receptor molecule along each of three clefts formed by neighboring monomers of the trimer with ligand trimerization a requiste for receptor binding.
• pfam TNF 112aa 3e-17 in ref transcript
  • TNF(Tumour Necrosis Factor) family.
• Changed! cd TNF 118aa 2e-17 in modified transcript

TNFSF14

• refseq_TNFSF14.F2 refseq_TNFSF14.R2 123 231
• NCBIGene 36.3 8740
• Alternative 5-prime, size difference: 108
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_003807

• cd TNF 145aa 2e-23 in ref transcript
  • Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT (lymphotoxin-alpha, TNF-beta), CD40 ligand, Apo2L (TRAIL), Fas ligand, and osteoprotegerin (OPG) ligand. These proteins generally have an intracellular N-terminal domain, a short transmembrane segment, an extracellular stalk, and a globular TNF-like extracellular domain of about 150 residues. They initiate apoptosis by binding to related receptors, some of which have intracellular death domains. They generally form homo- or hetero- trimeric complexes.TNF cytokines bind one elongated receptor molecule along each of three clefts formed by neighboring monomers of the trimer with ligand trimerization a requiste for receptor binding.
• smart TNF 129aa 2e-25 in ref transcript
  • Tumour necrosis factor family. Family of cytokines that form homotrimeric or heterotrimeric complexes. TNF mediates mature T-cell receptor-induced apoptosis through the p75 TNF receptor.

TNK2

• refseq_TNK2.F1 refseq_TNK2.R1 328 418
• NCBIGene 36.3 10188
• Single exon skipping, size difference: 90
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_001010938

• cd PTKc_Ack_like 258aa 1e-147 in ref transcript
  • Catalytic Domain of the Protein Tyrosine Kinase, Activated Cdc42-associated kinase. Protein Tyrosine Kinase (PTK) family; Activated Cdc42-associated kinase (Ack) subfamily; catalytic (c) domain. Ack subfamily members include Ack1, thirty-eight-negative kinase 1 (Tnk1), and similar proteins. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Ack subfamily members are cytoplasmic (or nonreceptor) tyr kinases containing an N-terminal catalytic domain, an SH3 domain, a Cdc42-binding CRIB domain, and a proline-rich region. They are mainly expressed in brain and skeletal tissues and are involved in the regulation of cell adhesion and growth, receptor degradation, and axonal guidance. Ack1 is also associated with androgen-independent prostate cancer progression. Tnk1 regulates TNFalpha signaling and may play an important role in cell death.
• cd SH3 52aa 6e-06 in ref transcript
  • Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
• smart TyrKc 260aa 1e-105 in ref transcript
  • Tyrosine kinase, catalytic domain. Phosphotransferases. Tyrosine-specific kinase subfamily.
• pfam GTPase_binding 68aa 2e-24 in ref transcript
  • GTPase binding. The GTPase binding domain binds to the G protein Cdc42, inhibiting both its intrinsic and stimulated GTPase activity. The domain is largely unstructured in the absence of Cdc42.
• smart SH3 54aa 2e-06 in ref transcript
  • Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.
• COG SPS1 266aa 6e-25 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].
• Changed! COG DedD 114aa 0.010 in modified transcript
  • Uncharacterized protein conserved in bacteria [Function unknown].

TNK2

• refseq_TNK2.F3 refseq_TNK2.R3 197 242
• NCBIGene 36.3 10188
• Single exon skipping, size difference: 45
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001010938

• cd PTKc_Ack_like 258aa 1e-147 in ref transcript
  • Catalytic Domain of the Protein Tyrosine Kinase, Activated Cdc42-associated kinase. Protein Tyrosine Kinase (PTK) family; Activated Cdc42-associated kinase (Ack) subfamily; catalytic (c) domain. Ack subfamily members include Ack1, thirty-eight-negative kinase 1 (Tnk1), and similar proteins. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Ack subfamily members are cytoplasmic (or nonreceptor) tyr kinases containing an N-terminal catalytic domain, an SH3 domain, a Cdc42-binding CRIB domain, and a proline-rich region. They are mainly expressed in brain and skeletal tissues and are involved in the regulation of cell adhesion and growth, receptor degradation, and axonal guidance. Ack1 is also associated with androgen-independent prostate cancer progression. Tnk1 regulates TNFalpha signaling and may play an important role in cell death.
• cd SH3 52aa 6e-06 in ref transcript
  • Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
• smart TyrKc 260aa 1e-105 in ref transcript
  • Tyrosine kinase, catalytic domain. Phosphotransferases. Tyrosine-specific kinase subfamily.
• pfam GTPase_binding 68aa 2e-24 in ref transcript
  • GTPase binding. The GTPase binding domain binds to the G protein Cdc42, inhibiting both its intrinsic and stimulated GTPase activity. The domain is largely unstructured in the absence of Cdc42.
• smart SH3 54aa 2e-06 in ref transcript
  • Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.
• COG SPS1 266aa 6e-25 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].

TNRC5

• refseq_TNRC5.F1 refseq_TNRC5.R1 171 295
• NCBIGene 36.2 10695
• Single exon skipping, size difference: 124
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_006586

TNRC6A

• refseq_TNRC6A.F1 refseq_TNRC6A.R1 148 273
• NCBIGene 36.2 27327
• Single exon skipping, size difference: 125
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_020847

• Changed! cd RRM 68aa 3e-05 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• Changed! pfam Ago_hook 69aa 6e-11 in ref transcript
  • Argonaute hook. This region has been called the argonaute hook. It has been shown to bind to the Piwi domain pfam02171 of Argnonaute proteins.

TPD52L1

• refseq_TPD52L1.F1 refseq_TPD52L1.R1 285 346
• NCBIGene 36.3 7164
• Single exon skipping, size difference: 61
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_003287

• Changed! pfam TPD52 185aa 4e-39 in ref transcript
  • Tumour protein D52 family. The hD52 gene was originally identified through its elevated expression level in human breast carcinoma. Cloning of D52 homologues from other species has indicated that D52 may play roles in calcium-mediated signal transduction and cell proliferation. Two human homologues of hD52, hD53 and hD54, have also been identified, demonstrating the existence of a novel gene/protein family. These proteins have an amino terminal coiled-coil that allows members to form homo- and heterodimers with each other.
• Changed! pfam TPD52 128aa 7e-27 in modified transcript

TPD52L2

• refseq_TPD52L2.F1 refseq_TPD52L2.R1 108 135
• NCBIGene 36.3 7165
• Single exon skipping, size difference: 27
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_199360

• Changed! pfam TPD52 163aa 4e-26 in ref transcript
  • Tumour protein D52 family. The hD52 gene was originally identified through its elevated expression level in human breast carcinoma. Cloning of D52 homologues from other species has indicated that D52 may play roles in calcium-mediated signal transduction and cell proliferation. Two human homologues of hD52, hD53 and hD54, have also been identified, demonstrating the existence of a novel gene/protein family. These proteins have an amino terminal coiled-coil that allows members to form homo- and heterodimers with each other.
• Changed! pfam TPD52 154aa 7e-27 in modified transcript

TPM1

• refseq_TPM1.F1 refseq_TPM1.R1 151 199
• NCBIGene 36.3 7168
• Alternative 5-prime, size difference: 48
• Exclusion of the stop codon
• Reference transcript: NM_000366

• Changed! pfam Tropomyosin 236aa 3e-45 in ref transcript
  • Tropomyosin.
• Changed! pfam Tropomyosin 237aa 1e-45 in modified transcript

TPO

• refseq_TPO.F1 refseq_TPO.R1 225 396
• NCBIGene 36.3 7173
• Single exon skipping, size difference: 171
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000547

• cd CCP 54aa 3e-06 in ref transcript
  • Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR); The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function.
• cd EGF_CA 44aa 3e-06 in ref transcript
  • Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements.
• Changed! pfam An_peroxidase 559aa 0.0 in ref transcript
  • Animal haem peroxidase.
• pfam EGF_CA 43aa 2e-09 in ref transcript
  • Calcium binding EGF domain.
• smart CCP 53aa 3e-06 in ref transcript
  • Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR). The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. A missense mutation in seventh CCP domain causes deficiency of the b subunit of factor XIII.
• Changed! pfam An_peroxidase 502aa 1e-163 in modified transcript

TPO

• refseq_TPO.F4 refseq_TPO.R4 115 247
• NCBIGene 36.3 7173
• Single exon skipping, size difference: 132
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000547

• cd CCP 54aa 3e-06 in ref transcript
  • Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR); The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function.
• Changed! cd EGF_CA 44aa 3e-06 in ref transcript
  • Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements.
• pfam An_peroxidase 559aa 0.0 in ref transcript
  • Animal haem peroxidase.
• Changed! pfam EGF_CA 43aa 2e-09 in ref transcript
  • Calcium binding EGF domain.
• smart CCP 53aa 3e-06 in ref transcript
  • Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR). The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. A missense mutation in seventh CCP domain causes deficiency of the b subunit of factor XIII.

TPO

• refseq_TPO.F6 refseq_TPO.R6 221 351
• NCBIGene 36.2 7173
• Single exon skipping, size difference: 130
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_000547

• cd CCP 54aa 3e-06 in ref transcript
  • Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR); The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function.
• cd EGF_CA 44aa 3e-06 in ref transcript
  • Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements.
• pfam An_peroxidase 559aa 0.0 in ref transcript
  • Animal haem peroxidase.
• pfam EGF_CA 43aa 2e-09 in ref transcript
  • Calcium binding EGF domain.
• smart CCP 53aa 3e-06 in ref transcript
  • Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR). The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. A missense mutation in seventh CCP domain causes deficiency of the b subunit of factor XIII.

TPTE

• refseq_TPTE.F2 refseq_TPTE.R2 213 273
• NCBIGene 36.3 7179
• Single exon skipping, size difference: 60
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_199259

• cd PTPc 53aa 0.002 in ref transcript
  • Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active.
• pfam PTEN_C2 131aa 5e-30 in ref transcript
  • C2 domain of PTEN tumour-suppressor protein. This is the C2 domain-like domain, in greek key form, of the PTEN protein, phosphatidyl-inositol triphosphate phosphatase, and it is the C-terminus. This domain may well include a CBR3 loop which means it plays a central role in membrane binding. This domain associates across an extensive interface with the N-terminal phosphatase domain DSPc (pfam00782) suggesting that the C2 domain productively positions the catalytic part of the protein on the membrane 1].
• smart PTPc_motif 59aa 2e-04 in ref transcript
  • Protein tyrosine phosphatase, catalytic domain motif.
• pfam Y_phosphatase 108aa 7e-04 in ref transcript
  • Protein-tyrosine phosphatase.
• COG CDC14 87aa 2e-06 in ref transcript
  • Predicted protein-tyrosine phosphatase [Signal transduction mechanisms].

TRAF3IP2

• refseq_TRAF3IP2.F2 refseq_TRAF3IP2.R2 283 394
• NCBIGene 36.3 10758
• Single exon skipping, size difference: 111
• Exclusion of the protein initiation site
• Reference transcript: NM_147200

• pfam SEFIR 139aa 1e-33 in ref transcript
  • SEFIR domain. This family comprises IL17 receptors (IL17Rs) and SEF proteins. The latter are feedback inhibitors of FGF signalling and are also thought to be receptors. Due to its similarity to the TIR domain (pfam01582), the SEFIR region is thought to be involved in homotypic interactions with other SEFIR/TIR-domain-containing proteins. Thus, SEFs and IL17Rs may be involved in TOLL/IL1R-like signalling pathways.

TRAF6

• refseq_TRAF6.F2 refseq_TRAF6.R2 296 389
• NCBIGene 36.3 7189
• Single exon skipping, size difference: 93
• Exclusion in 5'UTR
• Reference transcript: NM_145803

• cd MATH_TRAF6 150aa 2e-67 in ref transcript
  • Tumor Necrosis Factor Receptor (TNFR)-Associated Factor (TRAF) family, TRAF6 subfamily, TRAF domain, C-terminal MATH subdomain; composed of proteins with similarity to human TRAF6, including the Drosophila protein DTRAF2. TRAF molecules serve as adapter proteins that link TNFRs and downstream kinase cascades resulting in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses. TRAF6 is the most divergent in its TRAF domain among the mammalian TRAFs. In addition to mediating TNFR family signaling, it is also an essential signaling molecule of the interleukin-1/Toll-like receptor superfamily. Whereas other TRAF molecules display similar and overlapping TNFR-binding specificities, TRAF6 binds completely different sites on receptors such as CD40 and RANK. TRAF6 serves as a molecular bridge between innate and adaptive immunity and plays a central role in osteoimmunology. DTRAF2, as an activator of nuclear factor-kappaB, plays a pivotal role in Drosophila development and innate immunity. TRAF6 contains a RING finger domain, five zinc finger domains, and a TRAF domain. The TRAF domain can be divided into a more divergent N-terminal alpha helical region (TRAF-N), and a highly conserved C-terminal MATH subdomain (TRAF-C) with an eight-stranded beta-sandwich structure. TRAF-N mediates trimerization while TRAF-C interacts with receptors.
• cd RING 39aa 3e-04 in ref transcript
  • RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H).
• pfam MATH 143aa 1e-18 in ref transcript
  • MATH domain. This motif has been called the Meprin And TRAF-Homology (MATH) domain. This domain is hugely expanded in the nematode Caenorhabditis elegans.
• pfam zf-TRAF 58aa 9e-14 in ref transcript
  • TRAF-type zinc finger.
• smart RING 38aa 2e-06 in ref transcript
  • Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s).
• pfam zf-TRAF 57aa 1e-04 in ref transcript
• pfam Myosin_tail_1 46aa 0.007 in ref transcript
  • Myosin tail. The myosin molecule is a multi-subunit complex made up of two heavy chains and four light chains it is a fundamental contractile protein found in all eukaryote cell types. This family consists of the coiled-coil myosin heavy chain tail region. The coiled-coil is composed of the tail from two molecules of myosin. These can then assemble into the macromolecular thick filament. The coiled-coil region provides the structural backbone the thick filament.
• COG COG5222 65aa 1e-04 in ref transcript
  • Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only].

TRAF7

• refseq_TRAF7.F1 refseq_TRAF7.R1 145 194
• NCBIGene 36.2 84231
• Alternative 5-prime and 3-prime, size difference: 49
• Inclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_032271

• Changed! cd WD40 281aa 4e-47 in ref transcript
  • WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.
• Changed! pfam WD40 39aa 1e-06 in ref transcript
  • WD domain, G-beta repeat.
• Changed! TIGR rad18 34aa 4e-05 in ref transcript
  • This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
• Changed! pfam WD40 36aa 0.001 in ref transcript
• Changed! pfam WD40 41aa 0.002 in ref transcript
• Changed! pfam SMC_N 79aa 0.002 in ref transcript
  • RecF/RecN/SMC N terminal domain. This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.
• Changed! COG COG2319 330aa 2e-18 in ref transcript
  • FOG: WD40 repeat [General function prediction only].
• Changed! COG COG5152 36aa 4e-04 in ref transcript
  • Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only].

TRAPPC2

• refseq_TRAPPC2.F1 refseq_TRAPPC2.R1 109 251
• NCBIGene 36.3 6399
• Single exon skipping, size difference: 142
• Exclusion in 5'UTR
• Reference transcript: NM_001011658

• pfam Sedlin_N 128aa 9e-49 in ref transcript
  • Sedlin, N-terminal conserved region. Mutations in this protein are associated with the X-linked spondyloepiphyseal dysplasia tarda syndrome (OMIM:313400). This family represents an N-terminal conserved region.
• COG TRS20 133aa 4e-32 in ref transcript
  • Subunit of TRAPP, an ER-Golgi tethering complex [Cell motility and secretion].

TRERF1

• refseq_TRERF1.F1 refseq_TRERF1.R1 150 200
• NCBIGene 36.2 55809
• Alternative 5-prime, size difference: 50
• Inclusion in 5'UTR
• Reference transcript: NM_033502

• pfam ELM2 57aa 9e-10 in ref transcript
  • ELM2 domain. The ELM2 (Egl-27 and MTA1 homology 2) domain is a small domain of unknown function. It is found in the MTA1 protein that is part of the NuRD complex. The domain is usually found to the N terminus of a myb-like DNA binding domain pfam00249. ELM2 is also found associated with an ARID DNA binding domain pfam01388 in a protein from Arabidopsis thaliana. This suggests that ELM2 may also be involved in DNA binding, or perhaps is a protein-protein interaction domain.
• smart SANT 46aa 0.002 in ref transcript
  • SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.

TRERF1

• refseq_TRERF1.F3 refseq_TRERF1.R3 167 203
• NCBIGene 36.2 55809
• Alternative 3-prime, size difference: 36
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_033502

• pfam ELM2 57aa 9e-10 in ref transcript
  • ELM2 domain. The ELM2 (Egl-27 and MTA1 homology 2) domain is a small domain of unknown function. It is found in the MTA1 protein that is part of the NuRD complex. The domain is usually found to the N terminus of a myb-like DNA binding domain pfam00249. ELM2 is also found associated with an ARID DNA binding domain pfam01388 in a protein from Arabidopsis thaliana. This suggests that ELM2 may also be involved in DNA binding, or perhaps is a protein-protein interaction domain.
• smart SANT 46aa 0.002 in ref transcript
  • SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.

TRERF1

• refseq_TRERF1.F6 refseq_TRERF1.R6 165 414
• NCBIGene 36.2 55809
• Single exon skipping, size difference: 249
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_033502

• pfam ELM2 57aa 9e-10 in ref transcript
  • ELM2 domain. The ELM2 (Egl-27 and MTA1 homology 2) domain is a small domain of unknown function. It is found in the MTA1 protein that is part of the NuRD complex. The domain is usually found to the N terminus of a myb-like DNA binding domain pfam00249. ELM2 is also found associated with an ARID DNA binding domain pfam01388 in a protein from Arabidopsis thaliana. This suggests that ELM2 may also be involved in DNA binding, or perhaps is a protein-protein interaction domain.
• smart SANT 46aa 0.002 in ref transcript
  • SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.

TREX1

• refseq_TREX1.F1 refseq_TREX1.R1 157 242
• NCBIGene 36.2 11277
• Single exon skipping, size difference: 85
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_130384

ATRIP

• refseq_TREX1.F4 refseq_TREX1.R4 316 397
• NCBIGene 36.3 84126
• Single exon skipping, size difference: 81
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_130384

RNF216

• refseq_TRIAD3.F1 refseq_TRIAD3.R1 193 364
• NCBIGene 36.3 54476
• Alternative 3-prime, size difference: 171
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_207111

TRIM17

• refseq_TRIM17.F1 refseq_TRIM17.R1 116 152
• NCBIGene 36.3 51127
• Alternative 3-prime, size difference: 36
• Inclusion in 5'UTR
• Reference transcript: NM_001024940

• cd RING 53aa 6e-06 in ref transcript
  • RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H).
• cd BBOX 38aa 2e-05 in ref transcript
  • B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.
• smart SPRY 121aa 5e-25 in ref transcript
  • Domain in SPla and the RYanodine Receptor. Domain of unknown function. Distant homologues are domains in butyrophilin/marenostrin/pyrin homologues.
• pfam zf-B_box 41aa 2e-07 in ref transcript
  • B-box zinc finger.
• smart PRY 53aa 2e-07 in ref transcript
  • associated with SPRY domains.
• smart RING 50aa 2e-06 in ref transcript
  • Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s).
• COG PEX10 51aa 1e-04 in ref transcript
  • RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones].

TRIM24

• refseq_TRIM24.F1 refseq_TRIM24.R1 159 261
• NCBIGene 36.3 8805
• Alternative 5-prime, size difference: 102
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_015905

• cd Bromo_tif1_like 108aa 4e-46 in ref transcript
  • Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of the tripartite motif (TRIM) protein family, which is characterized by a particular domain architecture. It functions by recruiting coactivators and/or corepressors to modulate transcription. Vertebrate Tif1-gamma, also labeled E3 ubiquitin-protein ligase TRIM33, plays a role in the control of hematopoiesis. Its homologue in Xenopus laevis, Ectodermin, has been shown to function in germ-layer specification and control of cell growth during embryogenesis. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
• cd BBOX 39aa 1e-07 in ref transcript
  • B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.
• cd BAH_plant_2 62aa 0.006 in ref transcript
  • BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
• smart BBC 127aa 6e-32 in ref transcript
  • B-Box C-terminal domain. Coiled coil region C-terminal to (some) B-Box domains.
• smart BROMO 103aa 2e-29 in ref transcript
  • bromo domain.
• pfam zf-B_box 42aa 6e-10 in ref transcript
  • B-box zinc finger.
• pfam PHD 44aa 4e-08 in ref transcript
  • PHD-finger. PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
• pfam zf-B_box 46aa 0.003 in ref transcript
• COG COG5076 125aa 3e-14 in ref transcript
  • Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription].

TRIM3

• refseq_TRIM3.F1 refseq_TRIM3.R1 203 368
• NCBIGene 36.3 10612
• Single exon skipping, size difference: 165
• Exclusion in 5'UTR
• Reference transcript: NM_006458

• cd RING 44aa 2e-08 in ref transcript
  • RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H).
• cd BBOX 37aa 3e-06 in ref transcript
  • B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.
• cd WD40 261aa 9e-06 in ref transcript
  • WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.
• smart BBC 127aa 2e-32 in ref transcript
  • B-Box C-terminal domain. Coiled coil region C-terminal to (some) B-Box domains.
• smart IG_FLMN 98aa 2e-22 in ref transcript
  • Filamin-type immunoglobulin domains. These form a rod-like structure in the actin-binding cytoskeleton protein, filamin. The C-terminal repeats of filamin bind beta1-integrin (CD29).
• smart BBOX 42aa 4e-10 in ref transcript
  • B-Box-type zinc finger.
• smart RING 41aa 7e-10 in ref transcript
  • Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s).
• TIGR rad18 83aa 2e-07 in ref transcript
  • This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
• pfam NHL 28aa 2e-06 in ref transcript
  • NHL repeat. The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in the peptidyl-glycine alpha-amidating monooxygenase (PAM), proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. The human tripartite motif-containing protein 32 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats.
• pfam NHL 28aa 1e-04 in ref transcript
• pfam NHL 28aa 3e-04 in ref transcript
• pfam NHL 28aa 0.002 in ref transcript
• pfam NHL 28aa 0.003 in ref transcript
• COG COG3391 246aa 1e-11 in ref transcript
  • Uncharacterized conserved protein [Function unknown].
• COG RAD18 79aa 3e-05 in ref transcript
  • RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms].
• PRK PRK08268 82aa 0.006 in ref transcript
  • 3-hydroxybutyryl-CoA dehydrogenase; Validated.

TRIM31

• refseq_TRIM31.F1 refseq_TRIM31.R1 110 177
• NCBIGene 36.2 11074
• Exon skipping and alternative 3-prime or 5-prime, size difference: 67
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_007028

• cd RING 45aa 1e-06 in ref transcript
  • RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H).
• cd BBOX 37aa 7e-04 in ref transcript
  • B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.
• smart RING 41aa 2e-08 in ref transcript
  • Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s).
• pfam zf-B_box 42aa 2e-06 in ref transcript
  • B-box zinc finger.
• COG PEX10 50aa 4e-05 in ref transcript
  • RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones].

TRIM33

• refseq_TRIM33.F1 refseq_TRIM33.R1 229 280
• NCBIGene 36.3 51592
• Single exon skipping, size difference: 51
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_015906

• Changed! cd Bromo_tif1_like 126aa 8e-48 in ref transcript
  • Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of the tripartite motif (TRIM) protein family, which is characterized by a particular domain architecture. It functions by recruiting coactivators and/or corepressors to modulate transcription. Vertebrate Tif1-gamma, also labeled E3 ubiquitin-protein ligase TRIM33, plays a role in the control of hematopoiesis. Its homologue in Xenopus laevis, Ectodermin, has been shown to function in germ-layer specification and control of cell growth during embryogenesis. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
• cd BBOX 39aa 2e-07 in ref transcript
  • B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.
• smart BBC 127aa 2e-27 in ref transcript
  • B-Box C-terminal domain. Coiled coil region C-terminal to (some) B-Box domains.
• Changed! smart BROMO 122aa 3e-24 in ref transcript
  • bromo domain.
• pfam zf-B_box 42aa 2e-09 in ref transcript
  • B-box zinc finger.
• pfam PHD 44aa 3e-07 in ref transcript
  • PHD-finger. PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
• smart BBOX 37aa 0.004 in ref transcript
  • B-Box-type zinc finger.
• Changed! COG COG5076 121aa 3e-09 in ref transcript
  • Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription].
• Changed! cd Bromo_tif1_like 109aa 2e-50 in modified transcript
• Changed! smart BROMO 105aa 1e-27 in modified transcript
• Changed! COG COG5076 104aa 3e-12 in modified transcript

TRIM39

• refseq_TRIM39.F1 refseq_TRIM39.R1 124 214
• NCBIGene 36.3 56658
• Single exon skipping, size difference: 90
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_021253

• cd RING 45aa 5e-08 in ref transcript
  • RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H).
• cd BBOX 38aa 4e-05 in ref transcript
  • B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.
• smart SPRY 109aa 3e-31 in ref transcript
  • Domain in SPla and the RYanodine Receptor. Domain of unknown function. Distant homologues are domains in butyrophilin/marenostrin/pyrin homologues.
• smart PRY 52aa 3e-17 in ref transcript
  • associated with SPRY domains.
• smart RING 41aa 1e-09 in ref transcript
  • Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s).
• Changed! TIGR alt_F1F0_F0_B 178aa 1e-05 in ref transcript
  • CC and in principle may run in either direction. This model represents the F0 subunit B of this apparent second ATP synthase.
• pfam zf-B_box 38aa 1e-04 in ref transcript
  • B-box zinc finger.
• COG RAD18 151aa 1e-06 in ref transcript
  • RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms].
• Changed! PRK PRK02224 125aa 0.001 in ref transcript
  • chromosome segregation protein; Provisional.
• Changed! TIGR SMC_prok_A 148aa 8e-05 in modified transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent.
• Changed! PRK PRK02224 202aa 3e-04 in modified transcript

TRIM4

• refseq_TRIM4.F1 refseq_TRIM4.R1 224 302
• NCBIGene 36.3 89122
• Single exon skipping, size difference: 78
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_033017

• cd RING 45aa 8e-08 in ref transcript
  • RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H).
• cd BBOX 38aa 1e-05 in ref transcript
  • B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.
• smart SPRY 117aa 4e-13 in ref transcript
  • Domain in SPla and the RYanodine Receptor. Domain of unknown function. Distant homologues are domains in butyrophilin/marenostrin/pyrin homologues.
• smart RING 41aa 5e-08 in ref transcript
  • Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s).
• pfam zf-B_box 38aa 2e-05 in ref transcript
  • B-box zinc finger.
• smart PRY 70aa 0.002 in ref transcript
  • associated with SPRY domains.
• COG RAD18 69aa 6e-05 in ref transcript
  • RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms].

TRIM54

• refseq_TRIM54.F1 refseq_TRIM54.R1 172 298
• NCBIGene 36.3 57159
• Single exon skipping, size difference: 126
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_032546

• cd RING 60aa 3e-05 in ref transcript
  • RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H).
• pfam zf-C3HC4 25aa 0.010 in ref transcript
  • Zinc finger, C3HC4 type (RING finger). The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid. Many proteins containing a RING finger play a key role in the ubiquitination pathway.

TRIM55

• refseq_TRIM55.F2 refseq_TRIM55.R2 205 293
• NCBIGene 36.3 84675
• Single exon skipping, size difference: 88
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_184085

• cd RING 60aa 4e-06 in ref transcript
  • RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H).
• cd BBOX 40aa 0.007 in ref transcript
  • B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.
• pfam zf-B_box 40aa 2e-04 in ref transcript
  • B-box zinc finger.
• Changed! smart RING 56aa 0.001 in ref transcript
  • Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s).
• smart BBC 127aa 0.005 in ref transcript
  • B-Box C-terminal domain. Coiled coil region C-terminal to (some) B-Box domains.
• Changed! smart RING 35aa 0.002 in modified transcript

TRIM7

• refseq_TRIM7.F1 refseq_TRIM7.R1 121 398
• NCBIGene 36.3 81786
• Alternative 5-prime, size difference: 277
• Exclusion in 5'UTR
• Reference transcript: NM_203296

• smart SPRY 107aa 5e-22 in ref transcript
  • Domain in SPla and the RYanodine Receptor. Domain of unknown function. Distant homologues are domains in butyrophilin/marenostrin/pyrin homologues.
• smart PRY 48aa 5e-11 in ref transcript
  • associated with SPRY domains.

TRIM7

• refseq_TRIM7.F2 refseq_TRIM7.R2 226 294
• NCBIGene 36.3 81786
• Alternative 5-prime, size difference: 68
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_203293

• cd RING 56aa 1e-05 in ref transcript
  • RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H).
• cd BBOX 37aa 1e-04 in ref transcript
  • B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.
• Changed! smart SPRY 107aa 2e-22 in ref transcript
  • Domain in SPla and the RYanodine Receptor. Domain of unknown function. Distant homologues are domains in butyrophilin/marenostrin/pyrin homologues.
• Changed! smart PRY 48aa 2e-10 in ref transcript
  • associated with SPRY domains.
• Changed! smart RING 53aa 2e-06 in ref transcript
  • Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s).
• pfam zf-B_box 37aa 3e-06 in ref transcript
  • B-box zinc finger.
• COG RAD18 65aa 8e-05 in ref transcript
  • RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms].
• Changed! PRK PRK08476 53aa 0.001 in modified transcript
  • F0F1 ATP synthase subunit B'; Validated.

TRNT1

• refseq_TRNT1.F1 refseq_TRNT1.R1 283 343
• NCBIGene 36.2 51095
• Alternative 5-prime, size difference: 60
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_016000

• pfam PolyA_pol 124aa 3e-32 in ref transcript
  • Poly A polymerase head domain. This family includes nucleic acid independent RNA polymerases, such as Poly(A) polymerase, which adds the poly (A) tail to mRNA EC:2.7.7.19. This family also includes the tRNA nucleotidyltransferase that adds the CCA to the 3' of the tRNA EC:2.7.7.25.
• Changed! COG PcnB 394aa 2e-51 in ref transcript
  • tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis].
• Changed! COG PcnB 222aa 3e-49 in modified transcript

TRPC4AP

• refseq_TRPC4AP.F1 refseq_TRPC4AP.R1 133 157
• NCBIGene 36.3 26133
• Alternative 3-prime, size difference: 24
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_015638

TRPM3

• refseq_TRPM3.F2 refseq_TRPM3.R2 197 233
• NCBIGene 36.3 80036
• Single exon skipping, size difference: 36
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_001007471

• pfam Ion_trans 122aa 4e-07 in ref transcript
  • Ion transport protein. This family contains Sodium, Potassium, Calcium ion channels. This family is 6 transmembrane helices in which the last two helices flank a loop which determines ion selectivity. In some sub-families (e.g. Na channels) the domain is repeated four times, whereas in others (e.g. K channels) the protein forms as a tetramer in the membrane. A bacterial structure of the protein is known for the last two helices but is not the Pfam family due to it lacking the first four helices.
• TIGR trp 320aa 4e-05 in ref transcript
  • after chronic exposure to capsaicin. (McCleskey and Gold, 1999).

TRPM3

• refseq_TRPM3.F3 refseq_TRPM3.R3 149 179
• NCBIGene 36.3 80036
• Single exon skipping, size difference: 30
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001007471

• pfam Ion_trans 122aa 4e-07 in ref transcript
  • Ion transport protein. This family contains Sodium, Potassium, Calcium ion channels. This family is 6 transmembrane helices in which the last two helices flank a loop which determines ion selectivity. In some sub-families (e.g. Na channels) the domain is repeated four times, whereas in others (e.g. K channels) the protein forms as a tetramer in the membrane. A bacterial structure of the protein is known for the last two helices but is not the Pfam family due to it lacking the first four helices.
• TIGR trp 320aa 4e-05 in ref transcript
  • after chronic exposure to capsaicin. (McCleskey and Gold, 1999).

TRPM3

• refseq_TRPM3.F6 refseq_TRPM3.R6 130 205
• NCBIGene 36.3 80036
• Single exon skipping, size difference: 75
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_001007471

• pfam Ion_trans 122aa 4e-07 in ref transcript
  • Ion transport protein. This family contains Sodium, Potassium, Calcium ion channels. This family is 6 transmembrane helices in which the last two helices flank a loop which determines ion selectivity. In some sub-families (e.g. Na channels) the domain is repeated four times, whereas in others (e.g. K channels) the protein forms as a tetramer in the membrane. A bacterial structure of the protein is known for the last two helices but is not the Pfam family due to it lacking the first four helices.
• TIGR trp 320aa 4e-05 in ref transcript
  • after chronic exposure to capsaicin. (McCleskey and Gold, 1999).

TRPT1

• refseq_TRPT1.F2 refseq_TRPT1.R2 101 185
• NCBIGene 36.3 83707
• Single exon skipping, size difference: 84
• Exclusion of the protein initiation site
• Reference transcript: NM_001033678

• Changed! pfam PTS_2-RNA 179aa 2e-33 in ref transcript
  • RNA 2'-phosphotransferase, Tpt1 / KptA family. Tpt1 catalyses the last step of tRNA splicing in yeast. It transfers the splice junction 2'-phosphate from ligated tRNA to NAD, to produce ADP-ribose 1"-2"-cyclic phosphate. This is presumed to be followed by a transesterification step to release the RNA. The first step of this reaction is similar to that catalysed by some bacterial toxins. Escherichia coli KptA and mouse Tpt1 are likely to use the same reaction mechanism.
• Changed! PTZ PTZ00315 180aa 7e-39 in ref transcript
  • 2'-phosphotransferase; Provisional.
• Changed! pfam PTS_2-RNA 154aa 2e-27 in modified transcript
• Changed! PTZ PTZ00315 150aa 1e-31 in modified transcript

TRPV4

• refseq_TRPV4.F2 refseq_TRPV4.R2 165 345
• NCBIGene 36.3 59341
• Single exon skipping, size difference: 180
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_021625

• Changed! cd ANK 155aa 6e-11 in ref transcript
  • ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats.
• Changed! TIGR trp 651aa 1e-137 in ref transcript
  • after chronic exposure to capsaicin. (McCleskey and Gold, 1999).
• Changed! cd ANK 148aa 2e-10 in modified transcript
• Changed! TIGR trp 591aa 1e-119 in modified transcript

TSGA10

• refseq_TSGA10.F1 refseq_TSGA10.R1 155 199
• NCBIGene 36.3 80705
• Alternative 3-prime, size difference: 44
• Inclusion in 5'UTR
• Reference transcript: NM_182911

• TIGR SMC_prok_B 333aa 2e-12 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• TIGR SMC_prok_B 298aa 9e-09 in ref transcript
• pfam Macoilin 150aa 0.009 in ref transcript
  • Transmembrane protein. This entry is a highly conserved protein present in eukaryotes.
• COG Smc 363aa 5e-10 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].
• COG COG4372 204aa 2e-05 in ref transcript
  • Uncharacterized protein conserved in bacteria with the myosin-like domain [Function unknown].

TSPAN17

• refseq_TSPAN17.F1 refseq_TSPAN17.R1 125 157
• NCBIGene 36.3 26262
• Alternative 5-prime, size difference: 32
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_012171

• cd TM4SF9_like_LEL 124aa 7e-59 in ref transcript
  • Tetraspanin, extracellular domain or large extracellular loop (LEL), TM4SF9_like subfamily. Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. Tetraspanins are involved in diverse processes and their various functions may relate to their ability to act as molecular facilitators. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web". This subfamily contaions transmembrane 4 superfamily 9 (TM4SF9) or Tetraspanin-5 and related proteins. TM4SF9 is strongly expressed witin the central nervous system, and expression levels appear to correlate with differentiation status of particular neurons, hinting at a role in neuronal maturation.
• Changed! pfam Tetraspannin 252aa 2e-41 in ref transcript
  • Tetraspanin family.
• Changed! pfam Tetraspannin 245aa 1e-38 in modified transcript

TSPAN3

• refseq_TSPAN3.F2 refseq_TSPAN3.R2 187 262
• NCBIGene 36.3 10099
• Single exon skipping, size difference: 75
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_005724

• Changed! cd TM4SF8_like_LEL 107aa 6e-48 in ref transcript
  • Tetraspanin, extracellular domain or large extracellular loop (LEL), TM4SF8_like subfamily. Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. Tetraspanins are involved in diverse processes and their various functions may relate to their ability to act as molecular facilitators. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web". This subfamily contaions transmembrane 4 superfamily 8 (TM4SF8) or Tspan-3 and related proteins. Tspan-3 has been reported to form a complex with integrin beta1 and OSP/claudin-11, which may be involved in oligodendrocyte proliferation and migration.
• Changed! pfam Tetraspannin 228aa 1e-35 in ref transcript
  • Tetraspanin family.
• Changed! cd TM4SF8_like_LEL 102aa 8e-44 in modified transcript
• Changed! pfam Tetraspannin 203aa 8e-32 in modified transcript

TSPAN4

• refseq_TSPAN4.F1 refseq_TSPAN4.R1 117 217
• NCBIGene 36.3 7106
• Single exon skipping, size difference: 100
• Exclusion in 5'UTR
• Reference transcript: NM_003271

• cd NET-5_like_LEL 98aa 1e-40 in ref transcript
  • Tetraspanin, extracellular domain or large extracellular loop (LEL), NET-5_like family. Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. Tetraspanins are involved in diverse processes and their various functions may relate to their ability to act as molecular facilitators. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web". This sub-family contains proteins similar to human tetraspan NET-5.
• pfam Tetraspannin 222aa 3e-35 in ref transcript
  • Tetraspanin family.

TSPO

• refseq_TSPO.F1 refseq_TSPO.R1 189 400
• NCBIGene 36.3 706
• Single exon skipping, size difference: 211
• Exclusion of the protein initiation site
• Reference transcript: NM_000714

• Changed! pfam TspO_MBR 152aa 1e-43 in ref transcript
  • TspO/MBR family. Tryptophan-rich sensory protein (TspO) is an integral membrane protein that acts as a negative regulator of the expression of specific photosynthesis genes in response to oxygen/light. It is involved in the efflux of porphyrin intermediates from the cell. This reduces the activity of coproporphyrinogen III oxidase, which is thought to lead to the accumulation of a putative repressor molecule that inhibits the expression of specific photosynthesis genes. Several conserved aromatic residues are necessary for TspO function: they are thought to be involved in binding porphyrin intermediates. In, the rat mitochondrial peripheral benzodiazepine receptor (MBR) was shown to not only retain its structure within a bacterial outer membrane, but also to be able to functionally substitute for TspO in TspO- mutants, and to act in a similar manner to TspO in its in situ location: the outer mitochondrial membrane. The biological significance of MBR remains unclear, however. It is thought to be involved in a variety of cellular functions, including cholesterol transport in steroidogenic tissues.
• Changed! COG COG3476 150aa 5e-19 in ref transcript
  • Tryptophan-rich sensory protein (mitochondrial benzodiazepine receptor homolog) [Signal transduction mechanisms].

TTC8

• refseq_TTC8.F2 refseq_TTC8.R2 291 381
• NCBIGene 36.3 123016
• Single exon skipping, size difference: 90
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_144596

• cd TPR 93aa 1e-08 in ref transcript
  • Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here.
• cd TPR 90aa 1e-07 in ref transcript
• TIGR PEP_TPR_lipo 148aa 5e-06 in ref transcript
  • This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of tetratricopeptide repeats (TPR) suggests protein-protein interaction, possibly for the regulation of PEP-CTERM protein expression, since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator.
• TIGR type_IV_pilW 161aa 8e-04 in ref transcript
  • Members of this family are designated PilF in ref (PMID:8973346) and PilW in ref (PMID:15612916). This outer membrane protein is required both for pilus stability and for pilus function such as adherence to human cells. Members of this family contain copies of the TPR (tetratricopeptide repeat) domain.
• COG PilF 202aa 0.001 in ref transcript
  • Tfp pilus assembly protein PilF [Cell motility and secretion / Intracellular trafficking and secretion].

TTC8

• refseq_TTC8.F3 refseq_TTC8.R3 102 132
• NCBIGene 36.3 123016
• Single exon skipping, size difference: 30
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_144596

• cd TPR 93aa 1e-08 in ref transcript
  • Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here.
• cd TPR 90aa 1e-07 in ref transcript
• TIGR PEP_TPR_lipo 148aa 5e-06 in ref transcript
  • This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of tetratricopeptide repeats (TPR) suggests protein-protein interaction, possibly for the regulation of PEP-CTERM protein expression, since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator.
• TIGR type_IV_pilW 161aa 8e-04 in ref transcript
  • Members of this family are designated PilF in ref (PMID:8973346) and PilW in ref (PMID:15612916). This outer membrane protein is required both for pilus stability and for pilus function such as adherence to human cells. Members of this family contain copies of the TPR (tetratricopeptide repeat) domain.
• COG PilF 202aa 0.001 in ref transcript
  • Tfp pilus assembly protein PilF [Cell motility and secretion / Intracellular trafficking and secretion].

TTLL1

• refseq_TTLL1.F1 refseq_TTLL1.R1 199 271
• NCBIGene 36.3 25809
• Single exon skipping, size difference: 72
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_012263

• Changed! pfam TTL 306aa 1e-100 in ref transcript
  • Tubulin-tyrosine ligase family. Tubulins and microtubules are subjected to several post-translational modifications of which the reversible detyrosination/tyrosination of the carboxy-terminal end of most alpha-tubulins has been extensively analysed. This modification cycle involves a specific carboxypeptidase and the activity of the tubulin-tyrosine ligase (TTL). The true physiological function of TTL has so far not been established. Tubulin-tyrosine ligase (TTL) catalyses the ATP-dependent post-translational addition of a tyrosine to the carboxy terminal end of detyrosinated alpha-tubulin. In normally cycling cells, the tyrosinated form of tubulin predominates. However, in breast cancer cells, the detyrosinated form frequently predominates, with a correlation to tumour aggressiveness. On the other hand, 3-nitrotyrosine has been shown to be incorporated, by TTL, into the carboxy terminal end of detyrosinated alpha-tubulin. This reaction is not reversible by the carboxypeptidase enzyme. Cells cultured in 3-nitrotyrosine rich medium showed evidence of altered microtubule structure and function, including altered cell morphology, epithelial barrier dysfunction, and apoptosis.

TTLL3

• refseq_TTLL3.F1 refseq_TTLL3.R1 228 370
• NCBIGene 36.3 26140
• Single exon skipping, size difference: 142
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_001025930

• pfam TTL 292aa 7e-90 in ref transcript
  • Tubulin-tyrosine ligase family. Tubulins and microtubules are subjected to several post-translational modifications of which the reversible detyrosination/tyrosination of the carboxy-terminal end of most alpha-tubulins has been extensively analysed. This modification cycle involves a specific carboxypeptidase and the activity of the tubulin-tyrosine ligase (TTL). The true physiological function of TTL has so far not been established. Tubulin-tyrosine ligase (TTL) catalyses the ATP-dependent post-translational addition of a tyrosine to the carboxy terminal end of detyrosinated alpha-tubulin. In normally cycling cells, the tyrosinated form of tubulin predominates. However, in breast cancer cells, the detyrosinated form frequently predominates, with a correlation to tumour aggressiveness. On the other hand, 3-nitrotyrosine has been shown to be incorporated, by TTL, into the carboxy terminal end of detyrosinated alpha-tubulin. This reaction is not reversible by the carboxypeptidase enzyme. Cells cultured in 3-nitrotyrosine rich medium showed evidence of altered microtubule structure and function, including altered cell morphology, epithelial barrier dysfunction, and apoptosis.

TTYH1

• refseq_TTYH1.F1 refseq_TTYH1.R1 162 208
• NCBIGene 36.3 57348
• Single exon skipping, size difference: 46
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_001005367

• Changed! pfam Tweety 398aa 2e-71 in ref transcript
  • Tweety. The tweety (tty) gene has not been characterised at the protein level. However, it is thought to form a membrane protein with five potential membrane-spanning regions. A number of potential functions have been suggested.
• Changed! pfam Tweety 397aa 3e-71 in modified transcript

TUSC3

• refseq_TUSC3.F1 refseq_TUSC3.R1 159 224
• NCBIGene 36.3 7991
• Single exon skipping, size difference: 65
• Exclusion of the stop codon
• Reference transcript: NM_006765

• pfam OST3_OST6 308aa 1e-119 in ref transcript
  • OST3 / OST6 family. The proteins in this family are part of a complex of eight ER proteins that transfers core oligosaccharide from dolichol carrier to Asn-X-Ser/Thr motifs. This family includes both OST3 and OST6, each of which contains four predicted transmembrane helices. Disruption of OST3 and OST6 leads to a defect in the assembly of the complex. Hence, the function of these genes seems to be essential for recruiting a fully active complex necessary for efficient N-glycosylation.

TXNRD1

• refseq_TXNRD1.F2 refseq_TXNRD1.R2 279 389
• NCBIGene 36.3 7296
• Single exon skipping, size difference: 110
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_003330

• Changed! cd GRX_GRXh_1_2_like 47aa 5e-06 in ref transcript
  • Glutaredoxin (GRX) family, GRX human class 1 and 2 (h_1_2)-like subfamily; composed of proteins similar to human GRXs, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins such as ribonucleotide reductase. It contains a redox active CXXC motif in a TRX fold and uses a similar dithiol mechanism employed by TRXs for intramolecular disulfide bond reduction of protein substrates. Unlike TRX, GRX has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. The flow of reducing equivalents in the GRX system goes from NADPH -> GSH reductase -> GSH -> GRX -> protein substrates. By altering the redox state of target proteins, GRX is involved in many cellular functions including DNA synthesis, signal transduction and the defense against oxidative stress. Different classes are known including human GRX1 and GRX2, which are members of this subfamily. Also included in this subfamily are the N-terminal GRX domains of proteins similar to human thioredoxin reductase 1 and 3.
• Changed! TIGR TGR 487aa 0.0 in ref transcript
  • This homodimeric, FAD-containing member of the pyridine nucleotide disulfide oxidoreductase family contains a C-terminal motif Cys-SeCys-Gly, where SeCys is selenocysteine encoded by TGA (in some sequence reports interpreted as a stop codon). In some members of this subfamily, Cys-SeCys-Gly is replaced by Cys-Cys-Gly. The reach of the selenium atom at the C-term arm of the protein is proposed to allow broad substrate specificity.
• Changed! PTZ PTZ00052 487aa 1e-137 in ref transcript
  • thioredoxin reductase; Provisional.

TXNRD1

• refseq_TXNRD1.F3 refseq_TXNRD1.R3 156 393
• NCBIGene 36.3 7296
• Alternative 5-prime, size difference: 237
• Exclusion of the protein initiation site
• Reference transcript: NM_003330

• Changed! cd GRX_GRXh_1_2_like 47aa 5e-06 in ref transcript
  • Glutaredoxin (GRX) family, GRX human class 1 and 2 (h_1_2)-like subfamily; composed of proteins similar to human GRXs, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins such as ribonucleotide reductase. It contains a redox active CXXC motif in a TRX fold and uses a similar dithiol mechanism employed by TRXs for intramolecular disulfide bond reduction of protein substrates. Unlike TRX, GRX has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. The flow of reducing equivalents in the GRX system goes from NADPH -> GSH reductase -> GSH -> GRX -> protein substrates. By altering the redox state of target proteins, GRX is involved in many cellular functions including DNA synthesis, signal transduction and the defense against oxidative stress. Different classes are known including human GRX1 and GRX2, which are members of this subfamily. Also included in this subfamily are the N-terminal GRX domains of proteins similar to human thioredoxin reductase 1 and 3.
• TIGR TGR 487aa 0.0 in ref transcript
  • This homodimeric, FAD-containing member of the pyridine nucleotide disulfide oxidoreductase family contains a C-terminal motif Cys-SeCys-Gly, where SeCys is selenocysteine encoded by TGA (in some sequence reports interpreted as a stop codon). In some members of this subfamily, Cys-SeCys-Gly is replaced by Cys-Cys-Gly. The reach of the selenium atom at the C-term arm of the protein is proposed to allow broad substrate specificity.
• PTZ PTZ00052 487aa 1e-137 in ref transcript
  • thioredoxin reductase; Provisional.

TYSND1

• refseq_TYSND1.F1 refseq_TYSND1.R1 103 420
• NCBIGene 36.3 219743
• Multiple exon skipping, size difference: 317
• Exclusion in the protein causing a frameshift, Exclusion in the protein (no frameshift)
• Reference transcript: NM_173555

• Changed! TIGR protease_degS 165aa 4e-07 in ref transcript
  • This family consists of the periplasmic serine protease DegS (HhoB), a shorter paralog of protease DO (HtrA, DegP) and DegQ (HhoA). It is found in E. coli and several other Proteobacteria of the gamma subdivision. It contains a trypsin domain and a single copy of PDZ domain (in contrast to DegP with two copies). A critical role of this DegS is to sense stress in the periplasm and partially degrade an inhibitor of sigma(E).
• Changed! COG DegQ 173aa 2e-05 in ref transcript
  • Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones].

U2AF1

• refseq_U2AF1.F1 refseq_U2AF1.R1 100 167
• NCBIGene 36.3 7307
• Single exon skipping, size difference: 67
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_006758

• Changed! cd RRM 44aa 3e-04 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• Changed! smart RRM_1 44aa 6e-09 in ref transcript
  • RNA recognition motif.
• pfam zf-CCCH 27aa 0.010 in ref transcript
  • Zinc finger C-x8-C-x5-C-x3-H type (and similar).

U2AF1

• refseq_U2AF1.F4 refseq_U2AF1.R4 167 234
• NCBIGene 36.3 7307
• Single exon skipping, size difference: 67
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_001025203

• Changed! cd RRM 44aa 3e-04 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• Changed! smart RRM_1 44aa 7e-09 in ref transcript
  • RNA recognition motif.
• Changed! pfam zf-CCCH 27aa 0.006 in modified transcript
  • Zinc finger C-x8-C-x5-C-x3-H type (and similar).

U2AF1L4

• refseq_U2AF1L4.F1 refseq_U2AF1L4.R1 102 160
• NCBIGene 36.3 199746
• Alternative 5-prime, size difference: 58
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_144987

• cd RRM 63aa 1e-05 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• Changed! smart RRM_1 64aa 2e-11 in ref transcript
  • RNA recognition motif.
• Changed! pfam zf-CCCH 27aa 0.002 in ref transcript
  • Zinc finger C-x8-C-x5-C-x3-H type (and similar).
• Changed! smart RRM_1 66aa 2e-09 in modified transcript

UBA52

• refseq_UBA52.F1 refseq_UBA52.R1 112 134
• NCBIGene 36.3 7311
• Alternative 5-prime, size difference: 22
• Exclusion in 5'UTR
• Reference transcript: NM_001033930

• cd Ubiquitin 76aa 7e-37 in ref transcript
  • Ubiquitin (includes Ubq/RPL40e and Ubq/RPS27a fusions as well as homopolymeric multiubiquitin protein chains).
• pfam ubiquitin 69aa 2e-25 in ref transcript
  • Ubiquitin family. This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue), Nedd8, Elongin B, Rub1, and Parkin. A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites.
• pfam Ribosomal_L40e 52aa 2e-18 in ref transcript
  • Ribosomal L40e family. Bovine L40 has been identified as a secondary RNA binding protein. L40 is fused to a ubiquitin protein.
• PTZ PTZ00044 76aa 7e-20 in ref transcript
  • ubiquitin; Provisional.
• COG RPL40A 49aa 3e-07 in ref transcript
  • Ribosomal protein L40E [Translation, ribosomal structure and biogenesis].

UBASH3A

• refseq_UBASH3A.F1 refseq_UBASH3A.R1 192 306
• NCBIGene 36.3 53347
• Single exon skipping, size difference: 114
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_018961

• cd HP_PGM_like 213aa 2e-09 in ref transcript
  • Histidine phosphatase domain found in phosphoglycerate mutases and related proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction. Subgroup of the catalytic domain of a functionally diverse set of proteins, most of which are phosphatases. The conserved catalytic core of this domain contains a His residue which is phosphorylated in the reaction. This subgroup contains cofactor-dependent and cofactor-independent phosphoglycerate mutases (dPGM, and BPGM respectively), fructose-2,6-bisphosphatase (F26BP)ase, Sts-1, SixA, and related proteins. Functions include roles in metabolism, signaling, or regulation, for example, F26BPase affects glycolysis and gluconeogenesis through controlling the concentration of F26BP; BPGM controls the concentration of 2,3-BPG (the main allosteric effector of hemoglobin in human blood cells); human Sts-1 is a T-cell regulator; Escherichia coli Six A participates in the ArcB-dependent His-to-Asp phosphorelay signaling system. Deficiency and mutation in many of the human members result in disease, for example erythrocyte BPGM deficiency is a disease associated with a decrease in the concentration of 2,3-BPG.
• cd SH3 57aa 1e-06 in ref transcript
  • Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
• pfam PGAM 143aa 2e-14 in ref transcript
  • Phosphoglycerate mutase family. Y019_MYCTU and YK23_YEAST are not included in the Prosite entry. However these sequences are significantly similar and contain identical active site residues.
• smart SH3 57aa 8e-07 in ref transcript
  • Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.
• COG GpmB 189aa 4e-12 in ref transcript
  • Fructose-2,6-bisphosphatase [Carbohydrate transport and metabolism].
• COG UBP14 41aa 2e-05 in ref transcript
  • Isopeptidase T [Posttranslational modification, protein turnover, chaperones].

UBA3

• refseq_UBE1C.F1 refseq_UBE1C.R1 134 176
• NCBIGene 36.3 9039
• Single exon skipping, size difference: 42
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_003968

• cd Uba3_RUB 298aa 1e-157 in ref transcript
  • Ubiquitin activating enzyme (E1) subunit UBA3. UBA3 is part of the heterodimeric activating enzyme (E1), specific for the Rub family of ubiquitin-like proteins (Ubls). E1 enzymes are part of a conjugation cascade to attach Ub or Ubls, covalently to substrate proteins. consisting of activating (E1), conjugating (E2), and/or ligating (E3) enzymes. E1 activates ubiquitin(-like) by C-terminal adenylation, and subsequently forms a highly reactive thioester bond between its catalytic cysteine and Ubls C-terminus. E1 also associates with E2 and promotes ubiquitin transfer to the E2's catalytic cysteine. Post-translational modification by Rub family of ubiquitin-like proteins (Ublps) activates SCF ubiquitin ligases and is involved in cell cycle control, signaling and embryogenesis. UBA3 contains both the nucleotide-binding motif involved in adenylation and the catalytic cysteine involved in the thioester intermediate and Ublp transfer to E2.
• pfam ThiF 144aa 1e-38 in ref transcript
  • ThiF family. This family contains a repeated domain in ubiquitin activating enzyme E1 and members of the bacterial ThiF/MoeB/HesA family.
• pfam E2_bind 89aa 4e-25 in ref transcript
  • E2 binding domain. E1 and E2 enzymes play a central role in ubiquitin and ubiquitin-like protein transfer cascades. This is an E2 binding domain that is found on NEDD8 activating E1 enzyme. The domain resembles ubiquitin, and recruits the catalytic core of the E2 enzyme Ubc12 in a similar manner to that in which ubiquitin interacts with ubiquitin binding domains.
• pfam UBACT 66aa 4e-22 in ref transcript
  • Repeat in ubiquitin-activating (UBA) protein.
• COG ThiF 167aa 2e-34 in ref transcript
  • Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 2 [Coenzyme metabolism].

UBA5

• refseq_UBE1DC1.F1 refseq_UBE1DC1.R1 97 447
• NCBIGene 36.3 79876
• Alternative 5-prime, size difference: 350
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_024818

• Changed! cd ThiF_MoeB_HesA_family 246aa 2e-53 in ref transcript
  • ThiF_MoeB_HesA. Family of E1-like enzymes involved in molybdopterin and thiamine biosynthesis family. The common reaction mechanism catalyzed by MoeB and ThiF, like other E1 enzymes, begins with a nucleophilic attack of the C-terminal carboxylate of MoaD and ThiS, respectively, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of MoaD and ThiS. MoeB, as the MPT synthase (MoaE/MoaD complex) sulfurase, is involved in the biosynthesis of the molybdenum cofactor, a derivative of the tricyclic pterin, molybdopterin (MPT). ThiF catalyzes the adenylation of ThiS, as part of the biosynthesis pathway of thiamin pyrophosphate (vitamin B1).
• Changed! pfam ThiF 134aa 4e-23 in ref transcript
  • ThiF family. This family contains a repeated domain in ubiquitin activating enzyme E1 and members of the bacterial ThiF/MoeB/HesA family.
• Changed! COG ThiF 249aa 7e-20 in ref transcript
  • Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 2 [Coenzyme metabolism].

UBE2A

• refseq_UBE2A.F1 refseq_UBE2A.R1 102 192
• NCBIGene 36.3 7319
• Single exon skipping, size difference: 90
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_003336

• Changed! cd UBCc 135aa 6e-50 in ref transcript
  • Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin protein ligase enzymes, E3. This pathway regulates many fundamental cellular processes. There are also other E2s which form thiol-ester linkages without the use of E3s as well as several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) which lack the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways which were omitted from the scope of this CD.
• Changed! pfam UQ_con 138aa 3e-58 in ref transcript
  • Ubiquitin-conjugating enzyme. Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. TSG101 is one of several UBC homologues that lacks this active site cysteine.
• Changed! COG COG5078 151aa 4e-52 in ref transcript
  • Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones].
• Changed! cd UBCc 105aa 1e-30 in modified transcript
• Changed! pfam UQ_con 108aa 6e-37 in modified transcript
• Changed! COG COG5078 121aa 4e-33 in modified transcript

UBE2C

• refseq_UBE2C.F2 refseq_UBE2C.R2 210 264
• NCBIGene 36.3 11065
• Mutually exclusive exon skipping, size difference: 54
• Inclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_007019

• Changed! cd UBCc 138aa 6e-45 in ref transcript
  • Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin protein ligase enzymes, E3. This pathway regulates many fundamental cellular processes. There are also other E2s which form thiol-ester linkages without the use of E3s as well as several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) which lack the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways which were omitted from the scope of this CD.
• Changed! pfam UQ_con 137aa 5e-53 in ref transcript
  • Ubiquitin-conjugating enzyme. Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. TSG101 is one of several UBC homologues that lacks this active site cysteine.
• Changed! COG COG5078 140aa 3e-43 in ref transcript
  • Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones].
• Changed! cd UBCc 120aa 8e-13 in modified transcript
• Changed! pfam UQ_con 119aa 1e-12 in modified transcript
• Changed! COG COG5078 122aa 3e-07 in modified transcript

UBE2D2

• refseq_UBE2D2.F1 refseq_UBE2D2.R1 251 415
• NCBIGene 36.3 7322
• Single exon skipping, size difference: 164
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_003339

• Changed! cd UBCc 139aa 1e-50 in ref transcript
  • Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin protein ligase enzymes, E3. This pathway regulates many fundamental cellular processes. There are also other E2s which form thiol-ester linkages without the use of E3s as well as several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) which lack the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways which were omitted from the scope of this CD.
• Changed! pfam UQ_con 138aa 3e-57 in ref transcript
  • Ubiquitin-conjugating enzyme. Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. TSG101 is one of several UBC homologues that lacks this active site cysteine.
• Changed! COG COG5078 147aa 5e-56 in ref transcript
  • Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones].

UBE2D3

• refseq_UBE2D3.F2 refseq_UBE2D3.R2 102 254
• NCBIGene 36.3 7323
• Single exon skipping, size difference: 152
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_181893

• Changed! cd UBCc 137aa 2e-49 in ref transcript
  • Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin protein ligase enzymes, E3. This pathway regulates many fundamental cellular processes. There are also other E2s which form thiol-ester linkages without the use of E3s as well as several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) which lack the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways which were omitted from the scope of this CD.
• Changed! pfam UQ_con 137aa 4e-55 in ref transcript
  • Ubiquitin-conjugating enzyme. Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. TSG101 is one of several UBC homologues that lacks this active site cysteine.
• Changed! COG COG5078 147aa 2e-53 in ref transcript
  • Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones].

UBE2D3

• refseq_UBE2D3.F3 refseq_UBE2D3.R3 184 392
• NCBIGene 36.3 7323
• Alternative 3-prime, size difference: 208
• Inclusion in 5'UTR
• Reference transcript: NM_003340

• cd UBCc 139aa 4e-50 in ref transcript
  • Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin protein ligase enzymes, E3. This pathway regulates many fundamental cellular processes. There are also other E2s which form thiol-ester linkages without the use of E3s as well as several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) which lack the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways which were omitted from the scope of this CD.
• pfam UQ_con 138aa 4e-56 in ref transcript
  • Ubiquitin-conjugating enzyme. Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. TSG101 is one of several UBC homologues that lacks this active site cysteine.
• COG COG5078 147aa 7e-55 in ref transcript
  • Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones].

UBE2D3

• refseq_UBE2D3.F5 refseq_UBE2D3.R5 101 151
• NCBIGene 36.3 7323
• Single exon skipping, size difference: 50
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_181893

• Changed! cd UBCc 137aa 2e-49 in ref transcript
  • Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin protein ligase enzymes, E3. This pathway regulates many fundamental cellular processes. There are also other E2s which form thiol-ester linkages without the use of E3s as well as several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) which lack the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways which were omitted from the scope of this CD.
• Changed! pfam UQ_con 137aa 4e-55 in ref transcript
  • Ubiquitin-conjugating enzyme. Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. TSG101 is one of several UBC homologues that lacks this active site cysteine.
• Changed! COG COG5078 147aa 2e-53 in ref transcript
  • Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones].
• Changed! cd UBCc 137aa 8e-50 in modified transcript
• Changed! pfam UQ_con 137aa 1e-55 in modified transcript
• Changed! COG COG5078 147aa 3e-54 in modified transcript

UBE2D3

• refseq_UBE2D3.F7 refseq_UBE2D3.R3 187 395
• NCBIGene 36.3 7323
• Alternative 3-prime, size difference: 208
• Inclusion in 5'UTR
• Reference transcript: NM_181891

• cd UBCc 139aa 4e-50 in ref transcript
  • Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin protein ligase enzymes, E3. This pathway regulates many fundamental cellular processes. There are also other E2s which form thiol-ester linkages without the use of E3s as well as several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) which lack the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways which were omitted from the scope of this CD.
• pfam UQ_con 138aa 4e-56 in ref transcript
  • Ubiquitin-conjugating enzyme. Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. TSG101 is one of several UBC homologues that lacks this active site cysteine.
• COG COG5078 147aa 7e-55 in ref transcript
  • Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones].

UBE2E1

• refseq_UBE2E1.F1 refseq_UBE2E1.R1 196 247
• NCBIGene 36.3 7324
• Single exon skipping, size difference: 51
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_003341

• Changed! cd UBCc 139aa 2e-47 in ref transcript
  • Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin protein ligase enzymes, E3. This pathway regulates many fundamental cellular processes. There are also other E2s which form thiol-ester linkages without the use of E3s as well as several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) which lack the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways which were omitted from the scope of this CD.
• Changed! pfam UQ_con 138aa 4e-54 in ref transcript
  • Ubiquitin-conjugating enzyme. Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. TSG101 is one of several UBC homologues that lacks this active site cysteine.
• Changed! COG COG5078 147aa 1e-48 in ref transcript
  • Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones].
• Changed! cd UBCc 121aa 3e-41 in modified transcript
• Changed! pfam UQ_con 121aa 4e-48 in modified transcript
• Changed! COG COG5078 125aa 2e-42 in modified transcript

UBE2G1

• refseq_UBE2G1.F1 refseq_UBE2G1.R1 118 395
• NCBIGene 36.2 7326
• Multiple exon skipping, size difference: 277
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_003342

• Changed! cd UBCc 143aa 2e-41 in ref transcript
  • Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin protein ligase enzymes, E3. This pathway regulates many fundamental cellular processes. There are also other E2s which form thiol-ester linkages without the use of E3s as well as several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) which lack the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways which were omitted from the scope of this CD.
• Changed! pfam UQ_con 143aa 4e-48 in ref transcript
  • Ubiquitin-conjugating enzyme. Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. TSG101 is one of several UBC homologues that lacks this active site cysteine.
• Changed! COG COG5078 146aa 9e-45 in ref transcript
  • Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones].
• Changed! cd UBCc 30aa 0.002 in modified transcript
• Changed! smart UBCc 31aa 3e-05 in modified transcript
  • Ubiquitin-conjugating enzyme E2, catalytic domain homologues. Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. This pathway functions in regulating many fundamental processes required for cell viability.TSG101 is one of several UBC homologues that lacks this active site cysteine.
• Changed! COG COG5078 30aa 4e-05 in modified transcript

UBE2G2

• refseq_UBE2G2.F1 refseq_UBE2G2.R1 106 221
• NCBIGene 36.3 7327
• Single exon skipping, size difference: 115
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_003343

• Changed! cd UBCc 153aa 3e-43 in ref transcript
  • Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin protein ligase enzymes, E3. This pathway regulates many fundamental cellular processes. There are also other E2s which form thiol-ester linkages without the use of E3s as well as several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) which lack the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways which were omitted from the scope of this CD.
• Changed! pfam UQ_con 152aa 4e-50 in ref transcript
  • Ubiquitin-conjugating enzyme. Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. TSG101 is one of several UBC homologues that lacks this active site cysteine.
• Changed! COG COG5078 163aa 5e-48 in ref transcript
  • Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones].

UBE2H

• refseq_UBE2H.F2 refseq_UBE2H.R2 248 341
• NCBIGene 36.3 7328
• Multiple exon skipping, size difference: 93
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_003344

• Changed! cd UBCc 104aa 4e-30 in ref transcript
  • Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin protein ligase enzymes, E3. This pathway regulates many fundamental cellular processes. There are also other E2s which form thiol-ester linkages without the use of E3s as well as several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) which lack the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways which were omitted from the scope of this CD.
• Changed! pfam UQ_con 104aa 2e-34 in ref transcript
  • Ubiquitin-conjugating enzyme. Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. TSG101 is one of several UBC homologues that lacks this active site cysteine.
• Changed! COG COG5078 131aa 2e-29 in ref transcript
  • Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones].
• Changed! cd UBCc 73aa 6e-14 in modified transcript
• Changed! pfam UQ_con 73aa 8e-17 in modified transcript
• Changed! COG COG5078 100aa 7e-12 in modified transcript

UBE2I

• refseq_UBE2I.F1 refseq_UBE2I.R1 104 361
• NCBIGene 36.3 7329
• Single exon skipping, size difference: 257
• Exclusion in 5'UTR
• Reference transcript: NM_194259

• cd UBCc 146aa 5e-40 in ref transcript
  • Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin protein ligase enzymes, E3. This pathway regulates many fundamental cellular processes. There are also other E2s which form thiol-ester linkages without the use of E3s as well as several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) which lack the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways which were omitted from the scope of this CD.
• pfam UQ_con 145aa 1e-53 in ref transcript
  • Ubiquitin-conjugating enzyme. Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. TSG101 is one of several UBC homologues that lacks this active site cysteine.
• COG COG5078 156aa 4e-45 in ref transcript
  • Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones].

UBE2L3

• refseq_UBE2L3.F2 refseq_UBE2L3.R2 283 392
• NCBIGene 36.3 7332
• Single exon skipping, size difference: 109
• Exclusion in 5'UTR
• Reference transcript: NM_198157

UBE2V1

• refseq_UBE2V1.F1 refseq_UBE2V1.R1 147 296
• NCBIGene 36.3 7335
• Single exon skipping, size difference: 149
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_199144

• Changed! cd UBCc 117aa 1e-11 in ref transcript
  • Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin protein ligase enzymes, E3. This pathway regulates many fundamental cellular processes. There are also other E2s which form thiol-ester linkages without the use of E3s as well as several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) which lack the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways which were omitted from the scope of this CD.
• Changed! smart UBCc 128aa 3e-25 in ref transcript
  • Ubiquitin-conjugating enzyme E2, catalytic domain homologues. Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. This pathway functions in regulating many fundamental processes required for cell viability.TSG101 is one of several UBC homologues that lacks this active site cysteine.
• Changed! COG COG5078 131aa 4e-16 in ref transcript
  • Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones].

UBE2W

• refseq_UBE2W.F1 refseq_UBE2W.R1 198 301
• NCBIGene 36.2 55284
• Single exon skipping, size difference: 103
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_001001481

• Changed! cd UBCc 115aa 3e-25 in ref transcript
  • Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin protein ligase enzymes, E3. This pathway regulates many fundamental cellular processes. There are also other E2s which form thiol-ester linkages without the use of E3s as well as several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) which lack the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways which were omitted from the scope of this CD.
• Changed! pfam UQ_con 142aa 3e-30 in ref transcript
  • Ubiquitin-conjugating enzyme. Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. TSG101 is one of several UBC homologues that lacks this active site cysteine.
• Changed! COG COG5078 114aa 2e-25 in ref transcript
  • Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones].

UBE2W

• refseq_UBE2W.F2 refseq_UBE2W.R2 107 140
• NCBIGene 36.3 55284
• Single exon skipping, size difference: 33
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001001481

• Changed! cd UBCc 115aa 3e-25 in ref transcript
  • Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin protein ligase enzymes, E3. This pathway regulates many fundamental cellular processes. There are also other E2s which form thiol-ester linkages without the use of E3s as well as several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) which lack the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways which were omitted from the scope of this CD.
• pfam UQ_con 142aa 3e-30 in ref transcript
  • Ubiquitin-conjugating enzyme. Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. TSG101 is one of several UBC homologues that lacks this active site cysteine.
• Changed! COG COG5078 114aa 2e-25 in ref transcript
  • Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones].
• Changed! cd UBCc 114aa 3e-25 in modified transcript
• Changed! COG COG5078 114aa 2e-25 in modified transcript

UBE3B

• refseq_UBE3B.F1 refseq_UBE3B.R1 106 451
• NCBIGene 36.3 89910
• Alternative 5-prime, size difference: 345
• Exclusion in 5'UTR
• Reference transcript: NM_130466

• cd HECTc 385aa 1e-113 in ref transcript
  • HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ubiquitin molecules to the end of growing ubiquitin chains.
• pfam HECT 331aa 1e-94 in ref transcript
  • HECT-domain (ubiquitin-transferase). The name HECT comes from Homologous to the E6-AP Carboxyl Terminus.
• COG HUL4 399aa 2e-79 in ref transcript
  • Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones].

UBL7

• refseq_UBL7.F1 refseq_UBL7.R1 167 238
• NCBIGene 36.3 84993
• Alternative 5-prime, size difference: 71
• Exclusion in 5'UTR
• Reference transcript: NM_032907

• cd BMSC_UbP_N 75aa 1e-29 in ref transcript
  • BMSC_UbP (bone marrow stromal cell-derived ubiquitin-like protein) has an N-terminal ubiquitin-like (UBQ) domain and a C-terminal ubiquitin-associated (UBA) domain, a domain architecture similar to those of the UBIN, Chap1, and ubiquilin proteins. This CD represents the N-terminal ubiquitin-like domain.
• pfam ubiquitin 54aa 1e-07 in ref transcript
  • Ubiquitin family. This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue), Nedd8, Elongin B, Rub1, and Parkin. A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites.
• PTZ PTZ00044 34aa 0.001 in ref transcript
  • ubiquitin; Provisional.

UBOX5

• refseq_UBOX5.F2 refseq_UBOX5.R2 142 304
• NCBIGene 36.3 22888
• Single exon skipping, size difference: 162
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_014948

• cd RING 50aa 0.005 in ref transcript
  • RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H).
• pfam U-box 81aa 2e-23 in ref transcript
  • U-box domain. This domain is related to the Ring finger pfam00097 but lacks the zinc binding residues.
• COG UFD2 79aa 1e-05 in ref transcript
  • Ubiquitin fusion degradation protein 2 [Posttranslational modification, protein turnover, chaperones].

UBQLN1

• refseq_UBQLN1.F1 refseq_UBQLN1.R1 100 184
• NCBIGene 36.3 29979
• Single exon skipping, size difference: 84
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_013438

• cd hPLIC_N 58aa 4e-24 in ref transcript
  • hPLIC-1 and hPLIC-2 (human homologs of the yeast ubiquitin-like Dsk2 protein) are type2 UBL's (ubiquitin-like) proteins that are thought to serve as adaptors that link the ubiquitination machinery to the proteasome. The hPLIC's have an N-terminal UBL domain that binds the S5a subunit of the proteasome and a C-terminal UBA (ubiquitin-associated) domain that binds a ubiquitylated protein.
• cd UBA 38aa 6e-04 in ref transcript
  • Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
• pfam ubiquitin 59aa 3e-12 in ref transcript
  • Ubiquitin family. This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue), Nedd8, Elongin B, Rub1, and Parkin. A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites.
• smart UBA 37aa 4e-04 in ref transcript
  • Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.

UBXD5

• refseq_UBXD5.F2 refseq_UBXD5.R2 132 231
• NCBIGene 36.3 91544
• Single exon skipping, size difference: 99
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_183008

• pfam SEP 72aa 6e-19 in ref transcript
  • SEP domain. The SEP domain is named after Saccharomyces cerevisiae Shp1, Drosophila melanogaster eyes closed gene (eyc), and vertebrate p47. In p47, the SEP domain has been shown to bind to and inhibit the cysteine protease cathepsin L. Most SEP domains are succeeded closely by a UBX domain.
• PRK bchH 138aa 0.007 in ref transcript
  • magnesium chelatase subunit H; Provisional.

UBXD5

• refseq_UBXD5.F3 refseq_UBXD5.R3 121 246
• NCBIGene 36.3 91544
• Single exon skipping, size difference: 125
• Exclusion in 5'UTR
• Reference transcript: NM_183008

• pfam SEP 72aa 6e-19 in ref transcript
  • SEP domain. The SEP domain is named after Saccharomyces cerevisiae Shp1, Drosophila melanogaster eyes closed gene (eyc), and vertebrate p47. In p47, the SEP domain has been shown to bind to and inhibit the cysteine protease cathepsin L. Most SEP domains are succeeded closely by a UBX domain.
• PRK bchH 138aa 0.007 in ref transcript
  • magnesium chelatase subunit H; Provisional.

UCRC

• refseq_UCRC.F1 refseq_UCRC.R1 297 356
• NCBIGene 36.3 29796
• Alternative 5-prime, size difference: 59
• Exclusion in 5'UTR
• Reference transcript: NM_001003684

UFD1L

• refseq_UFD1L.F1 refseq_UFD1L.R1 175 208
• NCBIGene 36.3 7353
• Single exon skipping, size difference: 33
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_005659

• Changed! pfam UFD1 181aa 6e-88 in ref transcript
  • Ubiquitin fusion degradation protein UFD1. Post-translational ubiquitin-protein conjugates are recognised for degradation by the ubiquitin fusion degradation (UFD) pathway. Several proteins involved in this pathway have been identified. This family includes UFD1, a 40kD protein that is essential for vegetative cell viability. The human UFD1 gene is expressed at high levels during embryogenesis, especially in the eyes and in the inner ear primordia and is thought to be important in the determination of ectoderm-derived structures, including neural crest cells. In addition, this gene is deleted in the CATCH-22 (cardiac defects, abnormal facies, thymic hypoplasia, cleft palate and hypocalcaemia with deletions on chromosome 22) syndrome. This clinical syndrome is associated with a variety of developmental defects, all characterised by microdeletions on 22q11.2. Two such developmental defects are the DiGeorge syndrome OMIM:188400, and the velo-cardio- facial syndrome OMIM:145410. Several of the abnormalities associated with these conditions are thought to be due to defective neural crest cell differentiation.
• Changed! COG UFD1 285aa 1e-55 in ref transcript
  • Ubiquitin fusion-degradation protein [Posttranslational modification, protein turnover, chaperones].
• Changed! pfam UFD1 170aa 9e-79 in modified transcript
• Changed! COG UFD1 274aa 1e-48 in modified transcript

UGCGL1

• refseq_UGCGL1.F1 refseq_UGCGL1.R1 175 356
• NCBIGene 36.3 56886
• Alternative 5-prime, size difference: 181
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_020120

• Changed! cd GT8_HUGT1_C_like 248aa 1e-145 in ref transcript
  • The C-terminal domain of HUGT1-like is highly homologous to the GT 8 family. C-terminal domain of glycoprotein glucosyltransferase (UGT). UGT is a large glycoprotein whose C-terminus contains the catalytic activity. This catalytic C-terminal domain is highly homologous to Glycosyltransferase Family 8 (GT 8) and contains the DXD motif that coordinates donor sugar binding, characteristic for Family 8 glycosyltransferases. GT 8 proteins are retaining enzymes based on the relative anomeric stereochemistry of the substrate and product in the reaction catalyzed. The non-catalytic N-terminal portion of the human UTG1 (HUGT1) has been shown to monitor the protein folding status and activate its glucosyltransferase activity.
• Changed! pfam UDP-g_GGTase 209aa 3e-79 in ref transcript
  • UDP-glucose:Glycoprotein Glucosyltransferase. The N-terminal region of this group of proteins is required for correct folding of the ER UDP-Glc: glucosyltransferase.

UCHL5IP

• refseq_UIP1.F1 refseq_UIP1.R1 112 289
• NCBIGene 36.3 55559
• Single exon skipping, size difference: 177
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_207107

UIP1

• refseq_UIP1.F3 refseq_UIP1.R3 135 253
• NCBIGene 36.2 55559
• Alternative 3-prime, size difference: 118
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_207107

UNC45A

• refseq_UNC45A.F2 refseq_UNC45A.R2 158 203
• NCBIGene 36.3 55898
• Alternative 5-prime, size difference: 45
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_018671

• cd TPR 103aa 1e-12 in ref transcript
  • Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here.
• cd ARM 120aa 3e-05 in ref transcript
  • Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model.
• TIGR 3a0801s09 93aa 5e-10 in ref transcript
• COG NrfG 95aa 0.001 in ref transcript
  • FOG: TPR repeat [General function prediction only].

UNG2

• refseq_UNG2.F1 refseq_UNG2.R1 102 478
• NCBIGene 36.2 10309
• Alternative 5-prime, size difference: 376
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_021147

• Changed! cd CYCLIN 90aa 9e-11 in ref transcript
  • Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain.
• Changed! pfam Cyclin_N 125aa 5e-24 in ref transcript
  • Cyclin, N-terminal domain. Cyclins regulate cyclin dependent kinases (CDKs). One member is a Uracil-DNA glycosylase that is related to other cyclins. Cyclins contain two domains of similar all-alpha fold, of which this family corresponds with the N-terminal domain.
• Changed! COG COG5024 175aa 3e-20 in ref transcript
  • Cyclin [Cell division and chromosome partitioning].

UPF3A

• refseq_UPF3A.F1 refseq_UPF3A.R1 341 440
• NCBIGene 36.3 65110
• Single exon skipping, size difference: 99
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_023011

• Changed! pfam Smg4_UPF3 163aa 2e-48 in ref transcript
  • Smg-4/UPF3 family. This family contains proteins that are involved in nonsense mediated mRNA decay. A process that is triggered by premature stop codons in mRNA. The family includes Smg-4 and UPF3.
• Changed! pfam Smg4_UPF3 130aa 2e-35 in modified transcript

UPK3B

• refseq_UPK3B.F2 refseq_UPK3B.R2 185 265
• NCBIGene 36.3 80761
• Single exon skipping, size difference: 80
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_030570

USF1

• refseq_USF1.F2 refseq_USF1.R2 165 196
• NCBIGene 36.3 7391
• Alternative 5-prime, size difference: 31
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_007122

• Changed! cd HLH 63aa 2e-10 in ref transcript
  • Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins.
• Changed! pfam HLH 56aa 3e-12 in ref transcript
  • Helix-loop-helix DNA-binding domain.

USF2

• refseq_USF2.F1 refseq_USF2.R1 155 356
• NCBIGene 36.3 7392
• Single exon skipping, size difference: 201
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_003367

• cd HLH 63aa 7e-11 in ref transcript
  • Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins.
• pfam HLH 56aa 5e-12 in ref transcript
  • Helix-loop-helix DNA-binding domain.
• TIGR DNA_bind_RsfA 63aa 0.006 in ref transcript
  • In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.

USH1C

• refseq_USH1C.F1 refseq_USH1C.R1 114 223
• NCBIGene 36.3 10083
• Single exon skipping, size difference: 109
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_153676

• cd PDZ_signaling 81aa 7e-17 in ref transcript
  • PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of PDZ domains an N-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in proteases.
• cd PDZ_signaling 81aa 1e-14 in ref transcript
• cd PDZ_signaling 88aa 3e-08 in ref transcript
• smart PDZ 83aa 9e-16 in ref transcript
  • Domain present in PSD-95, Dlg, and ZO-1/2. Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities.
• smart PDZ 72aa 8e-14 in ref transcript
• TIGR degP_htrA_DO 194aa 2e-10 in ref transcript
  • This family consists of a set proteins various designated DegP, heat shock protein HtrA, and protease DO. The ortholog in Pseudomonas aeruginosa is designated MucD and is found in an operon that controls mucoid phenotype. This family also includes the DegQ (HhoA) paralog in E. coli which can rescue a DegP mutant, but not the smaller DegS paralog, which cannot. Members of this family are located in the periplasm and have separable functions as both protease and chaperone. Members have a trypsin domain and two copies of a PDZ domain. This protein protects bacteria from thermal and other stresses and may be important for the survival of bacterial pathogens.// The chaperone function is dominant at low temperatures, whereas the proteolytic activity is turned on at elevated temperatures.
• smart PDZ 87aa 6e-09 in ref transcript
• PRK PRK10942 172aa 2e-05 in ref transcript
  • serine endoprotease; Provisional.

USP1

• refseq_USP1.F1 refseq_USP1.R1 170 265
• NCBIGene 36.3 7398
• Alternative 5-prime, size difference: 95
• Exclusion in 5'UTR
• Reference transcript: NM_001017415

• cd Peptidase_C19O 176aa 2e-84 in ref transcript
  • A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
• cd Peptidase_C19O 208aa 5e-46 in ref transcript
• cd Peptidase_C19O 38aa 0.001 in ref transcript
• pfam UCH 196aa 1e-26 in ref transcript
  • Ubiquitin carboxyl-terminal hydrolase.
• pfam UCH 157aa 7e-18 in ref transcript
• COG UBP5 177aa 7e-11 in ref transcript
  • Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones].
• COG UBP5 150aa 1e-07 in ref transcript

USP14

• refseq_USP14.F1 refseq_USP14.R1 129 234
• NCBIGene 36.3 9097
• Single exon skipping, size difference: 105
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_005151

• cd Peptidase_C19A 376aa 1e-113 in ref transcript
  • A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
• Changed! cd UBP_N 70aa 8e-05 in ref transcript
  • The UBP (ubiquitin processing protease) domain (also referred to as USP which stands for "ubiquitin-specific protease") is present at in a large family of cysteine proteases that specifically cleave ubiquitin conjugates. This family includes Rpn11, UBP6 (USP14), USP7 (HAUSP). This domain is closely related to the amino-terminal ubiquitin-like domain of BAG1 (Bcl2-associated anthanogene1) protein and is found only in eukaryotes.
• pfam UCH 379aa 4e-59 in ref transcript
  • Ubiquitin carboxyl-terminal hydrolase.
• Changed! smart UBQ 63aa 3e-06 in ref transcript
  • Ubiquitin homologues. Ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression.
• Changed! COG UBP12 130aa 4e-07 in ref transcript
  • Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones].
• COG COG5077 117aa 3e-06 in ref transcript
  • Ubiquitin carboxyl-terminal hydrolase [Posttranslational modification, protein turnover, chaperones].
• Changed! cd UBP_N 64aa 0.009 in modified transcript
• Changed! smart UBQ 53aa 1e-05 in modified transcript
• Changed! COG UBP12 114aa 4e-07 in modified transcript

USP16

• refseq_USP16.F2 refseq_USP16.R2 181 244
• NCBIGene 36.3 10600
• Single exon skipping, size difference: 63
• Exclusion in 5'UTR
• Reference transcript: NM_001032410

• cd Peptidase_C19K 198aa 7e-64 in ref transcript
  • A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
• cd Peptidase_C19K 206aa 1e-37 in ref transcript
• pfam UCH 196aa 7e-32 in ref transcript
  • Ubiquitin carboxyl-terminal hydrolase.
• pfam UCH 200aa 7e-27 in ref transcript
• pfam zf-UBP 82aa 7e-08 in ref transcript
  • Zn-finger in ubiquitin-hydrolases and other protein.
• COG UBP12 204aa 3e-17 in ref transcript
  • Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones].
• COG UBP12 203aa 1e-16 in ref transcript

USP20

• refseq_USP20.F1 refseq_USP20.R1 122 220
• NCBIGene 36.3 10868
• Alternative 5-prime, size difference: 98
• Exclusion in 5'UTR
• Reference transcript: NM_001008563

• cd Peptidase_C19R 241aa 7e-49 in ref transcript
  • A subfamily of peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
• cd Peptidase_C19D 103aa 3e-12 in ref transcript
  • A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
• cd Peptidase_C19M 209aa 6e-09 in ref transcript
  • A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
• pfam UCH 240aa 4e-47 in ref transcript
  • Ubiquitin carboxyl-terminal hydrolase.
• pfam UCH 106aa 2e-25 in ref transcript
• smart DUSP 84aa 2e-25 in ref transcript
  • Domain in ubiquitin-specific proteases.
• smart DUSP 82aa 2e-19 in ref transcript
• pfam zf-UBP 64aa 8e-07 in ref transcript
  • Zn-finger in ubiquitin-hydrolases and other protein.
• COG UBP12 164aa 4e-29 in ref transcript
  • Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones].
• COG UBP12 108aa 2e-17 in ref transcript
• COG UBP14 238aa 4e-13 in ref transcript
  • Isopeptidase T [Posttranslational modification, protein turnover, chaperones].
• COG UBP12 62aa 8e-05 in ref transcript

USP21

• refseq_USP21.F1 refseq_USP21.R1 250 391
• NCBIGene 36.3 27005
• Single exon skipping, size difference: 141
• Exclusion in 5'UTR
• Reference transcript: NM_001014443

• cd Peptidase_C19R 259aa 1e-60 in ref transcript
  • A subfamily of peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
• cd Peptidase_C19R 22aa 5e-06 in ref transcript
• cd Peptidase_C19F 52aa 4e-04 in ref transcript
  • A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
• pfam UCH 344aa 1e-80 in ref transcript
  • Ubiquitin carboxyl-terminal hydrolase.
• COG UBP5 346aa 2e-50 in ref transcript
  • Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones].

USP33

• refseq_USP33.F1 refseq_USP33.R1 278 457
• NCBIGene 36.3 23032
• Single exon skipping, size difference: 179
• Exclusion of the protein initiation site
• Reference transcript: NM_015017

• cd Peptidase_C19R 241aa 7e-50 in ref transcript
  • A subfamily of peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
• cd Peptidase_C19E 100aa 7e-13 in ref transcript
  • A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
• cd Peptidase_C19M 215aa 5e-11 in ref transcript
  • A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
• pfam UCH 259aa 4e-49 in ref transcript
  • Ubiquitin carboxyl-terminal hydrolase.
• smart DUSP 83aa 1e-24 in ref transcript
  • Domain in ubiquitin-specific proteases.
• pfam UCH 102aa 2e-23 in ref transcript
• smart DUSP 70aa 1e-12 in ref transcript
• pfam zf-UBP 73aa 1e-07 in ref transcript
  • Zn-finger in ubiquitin-hydrolases and other protein.
• COG UBP12 155aa 1e-30 in ref transcript
  • Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones].
• COG UBP12 102aa 1e-14 in ref transcript
• COG UBP14 245aa 8e-14 in ref transcript
  • Isopeptidase T [Posttranslational modification, protein turnover, chaperones].
• COG UBP12 63aa 6e-05 in ref transcript

USP33

• refseq_USP33.F3 refseq_USP33.R3 136 160
• NCBIGene 36.3 23032
• Alternative 3-prime, size difference: 24
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_015017

• Changed! cd Peptidase_C19R 241aa 7e-50 in ref transcript
  • A subfamily of peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
• cd Peptidase_C19E 100aa 7e-13 in ref transcript
  • A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
• cd Peptidase_C19M 215aa 5e-11 in ref transcript
  • A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
• Changed! pfam UCH 259aa 4e-49 in ref transcript
  • Ubiquitin carboxyl-terminal hydrolase.
• smart DUSP 83aa 1e-24 in ref transcript
  • Domain in ubiquitin-specific proteases.
• pfam UCH 102aa 2e-23 in ref transcript
• smart DUSP 70aa 1e-12 in ref transcript
• pfam zf-UBP 73aa 1e-07 in ref transcript
  • Zn-finger in ubiquitin-hydrolases and other protein.
• COG UBP12 155aa 1e-30 in ref transcript
  • Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones].
• COG UBP12 102aa 1e-14 in ref transcript
• COG UBP14 245aa 8e-14 in ref transcript
  • Isopeptidase T [Posttranslational modification, protein turnover, chaperones].
• COG UBP12 63aa 6e-05 in ref transcript
• Changed! cd Peptidase_C19R 233aa 7e-51 in modified transcript
• Changed! pfam UCH 251aa 5e-50 in modified transcript
• Changed! COG UBP14 180aa 0.002 in modified transcript

USP4

• refseq_USP4.F1 refseq_USP4.R1 226 367
• NCBIGene 36.3 7375
• Single exon skipping, size difference: 141
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_003363

• cd Peptidase_C19R 146aa 1e-47 in ref transcript
  • A subfamily of peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
• cd Peptidase_C19E 170aa 1e-17 in ref transcript
  • A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
• pfam DUF1055 135aa 2e-57 in ref transcript
  • Domain of Unknown Function (DUF1055). This region is found in Ubiquitin-specific proteases.
• pfam UCH 150aa 4e-49 in ref transcript
  • Ubiquitin carboxyl-terminal hydrolase.
• pfam UCH 181aa 1e-43 in ref transcript
• smart DUSP 97aa 1e-25 in ref transcript
  • Domain in ubiquitin-specific proteases.
• Changed! COG UBP12 274aa 3e-65 in ref transcript
  • Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones].
• COG UBP12 149aa 1e-47 in ref transcript
• Changed! COG UBP12 150aa 0.009 in ref transcript
• Changed! COG UBP12 502aa 3e-71 in modified transcript

USP45

• refseq_USP45.F1 refseq_USP45.R1 209 383
• NCBIGene 36.2 85015
• Multiple exon skipping, size difference: 174
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: XM_931094

• cd Peptidase_C19K 209aa 1e-54 in ref transcript
  • A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
• Changed! cd Peptidase_C19K 197aa 1e-29 in ref transcript
• pfam UCH 195aa 1e-27 in ref transcript
  • Ubiquitin carboxyl-terminal hydrolase.
• Changed! pfam UCH 197aa 3e-20 in ref transcript
• pfam zf-UBP 56aa 6e-07 in ref transcript
  • Zn-finger in ubiquitin-hydrolases and other protein.
• Changed! COG UBP14 244aa 1e-15 in ref transcript
  • Isopeptidase T [Posttranslational modification, protein turnover, chaperones].
• COG UBP12 241aa 2e-13 in ref transcript
  • Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones].
• Changed! cd Peptidase_C19K 139aa 5e-21 in modified transcript
• Changed! pfam UCH 168aa 5e-14 in modified transcript
• Changed! COG UBP14 255aa 4e-16 in modified transcript

USP9X

• refseq_USP9X.F1 refseq_USP9X.R1 123 171
• NCBIGene 36.3 8239
• Alternative 5-prime, size difference: 48
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001039590

• cd peptidase_C19C 404aa 1e-119 in ref transcript
  • A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
• pfam UCH 399aa 1e-70 in ref transcript
  • Ubiquitin carboxyl-terminal hydrolase.
• COG COG5077 447aa 6e-45 in ref transcript
  • Ubiquitin carboxyl-terminal hydrolase [Posttranslational modification, protein turnover, chaperones].

VAPA

• refseq_VAPA.F1 refseq_VAPA.R1 151 286
• NCBIGene 36.3 9218
• Single exon skipping, size difference: 135
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_003574

• pfam Motile_Sperm 104aa 4e-29 in ref transcript
  • MSP (Major sperm protein) domain. Major sperm proteins are involved in sperm motility. These proteins oligomerise to form filaments. This family contains many other proteins.
• COG SCS2 110aa 9e-20 in ref transcript
  • VAMP-associated protein involved in inositol metabolism [Intracellular trafficking and secretion].

VCL

• refseq_VCL.F2 refseq_VCL.R2 196 400
• NCBIGene 36.3 7414
• Single exon skipping, size difference: 204
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_014000

• pfam Vinculin 358aa 1e-122 in ref transcript
  • Vinculin family.
• Changed! pfam Vinculin 541aa 2e-95 in ref transcript
• Changed! pfam Vinculin 241aa 4e-76 in ref transcript
• Changed! pfam Vinculin 692aa 1e-168 in modified transcript

VKORC1

• refseq_VKORC1.F1 refseq_VKORC1.R1 259 369
• NCBIGene 36.3 79001
• Single exon skipping, size difference: 110
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_024006

• Changed! smart VKc 149aa 3e-20 in ref transcript
  • Family of likely enzymes that includes the catalytic subunit of vitamin K epoxide reductase. Bacterial homologues are fused to members of the thioredoxin family of oxidoreductases.
• Changed! smart VKc 54aa 2e-06 in modified transcript

VLDLR

• refseq_VLDLR.F1 refseq_VLDLR.R1 152 236
• NCBIGene 36.3 7436
• Single exon skipping, size difference: 84
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_003383

• cd LDLa 35aa 7e-08 in ref transcript
  • Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure.
• cd LDLa 35aa 9e-08 in ref transcript
• cd LDLa 35aa 1e-07 in ref transcript
• cd LDLa 32aa 1e-06 in ref transcript
• cd LDLa 35aa 3e-06 in ref transcript
• cd LDLa 37aa 4e-04 in ref transcript
• cd LDLa 31aa 0.001 in ref transcript
• cd EGF_CA 31aa 0.008 in ref transcript
  • Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements.
• pfam Ldl_recept_b 41aa 6e-12 in ref transcript
  • Low-density lipoprotein receptor repeat class B. This domain is also known as the YWTD motif after the most conserved region of the repeat. The YWTD repeat is found in multiple tandem repeats and has been predicted to form a beta-propeller structure.
• pfam Ldl_recept_a 37aa 5e-10 in ref transcript
  • Low-density lipoprotein receptor domain class A.
• pfam Ldl_recept_a 36aa 1e-09 in ref transcript
• pfam Ldl_recept_a 36aa 5e-09 in ref transcript
• smart LY 43aa 5e-09 in ref transcript
  • Low-density lipoprotein-receptor YWTD domain. Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
• pfam Ldl_recept_a 37aa 1e-08 in ref transcript
• pfam Ldl_recept_a 34aa 6e-08 in ref transcript
• smart LY 43aa 5e-07 in ref transcript
• pfam Ldl_recept_a 39aa 2e-06 in ref transcript
• pfam Ldl_recept_a 31aa 7e-06 in ref transcript
• pfam Ldl_recept_b 40aa 6e-05 in ref transcript
• pfam Ldl_recept_b 41aa 9e-05 in ref transcript
• smart EGF_CA 31aa 2e-04 in ref transcript
  • Calcium-binding EGF-like domain.

VNN3

• refseq_VNN3.F2 refseq_VNN3.R2 195 241
• NCBIGene 36.3 55350
• Alternative 3-prime, size difference: 46
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_018399

• Changed! pfam CN_hydrolase 161aa 7e-17 in ref transcript
  • Carbon-nitrogen hydrolase. This family contains hydrolases that break carbon-nitrogen bonds. The family includes: Nitrilase EC:3.5.5.1, Aliphatic amidase EC:3.5.1.4, Biotidinase EC:3.5.1.12, Beta-ureidopropionase EC:3.5.1.6. Nitrilase-related proteins generally have a conserved E-K-C catalytic triad, and are multimeric alpha-beta-beta-alpha sandwich proteins.
• Changed! COG COG0388 160aa 3e-12 in ref transcript
  • Predicted amidohydrolase [General function prediction only].
• Changed! TIGR agmatine_aguB 27aa 0.008 in modified transcript
  • Members of this family are N-carbamoylputrescine amidase (3.5.1.53). Bacterial genes are designated AguB. The AguAB pathway replaces SpeB for conversion of agmatine to putrescine in two steps rather than one.

VPS13A

• refseq_VPS13A.F1 refseq_VPS13A.R1 115 232
• NCBIGene 36.3 23230
• Single exon skipping, size difference: 117
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_033305

• pfam DUF1162 279aa 2e-82 in ref transcript
  • Protein of unknown function (DUF1162). This family represents a conserved region within several hypothetical eukaryotic proteins. Family members might be vacuolar protein sorting related-proteins.
• Changed! COG MRS6 2101aa 2e-80 in ref transcript
  • Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion].
• COG MRS6 422aa 7e-33 in ref transcript
• Changed! COG MRS6 2062aa 1e-78 in modified transcript

VPS13C

• refseq_VPS13C.F1 refseq_VPS13C.R1 271 400
• NCBIGene 36.3 54832
• Multiple exon skipping, size difference: 129
• Exclusion in the protein (no frameshift), Exclusion in the protein (no frameshift)
• Reference transcript: NM_020821

• pfam DUF1162 284aa 1e-88 in ref transcript
  • Protein of unknown function (DUF1162). This family represents a conserved region within several hypothetical eukaryotic proteins. Family members might be vacuolar protein sorting related-proteins.
• Changed! COG MRS6 1049aa 1e-82 in ref transcript
  • Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion].
• COG MRS6 479aa 1e-32 in ref transcript
• COG MRS6 888aa 7e-09 in ref transcript
• Changed! COG MRS6 1006aa 1e-84 in modified transcript

VPS13D

• refseq_VPS13D.F1 refseq_VPS13D.R1 121 196
• NCBIGene 36.3 55187
• Single exon skipping, size difference: 75
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_015378

• cd UBA 36aa 0.001 in ref transcript
  • Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
• pfam DUF1162 284aa 6e-52 in ref transcript
  • Protein of unknown function (DUF1162). This family represents a conserved region within several hypothetical eukaryotic proteins. Family members might be vacuolar protein sorting related-proteins.
• pfam UBA 37aa 2e-04 in ref transcript
  • UBA/TS-N domain. This small domain is composed of three alpha helices. This family includes the previously defined UBA and TS-N domains. The UBA-domain (ubiquitin associated domain) is a novel sequence motif found in several proteins having connections to ubiquitin and the ubiquitination pathway. The structure of the UBA domain consists of a compact three helix bundle. This domain is found at the N terminus of EF-TS hence the name TS-N. The structure of EF-TS is known and this domain is implicated in its interaction with EF-TU. The domain has been found in non EF-TS proteins such as alpha-NAC and MJ0280.
• COG MRS6 1269aa 1e-53 in ref transcript
  • Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion].
• COG MRS6 463aa 3e-35 in ref transcript
• COG MRS6 167aa 0.004 in ref transcript

VPS24

• refseq_VPS24.F2 refseq_VPS24.R2 307 368
• NCBIGene 36.3 51652
• Single exon skipping, size difference: 61
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_016079

• Changed! pfam Snf7 171aa 9e-29 in ref transcript
  • Snf7. This family of proteins are involved in protein sorting and transport from the endosome to the vacuole/lysosome in eukaryotic cells. Vacuoles/lysosomes play an important role in the degradation of both lipids and cellular proteins. In order to perform this degradative function, vacuoles/lysosomes contain numerous hydrolases which have been transported in the form of inactive precursors via the biosynthetic pathway and are proteolytically activated upon delivery to the vacuole/lysosome. The delivery of transmembrane proteins, such as activated cell surface receptors to the lumen of the vacuole/lysosome, either for degradation/downregulation, or in the case of hydrolases, for proper localisation, requires the formation of multivesicular bodies (MVBs). These late endosomal structures are formed by invaginating and budding of the limiting membrane into the lumen of the compartment. During this process, a subset of the endosomal membrane proteins is sorted into the forming vesicles. Mature MVBs fuse with the vacuole/lysosome, thereby releasing cargo containing vesicles into its hydrolytic lumen for degradation. Endosomal proteins that are not sorted into the intralumenal MVB vesicles are either recycled back to the plasma membrane or Golgi complex, or remain in the limiting membrane of the MVB and are thereby transported to the limiting membrane of the vacuole/lysosome as a consequence of fusion. Therefore, the MVB sorting pathway plays a critical role in the decision between recycling and degradation of membrane proteins. A few archaeal sequences are also present within this family.
• Changed! COG VPS24 124aa 0.001 in ref transcript
  • Conserved protein implicated in secretion [Cell motility and secretion].

VPS41

• refseq_VPS41.F2 refseq_VPS41.R2 231 306
• NCBIGene 36.3 27072
• Single exon skipping, size difference: 75
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_014396

• smart CLH 138aa 4e-25 in ref transcript
  • Clathrin heavy chain repeat homology.

VPS54

• refseq_VPS54.F1 refseq_VPS54.R1 110 146
• NCBIGene 36.3 51542
• Alternative 3-prime, size difference: 36
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_016516

• pfam Vps54 135aa 2e-49 in ref transcript
  • Vps54-like protein. This family contains various proteins that are homologs of the yeast Vps54 protein, such as the rat homolog, the human homolog, and the mouse homolog. In yeast, Vps54 associates with Vps52 and Vps53 proteins to form a trimolecular complex that is involved in protein transport between Golgi, endosomal, and vacuolar compartments. All Vps54 homologs contain a coiled coil region (not found in the region featured in this family) and multiple dileucine motifs.

VRK3

• refseq_VRK3.F2 refseq_VRK3.R2 250 400
• NCBIGene 36.3 51231
• Single exon skipping, size difference: 150
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_016440

• cd S_TKc 205aa 8e-12 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• pfam Pkinase 187aa 2e-09 in ref transcript
  • Protein kinase domain.
• COG SPS1 207aa 9e-07 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].

VWA1

• refseq_VWA1.F2 refseq_VWA1.R2 100 495
• NCBIGene 36.3 64856
• Alternative 3-prime, size difference: 395
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_022834

• Changed! cd vWA_collagen 141aa 3e-29 in ref transcript
  • von Willebrand factor (vWF) type A domain; equivalent to the I-domain of integrins. This domain has a variety of functions including: intermolecular adhesion, cell migration, signalling, transcription, and DNA repair. In integrins these domains form heterodimers while in vWF it forms homodimers and multimers. There are different interaction surfaces of this domain as seen by its complexes with collagen with either integrin or human vWFA. In integrins collagen binding occurs via the metal ion-dependent adhesion site (MIDAS) and involves three surface loops located on the upper surface of the molecule. In human vWFA, collagen binding is thought to occur on the bottom of the molecule and does not involve the vestigial MIDAS motif.
• Changed! cd FN3 74aa 4e-06 in ref transcript
  • Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.
• Changed! pfam VWA 141aa 6e-28 in ref transcript
  • von Willebrand factor type A domain.
• Changed! pfam fn3 69aa 2e-07 in ref transcript
  • Fibronectin type III domain.
• Changed! pfam fn3 67aa 5e-05 in ref transcript

WAC

• refseq_WAC.F1 refseq_WAC.R1 103 412
• NCBIGene 36.3 51322
• Single exon skipping, size difference: 309
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_016628

• cd WW 30aa 3e-05 in ref transcript
  • Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
• smart WW 28aa 7e-05 in ref transcript
  • Domain with 2 conserved Trp (W) residues. Also known as the WWP or rsp5 domain. Binds proline-rich polypeptides.
• COG PRP40 40aa 0.007 in ref transcript
  • Splicing factor [RNA processing and modification].
• PRK PRK10856 86aa 0.008 in ref transcript
  • hypothetical protein; Provisional.

WARS

• refseq_WARS.F1 refseq_WARS.R1 145 317
• NCBIGene 36.3 7453
• Single exon skipping, size difference: 172
• Exclusion of the protein initiation site
• Reference transcript: NM_173701

• cd TrpRS_core 284aa 3e-74 in ref transcript
  • Tryptophanyl-tRNA synthetase (TrpRS) catalytic core domain. TrpRS is a homodimer, which attaches Tyr to the appropriate tRNA. TrpRS is a class I tRNA synthetases, so it aminoacylates the 2'-OH of the nucleotide at the 3' end of the tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains class I characteristic HIGH and KMSKS motifs, which are involved in ATP binding.
• Changed! cd WEPRS_RNA 50aa 1e-14 in ref transcript
  • WEPRS_RNA binding domain. This short RNA-binding domain is found in several higher eukaryote aminoacyl-tRNA synthetases (aaRSs). It is found in multiple copies in eukaryotic bifunctional glutamyl-prolyl-tRNA synthetases (EPRS) in a region that separates the N-terminal glutamyl-tRNA synthetase (GluRS) from the C-terminal prolyl-tRNA synthetase (ProRS). It is also found at the N-terminus of vertebrate tryptophanyl-tRNA synthetases (TrpRS). This domain consists of a helix-turn-helix structure, which is similar to other RNA-binding proteins. It is involved in both protein-RNA interactions by binding tRNA and protein-protein interactions, which are important for the formation of aaRSs into multienzyme complexes.
• TIGR trpS 318aa 1e-105 in ref transcript
  • This model represents tryptophanyl-tRNA synthetase. Some members of the family have a pfam00458 domain amino-terminal to the region described by this HMM.
• Changed! pfam WHEP-TRS 54aa 3e-17 in ref transcript
  • WHEP-TRS domain.
• PRK PRK12285 386aa 1e-110 in ref transcript
  • tryptophanyl-tRNA synthetase; Reviewed.

WARS

• refseq_WARS.F3 refseq_WARS.R3 235 407
• NCBIGene 36.3 7453
• Single exon skipping, size difference: 172
• Exclusion of the protein initiation site
• Reference transcript: NM_004184

• cd TrpRS_core 284aa 3e-74 in ref transcript
  • Tryptophanyl-tRNA synthetase (TrpRS) catalytic core domain. TrpRS is a homodimer, which attaches Tyr to the appropriate tRNA. TrpRS is a class I tRNA synthetases, so it aminoacylates the 2'-OH of the nucleotide at the 3' end of the tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains class I characteristic HIGH and KMSKS motifs, which are involved in ATP binding.
• Changed! cd WEPRS_RNA 50aa 1e-14 in ref transcript
  • WEPRS_RNA binding domain. This short RNA-binding domain is found in several higher eukaryote aminoacyl-tRNA synthetases (aaRSs). It is found in multiple copies in eukaryotic bifunctional glutamyl-prolyl-tRNA synthetases (EPRS) in a region that separates the N-terminal glutamyl-tRNA synthetase (GluRS) from the C-terminal prolyl-tRNA synthetase (ProRS). It is also found at the N-terminus of vertebrate tryptophanyl-tRNA synthetases (TrpRS). This domain consists of a helix-turn-helix structure, which is similar to other RNA-binding proteins. It is involved in both protein-RNA interactions by binding tRNA and protein-protein interactions, which are important for the formation of aaRSs into multienzyme complexes.
• TIGR trpS 318aa 1e-105 in ref transcript
  • This model represents tryptophanyl-tRNA synthetase. Some members of the family have a pfam00458 domain amino-terminal to the region described by this HMM.
• Changed! pfam WHEP-TRS 54aa 3e-17 in ref transcript
  • WHEP-TRS domain.
• PRK PRK12285 386aa 1e-110 in ref transcript
  • tryptophanyl-tRNA synthetase; Reviewed.

WARS2

• refseq_WARS2.F2 refseq_WARS2.R2 132 161
• NCBIGene 36.3 10352
• Alternative 3-prime, size difference: 29
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_015836

• Changed! cd TrpRS_core 278aa 3e-95 in ref transcript
  • Tryptophanyl-tRNA synthetase (TrpRS) catalytic core domain. TrpRS is a homodimer, which attaches Tyr to the appropriate tRNA. TrpRS is a class I tRNA synthetases, so it aminoacylates the 2'-OH of the nucleotide at the 3' end of the tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains class I characteristic HIGH and KMSKS motifs, which are involved in ATP binding.
• Changed! TIGR trpS 327aa 7e-76 in ref transcript
  • This model represents tryptophanyl-tRNA synthetase. Some members of the family have a pfam00458 domain amino-terminal to the region described by this HMM.
• Changed! PRK PRK00927 325aa 1e-123 in ref transcript
  • tryptophanyl-tRNA synthetase; Reviewed.
• Changed! cd TrpRS_core 178aa 1e-70 in modified transcript
• Changed! TIGR trpS 180aa 3e-60 in modified transcript
• Changed! PRK PRK00927 178aa 6e-89 in modified transcript

WASF1

• refseq_WASF1.F2 refseq_WASF1.R2 128 226
• NCBIGene 36.3 8936
• Single exon skipping, size difference: 98
• Exclusion in 5'UTR
• Reference transcript: NM_003931

WASF1

• refseq_WASF1.F4 refseq_WASF1.R4 129 274
• NCBIGene 36.3 8936
• Single exon skipping, size difference: 145
• Exclusion in 5'UTR
• Reference transcript: NM_003931

WBP5

• refseq_WBP5.F1 refseq_WBP5.R1 250 329
• NCBIGene 36.3 51186
• Single exon skipping, size difference: 79
• Exclusion in 5'UTR
• Reference transcript: NM_001006612

• pfam TFA 63aa 6e-18 in ref transcript
  • Transcription elongation factor A, SII-related family. The function of this family is unclear, but two members from Homo sapiesn are described as transcription elongation factor A, SII-like proteins.

EIF4H

• refseq_WBSCR1.F1 refseq_WBSCR1.R1 144 204
• NCBIGene 36.3 7458
• Single exon skipping, size difference: 60
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_022170

• cd RRM 70aa 2e-10 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• smart RRM 69aa 6e-11 in ref transcript
  • RNA recognition motif.
• Changed! COG COG0724 87aa 3e-07 in ref transcript
  • RNA-binding proteins (RRM domain) [General function prediction only].
• Changed! COG COG0724 81aa 1e-06 in modified transcript

WDHD1

• refseq_WDHD1.F1 refseq_WDHD1.R1 143 236
• NCBIGene 36.3 11169
• Single exon skipping, size difference: 93
• Exclusion of the protein initiation site
• Reference transcript: NM_007086

• Changed! cd WD40 248aa 5e-27 in ref transcript
  • WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.
• cd HMG-box 56aa 2e-06 in ref transcript
  • High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4; and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions.
• smart HMG 58aa 8e-08 in ref transcript
  • high mobility group.
• pfam WD40 38aa 3e-06 in ref transcript
  • WD domain, G-beta repeat.
• Changed! smart WD40 31aa 0.001 in ref transcript
  • WD40 repeats. Note that these repeats are permuted with respect to the structural repeats (blades) of the beta propeller domain.
• Changed! COG COG2319 289aa 5e-17 in ref transcript
  • FOG: WD40 repeat [General function prediction only].
• COG NHP6B 96aa 0.003 in ref transcript
  • Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics].
• Changed! cd WD40 161aa 3e-18 in modified transcript
• Changed! COG COG2319 175aa 4e-08 in modified transcript

WDR16

• refseq_WDR16.F1 refseq_WDR16.R1 167 357
• NCBIGene 36.2 146845
• Single exon skipping, size difference: 190
• Exclusion of the protein initiation site
• Reference transcript: NM_145054

• cd WD40 285aa 6e-34 in ref transcript
  • WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.
• cd WD40 343aa 2e-16 in ref transcript
• smart WD40 40aa 0.004 in ref transcript
  • WD40 repeats. Note that these repeats are permuted with respect to the structural repeats (blades) of the beta propeller domain.
• smart WD40 42aa 0.007 in ref transcript
• COG COG2319 286aa 2e-21 in ref transcript
  • FOG: WD40 repeat [General function prediction only].
• COG COG2319 353aa 6e-15 in ref transcript

WDR17

• refseq_WDR17.F1 refseq_WDR17.R1 106 229
• NCBIGene 36.3 116966
• Single exon skipping, size difference: 123
• Exclusion of the protein initiation site
• Reference transcript: NM_170710

• cd WD40 291aa 4e-48 in ref transcript
  • WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.
• cd WD40 348aa 2e-17 in ref transcript
• smart WD40 41aa 4e-06 in ref transcript
  • WD40 repeats. Note that these repeats are permuted with respect to the structural repeats (blades) of the beta propeller domain.
• smart WD40 38aa 4e-04 in ref transcript
• pfam WD40 40aa 0.002 in ref transcript
  • WD domain, G-beta repeat.
• pfam WD40 32aa 0.003 in ref transcript
• pfam WD40 40aa 0.004 in ref transcript
• COG COG2319 328aa 7e-32 in ref transcript
  • FOG: WD40 repeat [General function prediction only].
• COG COG2319 401aa 2e-14 in ref transcript

WDR21A

• refseq_WDR21A.F2 refseq_WDR21A.R2 197 297
• NCBIGene 36.3 26094
• Single exon skipping, size difference: 100
• Exclusion of the protein initiation site
• Reference transcript: NM_015604

• cd WD40 187aa 2e-11 in ref transcript
  • WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.
• COG COG2319 181aa 4e-07 in ref transcript
  • FOG: WD40 repeat [General function prediction only].

WDR21A

• refseq_WDR21A.F4 refseq_WDR21A.R4 218 401
• NCBIGene 36.3 26094
• Multiple exon skipping, size difference: 183
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_015604

• cd WD40 187aa 2e-11 in ref transcript
  • WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.
• COG COG2319 181aa 4e-07 in ref transcript
  • FOG: WD40 repeat [General function prediction only].

WDR21A

• refseq_WDR21A.F5 refseq_WDR21A.R5 102 429
• NCBIGene 36.3 26094
• Multiple exon skipping, size difference: 327
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift, Exclusion in the protein (no frameshift), Exclusion in the protein causing a frameshift
• Reference transcript: NM_015604

• Changed! cd WD40 187aa 2e-11 in ref transcript
  • WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.
• Changed! COG COG2319 181aa 4e-07 in ref transcript
  • FOG: WD40 repeat [General function prediction only].
• Changed! cd WD40 185aa 4e-11 in modified transcript
• Changed! COG COG2319 202aa 4e-07 in modified transcript

WDR23

• refseq_WDR23.F2 refseq_WDR23.R2 258 336
• NCBIGene 36.3 80344
• Alternative 5-prime and 3-prime, size difference: 78
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_025230

• cd WD40 343aa 8e-31 in ref transcript
  • WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.
• pfam WD40 38aa 2e-05 in ref transcript
  • WD domain, G-beta repeat.
• pfam WD40 38aa 0.002 in ref transcript
• COG COG2319 351aa 9e-19 in ref transcript
  • FOG: WD40 repeat [General function prediction only].

WDR35

• refseq_WDR35.F1 refseq_WDR35.R1 182 215
• NCBIGene 36.3 57539
• Single exon skipping, size difference: 33
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001006657

• cd WD40 301aa 2e-11 in ref transcript
  • WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.
• COG COG2319 186aa 7e-11 in ref transcript
  • FOG: WD40 repeat [General function prediction only].

WDR7

• refseq_WDR7.F2 refseq_WDR7.R2 109 208
• NCBIGene 36.3 23335
• Single exon skipping, size difference: 99
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_015285

• cd WD40 188aa 2e-14 in ref transcript
  • WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.
• cd WD40 266aa 1e-08 in ref transcript
• cd WD40 70aa 5e-08 in ref transcript
• smart WD40 39aa 3e-04 in ref transcript
  • WD40 repeats. Note that these repeats are permuted with respect to the structural repeats (blades) of the beta propeller domain.
• COG COG2319 252aa 5e-10 in ref transcript
  • FOG: WD40 repeat [General function prediction only].
• COG COG2319 178aa 8e-06 in ref transcript
• COG COG2319 120aa 2e-04 in ref transcript

WFDC10B

• refseq_WFDC10B.F1 refseq_WFDC10B.R1 157 312
• NCBIGene 36.3 280664
• Single exon skipping, size difference: 155
• Exclusion of the stop codon
• Reference transcript: NM_172006

WFDC2

• refseq_WFDC2.F1 refseq_WFDC2.R1 128 272
• NCBIGene 36.2 10406
• Single exon skipping, size difference: 144
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_006103

• Changed! cd WAP 63aa 4e-04 in ref transcript
  • whey acidic protein-type four-disulfide core domains. Members of the family include whey acidic protein, elafin (elastase-specific inhibitor), caltrin-like protein (a calcium transport inhibitor) and other extracellular proteinase inhibitors. A group of proteins containing 8 characteristically-spaced cysteine residuesforming disulphide bonds, have been termed '4-disulphide core' proteins. Protease inhibition occurs by insertion of the inhibitory loop into the active site pocket and interference with the catalytic residues of the protease.
• smart WAP 48aa 2e-07 in ref transcript
  • Four-disulfide core domains.
• Changed! pfam WAP 42aa 0.010 in ref transcript
  • WAP-type (Whey Acidic Protein) 'four-disulfide core'.
• Changed! cd WAP 50aa 0.001 in modified transcript

WFDC3

• refseq_WFDC3.F1 refseq_WFDC3.R1 200 335
• NCBIGene 36.2 140686
• Single exon skipping, size difference: 135
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_080614

• pfam WAP 42aa 0.002 in ref transcript
  • WAP-type (Whey Acidic Protein) 'four-disulfide core'.
• pfam WAP 41aa 0.002 in ref transcript
• pfam WAP 40aa 0.007 in ref transcript

WFDC3

• refseq_WFDC3.F3 refseq_WFDC3.R3 100 189
• NCBIGene 36.2 140686
• Single exon skipping, size difference: 89
• Exclusion of the protein initiation site
• Reference transcript: NM_080614

• Changed! pfam WAP 42aa 0.002 in ref transcript
  • WAP-type (Whey Acidic Protein) 'four-disulfide core'.
• Changed! pfam WAP 41aa 0.002 in ref transcript
• Changed! pfam WAP 40aa 0.007 in ref transcript

WFDC3

• refseq_WFDC3.F5 refseq_WFDC3.R5 164 311
• NCBIGene 36.2 140686
• Single exon skipping, size difference: 147
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_080614

• Changed! pfam WAP 42aa 0.002 in ref transcript
  • WAP-type (Whey Acidic Protein) 'four-disulfide core'.
• pfam WAP 41aa 0.002 in ref transcript
• pfam WAP 40aa 0.007 in ref transcript

WIPI2

• refseq_WIPI2.F1 refseq_WIPI2.R1 269 323
• NCBIGene 36.3 26100
• Single exon skipping, size difference: 54
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_015610

• Changed! cd WD40 194aa 2e-07 in ref transcript
  • WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.
• cd WD40 236aa 2e-05 in ref transcript
• Changed! COG COG2319 164aa 7e-05 in ref transcript
  • FOG: WD40 repeat [General function prediction only].
• Changed! cd WD40 245aa 8e-09 in modified transcript
• Changed! COG COG2319 242aa 3e-05 in modified transcript

WIPI2

• refseq_WIPI2.F2 refseq_WIPI2.R2 169 202
• NCBIGene 36.3 26100
• Alternative 5-prime, size difference: 33
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_015610

• cd WD40 194aa 2e-07 in ref transcript
  • WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.
• cd WD40 236aa 2e-05 in ref transcript
• COG COG2319 164aa 7e-05 in ref transcript
  • FOG: WD40 repeat [General function prediction only].

WNK3

• refseq_WNK3.F2 refseq_WNK3.R2 100 241
• NCBIGene 36.3 65267
• Alternative 5-prime, size difference: 141
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_020922

• cd S_TKc 254aa 5e-61 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• smart S_TKc 249aa 9e-61 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• COG SPS1 335aa 1e-27 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].

WNK3

• refseq_WNK3.F3 refseq_WNK3.R3 142 172
• NCBIGene 36.3 65267
• Single exon skipping, size difference: 30
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_020922

• cd S_TKc 254aa 5e-61 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• smart S_TKc 249aa 9e-61 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• COG SPS1 335aa 1e-27 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].

WRNIP1

• refseq_WRNIP1.F1 refseq_WRNIP1.R1 180 255
• NCBIGene 36.3 56897
• Alternative 3-prime, size difference: 75
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_020135

• Changed! cd AAA 131aa 2e-17 in ref transcript
  • The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.
• Changed! pfam AAA 137aa 2e-15 in ref transcript
  • ATPase family associated with various cellular activities (AAA). AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes.
• smart ZnF_Rad18 24aa 9e-07 in ref transcript
  • Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
• Changed! PRK PRK13342 437aa 1e-165 in ref transcript
  • recombination factor protein RarA; Reviewed.
• COG RAD18 25aa 0.007 in ref transcript
  • RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms].
• Changed! cd AAA 99aa 9e-13 in modified transcript
• Changed! pfam AAA 76aa 6e-12 in modified transcript
• Changed! TIGR dnaX_nterm 203aa 1e-06 in modified transcript
  • This model represents the well-conserved first ~ 365 amino acids of the translation of the dnaX gene. The full-length product of the dnaX gene in the model bacterium E. coli is the DNA polymerase III tau subunit. A translational frameshift leads to early termination and a truncated protein subunit gamma, about 1/3 shorter than tau and present in roughly equal amounts. This frameshift mechanism is not necessarily universal for species with DNA polymerase III but appears conserved in the exterme thermophile Thermus thermophilis.
• Changed! PRK PRK13342 412aa 1e-144 in modified transcript

XRCC4

• refseq_XRCC4.F2 refseq_XRCC4.R2 167 214
• NCBIGene 36.3 7518
• Alternative 5-prime, size difference: 47
• Inclusion in 5'UTR
• Reference transcript: NM_022406

• pfam XRCC4 334aa 1e-167 in ref transcript
  • DNA double-strand break repair and V(D)J recombination protein XRCC4. This family consists of several mammalian specific DNA double-strand break repair and V(D)J recombination protein XRCC4 sequences. In the non-homologous end joining pathway of DNA double-strand break repair, the ligation step is catalysed by a complex of XRCC4 and DNA ligase IV. It is thought that XRCC4 and ligase IV are essential for alignment-based gap filling, as well as for final ligation of the breaks.

YAF2

• refseq_YAF2.F2 refseq_YAF2.R2 125 297
• NCBIGene 36.2 10138
• Multiple exon skipping, size difference: 172
• Inclusion in the protein (no stop codon or frameshift), Inclusion in the protein causing a new stop codon
• Reference transcript: NM_005748

• smart ZnF_RBZ 21aa 7e-04 in ref transcript
  • Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.

YME1L1

• refseq_YME1L1.F2 refseq_YME1L1.R2 176 347
• NCBIGene 36.3 10730
• Single exon skipping, size difference: 171
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_139312

• cd AAA 123aa 8e-16 in ref transcript
  • The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.
• TIGR FtsH_fam 434aa 1e-162 in ref transcript
  • HflB(FtsH) is a pleiotropic protein required for correct cell division in bacteria. It has ATP-dependent zinc metalloprotease activity. It was formerly designated cell division protein FtsH.
• COG HflB 476aa 1e-142 in ref transcript
  • ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones].

YTHDC1

• refseq_YTHDC1.F1 refseq_YTHDC1.R1 303 357
• NCBIGene 36.3 91746
• Single exon skipping, size difference: 54
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001031732

• pfam YTH 94aa 2e-29 in ref transcript
  • YT521-B-like family. A protein of the YTH family has been shown to selectively remove transcripts of meiosis-specific genes expressed in mitotic cells. It has been speculated that in higher eukaryotic YTH-family members may be involved in similar mechanaisms to supress gene regulation during gametogenesis or general silencing. The rat protein YT521-B is a tyrosine-phosphorylated nuclear protein, that interacts with the nuclear transcriptosomal component scaffold attachment factor B, and the 68-kDa Src substrate associated during mitosis, Sam68. In vivo splicing assays demonstrated that YT521-B modulates alternative splice site selection in a concentration-dependent manner. The domain is predicted to have four alpha helices and six beta strands.

YWHAB

• refseq_YWHAB.F1 refseq_YWHAB.R1 307 402
• NCBIGene 36.3 7529
• Single exon skipping, size difference: 95
• Exclusion in 5'UTR
• Reference transcript: NM_003404

• pfam 14-3-3 234aa 1e-118 in ref transcript
  • 14-3-3 protein.
• COG BMH1 245aa 1e-81 in ref transcript
  • 14-3-3 family protein [Signal transduction mechanisms].

YY1AP1

• refseq_YY1AP1.F1 refseq_YY1AP1.R1 340 400
• NCBIGene 36.3 55249
• Alternative 3-prime, size difference: 60
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_139118

YY1AP1

• refseq_YY1AP1.F2 refseq_YY1AP1.R2 181 337
• NCBIGene 36.2 55249
• Single exon skipping, size difference: 156
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_139118

YY1AP1

• refseq_YY1AP1.F3 refseq_YY1AP1.R3 104 235
• NCBIGene 36.2 55249
• Single exon skipping, size difference: 131
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_139118

YY1AP1

• refseq_YY1AP1.F4 refseq_YY1AP1.R1 106 166
• NCBIGene 36.3 55249
• Alternative 3-prime, size difference: 60
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_139118

ZAN

• refseq_ZAN.F1 refseq_ZAN.R1 127 400
• NCBIGene 36.3 7455
• Exon skipping and alternative 3-prime or 5-prime, size difference: 273
• Inclusion in 3'UTR, Exclusion in 3'UTR, Exclusion in 3'UTR
• Reference transcript: NM_003386

• cd MAM 162aa 8e-32 in ref transcript
  • Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region.
• cd MAM 162aa 2e-28 in ref transcript
• cd MAM 155aa 1e-18 in ref transcript
• pfam VWD 153aa 1e-38 in ref transcript
  • von Willebrand factor type D domain. The Cypridina-type luciferase from Vargula hilgendorfii contains a vwd domain. Its function is unrelated but the similarity is very strong by several methods.
• pfam MAM 162aa 1e-36 in ref transcript
  • MAM domain. An extracellular domain found in many receptors.
• smart VWD 162aa 6e-35 in ref transcript
  • von Willebrand factor (vWF) type D domain. Von Willebrand factor contains several type D domains: D1 and D2 are present within the N-terminal propeptide whereas the remaining D domains are required for multimerisation.
• pfam MAM 164aa 7e-31 in ref transcript
• pfam MAM 158aa 8e-21 in ref transcript
• smart C8 73aa 2e-17 in ref transcript
  • C8 domain. This domain contains 8 conserved cysteine residues, but this family only contains 7 of them to overlaps with other domains. It is found in disease-related proteins including von Willebrand factor, Alpha tectorin, Zonadhesin and Mucin.
• smart C8 75aa 1e-15 in ref transcript
• pfam TIL 54aa 4e-06 in ref transcript
  • Trypsin Inhibitor like cysteine rich domain. This family contains trypsin inhibitors as well as a domain found in many extracellular proteins. The domain typically contains ten cysteine residues that form five disulphide bonds. The cysteine residues that form the disulphide bonds are 1-7, 2-6, 3-5, 4-10 and 8-9.
• pfam TIL 50aa 8e-06 in ref transcript

ZC3H14

• refseq_ZC3H14.F2 refseq_ZC3H14.R2 101 494
• NCBIGene 36.3 79882
• Multiple exon skipping, size difference: 393
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_024824

ZCCHC4

• refseq_ZCCHC4.F2 refseq_ZCCHC4.R2 303 397
• NCBIGene 36.2 29063
• Alternative 5-prime, size difference: 94
• Exclusion in the protein causing a frameshift
• Reference transcript: XM_376310

• pfam zf-GRF 41aa 4e-05 in ref transcript
  • GRF zinc finger. This presumed zinc binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to pfam01396.

ZDHHC13

• refseq_ZDHHC13.F1 refseq_ZDHHC13.R1 129 275
• NCBIGene 36.3 54503
• Single exon skipping, size difference: 146
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_019028

• Changed! cd ANK 114aa 2e-22 in ref transcript
  • ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats.
• Changed! cd ANK 152aa 4e-22 in ref transcript
• Changed! pfam zf-DHHC 53aa 5e-17 in ref transcript
  • DHHC zinc finger domain. This domain is also known as NEW1. This domain is predicted to be a zinc binding domain. The function of this domain is unknown, but it has been predicted to be involved in protein-protein or protein-DNA interactions, and palmitoyltransferase activity.
• Changed! pfam Ank 29aa 1e-05 in ref transcript
  • Ankyrin repeat. There's no clear separation between noise and signal on the HMM search Ankyrin repeats generally consist of a beta, alpha, alpha, beta order of secondary structures. The repeats associate to form a higher order structure.
• Changed! pfam Ank 32aa 3e-04 in ref transcript
• Changed! COG COG5273 248aa 4e-23 in ref transcript
  • Uncharacterized protein containing DHHC-type Zn finger [General function prediction only].
• Changed! COG Arp 146aa 1e-14 in ref transcript
  • FOG: Ankyrin repeat [General function prediction only].
• Changed! COG Arp 140aa 6e-14 in ref transcript

ZDHHC14

• refseq_ZDHHC14.F1 refseq_ZDHHC14.R1 236 281
• NCBIGene 36.3 79683
• Alternative 3-prime, size difference: 45
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_024630

• pfam zf-DHHC 63aa 6e-24 in ref transcript
  • DHHC zinc finger domain. This domain is also known as NEW1. This domain is predicted to be a zinc binding domain. The function of this domain is unknown, but it has been predicted to be involved in protein-protein or protein-DNA interactions, and palmitoyltransferase activity.
• COG COG5273 249aa 3e-31 in ref transcript
  • Uncharacterized protein containing DHHC-type Zn finger [General function prediction only].

ZDHHC16

• refseq_ZDHHC16.F2 refseq_ZDHHC16.R2 272 320
• NCBIGene 36.3 84287
• Single exon skipping, size difference: 48
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_032327

• pfam zf-DHHC 54aa 2e-21 in ref transcript
  • DHHC zinc finger domain. This domain is also known as NEW1. This domain is predicted to be a zinc binding domain. The function of this domain is unknown, but it has been predicted to be involved in protein-protein or protein-DNA interactions, and palmitoyltransferase activity.
• Changed! COG COG5273 88aa 1e-20 in ref transcript
  • Uncharacterized protein containing DHHC-type Zn finger [General function prediction only].
• Changed! COG COG5273 222aa 8e-22 in modified transcript

ZDHHC16

• refseq_ZDHHC16.F3 refseq_ZDHHC16.R3 220 400
• NCBIGene 36.3 84287
• Single exon skipping, size difference: 180
• Exclusion in 5'UTR
• Reference transcript: NM_198046

• pfam zf-DHHC 54aa 2e-21 in ref transcript
  • DHHC zinc finger domain. This domain is also known as NEW1. This domain is predicted to be a zinc binding domain. The function of this domain is unknown, but it has been predicted to be involved in protein-protein or protein-DNA interactions, and palmitoyltransferase activity.
• COG COG5273 88aa 1e-20 in ref transcript
  • Uncharacterized protein containing DHHC-type Zn finger [General function prediction only].

ZDHHC16

• refseq_ZDHHC16.F6 refseq_ZDHHC16.R6 123 240
• NCBIGene 36.3 84287
• Exon skipping and alternative 3-prime or 5-prime, size difference: 117
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_032327

• Changed! pfam zf-DHHC 54aa 2e-21 in ref transcript
  • DHHC zinc finger domain. This domain is also known as NEW1. This domain is predicted to be a zinc binding domain. The function of this domain is unknown, but it has been predicted to be involved in protein-protein or protein-DNA interactions, and palmitoyltransferase activity.
• Changed! COG COG5273 88aa 1e-20 in ref transcript
  • Uncharacterized protein containing DHHC-type Zn finger [General function prediction only].
• Changed! COG COG5273 50aa 0.001 in modified transcript

ZDHHC16

• refseq_ZDHHC16.F7 refseq_ZDHHC16.R7 127 322
• NCBIGene 36.3 84287
• Single exon skipping, size difference: 195
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_032327

• pfam zf-DHHC 54aa 2e-21 in ref transcript
  • DHHC zinc finger domain. This domain is also known as NEW1. This domain is predicted to be a zinc binding domain. The function of this domain is unknown, but it has been predicted to be involved in protein-protein or protein-DNA interactions, and palmitoyltransferase activity.
• Changed! COG COG5273 88aa 1e-20 in ref transcript
  • Uncharacterized protein containing DHHC-type Zn finger [General function prediction only].
• Changed! COG COG5273 63aa 2e-20 in modified transcript

ZFP64

• refseq_ZFP64.F1 refseq_ZFP64.R1 173 335
• NCBIGene 36.3 55734
• Single exon skipping, size difference: 162
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_018197

ZFYVE9

• refseq_ZFYVE9.F2 refseq_ZFYVE9.R2 221 398
• NCBIGene 36.3 9372
• Single exon skipping, size difference: 177
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_004799

• cd FYVE 54aa 1e-11 in ref transcript
  • FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;.
• pfam FYVE 66aa 8e-19 in ref transcript
  • FYVE zinc finger. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn++ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. We have included members which do not conserve these histidine residues but are clearly related.

ZGPAT

• refseq_ZGPAT.F1 refseq_ZGPAT.R1 185 255
• NCBIGene 36.3 84619
• Alternative 5-prime, size difference: 70
• Exclusion in 5'UTR
• Reference transcript: NM_032527

• cd TUDOR 31aa 0.005 in ref transcript
  • Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal.
• pfam G-patch 42aa 2e-08 in ref transcript
  • G-patch domain. This domain is found in a number of RNA binding proteins, and is also found in proteins that contain RNA binding domains. This suggests that this domain may have an RNA binding function. This domain has seven highly conserved glycines.
• smart ZnF_C3H1 22aa 6e-04 in ref transcript
  • zinc finger.
• smart TUDOR 36aa 0.006 in ref transcript
  • Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).

ZHX1

• refseq_ZHX1.F1 refseq_ZHX1.R1 121 216
• NCBIGene 36.3 11244
• Alternative 5-prime, size difference: 95
• Exclusion in 5'UTR
• Reference transcript: NM_001017926

• cd homeodomain 56aa 4e-07 in ref transcript
  • Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
• cd homeodomain 53aa 7e-07 in ref transcript
• cd homeodomain 41aa 0.002 in ref transcript
• cd homeodomain 48aa 0.002 in ref transcript
• cd homeodomain 44aa 0.009 in ref transcript
• smart HOX 52aa 5e-08 in ref transcript
  • Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes.
• smart HOX 53aa 1e-07 in ref transcript
• smart HOX 37aa 2e-04 in ref transcript
• smart HOX 41aa 3e-04 in ref transcript
• smart HOX 44aa 0.003 in ref transcript

ZMAT1

• refseq_ZMAT1.F2 refseq_ZMAT1.R2 152 273
• NCBIGene 36.2 84460
• Single exon skipping, size difference: 121
• Exclusion of the protein initiation site
• Reference transcript: NM_001011657

• smart ZnF_U1 35aa 0.001 in ref transcript
  • U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.

ZMAT3

• refseq_ZMAT3.F1 refseq_ZMAT3.R1 154 260
• NCBIGene 36.3 64393
• Alternative 5-prime and 3-prime, size difference: 106
• Inclusion in 5'UTR, Exclusion in 5'UTR
• Reference transcript: NM_022470

• smart ZnF_U1 35aa 2e-06 in ref transcript
  • U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
• smart ZnF_U1 34aa 2e-05 in ref transcript
• smart ZnF_U1 35aa 8e-05 in ref transcript

ZMAT5

• refseq_ZMAT5.F1 refseq_ZMAT5.R1 194 309
• NCBIGene 36.3 55954
• Single exon skipping, size difference: 115
• Exclusion in 5'UTR
• Reference transcript: NM_019103

• pfam zf-CCCH 23aa 6e-04 in ref transcript
  • Zinc finger C-x8-C-x5-C-x3-H type (and similar).
• pfam zf-U1 37aa 0.003 in ref transcript
  • U1 zinc finger. This family consists of several U1 small nuclear ribonucleoprotein C (U1-C) proteins. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site (ss) at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' ss is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' ss. Binding of TIA-1 in the vicinity of a 5' ss helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator. This domain is probably a zinc-binding. It is found in multiple copies in some members of the family.
• COG COG5136 43aa 0.002 in ref transcript
  • U1 snRNP-specific protein C [RNA processing and modification].

ZMYM2

• refseq_ZMYM2.F2 refseq_ZMYM2.R2 122 169
• NCBIGene 36.3 7750
• Single exon skipping, size difference: 47
• Exclusion in 5'UTR
• Reference transcript: NM_003453

• pfam zf-FCS 41aa 6e-06 in ref transcript
  • MYM-type Zinc finger with FCS sequence motif. MYM-type zinc fingers were identified in MYM family proteins. Human zinc finger protein 261 is involved in a chromosomal translocation and may be responsible for X-linked retardation in XQ13.1. Human zinc finger protein 198 is also involved in disease. In myeloproliferative disorders it is fused to FGF receptor 1; in atypical myeloproliferative disorders it is rearranged. Members of the family generally are involved in development. This Zn-finger domain functions as a transcriptional trans-activator of late vaccinia viral genes, and orthologues are also found in all nucleocytoplasmic large DNA viruses, NCLDV. This domain is also found fused to the C termini of recombinases from certain prokaryotic transposons.
• pfam zf-FCS 41aa 1e-05 in ref transcript
• pfam zf-FCS 44aa 8e-05 in ref transcript
• pfam zf-FCS 39aa 0.002 in ref transcript
• pfam zf-FCS 40aa 0.002 in ref transcript

ZNF16

• refseq_ZNF16.F1 refseq_ZNF16.R1 264 350
• NCBIGene 36.3 7564
• Single exon skipping, size difference: 86
• Exclusion in 5'UTR
• Reference transcript: NM_001029976

• COG COG5048 349aa 2e-09 in ref transcript
  • FOG: Zn-finger [General function prediction only].
• COG COG5048 210aa 6e-04 in ref transcript

ZNF160

• refseq_ZNF160.F1 refseq_ZNF160.R1 105 190
• NCBIGene 36.3 90338
• Single exon skipping, size difference: 85
• Exclusion in 5'UTR
• Reference transcript: NM_198893

• smart KRAB 61aa 1e-24 in ref transcript
  • krueppel associated box.
• COG COG5048 458aa 8e-12 in ref transcript
  • FOG: Zn-finger [General function prediction only].
• COG SFP1 117aa 0.007 in ref transcript
  • Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning].

ZNF182

• refseq_ZNF182.F2 refseq_ZNF182.R2 183 277
• NCBIGene 36.3 7569
• Single exon skipping, size difference: 94
• Exclusion of the protein initiation site
• Reference transcript: NM_006962

• smart KRAB 59aa 1e-23 in ref transcript
  • krueppel associated box.
• COG COG5048 399aa 7e-11 in ref transcript
  • FOG: Zn-finger [General function prediction only].

ZNF189

• refseq_ZNF189.F1 refseq_ZNF189.R1 190 284
• NCBIGene 36.3 7743
• Exon skipping and alternative 3-prime or 5-prime, size difference: 94
• Inclusion in the protein causing a new stop codon, Exclusion in the protein (no frameshift)
• Reference transcript: NM_003452

• Changed! pfam KRAB 41aa 2e-19 in ref transcript
  • KRAB box. The KRAB domain (or Kruppel-associated box) is present in about a third of zinc finger proteins containing C2H2 fingers. The KRAB domain is found to be involved in protein-protein interactions. The KRAB domain is generally encoded by two exons. The regions coded by the two exons are known as KRAB-A and KRAB-B. The A box plays an important role in repression by binding to corepressors, while the B box is thought to enhance this repression brought about by the A box. KRAB-containing proteins are thought to have critical functions in cell proliferation and differentiation, apoptosis and neoplastic transformation.
• Changed! COG COG5048 368aa 5e-09 in ref transcript
  • FOG: Zn-finger [General function prediction only].

ZNF2

• refseq_ZNF2.F2 refseq_ZNF2.R2 312 384
• NCBIGene 36.3 7549
• Single exon skipping, size difference: 72
• Exclusion of the protein initiation site
• Reference transcript: NM_021088

• Changed! smart KRAB 61aa 2e-23 in ref transcript
  • krueppel associated box.
• COG COG5048 158aa 2e-05 in ref transcript
  • FOG: Zn-finger [General function prediction only].
• Changed! smart KRAB 32aa 2e-08 in modified transcript

ZNF200

• refseq_ZNF200.F2 refseq_ZNF200.R2 107 458
• NCBIGene 36.3 7752
• Alternative 5-prime, size difference: 351
• Exclusion in 5'UTR
• Reference transcript: NM_003454

• pfam zf-C2H2 23aa 0.008 in ref transcript
  • Zinc finger, C2H2 type. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter.

ZNF207

• refseq_ZNF207.F1 refseq_ZNF207.R1 291 384
• NCBIGene 36.3 7756
• Single exon skipping, size difference: 93
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001098507

ZNF207

• refseq_ZNF207.F4 refseq_ZNF207.R4 205 253
• NCBIGene 36.3 7756
• Single exon skipping, size difference: 48
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001098507

ZNF211

• refseq_ZNF211.F1 refseq_ZNF211.R1 217 256
• NCBIGene 36.3 10520
• Single exon skipping, size difference: 39
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_006385

• pfam KRAB 41aa 4e-16 in ref transcript
  • KRAB box. The KRAB domain (or Kruppel-associated box) is present in about a third of zinc finger proteins containing C2H2 fingers. The KRAB domain is found to be involved in protein-protein interactions. The KRAB domain is generally encoded by two exons. The regions coded by the two exons are known as KRAB-A and KRAB-B. The A box plays an important role in repression by binding to corepressors, while the B box is thought to enhance this repression brought about by the A box. KRAB-containing proteins are thought to have critical functions in cell proliferation and differentiation, apoptosis and neoplastic transformation.
• COG SFP1 79aa 0.004 in ref transcript
  • Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning].

ZNF266

• refseq_ZNF266.F2 refseq_ZNF266.R2 124 404
• NCBIGene 36.3 10781
• Multiple exon skipping, size difference: 280
• Exclusion in 5'UTR, Exclusion in 5'UTR
• Reference transcript: NM_006631

• smart KRAB 28aa 2e-06 in ref transcript
  • krueppel associated box.
• COG COG5048 340aa 1e-05 in ref transcript
  • FOG: Zn-finger [General function prediction only].

ZNF274

• refseq_ZNF274.F1 refseq_ZNF274.R1 278 374
• NCBIGene 36.3 10782
• Single exon skipping, size difference: 96
• Exclusion in 5'UTR
• Reference transcript: NM_133502

• pfam KRAB 41aa 1e-18 in ref transcript
  • KRAB box. The KRAB domain (or Kruppel-associated box) is present in about a third of zinc finger proteins containing C2H2 fingers. The KRAB domain is found to be involved in protein-protein interactions. The KRAB domain is generally encoded by two exons. The regions coded by the two exons are known as KRAB-A and KRAB-B. The A box plays an important role in repression by binding to corepressors, while the B box is thought to enhance this repression brought about by the A box. KRAB-containing proteins are thought to have critical functions in cell proliferation and differentiation, apoptosis and neoplastic transformation.
• pfam zf-C2H2 23aa 8e-04 in ref transcript
  • Zinc finger, C2H2 type. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter.

PATZ1

• refseq_ZNF278.F1 refseq_ZNF278.R1 193 258
• NCBIGene 36.3 23598
• Alternative 3-prime, size difference: 65
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_014323

• pfam BTB 130aa 8e-22 in ref transcript
  • BTB/POZ domain. The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN.
• Changed! COG SFP1 58aa 0.004 in modified transcript
  • Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning].

ZNF302

• refseq_ZNF302.F1 refseq_ZNF302.R1 125 148
• NCBIGene 36.3 55900
• Alternative 5-prime, size difference: 23
• Exclusion in 5'UTR
• Reference transcript: NM_018443

• smart KRAB 61aa 1e-23 in ref transcript
  • krueppel associated box.

ZNF37B

• refseq_ZNF37B.F2 refseq_ZNF37B.R2 296 350
• NCBIGene 36.2 256112
• Alternative 3-prime, size difference: 54
• Inclusion in 5'UTR
• Reference transcript: XM_001127459

ZNF384

• refseq_ZNF384.F2 refseq_ZNF384.R2 203 251
• NCBIGene 36.3 171017
• Single exon skipping, size difference: 48
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001039917

ZNF451

• refseq_ZNF451.F2 refseq_ZNF451.R2 178 322
• NCBIGene 36.3 26036
• Single exon skipping, size difference: 144
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001031623

ZNF473

• refseq_ZNF473.F1 refseq_ZNF473.R1 232 354
• NCBIGene 36.3 25888
• Alternative 3-prime, size difference: 122
• Inclusion in 5'UTR
• Reference transcript: NM_001006656

• pfam KRAB 41aa 1e-08 in ref transcript
  • KRAB box. The KRAB domain (or Kruppel-associated box) is present in about a third of zinc finger proteins containing C2H2 fingers. The KRAB domain is found to be involved in protein-protein interactions. The KRAB domain is generally encoded by two exons. The regions coded by the two exons are known as KRAB-A and KRAB-B. The A box plays an important role in repression by binding to corepressors, while the B box is thought to enhance this repression brought about by the A box. KRAB-containing proteins are thought to have critical functions in cell proliferation and differentiation, apoptosis and neoplastic transformation.
• COG COG5048 405aa 4e-05 in ref transcript
  • FOG: Zn-finger [General function prediction only].
• COG COG5048 341aa 6e-04 in ref transcript

ZNF484

• refseq_ZNF484.F1 refseq_ZNF484.R1 133 178
• NCBIGene 36.3 83744
• Single exon skipping, size difference: 45
• Exclusion of the protein initiation site
• Reference transcript: NM_031486

• Changed! smart KRAB 60aa 1e-24 in ref transcript
  • krueppel associated box.
• COG COG5048 402aa 8e-10 in ref transcript
  • FOG: Zn-finger [General function prediction only].
• Changed! smart KRAB 31aa 4e-07 in modified transcript

ZNF107

• refseq_ZNF588.F2 refseq_ZNF588.R2 280 407
• NCBIGene 36.3 51427
• Single exon skipping, size difference: 127
• Exclusion in 5'UTR
• Reference transcript: NM_016220

• COG COG5048 313aa 1e-07 in ref transcript
  • FOG: Zn-finger [General function prediction only].
• COG COG5048 390aa 3e-07 in ref transcript

ZNF107

• refseq_ZNF588.F3 refseq_ZNF588.R3 109 251
• NCBIGene 36.3 51427
• Single exon skipping, size difference: 142
• Exclusion in 5'UTR
• Reference transcript: NM_016220

• COG COG5048 313aa 1e-07 in ref transcript
  • FOG: Zn-finger [General function prediction only].
• COG COG5048 390aa 3e-07 in ref transcript

ZNF599

• refseq_ZNF599.F1 refseq_ZNF599.R1 184 322
• NCBIGene 36.2 148103
• Single exon skipping, size difference: 138
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_001007248

• Changed! smart KRAB 61aa 7e-23 in ref transcript
  • krueppel associated box.
• Changed! COG COG5048 313aa 3e-13 in ref transcript
  • FOG: Zn-finger [General function prediction only].

ZNF655

• refseq_ZNF655.F1 refseq_ZNF655.R1 192 417
• NCBIGene 36.2 79027
• Multiple exon skipping, size difference: 225
• Inclusion in the protein causing a new stop codon, Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_138494

• Changed! COG COG5048 106aa 6e-04 in ref transcript
  • FOG: Zn-finger [General function prediction only].
• Changed! PRK truB 85aa 0.007 in ref transcript
  • tRNA pseudouridine synthase B; Provisional.

IKZF3

• refseq_ZNFN1A3.F2 refseq_ZNFN1A3.R2 190 307
• NCBIGene 36.3 22806
• Single exon skipping, size difference: 117
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_012481

IKZF3

• refseq_ZNFN1A3.F3 refseq_ZNFN1A3.R3 231 399
• NCBIGene 36.3 22806
• Single exon skipping, size difference: 168
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_012481

IKZF3

• refseq_ZNFN1A3.F5 refseq_ZNFN1A3.R5 146 263
• NCBIGene 36.3 22806
• Single exon skipping, size difference: 117
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_012481

ZPBP2

• refseq_ZPBP2.F1 refseq_ZPBP2.R1 184 250
• NCBIGene 36.3 124626
• Single exon skipping, size difference: 66
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_199321

• pfam Sp38 272aa 1e-142 in ref transcript
  • Zona-pellucida-binding protein (Sp38). This family contains a number of zona-pellucida-binding proteins that seem to be restricted to mammals. These are sperm proteins that bind to the 90-kDa family of zona pellucida glycoproteins in a calcium-dependent manner. These represent some of the specific molecules that mediate the first steps of gamete interaction, allowing fertilisation to occur.

ZRANB2

• refseq_ZRANB2.F1 refseq_ZRANB2.R1 209 284
• NCBIGene 36.3 9406
• Single exon skipping, size difference: 75
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_203350

• smart ZnF_RBZ 25aa 6e-04 in ref transcript
  • Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
• smart ZnF_RBZ 25aa 0.009 in ref transcript

ZWINT

• refseq_ZWINT.F2 refseq_ZWINT.R2 234 375
• NCBIGene 36.3 11130
• Alternative 5-prime and 3-prime, size difference: 141
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_007057

• Changed! PRK mukB 138aa 0.003 in ref transcript
  • cell division protein MukB; Provisional.

A26A1

• rs.A26A1.F1 rs.A26A1.R1 141 279
• NCBIGene 36.3 340441
• Single exon skipping, size difference: 138
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001005365

• cd ANK 126aa 2e-26 in ref transcript
  • ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats.
• Changed! cd ANK 125aa 3e-24 in ref transcript
• Changed! TIGR trp 175aa 6e-07 in ref transcript
  • after chronic exposure to capsaicin. (McCleskey and Gold, 1999).
• COG Arp 173aa 1e-11 in ref transcript
  • FOG: Ankyrin repeat [General function prediction only].
• Changed! TIGR trp 121aa 2e-05 in modified transcript

AADACL3

• rs.AADACL3.F1 rs.AADACL3.R1 160 377
• NCBIGene 36.3 126767
• Single exon skipping, size difference: 217
• Exclusion of the protein initiation site
• Reference transcript: NM_001103170

• Changed! pfam Abhydrolase_3 264aa 2e-43 in ref transcript
  • alpha/beta hydrolase fold. This catalytic domain is found in a very wide range of enzymes.
• Changed! COG Aes 342aa 2e-33 in ref transcript
  • Esterase/lipase [Lipid metabolism].
• Changed! pfam Abhydrolase_3 250aa 3e-35 in modified transcript
• Changed! COG Aes 277aa 7e-24 in modified transcript

ABCC1

• rs.ABCC1.F1 rs.ABCC1.R1 229 424
• NCBIGene 36.3 4363
• Single exon skipping, size difference: 195
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_004996

• Changed! cd ABCC_MRP_domain2 221aa 9e-96 in ref transcript
  • Domain 2 of the ABC subfamily C. This family is also known as MRP (mulrtidrug resisitance-associated protein). Some of the MRP members have five additional transmembrane segments in their N-terminus, but the function of these additional membrane-spanning domains is not clear. The MRP was found in the multidrug-resistance lung cancer cell in which p-glycoprotein was not overexpressed. MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions, such as glutathione, glucuronate, and sulfate.
• cd ABCC_MRP_domain1 202aa 6e-89 in ref transcript
  • Domain 1 of the ABC subfamily C. This family is also known as MRP (mulrtidrug resisitance-associated protein). Some of the MRP members have five additional transmembrane segments in their N-terminas, but the function of these additional membrane-spanning domains is not clear. The MRP was found in the multidrug-resisting lung cancer cell in which p-glycoprotein was not overexpressed. MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions, such as glutathione, glucuronate, and sulfate.
• Changed! TIGR MRP_assoc_pro 1524aa 0.0 in ref transcript
  • This model describes multi drug resistance-associated protein (MRP) in eukaryotes. The multidrug resistance-associated protein is an integral membrane protein that causes multidrug resistance when overexpressed in mammalian cells. It belongs to ABC transporter superfamily. The protein topology and function was experimentally demonstrated by epitope tagging and immunofluorescence. Insertion of tags in the critical regions associated with drug efflux, abrogated its function. The C-terminal domain seem to highly conserved.
• Changed! PTZ PTZ00243 869aa 1e-161 in ref transcript
  • ABC transporter; Provisional.
• COG MdlB 558aa 2e-56 in ref transcript
  • ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms].
• Changed! cd ABCC_MRP_domain2 142aa 2e-50 in modified transcript
• Changed! TIGR MRP_assoc_pro 1426aa 0.0 in modified transcript
• Changed! TIGR MRP_assoc_pro 35aa 5e-13 in modified transcript
• Changed! PTZ PTZ00243 772aa 1e-131 in modified transcript

ABCC1

• rs.ABCC1.F2 rs.ABCC1.R2 119 296
• NCBIGene 36.3 4363
• Single exon skipping, size difference: 177
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_004996

• cd ABCC_MRP_domain2 221aa 9e-96 in ref transcript
  • Domain 2 of the ABC subfamily C. This family is also known as MRP (mulrtidrug resisitance-associated protein). Some of the MRP members have five additional transmembrane segments in their N-terminus, but the function of these additional membrane-spanning domains is not clear. The MRP was found in the multidrug-resistance lung cancer cell in which p-glycoprotein was not overexpressed. MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions, such as glutathione, glucuronate, and sulfate.
• Changed! cd ABCC_MRP_domain1 202aa 6e-89 in ref transcript
  • Domain 1 of the ABC subfamily C. This family is also known as MRP (mulrtidrug resisitance-associated protein). Some of the MRP members have five additional transmembrane segments in their N-terminas, but the function of these additional membrane-spanning domains is not clear. The MRP was found in the multidrug-resisting lung cancer cell in which p-glycoprotein was not overexpressed. MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions, such as glutathione, glucuronate, and sulfate.
• Changed! TIGR MRP_assoc_pro 1524aa 0.0 in ref transcript
  • This model describes multi drug resistance-associated protein (MRP) in eukaryotes. The multidrug resistance-associated protein is an integral membrane protein that causes multidrug resistance when overexpressed in mammalian cells. It belongs to ABC transporter superfamily. The protein topology and function was experimentally demonstrated by epitope tagging and immunofluorescence. Insertion of tags in the critical regions associated with drug efflux, abrogated its function. The C-terminal domain seem to highly conserved.
• Changed! PTZ PTZ00243 869aa 1e-161 in ref transcript
  • ABC transporter; Provisional.
• Changed! COG MdlB 558aa 2e-56 in ref transcript
  • ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms].
• Changed! cd ABCC_MRP_domain1 97aa 3e-36 in modified transcript
• Changed! cd ABCC_MRP_domain1 63aa 1e-15 in modified transcript
• Changed! TIGR MRP_assoc_pro 1465aa 0.0 in modified transcript
• Changed! PTZ PTZ00243 766aa 1e-133 in modified transcript
• Changed! PTZ PTZ00243 326aa 8e-39 in modified transcript
• Changed! PRK PRK11160 68aa 4e-10 in modified transcript
  • cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed.
• Changed! COG COG1123 146aa 2e-07 in modified transcript
  • ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only].

ABCC1

• rs.ABCC1.F3 rs.ABCC1.R3 172 340
• NCBIGene 36.3 4363
• Single exon skipping, size difference: 168
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_004996

• cd ABCC_MRP_domain2 221aa 9e-96 in ref transcript
  • Domain 2 of the ABC subfamily C. This family is also known as MRP (mulrtidrug resisitance-associated protein). Some of the MRP members have five additional transmembrane segments in their N-terminus, but the function of these additional membrane-spanning domains is not clear. The MRP was found in the multidrug-resistance lung cancer cell in which p-glycoprotein was not overexpressed. MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions, such as glutathione, glucuronate, and sulfate.
• Changed! cd ABCC_MRP_domain1 202aa 6e-89 in ref transcript
  • Domain 1 of the ABC subfamily C. This family is also known as MRP (mulrtidrug resisitance-associated protein). Some of the MRP members have five additional transmembrane segments in their N-terminas, but the function of these additional membrane-spanning domains is not clear. The MRP was found in the multidrug-resisting lung cancer cell in which p-glycoprotein was not overexpressed. MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions, such as glutathione, glucuronate, and sulfate.
• Changed! TIGR MRP_assoc_pro 1524aa 0.0 in ref transcript
  • This model describes multi drug resistance-associated protein (MRP) in eukaryotes. The multidrug resistance-associated protein is an integral membrane protein that causes multidrug resistance when overexpressed in mammalian cells. It belongs to ABC transporter superfamily. The protein topology and function was experimentally demonstrated by epitope tagging and immunofluorescence. Insertion of tags in the critical regions associated with drug efflux, abrogated its function. The C-terminal domain seem to highly conserved.
• Changed! PTZ PTZ00243 869aa 1e-161 in ref transcript
  • ABC transporter; Provisional.
• Changed! COG MdlB 558aa 2e-56 in ref transcript
  • ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms].
• Changed! cd ABCC_MRP_domain1 146aa 2e-47 in modified transcript
• Changed! TIGR MRP_assoc_pro 758aa 0.0 in modified transcript
• Changed! TIGR MRP_assoc_pro 711aa 0.0 in modified transcript
• Changed! PTZ PTZ00243 813aa 1e-126 in modified transcript
• Changed! PTZ PTZ00243 326aa 9e-39 in modified transcript
• Changed! COG CydC 305aa 2e-19 in modified transcript
  • ABC-type transport system involved in cytochrome bd biosynthesis, fused ATPase and permease components [Energy production and conversion / Posttranslational modification, protein turnover, chaperones].

ABI1

• rs.ABI1.F1 rs.ABI1.R1 100 115
• NCBIGene 36.3 10006
• Single exon skipping, size difference: 15
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_005470

• cd SH3 52aa 3e-15 in ref transcript
  • Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
• Changed! pfam Abi_HHR 79aa 4e-32 in ref transcript
  • Abl-interactor HHR. The region featured in this family is found towards the N-terminus of a number of adaptor proteins that interact with Abl-family tyrosine kinases. More specifically, it is termed the homeo-domain homologous region (HHR), as it is similar to the DNA-binding region of homeo-domain proteins. Other homeo-domain proteins have been implicated in specifying positional information during embryonic development, and in the regulation of the expression of cell-type specific genes. The Abl-interactor proteins are thought to coordinate the cytoplasmic and nuclear functions of the Abl-family kinases, and seem to be involved in cytoskeletal reorganisation, but their precise role remains unclear.
• smart SH3 56aa 2e-17 in ref transcript
  • Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.
• Changed! pfam Abi_HHR 74aa 6e-30 in modified transcript

ABL2

• rs.ABL2.F1 rs.ABL2.R1 204 267
• NCBIGene 36.3 27
• Single exon skipping, size difference: 63
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001100108

• cd PTKc_Abl 263aa 1e-158 in ref transcript
  • Catalytic Domain of the Protein Tyrosine Kinase, Abelson kinase. Protein Tyrosine Kinase (PTK) family; Abelson (Abl) kinase; catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Abl (or c-Abl) is a ubiquitously-expressed cytoplasmic (or nonreceptor) tyr kinase that contains SH3, SH2, and tyr kinase domains in its N-terminal region, as well as nuclear localization motifs, a putative DNA-binding domain, and F- and G-actin binding domains in its C-terminal tail. It also contains a short autoinhibitory cap region in its N-terminus. Abl is normally inactive and requires phosphorylation and myristoylation for activation. Abl function depends on its subcellular localization. In the cytoplasm, Abl plays a role in cell proliferation and survival. In response to DNA damage or oxidative stress, Abl is transported to the nucleus where it induces apoptosis. In chronic myelogenous leukemia (CML) patients, an aberrant translocation results in the replacement of the first exon of Abl with the BCR (breakpoint cluster region) gene. The resulting BCR-Abl fusion protein is constitutively active and associates into tetramers, resulting in a hyperactive kinase sending a continuous signal. This leads to uncontrolled proliferation, morphological transformation and anti-apoptotic effects. BCR-Abl is the target of selective inhibitors, such as imatinib (Gleevec), used in the treatment of CML. Abl2, also known as ARG (Abelson-related gene), is thought to play a cooperative role with Abl in the proper development of the nervous system. The Tel-ARG fusion protein, resulting from reciprocal translocation between chromosomes 1 and 12, is associated with acute myeloid leukemia (AML). The TEL gene is a frequent fusion partner of other tyr kinase oncogenes, including Tel/Abl, Tel/PDGFRbeta, and Tel/Jak2, found in patients with leukemia and myeloproliferative disorders.
• cd SH2 90aa 5e-24 in ref transcript
  • Src homology 2 domains; Signal transduction, involved in recognition of phosphorylated tyrosine (pTyr). SH2 domains typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites.
• cd SH3 53aa 2e-09 in ref transcript
  • Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
• pfam Pkinase_Tyr 252aa 1e-112 in ref transcript
  • Protein tyrosine kinase.
• pfam F_actin_bind 163aa 1e-48 in ref transcript
  • F-actin binding. The F-actin binding domain forms a compact bundle of four antiparallel alpha-helices, which are arranged in a left-handed topology. Binding of F-actin to the F-actin binding domain may result in cytoplasmic retention and subcellular distribution of the protein, as well as possible inhibition of protein function.
• smart SH2 84aa 2e-27 in ref transcript
  • Src homology 2 domains. Src homology 2 domains bind phosphotyrosine-containing polypeptides via 2 surface pockets. Specificity is provided via interaction with residues that are distinct from the phosphotyrosine. Only a single occurrence of a SH2 domain has been found in S. cerevisiae.
• pfam SH3_1 54aa 1e-12 in ref transcript
  • SH3 domain. SH3 (Src homology 3) domains are often indicative of a protein involved in signal transduction related to cytoskeletal organisation. First described in the Src cytoplasmic tyrosine kinase. The structure is a partly opened beta barrel.
• COG SPS1 331aa 1e-20 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].

ACD

• rs.ACD.F1 rs.ACD.R1 173 212
• NCBIGene 36.3 65057
• Alternative 3-prime, size difference: 39
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001082486

ACOX3

• rs.ACOX3.F1 rs.ACOX3.R1 367 435
• NCBIGene 36.3 8310
• Single exon skipping, size difference: 68
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_003501

• Changed! cd AXO 654aa 0.0 in ref transcript
  • Peroxisomal acyl-CoA oxidases (AXO) catalyze the first set in the peroxisomal fatty acid beta-oxidation, the alpha,beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. In a second oxidative half-reaction, the reduced FAD is reoxidized by molecular oxygen. AXO is generally a homodimer, but it has been reported to form a different type of oligomer in yeast. There are several subtypes of AXO's, based on substrate specificity. Palmitoyl-CoA oxidase acts on straight-chain fatty acids and prostanoids; whereas, the closely related Trihydroxycoprostanoly-CoA oxidase has the greatest activity for 2-methyl branched side chains of bile precursors. Pristanoyl-CoA oxidase, acts on 2-methyl branched fatty acids. AXO has an additional domain, C-terminal to the region with similarity to acyl-CoA dehydrogenases, which is included in this alignment.
• Changed! pfam ACOX 190aa 1e-51 in ref transcript
  • Acyl-CoA oxidase. This is a family of Acyl-CoA oxidases EC:1.3.3.6. Acyl-coA oxidase converts acyl-CoA into trans-2- enoyl-CoA.
• pfam Acyl-CoA_dh_M 58aa 2e-09 in ref transcript
  • Acyl-CoA dehydrogenase, middle domain. Central domain of Acyl-CoA dehydrogenase has a beta-barrel fold.
• pfam Acyl-CoA_dh_1 162aa 1e-05 in ref transcript
  • Acyl-CoA dehydrogenase, C-terminal domain. C-terminal domain of Acyl-CoA dehydrogenase is an all-alpha, four helical up-and-down bundle.
• COG CaiA 373aa 6e-24 in ref transcript
  • Acyl-CoA dehydrogenases [Lipid metabolism].
• Changed! cd AXO 591aa 0.0 in modified transcript
• Changed! pfam ACOX 103aa 8e-24 in modified transcript

ACP1

• rs.ACP1.F1 rs.ACP1.R1 233 388
• NCBIGene 36.3 52
• Alternative 3-prime, size difference: 155
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_007099

• Changed! cd LMWPc 149aa 4e-43 in ref transcript
  • Low molecular weight phosphatase family;.
• Changed! pfam LMWPc 150aa 3e-41 in ref transcript
  • Low molecular weight phosphotyrosine protein phosphatase.
• Changed! COG Wzb 152aa 8e-31 in ref transcript
  • Protein-tyrosine-phosphatase [Signal transduction mechanisms].
• Changed! cd LMWPc 78aa 4e-23 in modified transcript
• Changed! pfam LMWPc 78aa 2e-21 in modified transcript
• Changed! COG Wzb 80aa 6e-19 in modified transcript

ACPL2

• rs.ACPL2.F1 rs.ACPL2.R1 206 380
• NCBIGene 36.3 92370
• Multiple exon skipping, size difference: 174
• Exclusion in 5'UTR, Exclusion in 5'UTR
• Reference transcript: NM_152282

• cd HP_HAP_like 81aa 3e-14 in ref transcript
  • Histidine phosphatase domain found in histidine acid phosphatases and phytases; contains a His residue which is phosphorylated during the reaction. Catalytic domain of HAP (histidine acid phosphatases) and phytases (myo-inositol hexakisphosphate phosphohydrolases). The conserved catalytic core of this domain contains a His residue which is phosphorylated in the reaction. Functions in this subgroup include roles in metabolism, signaling, or regulation, for example Escherichia coli glucose-1-phosphatase functions to scavenge glucose from glucose-1-phosphate and the signaling molecules inositol 1,3,4,5,6-pentakisphosphate (InsP5) and inositol hexakisphosphate (InsP6) are in vivo substrates for eukaryotic multiple inositol polyphosphate phosphatase 1 (Minpp1). Phytases scavenge phosphate from extracellular sources and are added to animal feed while prostatic acid phosphatase (PAP) has been used for many years as a serum marker for prostate cancer. Recently PAP has been shown in mouse models to suppress pain by functioning as an ecto-5prime-nucleotidase. In vivo it dephosphorylates extracellular adenosine monophosphate (AMP) generating adenosine,and leading to the activation of A1-adenosine receptors in dorsal spinal cord.
• cd HP_HAP_like 75aa 8e-13 in ref transcript
• pfam Acid_phosphat_A 338aa 3e-45 in ref transcript
  • Histidine acid phosphatase.

ACSM2B

• rs.ACSM2B.F1 rs.ACSM2B.R1 102 137
• NCBIGene 36.3 348158
• Single exon skipping, size difference: 35
• Exclusion in 5'UTR
• Reference transcript: NM_182617

• pfam AMP-binding 411aa 2e-81 in ref transcript
  • AMP-binding enzyme.
• COG Acs 526aa 1e-109 in ref transcript
  • Acyl-coenzyme A synthetases/AMP-(fatty) acid ligases [Lipid metabolism].

ACTR2

• rs.ACTR2.F1 rs.ACTR2.R1 102 117
• NCBIGene 36.3 10097
• Single exon skipping, size difference: 15
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001005386

• Changed! cd ACTIN 386aa 1e-122 in ref transcript
  • Actin; An ubiquitous protein involved in the formation of filaments that are a major component of the cytoskeleton. Interaction with myosin provides the basis of muscular contraction and many aspects of cell motility. Each actin protomer binds one molecule of ATP and either calcium or magnesium ions. Actin exists as a monomer in low salt concentrations, but filaments form rapidly as salt concentration rises, with the consequent hydrolysis of ATP. Polymerization is regulated by so-called capping proteins. The ATPase domain of actin shares similarity with ATPase domains of hexokinase and hsp70 proteins.
• Changed! smart ACTIN 388aa 1e-137 in ref transcript
  • Actin. ACTIN subfamily of ACTIN/mreB/sugarkinase/Hsp70 superfamily.
• Changed! PTZ PTZ00004 393aa 1e-106 in ref transcript
  • actin; Provisional.
• Changed! cd ACTIN 381aa 1e-122 in modified transcript
• Changed! smart ACTIN 383aa 1e-139 in modified transcript
• Changed! PTZ PTZ00004 388aa 1e-107 in modified transcript

ADAM15

• rs.ADAM15.F1 rs.ADAM15.R1 100 172
• NCBIGene 36.3 8751
• Single exon skipping, size difference: 72
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_207197

• cd ZnMc_adamalysin_II_like 200aa 3e-63 in ref transcript
  • Zinc-dependent metalloprotease; adamalysin_II_like subfamily. Adamalysin II is a snake venom zinc endopeptidase. This subfamily contains other snake venom metalloproteinases, as well as membrane-anchored metalloproteases belonging to the ADAM family. ADAMs (A Disintegrin And Metalloprotease) are glycoproteins, which play roles in cell signaling, cell fusion, and cell-cell interactions.
• pfam Reprolysin 199aa 2e-62 in ref transcript
  • Reprolysin (M12B) family zinc metalloprotease. The members of this family are enzymes that cleave peptides. These proteases require zinc for catalysis. Members of this family are also known as adamalysins. Most members of this family are snake venom endopeptidases, but there are also some mammalian proteins and fertilin. Fertilin and closely related proteins appear to not have some active site residues and may not be active enzymes.
• smart ACR 142aa 1e-38 in ref transcript
  • ADAM Cysteine-Rich Domain.
• pfam Pep_M12B_propep 143aa 3e-29 in ref transcript
  • Reprolysin family propeptide. This region is the propeptide for members of peptidase family M12B. The propeptide contains a sequence motif similar to the "cysteine switch" of the matrixins. This motif is found at the C terminus of the alignment but is not well aligned.
• pfam Disintegrin 75aa 4e-29 in ref transcript
  • Disintegrin.

ADAM9

• rs.ADAM9.F1 rs.ADAM9.R1 106 212
• NCBIGene 36.3 8754
• Single exon skipping, size difference: 106
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_003816

• cd ZnMc_adamalysin_II_like 193aa 3e-68 in ref transcript
  • Zinc-dependent metalloprotease; adamalysin_II_like subfamily. Adamalysin II is a snake venom zinc endopeptidase. This subfamily contains other snake venom metalloproteinases, as well as membrane-anchored metalloproteases belonging to the ADAM family. ADAMs (A Disintegrin And Metalloprotease) are glycoproteins, which play roles in cell signaling, cell fusion, and cell-cell interactions.
• pfam Reprolysin 195aa 2e-74 in ref transcript
  • Reprolysin (M12B) family zinc metalloprotease. The members of this family are enzymes that cleave peptides. These proteases require zinc for catalysis. Members of this family are also known as adamalysins. Most members of this family are snake venom endopeptidases, but there are also some mammalian proteins and fertilin. Fertilin and closely related proteins appear to not have some active site residues and may not be active enzymes.
• pfam Pep_M12B_propep 132aa 3e-52 in ref transcript
  • Reprolysin family propeptide. This region is the propeptide for members of peptidase family M12B. The propeptide contains a sequence motif similar to the "cysteine switch" of the matrixins. This motif is found at the C terminus of the alignment but is not well aligned.
• smart ACR 136aa 1e-50 in ref transcript
  • ADAM Cysteine-Rich Domain.
• pfam Disintegrin 77aa 4e-29 in ref transcript
  • Disintegrin.

ADAMTS13

• rs.ADAMTS13.F1 rs.ADAMTS13.R1 145 238
• NCBIGene 36.3 11093
• Alternative 3-prime, size difference: 93
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_139025

• Changed! cd ZnMc_ADAMTS_like 204aa 8e-68 in ref transcript
  • Zinc-dependent metalloprotease, ADAMTS_like subgroup. ADAMs (A Disintegrin And Metalloprotease) are glycoproteins, which play roles in cell signaling, cell fusion, and cell-cell interactions. This particular subfamily represents domain architectures that combine ADAM-like metalloproteinases with thrombospondin type-1 repeats. ADAMTS (a disintegrin and metalloproteinase with thrombospondin motifs) proteinases are inhibited by TIMPs (tissue inhibitors of metalloproteinases), and they play roles in coagulation, angiogenesis, development and progression of arthritis. They hydrolyze the von Willebrand factor precursor and various components of the extracellular matrix.
• Changed! pfam Reprolysin 206aa 1e-11 in ref transcript
  • Reprolysin (M12B) family zinc metalloprotease. The members of this family are enzymes that cleave peptides. These proteases require zinc for catalysis. Members of this family are also known as adamalysins. Most members of this family are snake venom endopeptidases, but there are also some mammalian proteins and fertilin. Fertilin and closely related proteins appear to not have some active site residues and may not be active enzymes.
• smart TSP1 53aa 3e-11 in ref transcript
  • Thrombospondin type 1 repeats. Type 1 repeats in thrombospondin-1 bind and activate TGF-beta.
• Changed! cd ZnMc_ADAMTS_like 198aa 4e-65 in modified transcript
• Changed! pfam Reprolysin 200aa 3e-10 in modified transcript

ADORA1

• rs.ADORA1.F1 rs.ADORA1.R1 138 293
• NCBIGene 36.3 134
• Single exon skipping, size difference: 155
• Exclusion in 5'UTR
• Reference transcript: NM_000674

• pfam 7tm_1 257aa 1e-20 in ref transcript
  • 7 transmembrane receptor (rhodopsin family). This family contains, amongst other G-protein-coupled receptors (GCPRs), members of the opsin family, which have been considered to be typical members of the rhodopsin superfamily. They share several motifs, mainly the seven transmembrane helices, GCPRs of the rhodopsin superfamily. All opsins bind a chromophore, such as 11-cis-retinal. The function of most opsins other than the photoisomerases is split into two steps: light absorption and G-protein activation. Photoisomerases, on the other hand, are not coupled to G-proteins - they are thought to generate and supply the chromophore that is used by visual opsins.

AFAP1L2

• rs.AFAP1L2.F1 rs.AFAP1L2.R1 100 112
• NCBIGene 36.3 84632
• Alternative 5-prime, size difference: 12
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001001936

• cd PH 89aa 8e-07 in ref transcript
  • Pleckstrin homology (PH) domain. PH domains are only found in eukaryotes. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes.
• cd PH 77aa 9e-07 in ref transcript
• pfam PH 75aa 1e-08 in ref transcript
  • PH domain. PH stands for pleckstrin homology.
• smart PH 88aa 6e-06 in ref transcript
  • Pleckstrin homology domain. Domain commonly found in eukaryotic signalling proteins. The domain family possesses multiple functions including the abilities to bind inositol phosphates, and various proteins. PH domains have been found to possess inserted domains (such as in PLC gamma, syntrophins) and to be inserted within other domains. Mutations in Brutons tyrosine kinase (Btk) within its PH domain cause X-linked agammaglobulinaemia (XLA) in patients. Point mutations cluster into the positively charged end of the molecule around the predicted binding site for phosphatidylinositol lipids.

AFF3

• rs.AFF3.F1 rs.AFF3.R1 113 188
• NCBIGene 36.3 3899
• Single exon skipping, size difference: 75
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001025108

• pfam AF-4 1204aa 0.0 in ref transcript
  • AF-4 proto-oncoprotein. This family consists of AF4 (Proto-oncogene AF4) and FMR2 (Fragile X E mental retardation syndrome) nuclear proteins. These proteins have been linked to human diseases such as acute lymphoblastic leukaemia and mental retardation. The family also contains a Drosophila AF4 protein homologue Lilliputian which contains an AT-hook domain. Lilliputian represents a novel pair-rule gene that acts in cytoskeleton regulation, segmentation and morphogenesis in Drosophila.

AGPAT2

• rs.AGPAT2.F1 rs.AGPAT2.R1 251 347
• NCBIGene 36.3 10555
• Single exon skipping, size difference: 96
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_006412

• Changed! pfam Acyltransferase 115aa 3e-28 in ref transcript
  • Acyltransferase. This family contains acyltransferases involved in phospholipid biosynthesis and other proteins of unknown function. This family also includes tafazzin, the Barth syndrome gene.
• Changed! COG PlsC 228aa 3e-19 in ref transcript
  • 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism].
• Changed! pfam Acyltransferase 88aa 3e-15 in modified transcript
• Changed! COG PlsC 129aa 5e-10 in modified transcript

AGTR1

• rs.AGTR1.F1 rs.AGTR1.R1 200 357
• NCBIGene 36.3 185
• Single exon skipping, size difference: 157
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_031850

• Changed! pfam 7tm_1 252aa 2e-42 in ref transcript
  • 7 transmembrane receptor (rhodopsin family). This family contains, amongst other G-protein-coupled receptors (GCPRs), members of the opsin family, which have been considered to be typical members of the rhodopsin superfamily. They share several motifs, mainly the seven transmembrane helices, GCPRs of the rhodopsin superfamily. All opsins bind a chromophore, such as 11-cis-retinal. The function of most opsins other than the photoisomerases is split into two steps: light absorption and G-protein activation. Photoisomerases, on the other hand, are not coupled to G-proteins - they are thought to generate and supply the chromophore that is used by visual opsins.

AGTR1

• rs.AGTR1.F2 rs.AGTR1.R2 223 281
• NCBIGene 36.3 185
• Single exon skipping, size difference: 58
• Exclusion of the protein initiation site
• Reference transcript: NM_031850

• pfam 7tm_1 252aa 2e-42 in ref transcript
  • 7 transmembrane receptor (rhodopsin family). This family contains, amongst other G-protein-coupled receptors (GCPRs), members of the opsin family, which have been considered to be typical members of the rhodopsin superfamily. They share several motifs, mainly the seven transmembrane helices, GCPRs of the rhodopsin superfamily. All opsins bind a chromophore, such as 11-cis-retinal. The function of most opsins other than the photoisomerases is split into two steps: light absorption and G-protein activation. Photoisomerases, on the other hand, are not coupled to G-proteins - they are thought to generate and supply the chromophore that is used by visual opsins.

AGTR1

• rs.AGTR1.F3 rs.AGTR1.R3 291 375
• NCBIGene 36.3 185
• Single exon skipping, size difference: 84
• Exclusion in 5'UTR
• Reference transcript: NM_031850

• pfam 7tm_1 252aa 2e-42 in ref transcript
  • 7 transmembrane receptor (rhodopsin family). This family contains, amongst other G-protein-coupled receptors (GCPRs), members of the opsin family, which have been considered to be typical members of the rhodopsin superfamily. They share several motifs, mainly the seven transmembrane helices, GCPRs of the rhodopsin superfamily. All opsins bind a chromophore, such as 11-cis-retinal. The function of most opsins other than the photoisomerases is split into two steps: light absorption and G-protein activation. Photoisomerases, on the other hand, are not coupled to G-proteins - they are thought to generate and supply the chromophore that is used by visual opsins.

AKAP13

• rs.AKAP13.F1 rs.AKAP13.R1 106 118
• NCBIGene 36.3 11214
• Mutually exclusive exon skipping, size difference: 12
• Inclusion in the protein (no stop codon or frameshift), Exclusion in the protein (no frameshift)
• Reference transcript: NM_006738

• cd RhoGEF 195aa 4e-37 in ref transcript
  • Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.
• cd PH 91aa 2e-05 in ref transcript
  • Pleckstrin homology (PH) domain. PH domains are only found in eukaryotes. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes.
• smart RhoGEF 192aa 5e-40 in ref transcript
  • Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases. Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains. Improved coverage.
• smart PH 102aa 5e-07 in ref transcript
  • Pleckstrin homology domain. Domain commonly found in eukaryotic signalling proteins. The domain family possesses multiple functions including the abilities to bind inositol phosphates, and various proteins. PH domains have been found to possess inserted domains (such as in PLC gamma, syntrophins) and to be inserted within other domains. Mutations in Brutons tyrosine kinase (Btk) within its PH domain cause X-linked agammaglobulinaemia (XLA) in patients. Point mutations cluster into the positively charged end of the molecule around the predicted binding site for phosphatidylinositol lipids.
• COG ROM1 305aa 5e-06 in ref transcript
  • RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms].

AKAP9

• rs.AKAP9.F1 rs.AKAP9.R1 129 153
• NCBIGene 36.3 10142
• Alternative 5-prime, size difference: 24
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_147171

• pfam PACT_coil_coil 83aa 2e-26 in ref transcript
  • Pericentrin-AKAP-450 domain of centrosomal targeting protein. This domain is a coiled-coil region close to the C-terminus of centrosomal proteins that is directly responsible for recruiting AKAP-450 and pericentrin to the centrosome. Hence the suggested name for this region is a PACT domain (pericentrin-AKAP-450 centrosomal targeting). This domain is also present at the C-terminus of coiled-coil proteins from Drosophila and S. pombe, and that from the Drosophila protein is sufficient for targeting to the centrosome in mammalian cells. The function of these proteins is unknown but they seem good candidates for having a centrosomal or spindle pole body location. The final 22 residues of this domain in AKAP-450 appear specifically to be a calmodulin-binding domain indicating that this member at least is likely to contribute to centrosome assembly.
• Changed! TIGR SMC_prok_B 404aa 6e-07 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• pfam SMC_N 259aa 6e-05 in ref transcript
  • RecF/RecN/SMC N terminal domain. This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.
• TIGR SMC_prok_A 252aa 0.001 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent.
• TIGR SMC_prok_B 709aa 0.002 in ref transcript
• COG Smc 264aa 3e-04 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].
• Changed! COG Smc 317aa 7e-04 in ref transcript
• PRK PRK05771 168aa 0.009 in ref transcript
  • V-type ATP synthase subunit I; Validated.
• Changed! TIGR SMC_prok_B 386aa 2e-07 in modified transcript
• Changed! COG Smc 308aa 4e-04 in modified transcript

AKR1C2

• rs.AKR1C2.F1 rs.AKR1C2.R1 245 345
• NCBIGene 36.3 1646
• Single exon skipping, size difference: 100
• Exclusion in 5'UTR
• Reference transcript: NM_001354

• cd Aldo_ket_red 289aa 1e-71 in ref transcript
  • Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial applications. Members have very distinct functions and include the prokaryotic 2,5-diketo-D-gluconic acid reductases and beta-keto ester reductases, the eukaryotic aldose reductases, aldehyde reductases, hydroxysteroid dehydrogenases, steroid 5beta-reductases, potassium channel beta-subunits and aflatoxin aldehyde reductases, among others.
• pfam Aldo_ket_red 292aa 1e-106 in ref transcript
  • Aldo/keto reductase family. This family includes a number of K+ ion channel beta chain regulatory domains - these are reported to have oxidoreductase activity.
• COG ARA1 298aa 9e-81 in ref transcript
  • Aldo/keto reductases, related to diketogulonate reductase [General function prediction only].

AKT1

• rs.AKT1.F1 rs.AKT1.R1 239 323
• NCBIGene 36.3 207
• Single exon skipping, size difference: 84
• Exclusion in 5'UTR
• Reference transcript: NM_001014432

• cd STKc_PKB_alpha 324aa 0.0 in ref transcript
  • STKc_PKB_alpha: Serine/Threonine Kinases (STKs), Protein Kinase B (PKB) or Akt subfamily, alpha (or Akt1) isoform, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The PKB subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. There are three PKB isoforms from different genes, PKB-alpha (or Akt1), PKB-beta (or Akt2), and PKB-gamma (or Akt3). PKB contains an N-terminal pleckstrin homology (PH) domain and a C-terminal catalytic domain. PKB-alpha is predominantly expressed in endothelial cells. It is critical for the regulation of angiogenesis and the maintenance of vascular integrity. It also plays a role in adipocyte differentiation. Mice deficient in PKB-alpha exhibit perinatal morbidity, growth retardation, reduction in body weight accompanied by reduced sizes of multiple organs, and enhanced apoptosis in some cell types. PKB-alpha activity has been reported to be frequently elevated in breast and prostate cancers. In some cancer cells, PKB-alpha may act as a suppressor of metastasis.
• cd PH_Akt 102aa 3e-52 in ref transcript
  • Akt pleckstrin homology (PH) domain. Akt (Protein Kinase B (PKB)) is a phosphatidylinositol 3'-kinase (PI3K)-dependent Ser/Thr kinase. The PH domain recruits Akt to the plasma membrane by binding to phosphoinositides (PtdIns-3,4-P2) and is required for activation. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
• smart S_TKc 249aa 2e-86 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• smart S_TK_X 68aa 7e-15 in ref transcript
  • Extension to Ser/Thr-type protein kinases.
• pfam PH 99aa 1e-11 in ref transcript
  • PH domain. PH stands for pleckstrin homology.
• PTZ PTZ00263 309aa 4e-80 in ref transcript
  • protein kinase A catalytic subunit; Provisional.

AKT1S1

• rs.AKT1S1.F1 rs.AKT1S1.R1 111 533
• NCBIGene 36.3 84335
• Alternative 5-prime, size difference: 422
• Exclusion of the protein initiation site
• Reference transcript: NM_032375

ALG9

• rs.ALG9.F1 rs.ALG9.R1 117 138
• NCBIGene 36.3 79796
• Alternative 3-prime, size difference: 21
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_024740

• Changed! pfam Glyco_transf_22 318aa 2e-57 in ref transcript
  • Alg9-like mannosyltransferase family. Members of this family are mannosyltransferase enzymes. At least some members are localised in endoplasmic reticulum and involved in GPI anchor biosynthesis.
• Changed! pfam Glyco_transf_22 311aa 8e-59 in modified transcript

ALPK1

• rs.ALPK1.F1 rs.ALPK1.R1 209 261
• NCBIGene 36.3 80216
• Alternative 3-prime, size difference: 52
• Inclusion in 5'UTR
• Reference transcript: NM_001102406

• pfam Alpha_kinase 205aa 4e-57 in ref transcript
  • Alpha-kinase family. This family is a novel family of eukaryotic protein kinase catalytic domains, which have no detectable similarity to conventional kinases. The family contains myosin heavy chain kinases and Elongation Factor-2 kinase and a bifunctional ion channel. This family is known as the alpha-kinase family. The structure of the kinase domain revealed unexpected similarity to eukaryotic protein kinases in the catalytic core as well as to metabolic enzymes with ATP-grasp domains.

ALS2CR8

• rs.ALS2CR8.F1 rs.ALS2CR8.R1 207 326
• NCBIGene 36.3 79800
• Single exon skipping, size difference: 119
• Exclusion in 5'UTR
• Reference transcript: NM_024744

AMELX

• rs.AMELX.F1 rs.AMELX.R1 245 287
• NCBIGene 36.3 265
• Single exon skipping, size difference: 42
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_182680

• Changed! pfam Amelogenin 66aa 4e-16 in ref transcript
  • Amelogenin. Amelogenins play a role in biomineralisation. They seem to regulate the formation of crystallites during the secretory stage of tooth enamel development. thought to play a major role in the structural organisation and mineralisation of developing enamel. They are found in the extracellular matrix. Mutations in X-chromosomal amelogenin can cause Amelogenesis imperfecta.
• Changed! pfam Amelogenin 52aa 1e-17 in modified transcript

AMPH

• rs.AMPH.F1 rs.AMPH.R1 297 423
• NCBIGene 36.3 273
• Single exon skipping, size difference: 126
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001635

• cd SH3 68aa 3e-06 in ref transcript
  • Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
• pfam BAR 220aa 3e-55 in ref transcript
  • BAR domain. BAR domains are dimerisation, lipid binding and curvature sensing modules found in many different protein families. A BAR domain with an additional N-terminal amphipathic helix (an N-BAR) can drive membrane curvature. These N-BAR domains are found in amphiphysin, endophilin, BRAP and Nadrin. BAR domains are also frequently found alongside domains that determine lipid specificity, like pfam00169 and pfam00787 domains in beta centaurins and sorting nexins respectively.
• smart SH3 70aa 7e-07 in ref transcript
  • Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.
• Changed! PRK rne 148aa 0.009 in ref transcript
  • ribonuclease E; Reviewed.
• Changed! PRK PRK05648 145aa 0.005 in modified transcript
  • DNA polymerase III subunits gamma and tau; Reviewed.

ANK1

• rs.ANK1.F1 rs.ANK1.R1 191 392
• NCBIGene 36.3 286
• Multiple exon skipping, size difference: 201
• Exclusion in the protein (no frameshift), Exclusion of the stop codon
• Reference transcript: NM_020478

ANKHD1

• rs.ANKHD1.F1 rs.ANKHD1.R1 143 176
• NCBIGene 36.3 54882
• Alternative 3-prime, size difference: 33
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_017747

• cd ANK 125aa 5e-28 in ref transcript
  • ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats.
• cd ANK 127aa 2e-26 in ref transcript
• cd ANK 127aa 3e-26 in ref transcript
• cd ANK 119aa 2e-25 in ref transcript
• cd ANK 128aa 4e-25 in ref transcript
• cd ANK 123aa 5e-23 in ref transcript
• cd KH-I 63aa 2e-11 in ref transcript
  • K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
• cd ANK 65aa 5e-08 in ref transcript
• pfam KH_1 63aa 2e-11 in ref transcript
  • KH domain. KH motifs can bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.
• TIGR trp 239aa 1e-06 in ref transcript
  • after chronic exposure to capsaicin. (McCleskey and Gold, 1999).
• TIGR trp 222aa 2e-05 in ref transcript
• pfam Ank 33aa 3e-05 in ref transcript
  • Ankyrin repeat. There's no clear separation between noise and signal on the HMM search Ankyrin repeats generally consist of a beta, alpha, alpha, beta order of secondary structures. The repeats associate to form a higher order structure.
• pfam Ank 29aa 9e-05 in ref transcript
• pfam Ank 31aa 4e-04 in ref transcript
• pfam Ank 29aa 0.001 in ref transcript
• pfam Ank 27aa 0.004 in ref transcript
• COG Arp 183aa 7e-16 in ref transcript
  • FOG: Ankyrin repeat [General function prediction only].
• COG Arp 196aa 1e-15 in ref transcript
• COG Arp 201aa 9e-15 in ref transcript
• COG Arp 228aa 2e-11 in ref transcript
• COG Arp 133aa 3e-11 in ref transcript

ANKRD12

• rs.ANKRD12.F1 rs.ANKRD12.R1 250 319
• NCBIGene 36.3 23253
• Single exon skipping, size difference: 69
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_015208

• cd ANK 113aa 4e-28 in ref transcript
  • ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats.
• pfam Ank 31aa 6e-06 in ref transcript
  • Ankyrin repeat. There's no clear separation between noise and signal on the HMM search Ankyrin repeats generally consist of a beta, alpha, alpha, beta order of secondary structures. The repeats associate to form a higher order structure.
• pfam Ank 28aa 4e-05 in ref transcript
• pfam Ank 33aa 1e-04 in ref transcript
• COG Arp 172aa 2e-12 in ref transcript
  • FOG: Ankyrin repeat [General function prediction only].

ANKRD16

• rs.ANKRD16.F1 rs.ANKRD16.R1 102 207
• NCBIGene 36.3 54522
• Alternative 5-prime and 3-prime, size difference: 105
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_019046

• cd ANK 121aa 5e-22 in ref transcript
  • ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats.
• Changed! cd ANK 156aa 5e-20 in ref transcript
• cd ANK 128aa 3e-19 in ref transcript
• TIGR trp 142aa 4e-05 in ref transcript
  • after chronic exposure to capsaicin. (McCleskey and Gold, 1999).
• Changed! TIGR trp 223aa 3e-04 in ref transcript
• Changed! COG Arp 184aa 7e-12 in ref transcript
  • FOG: Ankyrin repeat [General function prediction only].
• COG Arp 122aa 1e-10 in ref transcript
• Changed! cd ANK 121aa 1e-23 in modified transcript
• Changed! TIGR trp 177aa 0.003 in modified transcript
• Changed! COG Arp 169aa 3e-12 in modified transcript

ANKRD7

• rs.ANKRD7.F1 rs.ANKRD7.R1 177 237
• NCBIGene 36.3 56311
• Single exon skipping, size difference: 60
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001077708

• Changed! cd ANK 123aa 1e-26 in ref transcript
  • ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats.
• cd ANK 65aa 7e-10 in ref transcript
• pfam Ank 33aa 7e-07 in ref transcript
  • Ankyrin repeat. There's no clear separation between noise and signal on the HMM search Ankyrin repeats generally consist of a beta, alpha, alpha, beta order of secondary structures. The repeats associate to form a higher order structure.
• TIGR trp 102aa 1e-05 in ref transcript
  • after chronic exposure to capsaicin. (McCleskey and Gold, 1999).
• Changed! pfam Ank 30aa 4e-05 in ref transcript
• Changed! COG Arp 134aa 1e-10 in ref transcript
  • FOG: Ankyrin repeat [General function prediction only].
• Changed! cd ANK 126aa 2e-27 in modified transcript
• Changed! pfam Ank 30aa 5e-05 in modified transcript
• Changed! COG Arp 161aa 2e-11 in modified transcript

ANXA11

• rs.ANXA11.F1 rs.ANXA11.R1 220 416
• NCBIGene 36.3 311
• Single exon skipping, size difference: 196
• Exclusion in 5'UTR
• Reference transcript: NM_145869

• pfam Annexin 66aa 8e-22 in ref transcript
  • Annexin. This family of annexins also includes giardin that has been shown to function as an annexin.
• pfam Annexin 66aa 1e-21 in ref transcript
• pfam Annexin 66aa 4e-19 in ref transcript
• pfam Annexin 67aa 2e-17 in ref transcript

AP1S1

• rs.AP1S1.F1 rs.AP1S1.R1 139 416
• NCBIGene 36.3 1174
• Alternative 5-prime and 3-prime, size difference: 277
• Exclusion in the protein (no frameshift), Exclusion of the stop codon
• Reference transcript: NM_001283

• Changed! pfam Clat_adaptor_s 142aa 9e-58 in ref transcript
  • Clathrin adaptor complex small chain.
• Changed! COG APS2 150aa 7e-47 in ref transcript
  • Clathrin adaptor complex, small subunit [Intracellular trafficking and secretion].
• Changed! pfam Clat_adaptor_s 127aa 4e-54 in modified transcript
• Changed! COG APS2 129aa 2e-43 in modified transcript

AP3D1

• rs.AP3D1.F1 rs.AP3D1.R1 199 349
• NCBIGene 36.3 8943
• Multiple exon skipping, size difference: 150
• Inclusion in the protein (no stop codon or frameshift), Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_003938

• Changed! pfam BLVR 260aa 1e-141 in ref transcript
  • Bovine leukaemia virus receptor (BLVR). This family consists of several bovine specific leukaemia virus receptors which are thought to function as transmembrane proteins, although their exact function is unknown.
• pfam Adaptin_N 550aa 1e-132 in ref transcript
  • Adaptin N terminal region. This family consists of the N terminal region of various alpha, beta and gamma subunits of the AP-1, AP-2 and AP-3 adaptor protein complexes. The adaptor protein (AP) complexes are involved in the formation of clathrin-coated pits and vesicles. The N-terminal region of the various adaptor proteins (APs) is constant by comparison to the C-terminal which is variable within members of the AP-2 family; and it has been proposed that this constant region interacts with another uniform component of the coated vesicles.
• pfam BLVR 194aa 1e-79 in ref transcript
• COG COG5096 407aa 1e-12 in ref transcript
  • Vesicle coat complex, various subunits [Intracellular trafficking and secretion].
• Changed! pfam BLVR 253aa 1e-139 in modified transcript

AP3D1

• rs.AP3D1.F2 rs.AP3D1.R2 101 374
• NCBIGene 36.3 8943
• Exon skipping and alternative 3-prime or 5-prime, size difference: 273
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift, Exclusion in the protein (no frameshift)
• Reference transcript: NM_003938

• pfam BLVR 260aa 1e-141 in ref transcript
  • Bovine leukaemia virus receptor (BLVR). This family consists of several bovine specific leukaemia virus receptors which are thought to function as transmembrane proteins, although their exact function is unknown.
• Changed! pfam Adaptin_N 550aa 1e-132 in ref transcript
  • Adaptin N terminal region. This family consists of the N terminal region of various alpha, beta and gamma subunits of the AP-1, AP-2 and AP-3 adaptor protein complexes. The adaptor protein (AP) complexes are involved in the formation of clathrin-coated pits and vesicles. The N-terminal region of the various adaptor proteins (APs) is constant by comparison to the C-terminal which is variable within members of the AP-2 family; and it has been proposed that this constant region interacts with another uniform component of the coated vesicles.
• pfam BLVR 194aa 1e-79 in ref transcript
• Changed! COG COG5096 407aa 1e-12 in ref transcript
  • Vesicle coat complex, various subunits [Intracellular trafficking and secretion].
• Changed! pfam Adaptin_N 333aa 3e-61 in modified transcript
• Changed! COG COG5096 212aa 1e-06 in modified transcript

APAF1

• rs.APAF1.F1 rs.APAF1.R1 193 322
• NCBIGene 36.3 317
• Single exon skipping, size difference: 129
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_181861

• Changed! cd WD40 304aa 4e-60 in ref transcript
  • WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.
• cd WD40 274aa 5e-47 in ref transcript
• pfam NB-ARC 286aa 5e-73 in ref transcript
  • NB-ARC domain.
• pfam CARD 85aa 4e-14 in ref transcript
  • Caspase recruitment domain. Motif contained in proteins involved in apoptotic signaling. Predicted to possess a DEATH (pfam00531) domain-like fold.
• smart WD40 40aa 8e-08 in ref transcript
  • WD40 repeats. Note that these repeats are permuted with respect to the structural repeats (blades) of the beta propeller domain.
• smart WD40 40aa 2e-06 in ref transcript
• smart WD40 40aa 8e-05 in ref transcript
• smart WD40 42aa 1e-04 in ref transcript
• smart WD40 37aa 1e-04 in ref transcript
• Changed! pfam eIF2A 114aa 0.003 in ref transcript
  • Eukaryotic translation initiation factor eIF2A. This is a family of eukaryotic translation initiation factors.
• smart WD40 28aa 0.006 in ref transcript
• smart WD40 34aa 0.008 in ref transcript
• Changed! COG COG2319 398aa 4e-33 in ref transcript
  • FOG: WD40 repeat [General function prediction only].
• Changed! COG COG2319 408aa 5e-25 in ref transcript
• Changed! cd WD40 264aa 1e-55 in modified transcript
• Changed! COG COG2319 390aa 1e-33 in modified transcript

APAF1

• rs.APAF1.F2 rs.APAF1.R2 185 218
• NCBIGene 36.3 317
• Alternative 5-prime, size difference: 33
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_181861

• cd WD40 304aa 4e-60 in ref transcript
  • WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.
• cd WD40 274aa 5e-47 in ref transcript
• pfam NB-ARC 286aa 5e-73 in ref transcript
  • NB-ARC domain.
• pfam CARD 85aa 4e-14 in ref transcript
  • Caspase recruitment domain. Motif contained in proteins involved in apoptotic signaling. Predicted to possess a DEATH (pfam00531) domain-like fold.
• smart WD40 40aa 8e-08 in ref transcript
  • WD40 repeats. Note that these repeats are permuted with respect to the structural repeats (blades) of the beta propeller domain.
• smart WD40 40aa 2e-06 in ref transcript
• smart WD40 40aa 8e-05 in ref transcript
• smart WD40 42aa 1e-04 in ref transcript
• smart WD40 37aa 1e-04 in ref transcript
• pfam eIF2A 114aa 0.003 in ref transcript
  • Eukaryotic translation initiation factor eIF2A. This is a family of eukaryotic translation initiation factors.
• smart WD40 28aa 0.006 in ref transcript
• smart WD40 34aa 0.008 in ref transcript
• COG COG2319 398aa 4e-33 in ref transcript
  • FOG: WD40 repeat [General function prediction only].
• COG COG2319 408aa 5e-25 in ref transcript

APP

• rs.APP.F1 rs.APP.R1 245 302
• NCBIGene 36.3 351
• Single exon skipping, size difference: 57
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000484

• cd KU 52aa 9e-18 in ref transcript
  • BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
• pfam A4_EXTRA 165aa 8e-89 in ref transcript
  • Amyloid A4 extracellular domain.
• pfam Kunitz_BPTI 52aa 6e-19 in ref transcript
  • Kunitz/Bovine pancreatic trypsin inhibitor domain. Indicative of a protease inhibitor, usually a serine protease inhibitor. Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure. Certain family members are similar to the tick anticoagulant peptide (TAP). This is a highly selective inhibitor of factor Xa in the blood coagulation pathways. TAP molecules are highly dipolar, and are arranged to form a twisted two- stranded antiparallel beta-sheet followed by an alpha helix.
• pfam APP_amyloid 43aa 4e-18 in ref transcript
  • beta-amyloid precursor protein C-terminus. This is the amyloid, C-terminal, protein of the beta-Amyloid precursor protein (APP) which is a conserved and ubiquitous transmembrane glycoprotein strongly implicated in the pathogenesis of Alzheimer's disease but whose normal biological function is unknown. The C-terminal 100 residues are released and aggregate into amyloid deposits which are strongly implicated in the pathology of Alzheimer's disease plaque-formation. The domain is associated with family A4_EXTRA, pfam02177, further towards the N-terminus.
• pfam Beta-APP 34aa 9e-07 in ref transcript
  • Beta-amyloid peptide (beta-APP).
• pfam OmpH 81aa 0.005 in ref transcript
  • Outer membrane protein (OmpH-like). This family includes outer membrane proteins such as OmpH among others. Skp (OmpH) has been characterised as a molecular chaperone that interacts with unfolded proteins as they emerge in the periplasm from the Sec translocation machinery.
• Changed! COG SbcC 197aa 0.006 in ref transcript
  • ATPase involved in DNA repair [DNA replication, recombination, and repair].
• Changed! PRK xseA 173aa 0.001 in modified transcript
  • exodeoxyribonuclease VII large subunit; Reviewed.

ARFGAP1

• rs.ARFGAP1.F1 rs.ARFGAP1.R1 169 193
• NCBIGene 36.3 55738
• Single exon skipping, size difference: 30
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_175609

• pfam ArfGap 118aa 3e-48 in ref transcript
  • Putative GTPase activating protein for Arf. Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs.
• COG COG5347 159aa 4e-31 in ref transcript
  • GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion].

ARHGAP9

• rs.ARHGAP9.F1 rs.ARHGAP9.R1 295 401
• NCBIGene 36.3 64333
• Single exon skipping, size difference: 106
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_032496

• Changed! cd RhoGAP_ARHGAP27_15_12_9 205aa 6e-82 in ref transcript
  • RhoGAP_ARHGAP27_15_12_9: GTPase-activator protein (GAP) domain for Rho-like GTPases found in ARHGAP27 (also called CAMGAP1), ARHGAP15, 12 and 9-like proteins; This subgroup of ARHGAPs are multidomain proteins that contain RhoGAP, PH, SH3 and WW domains. Most members that are studied show GAP activity towards Rac1, some additionally show activity towards Cdc42. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
• cd PH 109aa 2e-09 in ref transcript
  • Pleckstrin homology (PH) domain. PH domains are only found in eukaryotes. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes.
• cd SH3 54aa 0.002 in ref transcript
  • Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
• Changed! pfam RhoGAP 171aa 7e-43 in ref transcript
  • RhoGAP domain. GTPase activator proteins towards Rho/Rac/Cdc42-like small GTPases.
• pfam PH 112aa 3e-08 in ref transcript
  • PH domain. PH stands for pleckstrin homology.
• pfam SH3_1 54aa 3e-05 in ref transcript
  • SH3 domain. SH3 (Src homology 3) domains are often indicative of a protein involved in signal transduction related to cytoskeletal organisation. First described in the Src cytoplasmic tyrosine kinase. The structure is a partly opened beta barrel.
• Changed! cd RhoGAP_ARHGAP27_15_12_9 119aa 2e-38 in modified transcript
• Changed! pfam RhoGAP 103aa 6e-16 in modified transcript

ARID4A

• rs.ARID4A.F1 rs.ARID4A.R1 146 308
• NCBIGene 36.3 5926
• Alternative 5-prime, size difference: 162
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_002892

• cd CHROMO 38aa 0.003 in ref transcript
  • Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence implicates the chromo domain in the binding activity of these proteins to methylated histone tails and maybe RNA. May occur as single instance, in a tandem arrangement or followd by a related "chromo shadow" domain.
• pfam ARID 96aa 1e-31 in ref transcript
  • ARID/BRIGHT DNA binding domain. This domain is know as ARID for AT-Rich Interaction Domain, and also known as the BRIGHT domain.
• pfam RBB1NT 93aa 8e-25 in ref transcript
  • RBB1NT (NUC162) domain. This domain is found N terminal to the ARID/BRIGHT domain in DNA-binding proteins of the Retinoblastoma-binding protein 1 family.
• smart TUDOR 56aa 1e-05 in ref transcript
  • Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).
• smart CHROMO 42aa 1e-04 in ref transcript
  • Chromatin organization modifier domain.

ARL13B

• rs.ARL13B.F1 rs.ARL13B.R1 136 457
• NCBIGene 36.3 200894
• Multiple exon skipping, size difference: 321
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_182896

• Changed! cd Arl2l1_Arl13_like 167aa 3e-79 in ref transcript
  • Arl2l1/Arl13 subfamily. Arl2l1 (Arl2-like protein 1) and Arl13 form a subfamily of the Arf family of small GTPases. Arl2l1 was identified in human cells during a search for the gene(s) responsible for Bardet-Biedl syndrome (BBS). Like Arl6, the identified BBS gene, Arl2l1 is proposed to have cilia-specific functions. Arl13 is found on the X chromosome, but its expression has not been confirmed; it may be a pseudogene.
• Changed! pfam Arf 171aa 4e-36 in ref transcript
  • ADP-ribosylation factor family. Pfam combines a number of different Prosite families together.
• Changed! pfam DUF1682 43aa 0.007 in ref transcript
  • Protein of unknown function (DUF1682). The members of this family are all hypothetical eukaryotic proteins of unknown function. One member is described as being an adipocyte-specific protein, but no evidence of this was found.
• TIGR major_cap_HK97 94aa 0.009 in ref transcript
  • This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease.
• Changed! PTZ PTZ00133 167aa 2e-23 in ref transcript
  • ADP-ribosylation factor; Provisional.
• PRK rne 46aa 0.002 in ref transcript
  • ribonuclease E; Reviewed.
• Changed! cd Arl2l1_Arl13_like 62aa 4e-25 in modified transcript
• Changed! pfam Arf 63aa 6e-05 in modified transcript

ARL5A

• rs.ARL5A.F1 rs.ARL5A.R1 100 358
• NCBIGene 36.3 26225
• Alternative 5-prime, size difference: 258
• Exclusion of the protein initiation site
• Reference transcript: NM_012097

• Changed! cd Arl5_Arl8 173aa 1e-94 in ref transcript
  • Arl5/Arl8 subfamily. Arl5 (Arf-like 5) and Arl8, like Arl4 and Arl7, are localized to the nucleus and nucleolus. Arl5 is developmentally regulated during embryogenesis in mice. Human Arl5 interacts with the heterochromatin protein 1-alpha (HP1alpha), a nonhistone chromosomal protein that is associated with heterochromatin and telomeres, and prevents telomere fusion. Arl5 may also play a role in embryonic nuclear dynamics and/or signaling cascades. Arl8 was identified from a fetal cartilage cDNA library. It is found in brain, heart, lung, cartilage, and kidney. No function has been assigned for Arl8 to date.
• Changed! pfam Arf 158aa 2e-61 in ref transcript
  • ADP-ribosylation factor family. Pfam combines a number of different Prosite families together.
• Changed! PTZ PTZ00133 179aa 5e-55 in ref transcript
  • ADP-ribosylation factor; Provisional.
• Changed! cd Arl5_Arl8 138aa 6e-76 in modified transcript
• Changed! pfam Arf 135aa 3e-50 in modified transcript
• Changed! PTZ PTZ00133 142aa 4e-43 in modified transcript

ARL6IP4

• rs.ARL6IP4.F1 rs.ARL6IP4.R1 101 125
• NCBIGene 36.3 51329
• Alternative 3-prime, size difference: 24
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_018694

• pfam SR-25 73aa 2e-19 in ref transcript
  • Nuclear RNA-splicing-associated protein. SR-25, otherwise known as ADP-ribosylation factor-like factor 6-interacting protein 4, is expressed in virtually all tissues. At the N-terminus there is a repeat of serine-arginine (SR repeat), and towards the middle of the protein there are clusters of both serines and of basic amino acids. The presence of many nuclear localisation signals strongly implies that this is a nuclear protein that may contribute to RNA splicing. SR-25 is also implicated, along with heat-shock-protein-27, as a mediator in the Rac1 (GTPase ras-related C3 botulinum toxin substrate 1) signalling pathway.

ARPC4

• rs.ARPC4.F1 rs.ARPC4.R1 103 522
• NCBIGene 36.3 10093
• Alternative 5-prime, size difference: 419
• Exclusion of the protein initiation site
• Reference transcript: NM_005718

• Changed! pfam ARPC4 168aa 1e-88 in ref transcript
  • ARP2/3 complex 20 kDa subunit (ARPC4). This family consists of several eukaryotic ARP2/3 complex 20 kDa subunit (P20-ARC) proteins. The Arp2/3 protein complex has been implicated in the control of actin polymerisation in cells. The human complex consists of seven subunits which include the actin related proteins Arp2 and Arp3 it has been suggested that the complex promotes actin assembly in lamellipodia and may participate in lamellipodial protrusion.
• Changed! PTZ PTZ00278 168aa 2e-59 in ref transcript
  • ARP2/3 complex subunit; Provisional.

ARTN

• rs.ARTN.F1 rs.ARTN.R1 150 174
• NCBIGene 36.3 9048
• Alternative 3-prime, size difference: 24
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_057090

• pfam TGF_beta 96aa 8e-06 in ref transcript
  • Transforming growth factor beta like domain.

ASGR2

• rs.ASGR2.F1 rs.ASGR2.R1 222 279
• NCBIGene 36.3 433
• Alternative 5-prime, size difference: 57
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_080912

• cd CLECT_DC-SIGN_like 126aa 1e-40 in ref transcript
  • CLECT_DC-SIGN_like: C-type lectin-like domain (CTLD) of the type found in human dendritic cell (DC)-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN) and the related receptor, DC-SIGN receptor (DC-SIGNR). This group also contains proteins similar to hepatic asialoglycoprotein receptor (ASGP-R) and langerin in human. These proteins are type II membrane proteins with a CTLD ectodomain. CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. DC-SIGN is thought to mediate the initial contact between dendritic cells and resting T cells, and may also mediate the rolling of DCs on epithelium. DC-SIGN and DC-SIGNR bind to oligosaccharides present on human tissues, as well as, on pathogens including parasites, bacteria, and viruses. DC-SIGN and DC-SIGNR bind to HIV enhancing viral infection of T cells. DC-SIGN and DC-SIGNR are homotetrameric, and contain four CTLDs stabilized by a coiled coil of alpha helices. The hepatic ASGP-R is an endocytic recycling receptor which binds and internalizes desialylated glycoproteins having a terminal galactose or N-acetylgalactosamine residues on their N-linked carbohydrate chains, via the clathrin-coated pit mediated endocytic pathway, and delivers them to lysosomes for degradation. It has been proposed that glycoproteins bearing terminal Sia (sialic acid) alpha2, 6GalNAc and Sia alpha2, 6Gal are endogenous ligands for ASGP-R and that ASGP-R participates in regulating the relative concentration of serum glycoproteins bearing alpha 2,6-linked Sia. The human ASGP-R is a hetero-oligomer composed of two subunits, both of which are found within this group. Langerin is expressed in a subset of dendritic leukocytes, the Langerhans cells (LC). Langerin induces the formation of Birbeck Granules (BGs) and associates with these BGs following internalization. Langerin binds, in a calcium-dependent manner, to glyco-conjugates containing mannose and related sugars mediating their uptake and degradation. Langerin molecules oligomerize as trimers with three CTLDs held together by a coiled-coil of alpha helices.
• Changed! pfam Lectin_N 143aa 5e-55 in ref transcript
  • Hepatic lectin, N-terminal domain.
• pfam Lectin_C 109aa 4e-32 in ref transcript
  • Lectin C-type domain. This family includes both long and short form C-type.
• Changed! pfam Lectin_N 143aa 4e-51 in modified transcript

ASGR2

• rs.ASGR2.F2 rs.ASGR2.R2 112 127
• NCBIGene 36.3 433
• Alternative 5-prime, size difference: 15
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_080912

• cd CLECT_DC-SIGN_like 126aa 1e-40 in ref transcript
  • CLECT_DC-SIGN_like: C-type lectin-like domain (CTLD) of the type found in human dendritic cell (DC)-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN) and the related receptor, DC-SIGN receptor (DC-SIGNR). This group also contains proteins similar to hepatic asialoglycoprotein receptor (ASGP-R) and langerin in human. These proteins are type II membrane proteins with a CTLD ectodomain. CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. DC-SIGN is thought to mediate the initial contact between dendritic cells and resting T cells, and may also mediate the rolling of DCs on epithelium. DC-SIGN and DC-SIGNR bind to oligosaccharides present on human tissues, as well as, on pathogens including parasites, bacteria, and viruses. DC-SIGN and DC-SIGNR bind to HIV enhancing viral infection of T cells. DC-SIGN and DC-SIGNR are homotetrameric, and contain four CTLDs stabilized by a coiled coil of alpha helices. The hepatic ASGP-R is an endocytic recycling receptor which binds and internalizes desialylated glycoproteins having a terminal galactose or N-acetylgalactosamine residues on their N-linked carbohydrate chains, via the clathrin-coated pit mediated endocytic pathway, and delivers them to lysosomes for degradation. It has been proposed that glycoproteins bearing terminal Sia (sialic acid) alpha2, 6GalNAc and Sia alpha2, 6Gal are endogenous ligands for ASGP-R and that ASGP-R participates in regulating the relative concentration of serum glycoproteins bearing alpha 2,6-linked Sia. The human ASGP-R is a hetero-oligomer composed of two subunits, both of which are found within this group. Langerin is expressed in a subset of dendritic leukocytes, the Langerhans cells (LC). Langerin induces the formation of Birbeck Granules (BGs) and associates with these BGs following internalization. Langerin binds, in a calcium-dependent manner, to glyco-conjugates containing mannose and related sugars mediating their uptake and degradation. Langerin molecules oligomerize as trimers with three CTLDs held together by a coiled-coil of alpha helices.
• Changed! pfam Lectin_N 143aa 5e-55 in ref transcript
  • Hepatic lectin, N-terminal domain.
• pfam Lectin_C 109aa 4e-32 in ref transcript
  • Lectin C-type domain. This family includes both long and short form C-type.
• Changed! pfam Lectin_N 138aa 1e-56 in modified transcript

ASRGL1

• rs.ASRGL1.F1 rs.ASRGL1.R1 213 290
• NCBIGene 36.3 80150
• Alternative 3-prime, size difference: 77
• Inclusion in 5'UTR
• Reference transcript: NM_025080

• cd ASRGL1_like 295aa 1e-100 in ref transcript
  • ASRGL1_like domains, a subfamily of the L-Asparaginase type 2-like enzymes. The wider family includes Glycosylasparaginase, Taspase 1 and L-Asparaginase type 2 enzymes. The proenzymes undergo autoproteolytic cleavage before a threonine to generate alpha and beta subunits. The threonine becomes the N-terminal residue of the beta subunit and is the catalytic residue. ASRGL1, or asparaginase-like 1, has been cloned from mammalian testis cDNA libraries. It has been identified as a sperm antigen that may induce the production of autoantibodies following obstruction of the male reproductive tract, e.g. vasectomy.
• pfam Asparaginase_2 250aa 5e-56 in ref transcript
  • Asparaginase.
• COG COG1446 292aa 1e-63 in ref transcript
  • Asparaginase [Amino acid transport and metabolism].

ASS1

• rs.ASS1.F1 rs.ASS1.R1 202 264
• NCBIGene 36.3 445
• Single exon skipping, size difference: 62
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_000050

• Changed! cd Argininosuccinate_Synthase 392aa 1e-161 in ref transcript
  • Argininosuccinate synthase. The Argininosuccinate synthase is a urea cycle enzyme that catalyzes the penultimate step in arginine biosynthesis: the ATP-dependent ligation of citrulline to aspartate to form argininosuccinate, AMP and pyrophosphate . In humans, a defect in the AS gene causes citrullinemia, a genetic disease characterized by severe vomiting spells and mental retardation. AS is a homotetrameric enzyme of chains of about 400 amino-acid residues. An arginine seems to be important for the enzyme's catalytic mechanism. The sequences of AS from various prokaryotes, archaebacteria and eukaryotes show significant similarity.
• Changed! pfam Arginosuc_synth 398aa 1e-180 in ref transcript
  • Arginosuccinate synthase. This family contains a PP-loop motif.
• Changed! PRK PRK00509 402aa 1e-170 in ref transcript
  • argininosuccinate synthase; Provisional.

ASTN2

• rs.ASTN2.F1 rs.ASTN2.R1 100 112
• NCBIGene 36.3 23245
• Alternative 3-prime, size difference: 12
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_198187

• smart MACPF 184aa 1e-36 in ref transcript
  • membrane-attack complex / perforin.

ATG4B

• rs.ATG4B.F1 rs.ATG4B.R1 101 121
• NCBIGene 36.3 23192
• Alternative 5-prime, size difference: 20
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_013325

• pfam Peptidase_C54 301aa 1e-101 in ref transcript
  • Peptidase family C54.

ATG9A

• rs.ATG9A.F1 rs.ATG9A.R1 125 177
• NCBIGene 36.3 79065
• Single exon skipping, size difference: 52
• Exclusion in 5'UTR
• Reference transcript: NM_001077198

• pfam APG9 359aa 1e-143 in ref transcript
  • Autophagy protein Apg9. In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg9 plays a direct role in the formation of the cytoplasm to vacuole targeting and autophagic vesicles, possibly serving as a marker for a specialised compartment essential for these vesicle-mediated alternative targeting pathways.

ATP11A

• rs.ATP11A.F1 rs.ATP11A.R1 142 169
• NCBIGene 36.3 23250
• Exon skipping and alternative 3-prime or 5-prime, size difference: 27
• Inclusion in the protein causing a new stop codon, Exclusion in the protein (no frameshift)
• Reference transcript: NM_032189

• TIGR ATPase-Plipid 1065aa 0.0 in ref transcript
  • This model describes the P-type ATPase responsible for transporting phospholipids from one leaflet of bilayer membranes to the other. These ATPases are found only in eukaryotes.
• COG MgtA 1061aa 1e-106 in ref transcript
  • Cation transport ATPase [Inorganic ion transport and metabolism].

ATP2A3

• rs.ATP2A3.F1 rs.ATP2A3.R1 104 117
• NCBIGene 36.3 489
• Alternative 5-prime, size difference: 13
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_174953

• cd HAD_like 118aa 0.002 in ref transcript
  • Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others, all of which use a nucleophilic aspartate in their phosphoryl transfer reaction. All members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. Members of this superfamily are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases.
• TIGR ATPase-IIA1_Ca 937aa 0.0 in ref transcript
  • The calcium P-type ATPases have been characterized as Type IIA based on a phylogenetic analysis which distinguishes this group from the Type IIB PMCA calcium pump modelled by TIGR01517. A separate analysis divides Type IIA into sub-types, SERCA and PMR1 the latter of which is modelled by TIGR01522.
• pfam Cation_ATPase_N 57aa 1e-12 in ref transcript
  • Cation transporter/ATPase, N-terminus. Members of this families are involved in Na+/K+, H+/K+, Ca++ and Mg++ transport.
• COG MgtA 980aa 0.0 in ref transcript
  • Cation transport ATPase [Inorganic ion transport and metabolism].

ATP2B1

• rs.ATP2B1.F1 rs.ATP2B1.R1 232 386
• NCBIGene 36.3 490
• Single exon skipping, size difference: 154
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_001682

• TIGR ATPase-IIB_Ca 707aa 0.0 in ref transcript
  • The calcium P-type ATPases have been characterized as Type IIB based on a phylogenetic analysis which distinguishes this group from the Type IIA SERCA calcium pump. A separate analysis divides Type IIA into sub-types (SERCA and PMR1) which are modelled by two corresponding HMMs (TIGR01116 and TIGR01522). This model is well separated from those.
• TIGR ATPase-IIB_Ca 281aa 1e-100 in ref transcript
• TIGR ATPase-IID_K-Na 297aa 7e-18 in ref transcript
  • The Leishmania sequence (GP|3192903), which falls between trusted and noise in this model, may very well turn out to be an active potassium pump.
• COG MgtA 703aa 1e-127 in ref transcript
  • Cation transport ATPase [Inorganic ion transport and metabolism].
• COG MgtA 237aa 2e-26 in ref transcript

ATP2B2

• rs.ATP2B2.F1 rs.ATP2B2.R1 176 311
• NCBIGene 36.3 491
• Multiple exon skipping, size difference: 135
• Exclusion in the protein (no frameshift), Exclusion in the protein (no frameshift), Exclusion in the protein (no frameshift)
• Reference transcript: NM_001001331

• Changed! TIGR ATPase-IIB_Ca 706aa 0.0 in ref transcript
  • The calcium P-type ATPases have been characterized as Type IIB based on a phylogenetic analysis which distinguishes this group from the Type IIA SERCA calcium pump. A separate analysis divides Type IIA into sub-types (SERCA and PMR1) which are modelled by two corresponding HMMs (TIGR01116 and TIGR01522). This model is well separated from those.
• Changed! TIGR ATPase-IIB_Ca 278aa 2e-78 in ref transcript
• Changed! COG MgtA 698aa 1e-126 in ref transcript
  • Cation transport ATPase [Inorganic ion transport and metabolism].
• Changed! COG MgtA 238aa 2e-24 in ref transcript
• Changed! TIGR ATPase-IIB_Ca 1031aa 0.0 in modified transcript
• Changed! COG MgtA 981aa 1e-151 in modified transcript

ATP2C1

• rs.ATP2C1.F1 rs.ATP2C1.R1 169 199
• NCBIGene 36.3 27032
• Alternative 5-prime, size difference: 30
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001001486

• cd HAD_like 111aa 2e-04 in ref transcript
  • Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others, all of which use a nucleophilic aspartate in their phosphoryl transfer reaction. All members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. Members of this superfamily are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases.
• TIGR ATPase-IIA2_Ca 881aa 0.0 in ref transcript
  • The calcium P-type ATPases have been characterized as Type IIA based on a phylogenetic analysis which distinguishes this group from the Type IIB PMCA calcium pump modelled by TIGR01517. A separate analysis divides Type IIA into sub-types, SERCA and PMR1 the former of which is modelled by TIGR01116.
• COG MgtA 865aa 0.0 in ref transcript
  • Cation transport ATPase [Inorganic ion transport and metabolism].

ATP6V0E2

• rs.ATP6V0E2.F1 rs.ATP6V0E2.R1 155 268
• NCBIGene 36.3 155066
• Single exon skipping, size difference: 113
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_001100592

• Changed! pfam ATP_synt_H 43aa 8e-14 in ref transcript
  • ATP synthase subunit H. ATP synthase subunit H is an extremely hydrophobic of approximately 9 kDa. This subunit may be required for assembly of vacuolar ATPase.
• Changed! pfam ATP_synt_H 65aa 2e-22 in modified transcript

ATP6V1C2

• rs.ATP6V1C2.F1 rs.ATP6V1C2.R1 139 277
• NCBIGene 36.3 245973
• Single exon skipping, size difference: 138
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001039362

• Changed! pfam V-ATPase_C 414aa 1e-129 in ref transcript
  • V-ATPase subunit C.
• Changed! COG COG5127 380aa 1e-54 in ref transcript
  • Vacuolar H+-ATPase V1 sector, subunit C [Energy production and conversion].
• Changed! pfam V-ATPase_C 368aa 1e-135 in modified transcript
• Changed! COG COG5127 334aa 3e-59 in modified transcript

ATP8A1

• rs.ATP8A1.F1 rs.ATP8A1.R1 100 145
• NCBIGene 36.3 10396
• Single exon skipping, size difference: 45
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_006095

• Changed! TIGR ATPase-Plipid 1038aa 0.0 in ref transcript
  • This model describes the P-type ATPase responsible for transporting phospholipids from one leaflet of bilayer membranes to the other. These ATPases are found only in eukaryotes.
• Changed! COG MgtA 1036aa 1e-121 in ref transcript
  • Cation transport ATPase [Inorganic ion transport and metabolism].
• Changed! TIGR ATPase-Plipid 1023aa 0.0 in modified transcript
• Changed! COG MgtA 1021aa 1e-122 in modified transcript

ATPAF1

• rs.ATPAF1.F1 rs.ATPAF1.R1 136 340
• NCBIGene 36.3 64756
• Multiple exon skipping, size difference: 204
• Exclusion in the protein (no frameshift), Exclusion in the protein (no frameshift)
• Reference transcript: NM_022745

• Changed! pfam ATP11 244aa 1e-102 in ref transcript
  • ATP11 protein. This family consists of several eukaryotic ATP11 proteins. In Saccharomyces cerevisiae, expression of functional F1-ATPase requires two proteins encoded by the ATP11 and ATP12 genes. Atp11p is a molecular chaperone of the mitochondrial matrix that participates in the biogenesis pathway to form F1, the catalytic unit of the ATP synthase.
• Changed! pfam ATP11 176aa 3e-49 in modified transcript

ATRX

• rs.ATRX.F1 rs.ATRX.R1 101 215
• NCBIGene 36.3 546
• Single exon skipping, size difference: 114
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000489

• cd HELICc 147aa 4e-16 in ref transcript
  • Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process.
• cd DEXDc 163aa 4e-11 in ref transcript
  • DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
• pfam SNF2_N 317aa 9e-84 in ref transcript
  • SNF2 family N-terminal domain. This domain is found in proteins involved in a variety of processes including transcription regulation (e.g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as well as a variety of other proteins with little functional information (e.g., lodestar, ETL1).
• pfam Helicase_C 77aa 4e-16 in ref transcript
  • Helicase conserved C-terminal domain. The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.
• COG HepA 321aa 1e-27 in ref transcript
  • Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair].
• COG HepA 194aa 6e-22 in ref transcript

ATXN3

• rs.ATXN3.F1 rs.ATXN3.R1 108 273
• NCBIGene 36.3 4287
• Single exon skipping, size difference: 165
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_004993

• Changed! pfam Josephin 161aa 2e-69 in ref transcript
  • Josephin.
• Changed! pfam Josephin 105aa 2e-45 in modified transcript

ATXN7L3

• rs.ATXN7L3.F1 rs.ATXN7L3.R1 107 128
• NCBIGene 36.3 56970
• Alternative 3-prime, size difference: 21
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_020218

• pfam Sgf11 45aa 1e-05 in ref transcript
  • Sgf11 (transcriptional regulation protein). The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae. The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation.
• pfam SCA7 30aa 0.006 in ref transcript
  • SCA7. This domain is found in the protein Sgf73/Sca7 which is a component of the multihistone acetyltransferase complexes SAGA and SILK. This domain is also found in Ataxin-7, a human protein which in its polyglutamine expanded pathological form, is responsible for the neurodegenerative disease spinocerebellar ataxia 7 (SCA7).

AURKA

• rs.AURKA.F1 rs.AURKA.R1 119 217
• NCBIGene 36.3 6790
• Single exon skipping, size difference: 98
• Exclusion in 5'UTR
• Reference transcript: NM_198433

• cd S_TKc 252aa 1e-80 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• smart S_TKc 240aa 2e-80 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• PTZ PTZ00263 244aa 4e-53 in ref transcript
  • protein kinase A catalytic subunit; Provisional.

AXIN1

• rs.AXIN1.F1 rs.AXIN1.R1 297 405
• NCBIGene 36.3 8312
• Single exon skipping, size difference: 108
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_003502

• pfam RGS 123aa 2e-31 in ref transcript
  • Regulator of G protein signaling domain. RGS family members are GTPase-activating proteins for heterotrimeric G-protein alpha-subunits.
• smart DAX 83aa 4e-27 in ref transcript
  • Domain present in Dishevelled and axin. Domain of unknown function.
• pfam Axin_b-cat_bind 33aa 2e-08 in ref transcript
  • Axin beta-catenin binding domain. This domain is found on the scaffolding protein Axin which is a component of the beta-catenin destruction complex. It competes with the tumour suppressor adenomatous polyposis coli protein (APC) for binding to beta-catenin.

B3GALT5

• rs.B3GALT5.F1 rs.B3GALT5.R1 237 397
• NCBIGene 36.3 10317
• Single exon skipping, size difference: 160
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_033172

• Changed! pfam Galactosyl_T 191aa 2e-44 in ref transcript
  • Galactosyltransferase. This family includes the galactosyltransferases UDP-galactose:2-acetamido-2-deoxy-D-glucose3beta- galactosyltrans ferase and UDP-Gal:beta-GlcNAc beta 1,3-galactosyltranferase. Specific galactosyltransferases transfer galactose to GlcNAc terminal chains in the synthesis of the lacto-series oligosaccharides types 1 and 2.

BACE2

• rs.BACE2.F1 rs.BACE2.R1 114 264
• NCBIGene 36.3 25825
• Single exon skipping, size difference: 150
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_012105

• Changed! cd beta_secretase_like 362aa 0.0 in ref transcript
  • Beta-secretase, aspartic-acid protease important in the pathogenesis of Alzheimer's disease. Beta-secretase also called BACE (beta-site of APP cleaving enzyme) or memapsin-2. Beta-secretase is an aspartic-acid protease important in the pathogenesis of Alzheimer's disease, and in the formation of myelin sheaths in peripheral nerve cells. It cleaves amyloid precursor protein (APP) to reveal the N-terminus of the beta-amyloid peptides. The beta-amyloid peptides are the major components of the amyloid plaques formed in the brain of patients with Alzheimer's disease (AD). Since BACE mediates one of the cleavages responsible for generation of AD, it is regarded as a potential target for pharmacological intervention in AD. Beta-secretase is a member of pepsin family of aspartic proteases. Same as other aspartic proteases, beta-secretase is a bilobal enzyme, each lobe contributing a catalytic Asp residue, with an extended active site cleft localized between the two lobes of the molecule. The N- and C-terminal domains, although structurally related by a 2-fold axis, have only limited sequence homology except the vicinity of the active site. This suggests that the enzymes evolved by an ancient duplication event. The enzymes specifically cleave bonds in peptides which have at least six residues in length with hydrophobic residues in both the P1 and P1' positions. The active site is located at the groove formed by the two lobes, with an extended loop projecting over the cleft to form an 11-residue flap, which encloses substrates and inhibitors in the active site. Specificity is determined by nearest-neighbor hydrophobic residues surrounding the catalytic aspartates, and by three residues in the flap. The enzymes are mostly secreted from cells as inactive proenzymes that activate autocatalytically at acidic pH. This family of aspartate proteases is classified by MEROPS as the peptidase family A1 (pepsin A, clan AA).
• Changed! pfam Asp 339aa 3e-34 in ref transcript
  • Eukaryotic aspartyl protease. Aspartyl (acid) proteases include pepsins, cathepsins, and renins. Two-domain structure, probably arising from ancestral duplication. This family does not include the retroviral nor retrotransposon proteases (pfam00077), which are much smaller and appear to be homologous to a single domain of the eukaryotic asp proteases.
• Changed! PTZ PTZ00147 338aa 6e-20 in ref transcript
  • histoaspartic protease (plasmepsin I or II); Provisional.
• Changed! cd beta_secretase_like 312aa 1e-165 in modified transcript
• Changed! pfam Asp 289aa 8e-33 in modified transcript
• Changed! PTZ PTZ00147 288aa 1e-17 in modified transcript

BACE2

• rs.BACE2.F2 rs.BACE2.R2 136 305
• NCBIGene 36.3 25825
• Single exon skipping, size difference: 169
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_012105

• Changed! cd beta_secretase_like 362aa 0.0 in ref transcript
  • Beta-secretase, aspartic-acid protease important in the pathogenesis of Alzheimer's disease. Beta-secretase also called BACE (beta-site of APP cleaving enzyme) or memapsin-2. Beta-secretase is an aspartic-acid protease important in the pathogenesis of Alzheimer's disease, and in the formation of myelin sheaths in peripheral nerve cells. It cleaves amyloid precursor protein (APP) to reveal the N-terminus of the beta-amyloid peptides. The beta-amyloid peptides are the major components of the amyloid plaques formed in the brain of patients with Alzheimer's disease (AD). Since BACE mediates one of the cleavages responsible for generation of AD, it is regarded as a potential target for pharmacological intervention in AD. Beta-secretase is a member of pepsin family of aspartic proteases. Same as other aspartic proteases, beta-secretase is a bilobal enzyme, each lobe contributing a catalytic Asp residue, with an extended active site cleft localized between the two lobes of the molecule. The N- and C-terminal domains, although structurally related by a 2-fold axis, have only limited sequence homology except the vicinity of the active site. This suggests that the enzymes evolved by an ancient duplication event. The enzymes specifically cleave bonds in peptides which have at least six residues in length with hydrophobic residues in both the P1 and P1' positions. The active site is located at the groove formed by the two lobes, with an extended loop projecting over the cleft to form an 11-residue flap, which encloses substrates and inhibitors in the active site. Specificity is determined by nearest-neighbor hydrophobic residues surrounding the catalytic aspartates, and by three residues in the flap. The enzymes are mostly secreted from cells as inactive proenzymes that activate autocatalytically at acidic pH. This family of aspartate proteases is classified by MEROPS as the peptidase family A1 (pepsin A, clan AA).
• Changed! pfam Asp 339aa 3e-34 in ref transcript
  • Eukaryotic aspartyl protease. Aspartyl (acid) proteases include pepsins, cathepsins, and renins. Two-domain structure, probably arising from ancestral duplication. This family does not include the retroviral nor retrotransposon proteases (pfam00077), which are much smaller and appear to be homologous to a single domain of the eukaryotic asp proteases.
• Changed! PTZ PTZ00147 338aa 6e-20 in ref transcript
  • histoaspartic protease (plasmepsin I or II); Provisional.
• Changed! cd beta_secretase_like 305aa 1e-163 in modified transcript
• Changed! pfam Asp 232aa 5e-29 in modified transcript
• Changed! PTZ PTZ00147 230aa 4e-16 in modified transcript

BAG5

• rs.BAG5.F1 rs.BAG5.R1 191 378
• NCBIGene 36.3 9529
• Alternative 5-prime, size difference: 187
• Exclusion of the protein initiation site
• Reference transcript: NM_001015049

• smart BAG 78aa 1e-14 in ref transcript
  • BAG domains, present in regulator of Hsp70 proteins. BAG domains, present in Bcl-2-associated athanogene 1 and silencer of death domains.
• smart BAG 79aa 5e-14 in ref transcript
• smart BAG 76aa 1e-10 in ref transcript
• smart BAG 78aa 6e-09 in ref transcript

BANP

• rs.BANP.F1 rs.BANP.R1 114 180
• NCBIGene 36.3 54971
• Single exon skipping, size difference: 66
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_079837

• pfam BEN 74aa 1e-13 in ref transcript
  • BEN domain. The BEN domain is found in diverse animal proteins such as BANP/SMAR1, NAC1 and the Drosophila mod(mdg4) isoform C, in the chordopoxvirus virosomal protein E5R and in several proteins of polydnaviruses. Computational analysis suggests that the BEN domain mediates protein-DNA and protein-protein interactions during chromatin organisation and transcription.

BBS9

• rs.BBS9.F1 rs.BBS9.R1 100 115
• NCBIGene 36.3 27241
• Single exon skipping, size difference: 15
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_198428

• COG COG1361 158aa 0.001 in ref transcript
  • S-layer domain [Cell envelope biogenesis, outer membrane].

BCAS3

• rs.BCAS3.F1 rs.BCAS3.R1 151 196
• NCBIGene 36.3 54828
• Single exon skipping, size difference: 45
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001099432

BCAS4

• rs.BCAS4.F1 rs.BCAS4.R1 264 361
• NCBIGene 36.3 55653
• Single exon skipping, size difference: 97
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_017843

BCL2L1

• rs.BCL2L1.F1 rs.BCL2L1.R1 198 387
• NCBIGene 36.3 598
• Alternative 5-prime, size difference: 189
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_138578

• Changed! cd Bcl-2_like 114aa 2e-40 in ref transcript
  • Apoptosis regulator proteins of the Bcl-2 family, named after B-cell lymphoma 2. This alignment model spans what have been described as Bcl-2 homology regions BH1, BH2, BH3, and BH4. Many members of this family have an additional C-terminal transmembrane segment. Some homologous proteins, which are not included in this model, may miss either the BH4 (Bax, Bak) or the BH2 (Bcl-X(S)) region, and some appear to only share the BH3 region (Bik, Bim, Bad, Bid, Egl-1). This family is involved in the regulation of the outer mitochondrial membrane's permeability and in promoting or preventing the release of apoptogenic factors, which in turn may trigger apoptosis by activating caspases. Bcl-2 and the closely related Bcl-X(L) are anti-apoptotic key regulators of programmed cell death. They are assumed to function via heterodimeric protein-protein interactions, binding pro-apoptotic proteins such as Bad (BCL2-antagonist of cell death), Bid, and Bim, by specifically interacting with their BH3 regions. Interfering with this heterodimeric interaction via small-molecule inhibitors may prove effective in targeting various cancers. This family also includes the Caenorhabditis elegans Bcl-2 homolog CED-9, which binds to CED-4, the C. Elegans homolog of mammalian Apaf-1. Apaf-1, however, does not seem to be inhibited by Bcl-2 directly.
• Changed! TIGR bcl-2 233aa 1e-89 in ref transcript
  • in artificial membranes at acidic pH, proapoptotic Bcl-2 family proteins (including Bax and Bak) probably induce the mitochondrial permeability transition and cytochrome c release by interacting with permeability transition pores, the most important component for pore fomation of which is VDAC.
• Changed! cd Bcl-2_like 45aa 1e-08 in modified transcript
• Changed! TIGR bcl-2 125aa 1e-35 in modified transcript
• Changed! TIGR bcl-2 45aa 6e-09 in modified transcript

BCLAF1

• rs.BCLAF1.F1 rs.BCLAF1.R1 161 308
• NCBIGene 36.3 9774
• Single exon skipping, size difference: 147
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_014739

BCS1L

• rs.BCS1L.F1 rs.BCS1L.R1 116 325
• NCBIGene 36.3 617
• Single exon skipping, size difference: 209
• Exclusion in 5'UTR
• Reference transcript: NM_004328

• cd AAA 157aa 3e-06 in ref transcript
  • The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.
• pfam BCS1_N 168aa 2e-50 in ref transcript
  • BCS1 N terminal. This domain is found at the N terminal of the mitochondrial ATPase BSC1. It encodes the import and intramitochondrial sorting for the protein.
• pfam AAA 175aa 2e-19 in ref transcript
  • ATPase family associated with various cellular activities (AAA). AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes.
• COG HflB 405aa 1e-18 in ref transcript
  • ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones].

BEST3

• rs.BEST3.F1 rs.BEST3.R1 323 476
• NCBIGene 36.3 144453
• Single exon skipping, size difference: 153
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_032735

• Changed! pfam Bestrophin 369aa 1e-161 in ref transcript
  • Bestrophin. Bestrophin is a 68-kDa basolateral plasma membrane protein expressed in retinal pigment epithelial cells (RPE). It is encoded by the VMD2 gene, which is mutated in Best macular dystrophy, a disease characterised by a depressed light peak in the electrooculogram. VMD2 encodes a 585-amino acid protein with an approximate mass of 68 kDa which has been designated bestrophin. Bestrophin shares homology with the Caenorhabditis elegans RFP gene family, named for the presence of a conserved arginine (R), phenylalanine (F), proline (P), amino acid sequence motif. Bestrophin is a plasma membrane protein, localised to the basolateral surface of RPE cells consistent with a role for bestrophin in the generation or regulation of the EOG light peak. Bestrophin and other RFP family members represent a new class of chloride channels, indicating a direct role for bestrophin in generating the light peak. The VMD2 gene underlying Best disease was shown to represent the first human member of the RFP-TM protein family. More than 97% of the disease-causing mutations are located in the N-terminal RFP-TM domain implying important functional properties.
• Changed! pfam Bestrophin 318aa 1e-128 in modified transcript

BID

• rs.BID.F1 rs.BID.R1 180 250
• NCBIGene 36.3 637
• Single exon skipping, size difference: 70
• Exclusion of the protein initiation site
• Reference transcript: NM_001196

• Changed! pfam BID 192aa 1e-76 in ref transcript
  • BH3 interacting domain (BID). BID is a member of the BCL-2 superfamily of proteins are key regulators of programmed cell death, hence this family is related to pfam00452. BID is a pro-apoptotic member of the Bcl-2 superfamily and as such posses the ability to target intracellular membranes and contains the BH3 death domain. The activity of BID is regulated by a Caspase 8-mediated cleavage event, exposing the BH3 domain and significantly changing the surface charge and hydrophobicity, which causes a change of cellular localisation.
• Changed! pfam BID 96aa 1e-33 in modified transcript

BIRC5

• rs.BIRC5.F1 rs.BIRC5.R1 375 444
• NCBIGene 36.3 332
• Single exon skipping, size difference: 69
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001012271

• Changed! cd BIR 95aa 3e-14 in ref transcript
  • Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger.
• Changed! smart BIR 97aa 4e-18 in ref transcript
  • Baculoviral inhibition of apoptosis protein repeat. Domain found in inhibitor of apoptosis proteins (IAPs) and other proteins. Acts as a direct inhibitor of caspase enzymes.
• Changed! cd BIR 72aa 1e-17 in modified transcript
• Changed! smart BIR 74aa 2e-21 in modified transcript

BIRC7

• rs.BIRC7.F1 rs.BIRC7.R1 400 454
• NCBIGene 36.3 79444
• Alternative 3-prime, size difference: 54
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_139317

• cd BIR 68aa 5e-23 in ref transcript
  • Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger.
• Changed! cd RING 39aa 0.007 in ref transcript
  • RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H).
• smart BIR 71aa 4e-23 in ref transcript
  • Baculoviral inhibition of apoptosis protein repeat. Domain found in inhibitor of apoptosis proteins (IAPs) and other proteins. Acts as a direct inhibitor of caspase enzymes.
• smart RING 34aa 0.003 in ref transcript
  • Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s).

BMP4

• rs.BMP4.F1 rs.BMP4.R1 132 341
• NCBIGene 36.3 652
• Alternative 5-prime, size difference: 209
• Exclusion in 5'UTR
• Reference transcript: NM_001202

• pfam TGFb_propeptide 236aa 9e-62 in ref transcript
  • TGF-beta propeptide. This propeptide is known as latency associated peptide (LAP) in TGF-beta. LAP is a homodimer which is disulfide linked to TGF-beta binding protein.
• smart TGFB 101aa 9e-48 in ref transcript
  • Transforming growth factor-beta (TGF-beta) family. Family members are active as disulphide-linked homo- or heterodimers. TGFB is a multifunctional peptide that controls proliferation, differentiation, and other functions in many cell types.

BPTF

• rs.BPTF.F1 rs.BPTF.R1 103 532
• NCBIGene 36.3 2186
• Alternative 5-prime, size difference: 429
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_182641

• cd Bromo_gcn5_like 101aa 1e-46 in ref transcript
  • Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates acetylation of histones at lysine residues; such acetylation is generally correlated with the activation of transcription. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
• cd BAH_plant_2 27aa 8e-04 in ref transcript
  • BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
• smart BROMO 102aa 1e-27 in ref transcript
  • bromo domain.
• pfam DDT 61aa 1e-20 in ref transcript
  • DDT domain. This domain is approximately 60 residues in length, and is predicted to be a DNA binding domain. The DDT domain is named after (DNA binding homeobox and Different Transcription factors). It is exclusively associated with nuclear domains, and is thought to be arranged into three alpha helices.
• pfam PHD 45aa 6e-10 in ref transcript
  • PHD-finger. PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
• smart PHD 47aa 5e-08 in ref transcript
  • PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RI NG finger and the FYV E finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BR OMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RI NG fingers misidentified as PHD fingers.
• COG COG5076 105aa 8e-14 in ref transcript
  • Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription].

BRCA1

• rs.BRCA1.F1 rs.BRCA1.R1 188 311
• NCBIGene 36.3 672
• Multiple exon skipping, size difference: 123
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_007296

• cd RING 46aa 1e-07 in ref transcript
  • RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H).
• cd BRCT 80aa 2e-04 in ref transcript
  • Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks.
• smart BRCT 84aa 6e-09 in ref transcript
  • breast cancer carboxy-terminal domain.
• smart RING 41aa 9e-09 in ref transcript
  • Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s).
• COG PEX10 43aa 1e-04 in ref transcript
  • RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones].
• COG RAD18 119aa 0.002 in ref transcript
  • RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms].

BTBD9

• rs.BTBD9.F1 rs.BTBD9.R1 211 411
• NCBIGene 36.3 114781
• Single exon skipping, size difference: 200
• Exclusion in 5'UTR
• Reference transcript: NM_052893

• pfam BTB 105aa 7e-23 in ref transcript
  • BTB/POZ domain. The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN.
• pfam BACK 99aa 2e-20 in ref transcript
  • BTB And C-terminal Kelch. This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation).
• pfam F5_F8_type_C 115aa 4e-06 in ref transcript
  • F5/8 type C domain. This domain is also known as the discoidin (DS) domain family.
• pfam F5_F8_type_C 102aa 1e-04 in ref transcript

BTLA

• rs.BTLA.F1 rs.BTLA.R1 108 252
• NCBIGene 36.3 151888
• Single exon skipping, size difference: 144
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_181780

• cd IG 75aa 7e-04 in ref transcript
  • Immunoglobulin domain family; members are components of immunoglobulins, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• smart IG_like 92aa 7e-06 in ref transcript
  • Immunoglobulin like. IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.

BTN2A2

• rs.BTN2A2.F1 rs.BTN2A2.R1 100 448
• NCBIGene 36.3 10385
• Single exon skipping, size difference: 348
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_006995

• smart SPRY 119aa 3e-27 in ref transcript
  • Domain in SPla and the RYanodine Receptor. Domain of unknown function. Distant homologues are domains in butyrophilin/marenostrin/pyrin homologues.
• smart PRY 52aa 4e-21 in ref transcript
  • associated with SPRY domains.
• Changed! pfam V-set 97aa 3e-10 in ref transcript
  • Immunoglobulin V-set domain. This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.
• pfam C2-set_2 82aa 0.007 in ref transcript
  • CD80-like C2-set immunoglobulin domain. These domains belong to the immunoglobulin superfamily.

BTNL8

• rs.BTNL8.F1 rs.BTNL8.R1 133 263
• NCBIGene 36.3 79908
• Alternative 5-prime, size difference: 130
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_001040462

• Changed! smart SPRY 123aa 3e-16 in ref transcript
  • Domain in SPla and the RYanodine Receptor. Domain of unknown function. Distant homologues are domains in butyrophilin/marenostrin/pyrin homologues.
• Changed! smart PRY 50aa 5e-11 in ref transcript
  • associated with SPRY domains.
• pfam V-set 106aa 6e-07 in ref transcript
  • Immunoglobulin V-set domain. This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.

C10orf125

• rs.C10orf125.F1 rs.C10orf125.R1 397 466
• NCBIGene 36.3 282969
• Alternative 3-prime, size difference: 69
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_001098483

• Changed! pfam RbsD_FucU 139aa 9e-28 in ref transcript
  • RbsD / FucU transport protein family. The Escherichia coli high-affinity ribose-transport system consists of six proteins encoded by the rbs operon (rbsD, rbsA, rbsC, rbsB, rbsK and rbsR). Of the six components, RbsD is the only one whose function is unknown although it is thought that it somehow plays a critical role in PtsG-mediated ribose transport. This family also includes FucU a protein from the fucose biosynthesis operon that is presumably also involved in fucose transport by similarity to RbsD.
• Changed! COG FucU 145aa 5e-40 in ref transcript
  • Fucose dissimilation pathway protein FucU [Carbohydrate transport and metabolism].
• Changed! pfam RbsD_FucU 125aa 2e-21 in modified transcript
• Changed! COG FucU 130aa 3e-33 in modified transcript

C10orf30

• rs.C10orf30.F1 rs.C10orf30.R1 219 389
• NCBIGene 36.3 222389
• Single exon skipping, size difference: 170
• Exclusion in 5'UTR
• Reference transcript: NM_152751

• pfam BEN 84aa 2e-09 in ref transcript
  • BEN domain. The BEN domain is found in diverse animal proteins such as BANP/SMAR1, NAC1 and the Drosophila mod(mdg4) isoform C, in the chordopoxvirus virosomal protein E5R and in several proteins of polydnaviruses. Computational analysis suggests that the BEN domain mediates protein-DNA and protein-protein interactions during chromatin organisation and transcription.

C10orf30

• rs.C10orf30.F1 rs.C10orf30.R2 411 542
• NCBIGene 36.3 222389
• Single exon skipping, size difference: 170
• Exclusion in 5'UTR
• Reference transcript: NM_152751

• pfam BEN 84aa 2e-09 in ref transcript
  • BEN domain. The BEN domain is found in diverse animal proteins such as BANP/SMAR1, NAC1 and the Drosophila mod(mdg4) isoform C, in the chordopoxvirus virosomal protein E5R and in several proteins of polydnaviruses. Computational analysis suggests that the BEN domain mediates protein-DNA and protein-protein interactions during chromatin organisation and transcription.

C11orf56

• rs.C11orf56.F1 rs.C11orf56.R1 151 193
• NCBIGene 36.3 84067
• Alternative 5-prime, size difference: 42
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_032127

• pfam RAI16-like 331aa 1e-88 in ref transcript
  • Retinoic acid induced 16-like protein. This is the conserved N-terminal 450 residues of a family of proteins described as retinoic acid-induced protein 16-like proteins. The exact function is not known. The proteins are found from worms to humans.

C12orf42

• rs.C12orf42.F1 rs.C12orf42.R1 380 515
• NCBIGene 36.3 374470
• Alternative 5-prime, size difference: 135
• Exclusion in 5'UTR
• Reference transcript: NM_001099336

C12orf44

• rs.C12orf44.F1 rs.C12orf44.R1 164 335
• NCBIGene 36.3 60673
• Alternative 5-prime, size difference: 171
• Exclusion in 5'UTR
• Reference transcript: NM_021934

• pfam DUF1649 167aa 1e-56 in ref transcript
  • Protein of unknown function (DUF1649). This family is made up of sequences derived from hypothetical eukaryotic proteins of unknown function.

C14orf100

• rs.C14orf100.F1 rs.C14orf100.R1 131 149
• NCBIGene 36.3 51528
• Alternative 3-prime, size difference: 18
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_016475

• pfam DUF766 293aa 1e-113 in ref transcript
  • Protein of unknown function (DUF766). This family consists of several eukaryotic proteins of unknown function.

C14orf104

• rs.C14orf104.F1 rs.C14orf104.R1 239 383
• NCBIGene 36.3 55172
• Single exon skipping, size difference: 144
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_018139

• pfam PIH1 299aa 3e-84 in ref transcript
  • pre-RNA processing PIH1/Nop17. This domain is involved in pre-rRNA processing. It has has been shown to be required either for nucleolar retention or correct assembly of the box C/D snoRNP in Saccharomyces cerevisiae.

C14orf118

• rs.C14orf118.F1 rs.C14orf118.R1 128 143
• NCBIGene 36.3 55668
• Mutually exclusive exon skipping, size difference: 15
• Inclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_017926

C14orf130

• rs.C14orf130.F1 rs.C14orf130.R1 313 447
• NCBIGene 36.3 55148
• Single exon skipping, size difference: 134
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_175748

• Changed! pfam zf-UBR 68aa 0.001 in ref transcript
  • Putative zinc finger in N-recognin (UBR box). This region is found in E3 ubiquitin ligases that recognise N-recognins.

C14orf138

• rs.C14orf138.F1 rs.C14orf138.R1 210 315
• NCBIGene 36.3 79609
• Single exon skipping, size difference: 105
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_024558

• Changed! pfam Methyltransf_16 172aa 9e-52 in ref transcript
  • Putative methyltransferase.
• COG COG3897 126aa 8e-04 in ref transcript
  • Predicted methyltransferase [General function prediction only].
• Changed! pfam Methyltransf_16 170aa 2e-51 in modified transcript

C14orf159

• rs.C14orf159.F1 rs.C14orf159.R1 100 115
• NCBIGene 36.3 80017
• Alternative 5-prime, size difference: 15
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001102368

• Changed! pfam DUF1445 143aa 2e-57 in ref transcript
  • Protein of unknown function (DUF1445). This family represents a conserved region approximately 150 residues long within a number of hypothetical bacterial and eukaryotic proteins of unknown function.
• Changed! PRK PRK05463 263aa 7e-46 in ref transcript
  • hypothetical protein; Provisional.
• Changed! pfam DUF1445 138aa 1e-54 in modified transcript
• Changed! PRK PRK05463 258aa 3e-44 in modified transcript

C14orf159

• rs.C14orf159.F2 rs.C14orf159.R2 124 202
• NCBIGene 36.3 80017
• Single exon skipping, size difference: 78
• Exclusion in 5'UTR
• Reference transcript: NM_001102366

• pfam DUF1445 138aa 1e-54 in ref transcript
  • Protein of unknown function (DUF1445). This family represents a conserved region approximately 150 residues long within a number of hypothetical bacterial and eukaryotic proteins of unknown function.
• PRK PRK05463 258aa 3e-44 in ref transcript
  • hypothetical protein; Provisional.

C14orf159

• rs.C14orf159.F3 rs.C14orf159.R3 167 287
• NCBIGene 36.3 80017
• Single exon skipping, size difference: 120
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001102368

• pfam DUF1445 143aa 2e-57 in ref transcript
  • Protein of unknown function (DUF1445). This family represents a conserved region approximately 150 residues long within a number of hypothetical bacterial and eukaryotic proteins of unknown function.
• PRK PRK05463 263aa 7e-46 in ref transcript
  • hypothetical protein; Provisional.

C14orf159

• rs.C14orf159.F4 rs.C14orf159.R4 211 382
• NCBIGene 36.3 80017
• Multiple exon skipping, size difference: 171
• Exclusion in 5'UTR, Exclusion in 5'UTR
• Reference transcript: NM_001102366

• pfam DUF1445 138aa 1e-54 in ref transcript
  • Protein of unknown function (DUF1445). This family represents a conserved region approximately 150 residues long within a number of hypothetical bacterial and eukaryotic proteins of unknown function.
• PRK PRK05463 258aa 3e-44 in ref transcript
  • hypothetical protein; Provisional.

C14orf159

• rs.C14orf159.F5 rs.C14orf159.R5 109 145
• NCBIGene 36.3 80017
• Alternative 5-prime, size difference: 36
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001102368

• Changed! pfam DUF1445 143aa 2e-57 in ref transcript
  • Protein of unknown function (DUF1445). This family represents a conserved region approximately 150 residues long within a number of hypothetical bacterial and eukaryotic proteins of unknown function.
• Changed! PRK PRK05463 263aa 7e-46 in ref transcript
  • hypothetical protein; Provisional.
• Changed! pfam DUF1445 131aa 5e-48 in modified transcript
• Changed! PRK PRK05463 251aa 2e-39 in modified transcript

C14orf159

• rs.C14orf159.F6 rs.C14orf159.R6 131 376
• NCBIGene 36.3 80017
• Alternative 5-prime, size difference: 245
• Exclusion in 5'UTR
• Reference transcript: NM_001102366

• pfam DUF1445 138aa 1e-54 in ref transcript
  • Protein of unknown function (DUF1445). This family represents a conserved region approximately 150 residues long within a number of hypothetical bacterial and eukaryotic proteins of unknown function.
• PRK PRK05463 258aa 3e-44 in ref transcript
  • hypothetical protein; Provisional.

C14orf179

• rs.C14orf179.F1 rs.C14orf179.R1 132 147
• NCBIGene 36.3 112752
• Mutually exclusive exon skipping, size difference: 15
• Inclusion in the protein (no stop codon or frameshift), Inclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_052873

C16orf13

• rs.C16orf13.F1 rs.C16orf13.R1 102 170
• NCBIGene 36.3 84326
• Single exon skipping, size difference: 68
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_001040160

• Changed! pfam DUF938 137aa 6e-48 in ref transcript
  • Protein of unknown function (DUF938). This family consists of several hypothetical proteins from both prokaryotes and eukaryotes. The function of this family is unknown.
• Changed! pfam DUF938 200aa 6e-81 in modified transcript

C16orf35

• rs.C16orf35.F1 rs.C16orf35.R1 169 374
• NCBIGene 36.3 8131
• Multiple exon skipping, size difference: 205
• Exclusion in the protein causing a frameshift, Exclusion in the protein (no frameshift)
• Reference transcript: NM_001077350

• Changed! pfam UPF0171 471aa 1e-161 in ref transcript
  • Uncharacterised protein family (UPF0171).
• Changed! pfam UPF0171 63aa 1e-16 in modified transcript

C16orf46

• rs.C16orf46.F1 rs.C16orf46.R1 318 407
• NCBIGene 36.3 123775
• Single exon skipping, size difference: 89
• Exclusion in 5'UTR
• Reference transcript: NM_152337

C17orf62

• rs.C17orf62.F1 rs.C17orf62.R1 114 164
• NCBIGene 36.3 79415
• Single exon skipping, size difference: 50
• Exclusion in 5'UTR
• Reference transcript: NM_001100407

C17orf62

• rs.C17orf62.F2 rs.C17orf62.R2 113 155
• NCBIGene 36.3 79415
• Single exon skipping, size difference: 42
• Exclusion in 5'UTR
• Reference transcript: NM_001033046

C17orf63

• rs.C17orf63.F1 rs.C17orf63.R1 175 209
• NCBIGene 36.3 55731
• Single exon skipping, size difference: 34
• Exclusion in 5'UTR
• Reference transcript: NM_018182

C17orf70

• rs.C17orf70.F1 rs.C17orf70.R1 109 305
• NCBIGene 36.3 80233
• Alternative 5-prime, size difference: 196
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_001109760

C17orf72

• rs.C17orf72.F1 rs.C17orf72.R1 100 121
• NCBIGene 36.3 92340
• Alternative 3-prime, size difference: 21
• Inclusion in 5'UTR
• Reference transcript: XM_001726843

C17orf80

• rs.C17orf80.F1 rs.C17orf80.R1 275 383
• NCBIGene 36.3 55028
• Single exon skipping, size difference: 108
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_017941

C18orf19

• rs.C18orf19.F1 rs.C18orf19.R1 223 363
• NCBIGene 36.3 125228
• Single exon skipping, size difference: 140
• Exclusion in 5'UTR
• Reference transcript: NM_001098801

• pfam DUF1279 88aa 2e-32 in ref transcript
  • Protein of unknown function (DUF1279). This family represents the C-terminus (approx. 120 residues) of a number of eukaryotic proteins of unknown function.

C18orf25

• rs.C18orf25.F1 rs.C18orf25.R1 202 385
• NCBIGene 36.3 147339
• Single exon skipping, size difference: 183
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_145055

C18orf34

• rs.C18orf34.F1 rs.C18orf34.R1 171 285
• NCBIGene 36.3 374864
• Single exon skipping, size difference: 114
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001105528

• COG Smc 233aa 0.005 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].

C18orf37

• rs.C18orf37.F1 rs.C18orf37.R1 333 441
• NCBIGene 36.3 125476
• Multiple exon skipping, size difference: 108
• Exclusion in the protein (no frameshift), Exclusion in the protein (no frameshift)
• Reference transcript: NM_001098817

• pfam YL1_C 30aa 1e-06 in ref transcript
  • YL1 nuclear protein C-terminal domain. This domain is found in proteins of the YL1 family. These proteins have been shown to be DNA-binding and may be a transcription factor. This domain is found in proteins that are not YL1 proteins.
• COG COG5195 88aa 7e-14 in ref transcript
  • Uncharacterized conserved protein [Function unknown].

C19orf28

• rs.C19orf28.F1 rs.C19orf28.R1 193 395
• NCBIGene 36.3 126321
• Single exon skipping, size difference: 202
• Exclusion of the stop codon
• Reference transcript: NM_021731

• TIGR gph 331aa 5e-08 in ref transcript
  • GPH:cation symporters catalyze uptake of sugars in symport with a monovalent cation (H+ or Na+). Members of this family includes transporters for melibiose, lactose, raffinose, glucuronides, pentosides and isoprimeverose. Mutants of two groups of these symporters (the melibiose permeases of enteric bacteria, and the lactose permease of Streptococcus thermophilus) have been isolated in which altered cation specificity is observed or in which sugar transport is uncoupled from cation symport (i.e., uniport is catalyzed). The various members of the family can use Na+, H+ or Li, Na+ or Li+, H+ or Li+, or only H+ as the symported cation. All of these proteins possess twelve putative transmembrane a-helical spanners.
• COG MelB 411aa 1e-15 in ref transcript
  • Na+/melibiose symporter and related transporters [Carbohydrate transport and metabolism].

C19orf60

• rs.C19orf60.F1 rs.C19orf60.R1 181 247
• NCBIGene 36.3 55049
• Alternative 3-prime, size difference: 66
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001100418

C19orf62

• rs.C19orf62.F1 rs.C19orf62.R1 140 178
• NCBIGene 36.3 29086
• Alternative 3-prime, size difference: 38
• Inclusion in 5'UTR
• Reference transcript: NM_014173

• TIGR acidobact_VWFA 74aa 0.004 in ref transcript
  • Members of this family are bacterial domains that include a region related to the von Willebrand factor type A (VWFA) domain (pfam00092). These domains are restricted to, and have undergone a large paralogous family expansion in, the Acidobacteria, including Solibacter usitatus and Acidobacterium capsulatum ATCC 51196.

C1D

• rs.C1D.F1 rs.C1D.R1 100 113
• NCBIGene 36.3 10438
• Alternative 5-prime, size difference: 13
• Exclusion in 5'UTR
• Reference transcript: NM_006333

• pfam Sas10_Utp3 80aa 4e-14 in ref transcript
  • Sas10/Utp3/C1D family. This family contains Utp3 and LCP5 which are components of the U3 ribonucleoprotein complex. It also includes the human C1D protein and Saccharomyces cerevisiae YHR081W (rrp47), an exosome-associated protein required for the 3' processing of stable RNAs, and Sas10 which has been identified as a regulator of chromatin silencing. This family also includes the human protein Neuroguidin an initiation factor 4E (eIF4E) binding protein.

C1orf116

• rs.C1orf116.F1 rs.C1orf116.R1 129 315
• NCBIGene 36.3 79098
• Single exon skipping, size difference: 186
• Exclusion of the protein initiation site
• Reference transcript: NM_023938

C1orf43

• rs.C1orf43.F1 rs.C1orf43.R1 291 393
• NCBIGene 36.3 25912
• Single exon skipping, size difference: 102
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001098616

• Changed! pfam NICE-3 189aa 1e-85 in ref transcript
  • NICE-3 protein. This family consists of several eukaryotic NICE-3 and related proteins. The gene coding for NICE-3 is part of the epidermal differentiation complex (EDC) which comprises a large number of genes that are of crucial importance for the maturation of the human epidermis. The function of NICE-3 is unknown.
• Changed! pfam NICE-3 155aa 6e-59 in modified transcript

C20orf71

• rs.C20orf71.F1 rs.C20orf71.R1 309 417
• NCBIGene 36.3 128861
• Single exon skipping, size difference: 108
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_178466

• Changed! pfam LBP_BPI_CETP 156aa 1e-15 in ref transcript
  • LBP / BPI / CETP family, N-terminal domain. The N and C terminal domains of the LBP/BPI/CETP family are structurally similar.
• Changed! pfam LBP_BPI_CETP 79aa 2e-10 in modified transcript

C21orf33

• rs.C21orf33.F1 rs.C21orf33.R1 205 298
• NCBIGene 36.3 8209
• Single exon skipping, size difference: 93
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_004649

• Changed! cd GATase1_ES1 222aa 6e-89 in ref transcript
  • Type 1 glutamine amidotransferase (GATase1)-like domain found in zebrafish ES1. This group includes, proteins similar to ES1, Escherichia coli enhancing lycopene biosynthesis protein 2, Azospirillum brasilense iaaC and, human HES1. The catalytic triad typical of GATase1domains is not conserved in this GATase1-like domain. However, in common with GATase1domains a reactive cys residue is found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow. Zebrafish ES1 is expressed specifically in adult photoreceptor cells and appears to be a cytoplasmic protein. A. brasilense iaaC is involved in controlling IAA biosynthesis.
• Changed! pfam DJ-1_PfpI 168aa 2e-14 in ref transcript
  • DJ-1/PfpI family. The family includes the protease PfpI. This domain is also found in transcriptional regulators.
• Changed! PRK PRK11780 224aa 1e-83 in ref transcript
  • isoprenoid biosynthesis protein with amidotransferase-like domain; Provisional.
• Changed! cd GATase1_ES1 191aa 4e-69 in modified transcript
• Changed! pfam DJ-1_PfpI 137aa 7e-06 in modified transcript
• Changed! PRK PRK11780 193aa 6e-64 in modified transcript

C21orf34

• rs.C21orf34.F1 rs.C21orf34.R1 240 283
• NCBIGene 36.3 388815
• Single exon skipping, size difference: 115
• Inclusion in 3'UTR
• Reference transcript: NM_001005734

C21orf91

• rs.C21orf91.F1 rs.C21orf91.R1 209 272
• NCBIGene 36.3 54149
• Single exon skipping, size difference: 63
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001100420

• Changed! pfam EURL 291aa 1e-145 in ref transcript
  • EURL protein. This family consists of several animal EURL proteins. EURL is preferentially expressed in chick retinal precursor cells as well as in the anterior epithelial cells of the lens at early stages of development. EURL transcripts are found primarily in the peripheral dorsal retina, i.e., the most undifferentiated part of the dorsal retina. EURL transcripts are also detected in the lens at stage 18 and remain abundant in the proliferating epithelial cells of the lens until at least day 11. The distribution pattern of EURL in the developing retina and lens suggest a role before the events leading to cell determination and differentiation.
• Changed! pfam EURL 221aa 1e-108 in modified transcript

C2orf56

• rs.C2orf56.F1 rs.C2orf56.R1 349 430
• NCBIGene 36.3 55471
• Single exon skipping, size difference: 81
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_144736

• pfam DUF185 247aa 5e-33 in ref transcript
  • Uncharacterized ACR, COG1565. This family contains several uncharacterised proteins. One member has been described as an ATP synthase beta subunit transcription termination factor rho protein.
• Changed! COG COG1565 357aa 4e-61 in ref transcript
  • Uncharacterized conserved protein [Function unknown].
• Changed! COG COG1565 330aa 1e-44 in modified transcript

C5orf5

• rs.C5orf5.F1 rs.C5orf5.R1 225 291
• NCBIGene 36.3 51306
• Single exon skipping, size difference: 66
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_016603

• cd RhoGAP_FAM13A1a 185aa 3e-78 in ref transcript
  • RhoGAP_FAM13A1a: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of FAM13A1, isoform a-like proteins. The function of FAM13A1a is unknown. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by up several orders of magnitude.
• pfam RhoGAP 152aa 3e-37 in ref transcript
  • RhoGAP domain. GTPase activator proteins towards Rho/Rac/Cdc42-like small GTPases.

C5orf5

• rs.C5orf5.F2 rs.C5orf5.R2 302 494
• NCBIGene 36.3 51306
• Single exon skipping, size difference: 192
• Exclusion of the protein initiation site
• Reference transcript: NM_016603

• Changed! cd RhoGAP_FAM13A1a 185aa 3e-78 in ref transcript
  • RhoGAP_FAM13A1a: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of FAM13A1, isoform a-like proteins. The function of FAM13A1a is unknown. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by up several orders of magnitude.
• Changed! pfam RhoGAP 152aa 3e-37 in ref transcript
  • RhoGAP domain. GTPase activator proteins towards Rho/Rac/Cdc42-like small GTPases.
• Changed! cd RhoGAP_FAM13A1a 85aa 4e-32 in modified transcript
• Changed! pfam RhoGAP 67aa 2e-12 in modified transcript

C5orf5

• rs.C5orf5.F3 rs.C5orf5.R3 293 377
• NCBIGene 36.3 51306
• Single exon skipping, size difference: 84
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_016603

• cd RhoGAP_FAM13A1a 185aa 3e-78 in ref transcript
  • RhoGAP_FAM13A1a: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of FAM13A1, isoform a-like proteins. The function of FAM13A1a is unknown. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by up several orders of magnitude.
• pfam RhoGAP 152aa 3e-37 in ref transcript
  • RhoGAP domain. GTPase activator proteins towards Rho/Rac/Cdc42-like small GTPases.

C6orf162

• rs.C6orf162.F1 rs.C6orf162.R1 101 122
• NCBIGene 36.3 57150
• Single exon skipping, size difference: 21
• Exclusion in 5'UTR
• Reference transcript: NM_001042493

C6orf25

• rs.C6orf25.F1 rs.C6orf25.R1 107 126
• NCBIGene 36.3 80739
• Alternative 3-prime, size difference: 19
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_138272

C6orf60

• rs.C6orf60.F1 rs.C6orf60.R1 174 321
• NCBIGene 36.3 79632
• Single exon skipping, size difference: 147
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_024581

• TIGR SMC_prok_A 303aa 7e-06 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent.
• Changed! TIGR SMC_prok_B 226aa 2e-04 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• COG Smc 356aa 3e-04 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].

C8orf59

• rs.C8orf59.F1 rs.C8orf59.R1 136 223
• NCBIGene 36.3 401466
• Alternative 5-prime, size difference: 87
• Exclusion in 5'UTR
• Reference transcript: NM_001099670

C8orf79

• rs.C8orf79.F1 rs.C8orf79.R1 278 342
• NCBIGene 36.3 57604
• Alternative 5-prime, size difference: 64
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_020844

• Changed! cd AdoMet_MTases 92aa 6e-10 in ref transcript
  • S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.).
• Changed! pfam Methyltransf_11 90aa 1e-18 in ref transcript
  • Methyltransferase domain. Members of this family are SAM dependent methyltransferases.
• Changed! COG UbiE 139aa 3e-19 in ref transcript
  • Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism].
• Changed! pfam Methyltransf_11 38aa 0.006 in modified transcript
• Changed! COG UbiE 95aa 1e-06 in modified transcript

C9orf116

• rs.C9orf116.F1 rs.C9orf116.R1 184 230
• NCBIGene 36.3 138162
• Alternative 3-prime, size difference: 46
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_001048265

C9orf127

• rs.C9orf127.F1 rs.C9orf127.R1 237 309
• NCBIGene 36.3 51754
• Alternative 5-prime, size difference: 72
• Inclusion in 5'UTR
• Reference transcript: NM_001042589

C9orf131

• rs.C9orf131.F1 rs.C9orf131.R1 249 324
• NCBIGene 36.3 138724
• Single exon skipping, size difference: 75
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001040412

C9orf5

• rs.C9orf5.F1 rs.C9orf5.R1 147 171
• NCBIGene 36.3 23731
• Single exon skipping, size difference: 24
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_032012

• COG PerM 163aa 0.009 in ref transcript
  • Predicted permease [General function prediction only].

CADM1

• rs.CADM1.F1 rs.CADM1.R1 222 306
• NCBIGene 36.3 23705
• Single exon skipping, size difference: 84
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_014333

• cd IGcam 71aa 1e-07 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• cd IG 72aa 0.004 in ref transcript
  • Immunoglobulin domain family; members are components of immunoglobulins, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• smart IG_like 80aa 3e-10 in ref transcript
  • Immunoglobulin like. IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
• pfam C2-set_2 70aa 3e-08 in ref transcript
  • CD80-like C2-set immunoglobulin domain. These domains belong to the immunoglobulin superfamily.
• smart IG_like 92aa 9e-08 in ref transcript

CADPS2

• rs.CADPS2.F1 rs.CADPS2.R1 406 535
• NCBIGene 36.3 93664
• Single exon skipping, size difference: 120
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_017954

• cd PH_CADPS 110aa 2e-52 in ref transcript
  • CADPS (Ca2+-dependent activator protein) Pleckstrin homology (PH) domain. CADPS is a calcium-dependent activator involved in secretion. It contains a central PH domain that binds to phosphoinositide 4,5 bisphosphate containing liposomes. However, membrane association may also be mediated by binding to phosphatidlyserine via general electrostatic interactions. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
• pfam DUF1041 95aa 1e-13 in ref transcript
  • Domain of Unknown Function (DUF1041). This family consists of several eukaryotic domains of unknown function. Members of this family are often found in tandem repeats and co-occur with pfam00168, pfam00130 and pfam00169 domains.
• smart PH 102aa 2e-09 in ref transcript
  • Pleckstrin homology domain. Domain commonly found in eukaryotic signalling proteins. The domain family possesses multiple functions including the abilities to bind inositol phosphates, and various proteins. PH domains have been found to possess inserted domains (such as in PLC gamma, syntrophins) and to be inserted within other domains. Mutations in Brutons tyrosine kinase (Btk) within its PH domain cause X-linked agammaglobulinaemia (XLA) in patients. Point mutations cluster into the positively charged end of the molecule around the predicted binding site for phosphatidylinositol lipids.

CALCA

• rs.CALCA.F1 rs.CALCA.R1 104 128
• NCBIGene 36.3 796
• Alternative 5-prime, size difference: 24
• Exclusion in 5'UTR
• Reference transcript: NM_001033952

• smart CALCITONIN 38aa 8e-14 in ref transcript
  • calcitonin. This family is formed by calcitonin, the calcitonin gene-related peptide, and amylin. They are short polypeptide hormones.

CAMK2A

• rs.CAMK2A.F1 rs.CAMK2A.R1 114 147
• NCBIGene 36.3 815
• Single exon skipping, size difference: 33
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_015981

• cd S_TKc 260aa 1e-81 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• smart S_TKc 249aa 2e-84 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• pfam CaMKII_AD 128aa 8e-62 in ref transcript
  • Calcium/calmodulin dependent protein kinase II Association. This domain is found at the C-terminus of the Calcium/calmodulin dependent protein kinases II (CaMKII). These proteins also have a Ser/Thr protein kinase domain (pfam00069) at their N-terminus. The function of the CaMKII association domain is the assembly of the single proteins into large (8 to 14 subunits) multimers.
• PTZ PTZ00263 261aa 3e-41 in ref transcript
  • protein kinase A catalytic subunit; Provisional.

CAMK2B

• rs.CAMK2B.F1 rs.CAMK2B.R1 117 162
• NCBIGene 36.3 816
• Single exon skipping, size difference: 45
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001220

• cd S_TKc 260aa 2e-82 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• smart S_TKc 249aa 1e-85 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• pfam CaMKII_AD 128aa 1e-58 in ref transcript
  • Calcium/calmodulin dependent protein kinase II Association. This domain is found at the C-terminus of the Calcium/calmodulin dependent protein kinases II (CaMKII). These proteins also have a Ser/Thr protein kinase domain (pfam00069) at their N-terminus. The function of the CaMKII association domain is the assembly of the single proteins into large (8 to 14 subunits) multimers.
• PTZ PTZ00263 249aa 6e-40 in ref transcript
  • protein kinase A catalytic subunit; Provisional.

CAMK2G

• rs.CAMK2G.F1 rs.CAMK2G.R1 111 153
• NCBIGene 36.3 818
• Alternative 5-prime, size difference: 42
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_172171

• cd S_TKc 260aa 5e-84 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• smart S_TKc 249aa 2e-86 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• pfam CaMKII_AD 128aa 5e-59 in ref transcript
  • Calcium/calmodulin dependent protein kinase II Association. This domain is found at the C-terminus of the Calcium/calmodulin dependent protein kinases II (CaMKII). These proteins also have a Ser/Thr protein kinase domain (pfam00069) at their N-terminus. The function of the CaMKII association domain is the assembly of the single proteins into large (8 to 14 subunits) multimers.
• PTZ PTZ00263 249aa 3e-43 in ref transcript
  • protein kinase A catalytic subunit; Provisional.

CAP1

• rs.CAP1.F1 rs.CAP1.R1 104 122
• NCBIGene 36.3 10487
• Alternative 5-prime, size difference: 18
• Exclusion in 5'UTR
• Reference transcript: NM_006367

• pfam CAP_N 302aa 1e-109 in ref transcript
  • Adenylate cyclase associated (CAP) N terminal.
• pfam CAP_C 156aa 5e-71 in ref transcript
  • DE Adenylate cyclase associated (CAP) C terminal.

CAPN3

• rs.CAPN3.F1 rs.CAPN3.R1 104 122
• NCBIGene 36.3 825
• Single exon skipping, size difference: 18
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000070

• cd CysPc 353aa 1e-106 in ref transcript
  • Calpains, domains IIa, IIb; calcium-dependent cytoplasmic cysteine proteinases, papain-like. Functions in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction.
• cd Calpain_III 158aa 1e-54 in ref transcript
  • Calpain, subdomain III. Calpains are calcium-activated cytoplasmic cysteine proteinases, participate in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction. Catalytic domain and the two calmodulin-like domains are separated by C2-like domain III. Domain III plays an important role in calcium-induced activation of calpain involving electrostatic interactions with subdomain II. Proposed to mediate calpain's interaction with phospholipids and translocation to cytoplasmic/nuclear membranes. CD includes subdomain III of typical and atypical calpains.
• cd EFh 55aa 2e-06 in ref transcript
  • EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers.
• cd EFh 68aa 0.004 in ref transcript
• cd EFh 56aa 0.008 in ref transcript
• pfam Peptidase_C2 343aa 1e-158 in ref transcript
  • Calpain family cysteine protease.
• pfam Calpain_III 155aa 8e-65 in ref transcript
  • Calpain large subunit, domain III. The function of the domain III and I are currently unknown. Domain II is a cysteine protease and domain IV is a calcium binding domain. Calpains are believed to participate in intracellular signaling pathways mediated by calcium ions.
• COG FRQ1 99aa 6e-06 in ref transcript
  • Ca2+-binding protein (EF-Hand superfamily) [Signal transduction mechanisms / Cytoskeleton / Cell division and chromosome partitioning / General function prediction only].

CAPN3

• rs.CAPN3.F2 rs.CAPN3.R2 123 401
• NCBIGene 36.3 825
• Single exon skipping, size difference: 278
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_000070

• Changed! cd CysPc 353aa 1e-106 in ref transcript
  • Calpains, domains IIa, IIb; calcium-dependent cytoplasmic cysteine proteinases, papain-like. Functions in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction.
• Changed! cd Calpain_III 158aa 1e-54 in ref transcript
  • Calpain, subdomain III. Calpains are calcium-activated cytoplasmic cysteine proteinases, participate in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction. Catalytic domain and the two calmodulin-like domains are separated by C2-like domain III. Domain III plays an important role in calcium-induced activation of calpain involving electrostatic interactions with subdomain II. Proposed to mediate calpain's interaction with phospholipids and translocation to cytoplasmic/nuclear membranes. CD includes subdomain III of typical and atypical calpains.
• Changed! cd EFh 55aa 2e-06 in ref transcript
  • EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers.
• Changed! cd EFh 68aa 0.004 in ref transcript
• Changed! cd EFh 56aa 0.008 in ref transcript
• Changed! pfam Peptidase_C2 343aa 1e-158 in ref transcript
  • Calpain family cysteine protease.
• Changed! pfam Calpain_III 155aa 8e-65 in ref transcript
  • Calpain large subunit, domain III. The function of the domain III and I are currently unknown. Domain II is a cysteine protease and domain IV is a calcium binding domain. Calpains are believed to participate in intracellular signaling pathways mediated by calcium ions.
• Changed! COG FRQ1 99aa 6e-06 in ref transcript
  • Ca2+-binding protein (EF-Hand superfamily) [Signal transduction mechanisms / Cytoskeleton / Cell division and chromosome partitioning / General function prediction only].
• Changed! cd CysPc 99aa 4e-15 in modified transcript
• Changed! smart CysPc 101aa 3e-27 in modified transcript
  • Calpain-like thiol protease family. Calpain-like thiol protease family (peptidase family C2). Calcium activated neutral protease (large subunit).

CAPN3

• rs.CAPN3.F3 rs.CAPN3.R3 103 121
• NCBIGene 36.3 825
• Single exon skipping, size difference: 18
• Exclusion in 5'UTR
• Reference transcript: NM_173090

• cd EFh 55aa 6e-06 in ref transcript
  • EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers.
• COG FRQ1 91aa 2e-06 in ref transcript
  • Ca2+-binding protein (EF-Hand superfamily) [Signal transduction mechanisms / Cytoskeleton / Cell division and chromosome partitioning / General function prediction only].

CAPN3

• rs.CAPN3.F4 rs.CAPN3.R4 188 332
• NCBIGene 36.3 825
• Single exon skipping, size difference: 144
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000070

• Changed! cd CysPc 353aa 1e-106 in ref transcript
  • Calpains, domains IIa, IIb; calcium-dependent cytoplasmic cysteine proteinases, papain-like. Functions in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction.
• cd Calpain_III 158aa 1e-54 in ref transcript
  • Calpain, subdomain III. Calpains are calcium-activated cytoplasmic cysteine proteinases, participate in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction. Catalytic domain and the two calmodulin-like domains are separated by C2-like domain III. Domain III plays an important role in calcium-induced activation of calpain involving electrostatic interactions with subdomain II. Proposed to mediate calpain's interaction with phospholipids and translocation to cytoplasmic/nuclear membranes. CD includes subdomain III of typical and atypical calpains.
• cd EFh 55aa 2e-06 in ref transcript
  • EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers.
• cd EFh 68aa 0.004 in ref transcript
• cd EFh 56aa 0.008 in ref transcript
• Changed! pfam Peptidase_C2 343aa 1e-158 in ref transcript
  • Calpain family cysteine protease.
• pfam Calpain_III 155aa 8e-65 in ref transcript
  • Calpain large subunit, domain III. The function of the domain III and I are currently unknown. Domain II is a cysteine protease and domain IV is a calcium binding domain. Calpains are believed to participate in intracellular signaling pathways mediated by calcium ions.
• COG FRQ1 99aa 6e-06 in ref transcript
  • Ca2+-binding protein (EF-Hand superfamily) [Signal transduction mechanisms / Cytoskeleton / Cell division and chromosome partitioning / General function prediction only].
• Changed! cd CysPc 305aa 1e-111 in modified transcript
• Changed! pfam Peptidase_C2 295aa 1e-165 in modified transcript

CASC1

• rs.CASC1.F1 rs.CASC1.R1 286 348
• NCBIGene 36.3 55259
• Alternative 3-prime, size difference: 62
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_018272

CASC4

• rs.CASC4.F1 rs.CASC4.R1 369 537
• NCBIGene 36.3 113201
• Single exon skipping, size difference: 168
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_138423

• TIGR SMC_prok_B 159aa 3e-06 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• COG Smc 157aa 9e-05 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].
• COG FlaD 98aa 0.003 in ref transcript
  • Putative archaeal flagellar protein D/E [Cell motility and secretion].

CASP1

• rs.CASP1.F1 rs.CASP1.R1 333 477
• NCBIGene 36.3 834
• Single exon skipping, size difference: 144
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_033292

• Changed! cd CASc 250aa 1e-72 in ref transcript
  • Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs.
• Changed! smart CASc 250aa 5e-94 in ref transcript
  • Caspase, interleukin-1 beta converting enzyme (ICE) homologues. Cysteine aspartases that mediate programmed cell death (apoptosis). Caspases are synthesised as zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologues.
• pfam CARD 88aa 5e-20 in ref transcript
  • Caspase recruitment domain. Motif contained in proteins involved in apoptotic signaling. Predicted to possess a DEATH (pfam00531) domain-like fold.
• Changed! cd CASc 202aa 7e-58 in modified transcript
• Changed! smart CASc 202aa 6e-76 in modified transcript

CASP10

• rs.CASP10.F1 rs.CASP10.R1 165 294
• NCBIGene 36.3 843
• Multiple exon skipping, size difference: 129
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_032977

• cd CASc 240aa 1e-82 in ref transcript
  • Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs.
• cd DED 79aa 2e-12 in ref transcript
  • Death effector domain. DED is part of a superfamily of death domains which also includes death-domain (DD) and caspase recruitment domain (CARD). Protein-protein interactions involving these domains occur through homotypic interactions, such as DED-DED. Caspases are the primary executioners of apoptosis via proteolytic cascades, and upstream caspases such as caspase-8 and caspase-9 are activated by signaling complexes such as the death inducing signaling complex (DISC) and the apoptosome. Binding of caspases to specific adaptor molecules via DED or CARD domains leads to autoactivation of caspases.
• cd DED 74aa 1e-11 in ref transcript
• smart CASc 239aa 4e-97 in ref transcript
  • Caspase, interleukin-1 beta converting enzyme (ICE) homologues. Cysteine aspartases that mediate programmed cell death (apoptosis). Caspases are synthesised as zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologues.
• pfam DED 83aa 7e-17 in ref transcript
  • Death effector domain.
• pfam DED 77aa 1e-15 in ref transcript

CASP2

• rs.CASP2.F1 rs.CASP2.R1 296 514
• NCBIGene 36.3 835
• Exon skipping and alternative 3-prime or 5-prime, size difference: 218
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_032982

• Changed! cd CASc 256aa 3e-74 in ref transcript
  • Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs.
• Changed! smart CASc 256aa 9e-86 in ref transcript
  • Caspase, interleukin-1 beta converting enzyme (ICE) homologues. Cysteine aspartases that mediate programmed cell death (apoptosis). Caspases are synthesised as zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologues.
• Changed! smart CARD 89aa 9e-16 in ref transcript
  • Caspase recruitment domain. Motif contained in proteins involved in apoptotic signalling. Mediates homodimerisation. Structure consists of six antiparallel helices arranged in a topology homologue to the DEATH and the DED domain.
• Changed! smart CARD 75aa 6e-13 in modified transcript

CASP3

• rs.CASP3.F1 rs.CASP3.R1 119 286
• NCBIGene 36.3 836
• Single exon skipping, size difference: 167
• Exclusion in 5'UTR
• Reference transcript: NM_004346

• cd CASc 239aa 3e-86 in ref transcript
  • Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs.
• smart CASc 241aa 3e-97 in ref transcript
  • Caspase, interleukin-1 beta converting enzyme (ICE) homologues. Cysteine aspartases that mediate programmed cell death (apoptosis). Caspases are synthesised as zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologues.

CASP4

• rs.CASP4.F1 rs.CASP4.R1 110 209
• NCBIGene 36.3 837
• Single exon skipping, size difference: 99
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_001225

• Changed! cd CASc 250aa 3e-69 in ref transcript
  • Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs.
• Changed! smart CASc 250aa 2e-93 in ref transcript
  • Caspase, interleukin-1 beta converting enzyme (ICE) homologues. Cysteine aspartases that mediate programmed cell death (apoptosis). Caspases are synthesised as zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologues.
• Changed! smart CARD 89aa 2e-10 in ref transcript
  • Caspase recruitment domain. Motif contained in proteins involved in apoptotic signalling. Mediates homodimerisation. Structure consists of six antiparallel helices arranged in a topology homologue to the DEATH and the DED domain.

CASP7

• rs.CASP7.F1 rs.CASP7.R1 111 144
• NCBIGene 36.3 840
• Alternative 3-prime, size difference: 33
• Exclusion of the protein initiation site
• Reference transcript: NM_033338

• cd CASc 242aa 4e-84 in ref transcript
  • Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs.
• smart CASc 243aa 2e-90 in ref transcript
  • Caspase, interleukin-1 beta converting enzyme (ICE) homologues. Cysteine aspartases that mediate programmed cell death (apoptosis). Caspases are synthesised as zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologues.

CASP8

• rs.CASP8.F1 rs.CASP8.R1 149 175
• NCBIGene 36.3 841
• Alternative 3-prime, size difference: 26
• Exclusion in 5'UTR
• Reference transcript: NM_001228

• cd CASc 253aa 2e-84 in ref transcript
  • Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs.
• cd DED 75aa 6e-17 in ref transcript
  • Death effector domain. DED is part of a superfamily of death domains which also includes death-domain (DD) and caspase recruitment domain (CARD). Protein-protein interactions involving these domains occur through homotypic interactions, such as DED-DED. Caspases are the primary executioners of apoptosis via proteolytic cascades, and upstream caspases such as caspase-8 and caspase-9 are activated by signaling complexes such as the death inducing signaling complex (DISC) and the apoptosome. Binding of caspases to specific adaptor molecules via DED or CARD domains leads to autoactivation of caspases.
• cd DED 75aa 2e-11 in ref transcript
• smart CASc 252aa 4e-89 in ref transcript
  • Caspase, interleukin-1 beta converting enzyme (ICE) homologues. Cysteine aspartases that mediate programmed cell death (apoptosis). Caspases are synthesised as zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologues.
• pfam DED 84aa 8e-23 in ref transcript
  • Death effector domain.
• pfam DED 81aa 1e-16 in ref transcript

CASP8

• rs.CASP8.F2 rs.CASP8.R2 107 175
• NCBIGene 36.3 841
• Alternative 5-prime, size difference: 68
• Exclusion in 5'UTR
• Reference transcript: NM_001228

• cd CASc 253aa 2e-84 in ref transcript
  • Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs.
• cd DED 75aa 6e-17 in ref transcript
  • Death effector domain. DED is part of a superfamily of death domains which also includes death-domain (DD) and caspase recruitment domain (CARD). Protein-protein interactions involving these domains occur through homotypic interactions, such as DED-DED. Caspases are the primary executioners of apoptosis via proteolytic cascades, and upstream caspases such as caspase-8 and caspase-9 are activated by signaling complexes such as the death inducing signaling complex (DISC) and the apoptosome. Binding of caspases to specific adaptor molecules via DED or CARD domains leads to autoactivation of caspases.
• cd DED 75aa 2e-11 in ref transcript
• smart CASc 252aa 4e-89 in ref transcript
  • Caspase, interleukin-1 beta converting enzyme (ICE) homologues. Cysteine aspartases that mediate programmed cell death (apoptosis). Caspases are synthesised as zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologues.
• pfam DED 84aa 8e-23 in ref transcript
  • Death effector domain.
• pfam DED 81aa 1e-16 in ref transcript

CASP8

• rs.CASP8.F3 rs.CASP8.R3 147 212
• NCBIGene 36.3 841
• Single exon skipping, size difference: 65
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_001080125

• Changed! cd CASc 253aa 3e-85 in ref transcript
  • Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs.
• cd DED 75aa 3e-17 in ref transcript
  • Death effector domain. DED is part of a superfamily of death domains which also includes death-domain (DD) and caspase recruitment domain (CARD). Protein-protein interactions involving these domains occur through homotypic interactions, such as DED-DED. Caspases are the primary executioners of apoptosis via proteolytic cascades, and upstream caspases such as caspase-8 and caspase-9 are activated by signaling complexes such as the death inducing signaling complex (DISC) and the apoptosome. Binding of caspases to specific adaptor molecules via DED or CARD domains leads to autoactivation of caspases.
• cd DED 78aa 7e-13 in ref transcript
• Changed! smart CASc 252aa 4e-90 in ref transcript
  • Caspase, interleukin-1 beta converting enzyme (ICE) homologues. Cysteine aspartases that mediate programmed cell death (apoptosis). Caspases are synthesised as zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologues.
• pfam DED 84aa 5e-23 in ref transcript
  • Death effector domain.
• pfam DED 82aa 2e-17 in ref transcript

CASP8

• rs.CASP8.F4 rs.CASP8.R4 288 333
• NCBIGene 36.3 841
• Single exon skipping, size difference: 45
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001080125

• cd CASc 253aa 3e-85 in ref transcript
  • Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs.
• cd DED 75aa 3e-17 in ref transcript
  • Death effector domain. DED is part of a superfamily of death domains which also includes death-domain (DD) and caspase recruitment domain (CARD). Protein-protein interactions involving these domains occur through homotypic interactions, such as DED-DED. Caspases are the primary executioners of apoptosis via proteolytic cascades, and upstream caspases such as caspase-8 and caspase-9 are activated by signaling complexes such as the death inducing signaling complex (DISC) and the apoptosome. Binding of caspases to specific adaptor molecules via DED or CARD domains leads to autoactivation of caspases.
• cd DED 78aa 7e-13 in ref transcript
• smart CASc 252aa 4e-90 in ref transcript
  • Caspase, interleukin-1 beta converting enzyme (ICE) homologues. Cysteine aspartases that mediate programmed cell death (apoptosis). Caspases are synthesised as zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologues.
• pfam DED 84aa 5e-23 in ref transcript
  • Death effector domain.
• pfam DED 82aa 2e-17 in ref transcript

CASP9

• rs.CASP9.F1 rs.CASP9.R1 100 550
• NCBIGene 36.3 842
• Multiple exon skipping, size difference: 450
• Exclusion in the protein causing a frameshift, Exclusion in the protein (no frameshift), Exclusion in the protein (no frameshift), Exclusion in the protein causing a frameshift
• Reference transcript: NM_001229

• Changed! cd CASc 263aa 5e-78 in ref transcript
  • Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs.
• Changed! smart CASc 261aa 6e-81 in ref transcript
  • Caspase, interleukin-1 beta converting enzyme (ICE) homologues. Cysteine aspartases that mediate programmed cell death (apoptosis). Caspases are synthesised as zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologues.
• smart CARD 91aa 7e-16 in ref transcript
  • Caspase recruitment domain. Motif contained in proteins involved in apoptotic signalling. Mediates homodimerisation. Structure consists of six antiparallel helices arranged in a topology homologue to the DEATH and the DED domain.
• Changed! cd CASc 125aa 2e-26 in modified transcript
• Changed! smart CASc 124aa 3e-26 in modified transcript

CAST

• rs.CAST.F1 rs.CAST.R1 135 192
• NCBIGene 36.3 831
• Single exon skipping, size difference: 57
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001750

• pfam Calpain_inhib 127aa 5e-19 in ref transcript
  • Calpain inhibitor. This region is found multiple times in calpain inhibitor proteins.
• pfam Calpain_inhib 118aa 3e-16 in ref transcript
• pfam Calpain_inhib 99aa 2e-13 in ref transcript
• pfam Calpain_inhib 126aa 3e-11 in ref transcript

CAST

• rs.CAST.F2 rs.CAST.R2 102 141
• NCBIGene 36.3 831
• Single exon skipping, size difference: 39
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001750

• pfam Calpain_inhib 127aa 5e-19 in ref transcript
  • Calpain inhibitor. This region is found multiple times in calpain inhibitor proteins.
• pfam Calpain_inhib 118aa 3e-16 in ref transcript
• pfam Calpain_inhib 99aa 2e-13 in ref transcript
• Changed! pfam Calpain_inhib 126aa 3e-11 in ref transcript
• Changed! pfam Calpain_inhib 113aa 2e-09 in modified transcript

CAST

• rs.CAST.F3 rs.CAST.R3 101 167
• NCBIGene 36.3 831
• Single exon skipping, size difference: 66
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001750

• pfam Calpain_inhib 127aa 5e-19 in ref transcript
  • Calpain inhibitor. This region is found multiple times in calpain inhibitor proteins.
• pfam Calpain_inhib 118aa 3e-16 in ref transcript
• pfam Calpain_inhib 99aa 2e-13 in ref transcript
• pfam Calpain_inhib 126aa 3e-11 in ref transcript

CBFA2T2

• rs.CBFA2T2.F1 rs.CBFA2T2.R1 127 415
• NCBIGene 36.3 9139
• Single exon skipping, size difference: 288
• Exclusion of the protein initiation site
• Reference transcript: NM_005093

• pfam TAFH 96aa 3e-38 in ref transcript
  • NHR1 homology to TAF. This corresponds to the region NHR1 that is conserved between the product of the nervy gene in Drosophila and the human mtg8b protein, which is hypothesised to be a transcription factor.
• pfam NHR2 67aa 2e-32 in ref transcript
  • NHR2 domain like. The NHR2 (Nervy homology 2) domain is found in the ETO protein where it mediates oligomerisation and protein-protein interactions. It forms an alpha-helical tetramer.
• pfam zf-MYND 37aa 5e-11 in ref transcript
  • MYND finger.

CBFA2T3

• rs.CBFA2T3.F1 rs.CBFA2T3.R1 348 423
• NCBIGene 36.3 863
• Single exon skipping, size difference: 75
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_005187

• pfam TAFH 96aa 5e-38 in ref transcript
  • NHR1 homology to TAF. This corresponds to the region NHR1 that is conserved between the product of the nervy gene in Drosophila and the human mtg8b protein, which is hypothesised to be a transcription factor.
• pfam NHR2 67aa 3e-24 in ref transcript
  • NHR2 domain like. The NHR2 (Nervy homology 2) domain is found in the ETO protein where it mediates oligomerisation and protein-protein interactions. It forms an alpha-helical tetramer.
• pfam zf-MYND 37aa 5e-11 in ref transcript
  • MYND finger.
• COG NtpE 60aa 0.003 in ref transcript
  • Archaeal/vacuolar-type H+-ATPase subunit E [Energy production and conversion].

CCDC32

• rs.CCDC32.F1 rs.CCDC32.R1 121 146
• NCBIGene 36.3 90416
• Alternative 5-prime, size difference: 25
• Exclusion of the protein initiation site
• Reference transcript: NM_001080791

CCDC33

• rs.CCDC33.F1 rs.CCDC33.R1 111 213
• NCBIGene 36.3 80125
• Single exon skipping, size difference: 102
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_025055

CCDC41

• rs.CCDC41.F1 rs.CCDC41.R1 236 289
• NCBIGene 36.3 51134
• Single exon skipping, size difference: 53
• Exclusion in 5'UTR
• Reference transcript: NM_016122

• TIGR SMC_prok_B 327aa 1e-11 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• COG Smc 324aa 5e-06 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].

CCDC43

• rs.CCDC43.F1 rs.CCDC43.R1 270 329
• NCBIGene 36.3 124808
• Single exon skipping, size difference: 59
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_144609

CCHCR1

• rs.CCHCR1.F1 rs.CCHCR1.R1 148 256
• NCBIGene 36.3 54535
• Alternative 3-prime, size difference: 108
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001105564

• Changed! pfam HCR 756aa 0.0 in ref transcript
  • Alpha helical coiled-coil rod protein (HCR). This family consists of several mammalian alpha helical coiled-coil rod HCR proteins. The function of HCR is unknown but it has been implicated in psoriasis in humans and is thought to affect keratinocyte proliferation.
• Changed! COG Smc 377aa 0.003 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].
• Changed! pfam HCR 750aa 0.0 in modified transcript

CCNB1IP1

• rs.CCNB1IP1.F1 rs.CCNB1IP1.R1 246 446
• NCBIGene 36.3 57820
• Single exon skipping, size difference: 200
• Exclusion in 5'UTR
• Reference transcript: NM_021178

CCNC

• rs.CCNC.F1 rs.CCNC.R1 140 362
• NCBIGene 36.3 892
• Alternative 5-prime, size difference: 222
• Exclusion of the protein initiation site
• Reference transcript: NM_005190

• Changed! cd CYCLIN 52aa 4e-06 in ref transcript
  • Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain.
• cd CYCLIN 84aa 0.008 in ref transcript
• Changed! TIGR ccl1 250aa 7e-21 in ref transcript
  • University).
• Changed! COG CCL1 243aa 4e-30 in ref transcript
  • Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH/TFIIK, cyclin H subunit [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair].
• Changed! TIGR ccl1 169aa 4e-12 in modified transcript
• Changed! COG CCL1 157aa 2e-18 in modified transcript

CCR5

• rs.CCR5.F1 rs.CCR5.R1 100 335
• NCBIGene 36.3 1234
• Alternative 3-prime, size difference: 235
• Inclusion in 5'UTR
• Reference transcript: NM_001100168

• pfam 7tm_1 239aa 8e-30 in ref transcript
  • 7 transmembrane receptor (rhodopsin family). This family contains, amongst other G-protein-coupled receptors (GCPRs), members of the opsin family, which have been considered to be typical members of the rhodopsin superfamily. They share several motifs, mainly the seven transmembrane helices, GCPRs of the rhodopsin superfamily. All opsins bind a chromophore, such as 11-cis-retinal. The function of most opsins other than the photoisomerases is split into two steps: light absorption and G-protein activation. Photoisomerases, on the other hand, are not coupled to G-proteins - they are thought to generate and supply the chromophore that is used by visual opsins.

CD1E

• rs.CD1E.F1 rs.CD1E.R1 129 233
• NCBIGene 36.3 913
• Alternative 5-prime, size difference: 104
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_030893

• Changed! cd IGc 93aa 3e-11 in ref transcript
  • Immunoglobulin domain constant region subfamily; members of the IGc subfamily are components of immunoglobulins, T-cell receptors, CD1 cell surface glycoproteins, secretory glycoproteins A/C, and Major Histocompatibility Complex (MHC) class I/II molecules. In immunoglobulins, each chain is composed of one variable domain (IGv) and one or more constant domains (IGc); these names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. T-cell receptors form heterodimers, pairing two chains (alpha/beta or gamma/delta), each with a IGv and IGc domain. MHCs form heterodimers pairing two chains (alpha/beta or delta/epsilon), each with a MHC and IGc domain. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• Changed! smart IGc1 69aa 7e-16 in ref transcript
  • Immunoglobulin C-Type.
• Changed! cd IGc 59aa 1e-06 in modified transcript
• Changed! smart IGc1 45aa 8e-10 in modified transcript

CD1E

• rs.CD1E.F2 rs.CD1E.R2 193 229
• NCBIGene 36.3 913
• Alternative 3-prime, size difference: 36
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_030893

• cd IGc 93aa 3e-11 in ref transcript
  • Immunoglobulin domain constant region subfamily; members of the IGc subfamily are components of immunoglobulins, T-cell receptors, CD1 cell surface glycoproteins, secretory glycoproteins A/C, and Major Histocompatibility Complex (MHC) class I/II molecules. In immunoglobulins, each chain is composed of one variable domain (IGv) and one or more constant domains (IGc); these names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. T-cell receptors form heterodimers, pairing two chains (alpha/beta or gamma/delta), each with a IGv and IGc domain. MHCs form heterodimers pairing two chains (alpha/beta or delta/epsilon), each with a MHC and IGc domain. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• smart IGc1 69aa 7e-16 in ref transcript
  • Immunoglobulin C-Type.

CD33

• rs.CD33.F1 rs.CD33.R1 125 506
• NCBIGene 36.3 945
• Single exon skipping, size difference: 381
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001772

• Changed! pfam V-set 114aa 7e-09 in ref transcript
  • Immunoglobulin V-set domain. This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.
• pfam C2-set_2 74aa 4e-04 in ref transcript
  • CD80-like C2-set immunoglobulin domain. These domains belong to the immunoglobulin superfamily.

CD3D

• rs.CD3D.F1 rs.CD3D.R1 306 438
• NCBIGene 36.3 915
• Single exon skipping, size difference: 132
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000732

• smart ITAM 21aa 0.001 in ref transcript
  • Immunoreceptor tyrosine-based activation motif. Motif that may be dually phosphorylated on tyrosine that links antigen receptors to downstream signalling machinery.

CD40

• rs.CD40.F1 rs.CD40.R1 142 204
• NCBIGene 36.3 958
• Single exon skipping, size difference: 62
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_001250

• cd TNFR 98aa 8e-16 in ref transcript
  • Tumor necrosis factor receptor (TNFR) domain; superfamily of TNF-like receptor domains. When bound to TNF-like cytokines, TNFRs trigger multiple signal transduction pathways, they are involved in inflammation response, apoptosis, autoimmunity and organogenesis. TNFRs domains are elongated with generally three tandem repeats of cysteine-rich domains (CRDs). They fit in the grooves between protomers within the ligand trimer. Some TNFRs, such as NGFR and HveA, bind ligands with no structural similarity to TNF and do not bind ligand trimers.
• Changed! cd TNFR 63aa 3e-04 in ref transcript
• smart TNFR 39aa 0.004 in ref transcript
  • Tumor necrosis factor receptor / nerve growth factor receptor repeats. Repeats in growth factor receptors that are involved in growth factor binding. TNF/TNFR.

CD44

• rs.CD44.F1 rs.CD44.R1 225 354
• NCBIGene 36.3 960
• Single exon skipping, size difference: 129
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000610

• cd Link_domain_CD44_like 145aa 3e-50 in ref transcript
  • This domain is a hyaluronan (HA)-binding domain. It is found in CD44 receptor and mediates adhesive interactions during inflammatory leukocyte homing and tumor metastasis. It also plays an important role in arteriogenesis. The functional HA-binding domain of CD44 is an extended domain comprised of a single link module flanked with N-and C- extensions. These extensions are essential for folding and for functional activity. This group also contains the cell surface retention sequence (CRS) binding protein-1 (CRSBP-1) and lymph vessel endothelial receptor-1 (LYVE-1). CRSBP-1 is a cell surface binding protein for the CRS motif of PDGF-BB (platelet-derived growth factor-BB) and is responsible for the cell surface retention of PDGF-BB in SSV-transformed cells. CRSBP-1 may play a role in autocrine regulation of cell growth mediated by CRS containing growth regulators. LYVE-1 is preferentially expressed on the lymphatic endothelium and is used as a molecular marker for the detection and characterization of lymphatic vessels in tumors.
• smart LINK 91aa 1e-32 in ref transcript
  • Link (Hyaluronan-binding).

CD47

• rs.CD47.F1 rs.CD47.R1 168 201
• NCBIGene 36.3 961
• Single exon skipping, size difference: 33
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001777

• pfam CD47 158aa 2e-40 in ref transcript
  • CD47 transmembrane region. This family represents the transmembrane region of CD47 leukocyte antigen.
• pfam V-set_CD47 135aa 2e-38 in ref transcript
  • CD47 immunoglobulin-like domain. This family represents the CD47 leukocyte antigen V-set like Ig domain.

CD59

• rs.CD59.F1 rs.CD59.R1 105 221
• NCBIGene 36.3 966
• Single exon skipping, size difference: 116
• Exclusion in 5'UTR
• Reference transcript: NM_203330

• cd LU 72aa 2e-08 in ref transcript
  • Ly-6 antigen / uPA receptor -like domain; occurs singly in GPI-linked cell-surface glycoproteins (Ly-6 family,CD59, thymocyte B cell antigen, Sgp-2) or as three-fold repeated domain in urokinase-type plasminogen activator receptor. Topology of these domains is similar to that of snake venom neurotoxins.
• pfam UPAR_LY6 68aa 7e-12 in ref transcript
  • u-PAR/Ly-6 domain. This extracellular disulphide bond rich domain is related to pfam00087.

CD82

• rs.CD82.F1 rs.CD82.R1 475 550
• NCBIGene 36.3 3732
• Single exon skipping, size difference: 75
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_002231

• Changed! cd CD37_CD82_like_LEL 122aa 5e-39 in ref transcript
  • Tetraspanin, extracellular domain or large extracellular loop (LEL), CD37_CD82_Like family. Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. Tetraspanins are involved in diverse processes and their various functions may relate to their ability to act as molecular facilitators. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web". CD37 is a leukocyte-specific protein, and its restricted expression pattern suggests a role in the immune system. A regulatory role in T-cell proliferation has been suggested. CD82 is a metastasis suppressor implicated in biological processes ranging from fusion, adhesion, and migration to apoptosis and alterations of cell morphology.
• Changed! pfam Tetraspannin 250aa 4e-28 in ref transcript
  • Tetraspanin family.
• Changed! cd CD37_CD82_like_LEL 117aa 1e-36 in modified transcript
• Changed! pfam Tetraspannin 225aa 6e-24 in modified transcript

CDC2

• rs.CDC2.F1 rs.CDC2.R1 111 282
• NCBIGene 36.3 983
• Single exon skipping, size difference: 171
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001786

• Changed! cd S_TKc 285aa 6e-76 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• Changed! pfam Pkinase 284aa 4e-82 in ref transcript
  • Protein kinase domain.
• Changed! PTZ PTZ00024 278aa 3e-51 in ref transcript
  • cyclin-dependent protein kinase; Provisional.
• Changed! cd S_TKc 228aa 7e-41 in modified transcript
• Changed! pfam Pkinase 227aa 1e-48 in modified transcript
• Changed! PTZ PTZ00024 141aa 2e-27 in modified transcript
• Changed! PTZ PTZ00266 82aa 6e-09 in modified transcript
  • NIMA-related protein kinase; Provisional.

CDC2L1

• rs.CDC2L1.F1 rs.CDC2L1.R1 107 154
• NCBIGene 36.3 984
• Single exon skipping, size difference: 47
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_033486

• Changed! cd S_TKc 287aa 3e-68 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• Changed! smart S_TKc 276aa 1e-68 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• Changed! PTZ PTZ00024 295aa 4e-55 in ref transcript
  • cyclin-dependent protein kinase; Provisional.

CDC42BPA

• rs.CDC42BPA.F1 rs.CDC42BPA.R1 172 415
• NCBIGene 36.3 8476
• Single exon skipping, size difference: 243
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_003607

• cd STKc_MRCK_alpha 332aa 0.0 in ref transcript
  • STKc_MRCK_alpha: Serine/Threonine Kinases (STKs), DMPK-like subfamily, DMPK-related cell division control protein 42 (Cdc42) binding kinase (MRCK) alpha isoform, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The DMPK-like subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. MRCK is activated via interaction with the small GTPase Cdc42. MRCK/Cdc42 signaling mediates myosin-dependent cell motility. MRCKalpha is expressed ubiquitously in many tissues. It plays a role in the regulation of peripheral actin reorganization and neurite outgrowth. It may also play a role in the transferrin iron uptake pathway.
• cd PH_MRCK 122aa 2e-61 in ref transcript
  • MRCK (myotonic dystrophy-related Cdc42-binding kinase) pleckstrin homology (PH) domain. MRCK consists of a serine/threonine kinase domain, a cysteine rich (C1) region, a PH domain and a p21 binding motif. It has been shown to promote cytoskeletal reorganization, which affects many biological processes. The MRCK PH domain is responsible for its targeting to cell to cell junctions. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
• cd C1 50aa 1e-09 in ref transcript
  • Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
• cd CRIB 36aa 3e-04 in ref transcript
  • PAK (p21 activated kinase) Binding Domain (PBD), binds Cdc42p- and/or Rho-like small GTPases; also known as the Cdc42/Rac interactive binding (CRIB) motif; has been shown to inhibit transcriptional activation and cell transformation mediated by the Ras-Rac pathway. CRIB-containing effector proteins are functionally diverse and include serine/threonine kinases, tyrosine kinases, actin-binding proteins, and adapter molecules.
• smart S_TKc 257aa 2e-68 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• pfam CNH 264aa 6e-64 in ref transcript
  • CNH domain. Domain found in NIK1-like kinase, mouse citron and yeast ROM1, ROM2. Unpublished observations.
• pfam DMPK_coil 61aa 1e-17 in ref transcript
  • DMPK coiled coil domain like. This domain is found in the myotonic dystrophy protein kinase (DMPK) and adopts a coiled coil structure. It plays a role in dimerisation.
• Changed! TIGR SMC_prok_B 306aa 4e-14 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• smart S_TK_X 60aa 1e-11 in ref transcript
  • Extension to Ser/Thr-type protein kinases.
• pfam C1_1 51aa 8e-10 in ref transcript
  • Phorbol esters/diacylglycerol binding domain (C1 domain). This domain is also known as the Protein kinase C conserved region 1 (C1) domain.
• Changed! pfam SMC_N 338aa 1e-08 in ref transcript
  • RecF/RecN/SMC N terminal domain. This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.
• smart PBD 36aa 3e-05 in ref transcript
  • P21-Rho-binding domain. Small domains that bind Cdc42p- and/or Rho-like small GTPases. Also known as the Cdc42/Rac interactive binding (CRIB).
• smart PH 117aa 2e-04 in ref transcript
  • Pleckstrin homology domain. Domain commonly found in eukaryotic signalling proteins. The domain family possesses multiple functions including the abilities to bind inositol phosphates, and various proteins. PH domains have been found to possess inserted domains (such as in PLC gamma, syntrophins) and to be inserted within other domains. Mutations in Brutons tyrosine kinase (Btk) within its PH domain cause X-linked agammaglobulinaemia (XLA) in patients. Point mutations cluster into the positively charged end of the molecule around the predicted binding site for phosphatidylinositol lipids.
• PTZ PTZ00263 335aa 3e-63 in ref transcript
  • protein kinase A catalytic subunit; Provisional.
• Changed! COG SbcC 545aa 5e-17 in ref transcript
  • ATPase involved in DNA repair [DNA replication, recombination, and repair].
• COG ROM1 138aa 3e-07 in ref transcript
  • RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms].
• Changed! pfam SMC_N 329aa 6e-09 in modified transcript
• Changed! COG SbcC 464aa 3e-11 in modified transcript

CDKN1A

• rs.CDKN1A.F1 rs.CDKN1A.R1 243 384
• NCBIGene 36.3 1026
• Alternative 5-prime, size difference: 141
• Exclusion in 5'UTR
• Reference transcript: NM_078467

• pfam CDI 50aa 8e-13 in ref transcript
  • Cyclin-dependent kinase inhibitor. Cell cycle progression is negatively controlled by cyclin-dependent kinases inhibitors (CDIs). CDIs are involved in cell cycle arrest at the G1 phase.

CDKN2A

• rs.CDKN2A.F1 rs.CDKN2A.R1 127 401
• NCBIGene 36.3 1029
• Alternative 5-prime, size difference: 274
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_000077

• Changed! cd ANK 100aa 1e-12 in ref transcript
  • ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats.
• Changed! PTZ PTZ00322 81aa 1e-05 in ref transcript
  • 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase; Provisional.

CEACAM20

• rs.CEACAM20.F1 rs.CEACAM20.R1 102 138
• NCBIGene 36.3 125931
• Single exon skipping, size difference: 36
• Exclusion in 3'UTR
• Reference transcript: NM_001102597

• cd IGcam 71aa 1e-05 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• cd IGcam 80aa 3e-04 in ref transcript
• cd IGcam 73aa 6e-04 in ref transcript
• pfam I-set 84aa 4e-06 in ref transcript
  • Immunoglobulin I-set domain.
• smart IGc2 59aa 6e-06 in ref transcript
  • Immunoglobulin C-2 Type.
• smart IG_like 74aa 7e-06 in ref transcript
  • Immunoglobulin like. IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.

CEACAM20

• rs.CEACAM20.F2 rs.CEACAM20.R2 124 403
• NCBIGene 36.3 125931
• Single exon skipping, size difference: 279
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001102597

• Changed! cd IGcam 71aa 1e-05 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• cd IGcam 80aa 3e-04 in ref transcript
• cd IGcam 73aa 6e-04 in ref transcript
• pfam I-set 84aa 4e-06 in ref transcript
  • Immunoglobulin I-set domain.
• smart IGc2 59aa 6e-06 in ref transcript
  • Immunoglobulin C-2 Type.
• Changed! smart IG_like 74aa 7e-06 in ref transcript
  • Immunoglobulin like. IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.

CENPA

• rs.CENPA.F1 rs.CENPA.R1 390 468
• NCBIGene 36.3 1058
• Single exon skipping, size difference: 78
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001809

• Changed! smart H3 100aa 6e-34 in ref transcript
  • Histone H3.
• Changed! PTZ PTZ00018 87aa 2e-16 in ref transcript
  • histone 3; Provisional.
• Changed! smart H3 74aa 3e-25 in modified transcript
• Changed! PTZ PTZ00018 61aa 5e-14 in modified transcript

CEP170

• rs.CEP170.F1 rs.CEP170.R1 250 358
• NCBIGene 36.3 9859
• Alternative 3-prime, size difference: 108
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_014812

• cd FHA 89aa 4e-10 in ref transcript
  • Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins localize to the nucleus, where they participate in establishing or maintaining cell cycle checkpoints, DNA repair, or transcriptional regulation. Members of the FHA family include: Dun1, Rad53, Cds1, Mek1, KAPP(kinase-associated protein phosphatase),and Ki-67 (a human nuclear protein related to cell proliferation).
• pfam FHA 68aa 3e-11 in ref transcript
  • FHA domain. The FHA (Forkhead-associated) domain is a phosphopeptide binding motif.
• COG COG1716 79aa 1e-04 in ref transcript
  • FOG: FHA domain [Signal transduction mechanisms].

CEP170

• rs.CEP170.F2 rs.CEP170.R2 148 178
• NCBIGene 36.3 9859
• Alternative 5-prime, size difference: 30
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_014812

• cd FHA 89aa 4e-10 in ref transcript
  • Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins localize to the nucleus, where they participate in establishing or maintaining cell cycle checkpoints, DNA repair, or transcriptional regulation. Members of the FHA family include: Dun1, Rad53, Cds1, Mek1, KAPP(kinase-associated protein phosphatase),and Ki-67 (a human nuclear protein related to cell proliferation).
• pfam FHA 68aa 3e-11 in ref transcript
  • FHA domain. The FHA (Forkhead-associated) domain is a phosphopeptide binding motif.
• COG COG1716 79aa 1e-04 in ref transcript
  • FOG: FHA domain [Signal transduction mechanisms].

CEP170

• rs.CEP170.F3 rs.CEP170.R3 234 528
• NCBIGene 36.3 9859
• Single exon skipping, size difference: 294
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_014812

• cd FHA 89aa 4e-10 in ref transcript
  • Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins localize to the nucleus, where they participate in establishing or maintaining cell cycle checkpoints, DNA repair, or transcriptional regulation. Members of the FHA family include: Dun1, Rad53, Cds1, Mek1, KAPP(kinase-associated protein phosphatase),and Ki-67 (a human nuclear protein related to cell proliferation).
• pfam FHA 68aa 3e-11 in ref transcript
  • FHA domain. The FHA (Forkhead-associated) domain is a phosphopeptide binding motif.
• COG COG1716 79aa 1e-04 in ref transcript
  • FOG: FHA domain [Signal transduction mechanisms].

CEP250

• rs.CEP250.F1 rs.CEP250.R1 185 353
• NCBIGene 36.3 11190
• Single exon skipping, size difference: 168
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_007186

• TIGR SMC_prok_B 407aa 8e-12 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• TIGR SMC_prok_B 282aa 3e-07 in ref transcript
• TIGR SMC_prok_B 209aa 2e-04 in ref transcript
• pfam SMC_N 108aa 0.009 in ref transcript
  • RecF/RecN/SMC N terminal domain. This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.
• Changed! COG Smc 379aa 6e-10 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].
• COG Smc 261aa 5e-04 in ref transcript
• Changed! COG Smc 372aa 6e-10 in modified transcript

CEP63

• rs.CEP63.F1 rs.CEP63.R1 122 260
• NCBIGene 36.3 80254
• Single exon skipping, size difference: 138
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_025180

• Changed! TIGR SMC_prok_B 289aa 9e-09 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• Changed! TIGR SMC_prok_A 224aa 7e-04 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent.
• Changed! COG Smc 345aa 3e-07 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].
• Changed! TIGR SMC_prok_A 346aa 8e-09 in modified transcript
• Changed! TIGR SMC_prok_B 219aa 1e-07 in modified transcript
• Changed! COG Smc 299aa 2e-06 in modified transcript
• Changed! COG Smc 222aa 0.001 in modified transcript

CEP78

• rs.CEP78.F1 rs.CEP78.R1 108 156
• NCBIGene 36.3 84131
• Single exon skipping, size difference: 48
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001098802

• cd LRR_RI 170aa 1e-09 in ref transcript
  • Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1).

CHCHD4

• rs.CHCHD4.F1 rs.CHCHD4.R1 193 363
• NCBIGene 36.3 131474
• Single exon skipping, size difference: 170
• Exclusion of the protein initiation site
• Reference transcript: NM_144636

• pfam CHCH 44aa 5e-06 in ref transcript
  • CHCH domain. we have identified a conserved motif in the LOC118487 protein that we have called the CHCH motif. Alignment of this protein with related members showed the presence of three subgroups of proteins, which are called the S (Small), N (N-terminal extended) and C (C-terminal extended) subgroups. All three sub-groups of proteins have in common that they contain a predicted conserved [coiled coil 1]-[helix 1]-[coiled coil 2]-[helix 2] domain (CHCH domain). Within each helix of the CHCH domain, there are two cysteines present in a C-X9-C motif. The N-group contains an additional double helix domain, and each helix contains the C-X9-C motif. This family contains a number of characterised proteins: Cox19 protein - a nuclear gene of Saccharomyces cerevisiae, codes for an 11-kDa protein (Cox19p) required for expression of cytochrome oxidase. Because cox19 mutants are able to synthesise the mitochondrial and nuclear gene products of cytochrome oxidase, Cox19p probably functions post-translationally during assembly of the enzyme. Cox19p is present in the cytoplasm and mitochondria, where it exists as a soluble intermembrane protein. This dual location is similar to what was previously reported for Cox17p, a low molecular weight copper protein thought to be required for maturation of the CuA centre of subunit 2 of cytochrome oxidase. Cox19p have four conserved potential metal ligands, these are three cysteines and one histidine. Mrp10 - belongs to the class of yeast mitochondrial ribosomal proteins that are essential for translation. Eukaryotic NADH-ubiquinone oxidoreductase 19 kDa (NDUFA8) subunit. The CHCH domain was previously called DUF657.

CHEK2

• rs.CHEK2.F1 rs.CHEK2.R1 231 360
• NCBIGene 36.3 11200
• Single exon skipping, size difference: 129
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001005735

• cd S_TKc 268aa 7e-68 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• Changed! cd FHA 89aa 5e-07 in ref transcript
  • Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins localize to the nucleus, where they participate in establishing or maintaining cell cycle checkpoints, DNA repair, or transcriptional regulation. Members of the FHA family include: Dun1, Rad53, Cds1, Mek1, KAPP(kinase-associated protein phosphatase),and Ki-67 (a human nuclear protein related to cell proliferation).
• smart S_TKc 257aa 4e-75 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• pfam FHA 79aa 8e-08 in ref transcript
  • FHA domain. The FHA (Forkhead-associated) domain is a phosphopeptide binding motif.
• PTZ PTZ00263 226aa 5e-43 in ref transcript
  • protein kinase A catalytic subunit; Provisional.
• Changed! cd FHA 109aa 1e-07 in modified transcript

CHEK2

• rs.CHEK2.F2 rs.CHEK2.R2 157 244
• NCBIGene 36.3 11200
• Single exon skipping, size difference: 87
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001005735

• Changed! cd S_TKc 268aa 7e-68 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• cd FHA 89aa 5e-07 in ref transcript
  • Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins localize to the nucleus, where they participate in establishing or maintaining cell cycle checkpoints, DNA repair, or transcriptional regulation. Members of the FHA family include: Dun1, Rad53, Cds1, Mek1, KAPP(kinase-associated protein phosphatase),and Ki-67 (a human nuclear protein related to cell proliferation).
• Changed! smart S_TKc 257aa 4e-75 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• pfam FHA 79aa 8e-08 in ref transcript
  • FHA domain. The FHA (Forkhead-associated) domain is a phosphopeptide binding motif.
• Changed! PTZ PTZ00263 226aa 5e-43 in ref transcript
  • protein kinase A catalytic subunit; Provisional.
• Changed! cd S_TKc 239aa 4e-50 in modified transcript
• Changed! smart S_TKc 228aa 6e-56 in modified transcript
• Changed! PTZ PTZ00263 197aa 9e-29 in modified transcript

CHMP1A

• rs.CHMP1A.F1 rs.CHMP1A.R1 100 120
• NCBIGene 36.3 5119
• Single exon skipping, size difference: 20
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_001083314

• Changed! pfam Snf7 140aa 3e-11 in modified transcript
  • Snf7. This family of proteins are involved in protein sorting and transport from the endosome to the vacuole/lysosome in eukaryotic cells. Vacuoles/lysosomes play an important role in the degradation of both lipids and cellular proteins. In order to perform this degradative function, vacuoles/lysosomes contain numerous hydrolases which have been transported in the form of inactive precursors via the biosynthetic pathway and are proteolytically activated upon delivery to the vacuole/lysosome. The delivery of transmembrane proteins, such as activated cell surface receptors to the lumen of the vacuole/lysosome, either for degradation/downregulation, or in the case of hydrolases, for proper localisation, requires the formation of multivesicular bodies (MVBs). These late endosomal structures are formed by invaginating and budding of the limiting membrane into the lumen of the compartment. During this process, a subset of the endosomal membrane proteins is sorted into the forming vesicles. Mature MVBs fuse with the vacuole/lysosome, thereby releasing cargo containing vesicles into its hydrolytic lumen for degradation. Endosomal proteins that are not sorted into the intralumenal MVB vesicles are either recycled back to the plasma membrane or Golgi complex, or remain in the limiting membrane of the MVB and are thereby transported to the limiting membrane of the vacuole/lysosome as a consequence of fusion. Therefore, the MVB sorting pathway plays a critical role in the decision between recycling and degradation of membrane proteins. A few archaeal sequences are also present within this family.
• Changed! COG VPS24 148aa 1e-06 in modified transcript
  • Conserved protein implicated in secretion [Cell motility and secretion].

CHRFAM7A

• rs.CHRFAM7A.F1 rs.CHRFAM7A.R1 328 392
• NCBIGene 36.3 89832
• Single exon skipping, size difference: 64
• Exclusion of the protein initiation site
• Reference transcript: NM_139320

• Changed! TIGR LIC 373aa 1e-107 in ref transcript
  • selective while glycine receptors are anion selective).
• Changed! TIGR LIC 307aa 3e-78 in modified transcript

CLCC1

• rs.CLCC1.F1 rs.CLCC1.R1 90 100
• NCBIGene 36.3 23155
• Alternative 3-prime, size difference: 10
• Inclusion in 5'UTR
• Reference transcript: NM_001048210

• pfam MCLC 538aa 0.0 in ref transcript
  • Mid-1-related chloride channel (MCLC). This family consists of several mid-1-related chloride channels. mid-1-related chloride channel (MCLC) proteins function as a chloride channel when incorporated in the planar lipid bilayer.

CLCC1

• rs.CLCC1.F2 rs.CLCC1.R2 101 251
• NCBIGene 36.3 23155
• Alternative 3-prime, size difference: 150
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001048210

• Changed! pfam MCLC 538aa 0.0 in ref transcript
  • Mid-1-related chloride channel (MCLC). This family consists of several mid-1-related chloride channels. mid-1-related chloride channel (MCLC) proteins function as a chloride channel when incorporated in the planar lipid bilayer.
• Changed! pfam MCLC 488aa 0.0 in modified transcript

CLCN6

• rs.CLCN6.F1 rs.CLCN6.R1 90 100
• NCBIGene 36.3 1185
• Alternative 5-prime, size difference: 10
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_001286

• Changed! cd ClC_6_like 322aa 1e-105 in ref transcript
  • ClC-6-like chloride channel proteins. This CD includes ClC-6, ClC-7 and ClC-B, C, D in plants. Proteins in this family are ubiquitous in eukarotes and their functions are unclear. They are expressed in intracellular organelles membranes. This family belongs to the ClC superfamily of chloride ion channels, which share the unique double-barreled architecture and voltage-dependent gating mechanism. The gating is conferred by the permeating anion itself, acting as the gating charge. ClC chloride ion channel superfamily perform a variety of functions including cellular excitability regulation, cell volume regulation, membrane potential stabilization, acidification of intracellular organelles, signal transduction, and transepithelial transport in animals.
• Changed! cd ClC_6_like 112aa 5e-39 in ref transcript
• Changed! cd CBS_pair_EriC_assoc_euk_bac 54aa 2e-13 in ref transcript
  • This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the EriC CIC-type chloride channels in eukaryotes and bacteria. These ion channels are proteins with a seemingly simple task of allowing the passive flow of chloride ions across biological membranes. CIC-type chloride channels come from all kingdoms of life, have several gene families, and can be gated by voltage. The members of the CIC-type chloride channel are double-barreled: two proteins forming homodimers at a broad interface formed by four helices from each protein. The two pores are not found at this interface, but are completely contained within each subunit, as deduced from the mutational analyses, unlike many other channels, in which four or five identical or structurally related subunits jointly form one pore. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain in CLC chloride channel family members have been associated with classic Bartter syndrome, Osteopetrosis, Dent's disease, idiopathic generalized epilepsy, and myotonia.
• Changed! pfam Voltage_CLC 231aa 4e-28 in ref transcript
  • Voltage gated chloride channel. This family of ion channels contains 10 or 12 transmembrane helices. Each protein forms a single pore. It has been shown that some members of this family form homodimers. In terms of primary structure, they are unrelated to known cation channels or other types of anion channels. Three ClC subfamilies are found in animals. ClC-1 is involved in setting and restoring the resting membrane potential of skeletal muscle, while other channels play important parts in solute concentration mechanisms in the kidney. These proteins contain two pfam00571 domains.
• Changed! pfam Voltage_CLC 129aa 2e-15 in ref transcript
• Changed! pfam CBS 58aa 3e-08 in ref transcript
  • CBS domain pair. CBS domains are small intracellular modules that pair together to form a stable globular domain. This family represents a pair of CBS domains, that has been termed a Bateman domain. CBS domains have been shown to bind ligands with an adenosyl group such as AMP, ATP and S-AdoMet. CBS domains are found attached to a wide range of other protein domains suggesting that CBS domains may play a regulatory role making proteins sensitive to adenosyl carrying ligands. The region containing the CBS domains in Cystathionine-beta synthase is involved in regulation by S-AdoMet. CBS domain pairs from AMPK bind AMP or ATP. The CBS domains from IMPDH and the chloride channel CLC2 bind ATP.
• Changed! smart CBS 48aa 0.009 in ref transcript
  • Domain in cystathionine beta-synthase and other proteins. Domain present in all 3 forms of cellular life. Present in two copies in inosine monophosphate dehydrogenase, of which one is disordered in the crystal structure [3]. A number of disease states are associated with CBS-containing proteins including homocystinuria, Becker's and Thomsen disease.
• Changed! COG EriC 287aa 2e-13 in ref transcript
  • Chloride channel protein EriC [Inorganic ion transport and metabolism].
• Changed! COG EriC 111aa 3e-09 in ref transcript
• Changed! PRK PRK05567 58aa 3e-05 in ref transcript
  • inositol-5'-monophosphate dehydrogenase; Reviewed.
• Changed! cd ClC_6_like 188aa 1e-59 in modified transcript
• Changed! pfam Voltage_CLC 78aa 1e-14 in modified transcript
• Changed! COG EriC 136aa 2e-07 in modified transcript

CLEC12A

• rs.CLEC12A.F1 rs.CLEC12A.R1 211 310
• NCBIGene 36.3 160364
• Single exon skipping, size difference: 99
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_138337

• cd CLECT_NK_receptors_like 118aa 8e-30 in ref transcript
  • CLECT_NK_receptors_like: C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs), including proteins similar to oxidized low density lipoprotein (OxLDL) receptor (LOX-1), CD94, CD69, NKG2-A and -D, osteoclast inhibitory lectin (OCIL), dendritic cell-associated C-type lectin-1 (dectin-1), human myeloid inhibitory C-type lectin-like receptor (MICL), mast cell-associated functional antigen (MAFA), killer cell lectin-like receptors: subfamily F, member 1 (KLRF1) and subfamily B, member 1 (KLRB1), and lys49 receptors. CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. NKRs are variously associated with activation or inhibition of natural killer (NK) cells. Activating NKRs stimulate cytolysis by NK cells of virally infected or transformed cells; inhibitory NKRs block cytolysis upon recognition of markers of healthy self cells. Most Lys49 receptors are inhibitory; some are stimulatory. OCIL inhibits NK cell function via binding to the receptor NKRP1D. Murine OCIL in addition to inhibiting NK cell function inhibits osteoclast differentiation. MAFA clusters with the type I Fc epsilon receptor (FcepsilonRI) and inhibits the mast cells secretory response to FcepsilonRI stimulus. CD72 is a negative regulator of B cell receptor signaling. NKG2D is an activating receptor for stress-induced antigens; human NKG2D ligands include the stress induced MHC-I homologs, MICA, MICB, and ULBP family of glycoproteins Several NKRs have a carbohydrate-binding capacity which is not mediated through calcium ions (e.g. OCIL binds a range of high molecular weight sulfated glycosaminoglycans including dextran sulfate, fucoidan, and gamma-carrageenan sugars). Dectin-1 binds fungal beta-glucans and in involved in the innate immune responses to fungal pathogens. MAFA binds saccharides having terminal alpha-D mannose residues in a calcium-dependent manner. LOX-1 is the major receptor for OxLDL in endothelial cells and thought to play a role in the pathology of atherosclerosis. Some NKRs exist as homodimers (e.g.Lys49, NKG2D, CD69, LOX-1) and some as heterodimers (e.g. CD94/NKG2A). Dectin-1 can function as a monomer in vitro.
• smart CLECT 117aa 4e-15 in ref transcript
  • C-type lectin (CTL) or carbohydrate-recognition domain (CRD). Many of these domains function as calcium-dependent carbohydrate binding modules.

CLEC1B

• rs.CLEC1B.F1 rs.CLEC1B.R1 268 367
• NCBIGene 36.3 51266
• Single exon skipping, size difference: 99
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_016509

• cd CLECT_NK_receptors_like 117aa 8e-29 in ref transcript
  • CLECT_NK_receptors_like: C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs), including proteins similar to oxidized low density lipoprotein (OxLDL) receptor (LOX-1), CD94, CD69, NKG2-A and -D, osteoclast inhibitory lectin (OCIL), dendritic cell-associated C-type lectin-1 (dectin-1), human myeloid inhibitory C-type lectin-like receptor (MICL), mast cell-associated functional antigen (MAFA), killer cell lectin-like receptors: subfamily F, member 1 (KLRF1) and subfamily B, member 1 (KLRB1), and lys49 receptors. CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. NKRs are variously associated with activation or inhibition of natural killer (NK) cells. Activating NKRs stimulate cytolysis by NK cells of virally infected or transformed cells; inhibitory NKRs block cytolysis upon recognition of markers of healthy self cells. Most Lys49 receptors are inhibitory; some are stimulatory. OCIL inhibits NK cell function via binding to the receptor NKRP1D. Murine OCIL in addition to inhibiting NK cell function inhibits osteoclast differentiation. MAFA clusters with the type I Fc epsilon receptor (FcepsilonRI) and inhibits the mast cells secretory response to FcepsilonRI stimulus. CD72 is a negative regulator of B cell receptor signaling. NKG2D is an activating receptor for stress-induced antigens; human NKG2D ligands include the stress induced MHC-I homologs, MICA, MICB, and ULBP family of glycoproteins Several NKRs have a carbohydrate-binding capacity which is not mediated through calcium ions (e.g. OCIL binds a range of high molecular weight sulfated glycosaminoglycans including dextran sulfate, fucoidan, and gamma-carrageenan sugars). Dectin-1 binds fungal beta-glucans and in involved in the innate immune responses to fungal pathogens. MAFA binds saccharides having terminal alpha-D mannose residues in a calcium-dependent manner. LOX-1 is the major receptor for OxLDL in endothelial cells and thought to play a role in the pathology of atherosclerosis. Some NKRs exist as homodimers (e.g.Lys49, NKG2D, CD69, LOX-1) and some as heterodimers (e.g. CD94/NKG2A). Dectin-1 can function as a monomer in vitro.
• smart CLECT 116aa 8e-19 in ref transcript
  • C-type lectin (CTL) or carbohydrate-recognition domain (CRD). Many of these domains function as calcium-dependent carbohydrate binding modules.

CLIP1

• rs.CLIP1.F1 rs.CLIP1.R1 280 385
• NCBIGene 36.3 6249
• Single exon skipping, size difference: 105
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_002956

• pfam CAP_GLY 66aa 6e-27 in ref transcript
  • CAP-Gly domain. Cytoskeleton-associated proteins (CAPs) are involved in the organisation of microtubules and transportation of vesicles and organelles along the cytoskeletal network. A conserved motif, CAP-Gly, has been identified in a number of CAPs, including CLIP-170 and dynactins. The crystal structure of Caenorhabditis elegans F53F4.3 protein CAP-Gly domain was recently solved. The domain contains three beta-strands. The most conserved sequence, GKNDG, is located in two consecutive sharp turns on the surface, forming the entrance to a groove.
• pfam CAP_GLY 66aa 6e-26 in ref transcript
• TIGR SMC_prok_A 315aa 9e-14 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent.
• Changed! TIGR SMC_prok_B 178aa 8e-08 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• Changed! TIGR SMC_prok_B 349aa 2e-07 in ref transcript
• COG NIP100 61aa 2e-11 in ref transcript
  • Dynactin complex subunit involved in mitotic spindle partitioning in anaphase B [Cell division and chromosome partitioning].
• COG Smc 306aa 4e-11 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].
• COG NIP100 62aa 2e-10 in ref transcript
• Changed! PRK PRK03918 578aa 5e-07 in ref transcript
  • chromosome segregation protein; Provisional.
• Changed! TIGR SMC_prok_B 144aa 9e-06 in modified transcript
• Changed! pfam SMC_N 392aa 1e-05 in modified transcript
  • RecF/RecN/SMC N terminal domain. This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.
• Changed! PRK PRK03918 543aa 3e-06 in modified transcript

CMTM1

• rs.CMTM1.F1 rs.CMTM1.R1 109 460
• NCBIGene 36.3 113540
• Alternative 5-prime, size difference: 351
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_052999

• Changed! pfam MARVEL 114aa 0.006 in ref transcript
  • Membrane-associating domain. MARVEL domain-containing proteins are often found in lipid-associating proteins - such as Occludin and MAL family proteins. It may be part of the machinery of membrane apposition events, such as transport vesicle biogenesis.

CNGA3

• rs.CNGA3.F1 rs.CNGA3.R1 480 534
• NCBIGene 36.3 1261
• Single exon skipping, size difference: 54
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001298

• cd CAP_ED 117aa 8e-17 in ref transcript
  • effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels. Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels.
• smart cNMP 120aa 1e-17 in ref transcript
  • Cyclic nucleotide-monophosphate binding domain. Catabolite gene activator protein (CAP) is a prokaryotic homologue of eukaryotic cNMP-binding domains, present in ion channels, and cNMP-dependent kinases.
• pfam Ion_trans 140aa 3e-09 in ref transcript
  • Ion transport protein. This family contains Sodium, Potassium, Calcium ion channels. This family is 6 transmembrane helices in which the last two helices flank a loop which determines ion selectivity. In some sub-families (e.g. Na channels) the domain is repeated four times, whereas in others (e.g. K channels) the protein forms as a tetramer in the membrane. A bacterial structure of the protein is known for the last two helices but is not the Pfam family due to it lacking the first four helices.
• COG Crp 123aa 1e-06 in ref transcript
  • cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms].

CNTN5

• rs.CNTN5.F1 rs.CNTN5.R1 176 398
• NCBIGene 36.3 53942
• Single exon skipping, size difference: 222
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_014361

• cd IGcam 77aa 2e-14 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• cd IGcam 86aa 3e-13 in ref transcript
• cd FN3 92aa 1e-11 in ref transcript
  • Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.
• cd IGcam 87aa 4e-11 in ref transcript
• cd IGcam 92aa 1e-10 in ref transcript
• cd FN3 84aa 2e-09 in ref transcript
• cd FN3 93aa 4e-05 in ref transcript
• cd IGcam 84aa 5e-05 in ref transcript
• cd FN3 86aa 2e-04 in ref transcript
• cd IGcam 93aa 0.002 in ref transcript
• pfam I-set 89aa 1e-16 in ref transcript
  • Immunoglobulin I-set domain.
• pfam I-set 86aa 2e-15 in ref transcript
• smart IGc2 62aa 2e-13 in ref transcript
  • Immunoglobulin C-2 Type.
• pfam fn3 85aa 4e-10 in ref transcript
  • Fibronectin type III domain.
• pfam I-set 93aa 1e-09 in ref transcript
• pfam fn3 78aa 7e-07 in ref transcript
• smart IG_like 74aa 7e-06 in ref transcript
  • Immunoglobulin like. IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
• pfam I-set 91aa 1e-04 in ref transcript
• pfam fn3 88aa 6e-04 in ref transcript
• smart FN3 78aa 7e-04 in ref transcript
  • Fibronectin type 3 domain. One of three types of internal repeat within the plasma protein, fibronectin. The tenth fibronectin type III repeat contains a RGD cell recognition sequence in a flexible loop between 2 strands. Type III modules are present in both extracellular and intracellular proteins.

CNTNAP4

• rs.CNTNAP4.F1 rs.CNTNAP4.R1 173 317
• NCBIGene 36.3 85445
• Single exon skipping, size difference: 144
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_138994

• cd FA58C 123aa 2e-24 in ref transcript
  • Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes.
• cd LamG 145aa 1e-21 in ref transcript
  • Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules.
• cd LamG 151aa 1e-17 in ref transcript
• Changed! cd LamG 96aa 3e-10 in ref transcript
• cd LamG 140aa 1e-09 in ref transcript
• cd FReD 48aa 0.006 in ref transcript
  • Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation.
• smart LamG 127aa 6e-25 in ref transcript
  • Laminin G domain.
• pfam F5_F8_type_C 121aa 1e-23 in ref transcript
  • F5/8 type C domain. This domain is also known as the discoidin (DS) domain family.
• pfam Laminin_G_2 124aa 1e-20 in ref transcript
  • Laminin G domain. This family includes the Thrombospondin N-terminal-like domain, a Laminin G subfamily.
• pfam Laminin_G_2 128aa 5e-13 in ref transcript
• Changed! pfam Laminin_G_2 98aa 9e-12 in ref transcript
• smart FBG 45aa 4e-04 in ref transcript
  • Fibrinogen-related domains (FReDs). Domain present at the C-termini of fibrinogen beta and gamma chains, and a variety of fibrinogen-related proteins, including tenascin and Drosophila scabrous.
• smart COLFI 84aa 0.003 in ref transcript
  • Fibrillar collagens C-terminal domain. Found at C-termini of fibrillar collagens: Ephydatia muelleri procollagen EMF1alpha, vertebrate collagens alpha(1)III, alpha(1)II, alpha(2)V etc.
• pfam EGF 33aa 0.005 in ref transcript
  • EGF-like domain. There is no clear separation between noise and signal. pfam00053 is very similar, but has 8 instead of 6 conserved cysteines. Includes some cytokine receptors. The EGF domain misses the N-terminus regions of the Ca2+ binding EGF domains (this is the main reason of discrepancy between Swiss-Prot domain start/end and Pfam). The family is hard to model due to many similar but different sub-types of EGF domains. Pfam certainly misses a number of EGF domains.
• Changed! cd LamG 146aa 7e-18 in modified transcript
• Changed! pfam Laminin_G_2 127aa 7e-20 in modified transcript

COL11A2

• rs.COL11A2.F1 rs.COL11A2.R1 193 271
• NCBIGene 36.3 1302
• Single exon skipping, size difference: 78
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_080680

• cd LamG 152aa 1e-05 in ref transcript
  • Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules.
• smart COLFI 196aa 6e-85 in ref transcript
  • Fibrillar collagens C-terminal domain. Found at C-termini of fibrillar collagens: Ephydatia muelleri procollagen EMF1alpha, vertebrate collagens alpha(1)III, alpha(1)II, alpha(2)V etc.
• smart TSPN 183aa 7e-56 in ref transcript
  • Thrombospondin N-terminal -like domains. Heparin-binding and cell adhesion domain of thrombospondin.

COL13A1

• rs.COL13A1.F1 rs.COL13A1.R1 123 165
• NCBIGene 36.3 1305
• Single exon skipping, size difference: 42
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_005203

COL13A1

• rs.COL13A1.F2 rs.COL13A1.R2 101 146
• NCBIGene 36.3 1305
• Single exon skipping, size difference: 45
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_005203

COL13A1

• rs.COL13A1.F3 rs.COL13A1.R3 134 170
• NCBIGene 36.3 1305
• Single exon skipping, size difference: 36
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_005203

COLQ

• rs.COLQ.F1 rs.COLQ.R1 137 239
• NCBIGene 36.3 8292
• Single exon skipping, size difference: 102
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_005677

• TIGR myxo_disulf_rpt 25aa 5e-04 in ref transcript
  • This model represents a sequence region shared between several proteins of Myxococcus xanthus DK 1622 and some eukaryotic proteins that include human pappalysin-1. The region of about 40 amino acids contains several conserved Cys residues presumed to form disulfide bonds. The region appears in up to 13 repeats in Myxococcus.
• pfam Collagen 63aa 0.004 in ref transcript
  • Collagen triple helix repeat (20 copies). Members of this family belong to the collagen superfamily. Collagens are generally extracellular structural proteins involved in formation of connective tissue structure. The alignment contains 20 copies of the G-X-Y repeat that forms a triple helix. The first position of the repeat is glycine, the second and third positions can be any residue but are frequently proline and hydroxyproline. Collagens are post translationally modified by proline hydroxylase to form the hydroxyproline residues. Defective hydroxylation is the cause of scurvy. Some members of the collagen superfamily are not involved in connective tissue structure but share the same triple helical structure.

COMMD5

• rs.COMMD5.F1 rs.COMMD5.R1 256 410
• NCBIGene 36.3 28991
• Alternative 5-prime, size difference: 154
• Exclusion in 5'UTR
• Reference transcript: NM_014066

• cd Commd5_HCaRG 110aa 3e-46 in ref transcript
  • COMM_Domain containing protein 5, also called HCaRG (hypertension-related, calcium-regulated gene). HCaRG is a nuclear protein that might be involved in cell proliferation; it is negatively regulated by extracellular calcium concentration, and its basal mRNA levels are higher in hypertensive animals. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
• cd Commd10 147aa 3e-06 in ref transcript
  • COMM_Domain containing protein 10. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
• pfam HCaRG 176aa 1e-43 in ref transcript
  • HCaRG protein. This family consists of several mammalian HCaRG(hypertension-related, calcium-regulated gene) proteins. HCaRG is negatively regulated by extracellular calcium concentration, and its basal mRNA levels are higher in hypertensive animals. HCaRG is a nuclear protein potentially involved in the control of cell proliferation.

COMMD9

• rs.COMMD9.F1 rs.COMMD9.R1 165 291
• NCBIGene 36.3 29099
• Single exon skipping, size difference: 126
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_014186

• cd Commd9 108aa 2e-42 in ref transcript
  • COMM_Domain containing protein 9. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
• Changed! pfam HCaRG 183aa 9e-27 in ref transcript
  • HCaRG protein. This family consists of several mammalian HCaRG(hypertension-related, calcium-regulated gene) proteins. HCaRG is negatively regulated by extracellular calcium concentration, and its basal mRNA levels are higher in hypertensive animals. HCaRG is a nuclear protein potentially involved in the control of cell proliferation.
• Changed! pfam HCaRG 125aa 4e-24 in modified transcript

COPA

• rs.COPA.F1 rs.COPA.R1 119 146
• NCBIGene 36.3 1314
• Alternative 3-prime, size difference: 27
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001098398

• cd WD40 310aa 9e-60 in ref transcript
  • WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.
• pfam COPI_C 410aa 0.0 in ref transcript
  • Coatomer (COPI) alpha subunit C-terminus. This family represents the C-terminus (approximately 500 residues) of the eukaryotic coatomer alpha subunit. Coatomer (COPI) is a large cytosolic protein complex which forms a coat around vesicles budding from the Golgi apparatus. Such coatomer-coated vesicles have been proposed to play a role in many distinct steps of intracellular transport. Note that many family members also contain the pfam04053 domain.
• Changed! pfam Coatomer_WDAD 452aa 0.0 in ref transcript
  • Coatomer WD associated region.
• smart WD40 40aa 3e-07 in ref transcript
  • WD40 repeats. Note that these repeats are permuted with respect to the structural repeats (blades) of the beta propeller domain.
• pfam WD40 34aa 6e-05 in ref transcript
  • WD domain, G-beta repeat.
• pfam WD40 39aa 6e-05 in ref transcript
• smart WD40 36aa 1e-04 in ref transcript
• smart WD40 39aa 5e-04 in ref transcript
• COG COG2319 316aa 4e-32 in ref transcript
  • FOG: WD40 repeat [General function prediction only].
• Changed! pfam Coatomer_WDAD 443aa 0.0 in modified transcript

COPE

• rs.COPE.F1 rs.COPE.R1 101 254
• NCBIGene 36.3 11316
• Single exon skipping, size difference: 153
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_007263

• cd TPR 83aa 0.007 in ref transcript
  • Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here.
• Changed! pfam Coatomer_E 291aa 1e-109 in ref transcript
  • Coatomer epsilon subunit. This family represents the epsilon subunit of the coatomer complex, which is involved in the regulation of intracellular protein trafficking between the endoplasmic reticulum and the Golgi complex.
• Changed! pfam Coatomer_E 240aa 4e-84 in modified transcript

CPEB1

• rs.CPEB1.F1 rs.CPEB1.R1 100 115
• NCBIGene 36.3 64506
• Alternative 5-prime, size difference: 15
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_030594

• Changed! cd RRM 68aa 5e-05 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• cd RRM 60aa 0.005 in ref transcript
• Changed! smart RRM_2 63aa 0.001 in ref transcript
  • RNA recognition motif.
• Changed! cd RRM 73aa 1e-04 in modified transcript
• Changed! smart RRM_2 68aa 0.005 in modified transcript

CPSF4

• rs.CPSF4.F1 rs.CPSF4.R1 112 187
• NCBIGene 36.3 10898
• Alternative 3-prime, size difference: 75
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_006693

• smart ZnF_C3H1 26aa 0.002 in ref transcript
  • zinc finger.
• COG YTH1 152aa 1e-21 in ref transcript
  • Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only].

CPZ

• rs.CPZ.F1 rs.CPZ.R1 132 395
• NCBIGene 36.3 8532
• Alternative 5-prime and 3-prime, size difference: 263
• Inclusion in the protein causing a new stop codon, Inclusion in the protein causing a frameshift
• Reference transcript: NM_001014447

• Changed! cd M14_CPZ 395aa 0.0 in ref transcript
  • Peptidase M14-like domain of carboxypeptidase (CP) Z (CPZ), CPZ belongs to the N/E subfamily of the M14 family of metallocarboxypeptidases (MCPs). The M14 family are zinc-binding CPs which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. CPZ is a secreted Zn-dependent enzyme whose biological function is largely unknown. Unlike other members of the N/E subfamily, CPZ has a bipartite structure, which consists of an N-terminal cysteine-rich domain (CRD) whose sequence is similar to Wnt-binding proteins, and a C-terminal CP catalytic domain that removes C-terminal Arg residues from substrates. CPZ is enriched in the extracellular matrix and is widely distributed during early embryogenesis. That the CRD of CPZ can bind to Wnt4 suggests that CPZ plays a role in Wnt signaling.
• Changed! pfam Peptidase_M14 302aa 1e-62 in ref transcript
  • Zinc carboxypeptidase.
• Changed! smart FRI 118aa 2e-36 in ref transcript
  • Frizzled. Drosophila melanogaster frizzled mediates signalling that polarises a precursor cell along the anteroposterior axis. Homologues of the N-terminal region of frizzled exist either as transmembrane or secreted molecules. Frizzled homologues are reported to be receptors for the Wnt growth factors. (Not yet in MEDLINE: the FRI domain occurs in several receptor tyrosine kinases [Xu, Y.K. and Nusse, Curr. Biol. 8 R405-R406 (1998); Masiakowski, P. and Yanopoulos, G.D., Curr. Biol. 8, R407 (1998)].
• Changed! COG COG2866 185aa 2e-06 in ref transcript
  • Predicted carboxypeptidase [Amino acid transport and metabolism].

CREBBP

• rs.CREBBP.F1 rs.CREBBP.R1 209 323
• NCBIGene 36.3 1387
• Single exon skipping, size difference: 114
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_004380

• cd Bromo_cbp_like 108aa 1e-63 in ref transcript
  • Bromodomain, cbp_like subfamily. Cbp (CREB binding protein or CREBBP) is an acetyltransferase acting on histone, which gives a specific tag for transcriptional activation and also acetylates non-histone proteins. CREBBP binds specifically to phosphorylated CREB protein and augments the activity of phosphorylated CREB to activate transcription of cAMP-responsive genes. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
• cd ZZ_CBP 41aa 2e-19 in ref transcript
  • Zinc finger, ZZ type. Zinc finger present in CBP/p300 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. CREB-binding protein (CBP) is a large multidomain protein that provides binding sites for transcriptional coactivators, the role of the ZZ domain in CBP/p300 is unclear.
• pfam DUF906 234aa 1e-136 in ref transcript
  • Domain of Unknown Function (DUF906).
• pfam KIX 81aa 4e-38 in ref transcript
  • KIX domain. CBP and P300 bind to the CREB via a domain known as KIX. The KIX domain of CBP also binds to transactivation domains of other nuclear factors including Myb and Jun.
• Changed! pfam zf-TAZ 85aa 1e-35 in ref transcript
  • TAZ zinc finger. The TAZ2 domain of CBP binds to other transcription factors such as the p53 tumour suppressor protein, E1A oncoprotein, MyoD, and GATA-1. The zinc coordinating motif that is necessary for binding to target DNA sequences consists of HCCC.
• pfam DUF902 61aa 6e-31 in ref transcript
  • Domain of Unknown Function (DUF902).
• smart BROMO 109aa 5e-29 in ref transcript
  • bromo domain.
• pfam zf-TAZ 80aa 5e-25 in ref transcript
• pfam Creb_binding 73aa 6e-16 in ref transcript
  • Creb binding. The Creb binding domain assumes a structure comprising of three alpha-helices which pack in a bundle, exposing a hydrophobic groove between alpha-1 and alpha-3 within which complimentary domains found in the protein 'activator for thyroid hormone and retinoid receptors' (ACTR) can dock. Docking of these domains is required for the recruitment of RNA polymerase II and the basal transcription machinery.
• smart ZnF_ZZ 43aa 1e-12 in ref transcript
  • Zinc-binding domain, present in Dystrophin, CREB-binding protein. Putative zinc-binding domain present in dystrophin-like proteins, and CREB-binding protein/p300 homologues. The ZZ in dystrophin appears to bind calmodulin. A missense mutation of one of the conserved cysteines in dystrophin results in a patient with Duchenne muscular dystrophy [3].
• pfam PAT1 136aa 2e-04 in ref transcript
  • Topoisomerase II-associated protein PAT1. Members of this family are necessary for accurate chromosome transmission during cell division.
• COG COG5076 109aa 1e-12 in ref transcript
  • Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription].
• PRK PRK08853 109aa 0.001 in ref transcript
  • DNA polymerase III subunits gamma and tau; Validated.
• Changed! pfam zf-TAZ 58aa 5e-20 in modified transcript

CREM

• rs.CREM.F1 rs.CREM.R1 210 246
• NCBIGene 36.3 1390
• Single exon skipping, size difference: 36
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_182717

• pfam bZIP_1 53aa 4e-05 in ref transcript
  • bZIP transcription factor. The Pfam entry includes the basic region and the leucine zipper region.

CRKRS

• rs.CRKRS.F1 rs.CRKRS.R1 129 156
• NCBIGene 36.3 51755
• Alternative 3-prime, size difference: 27
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_016507

• cd S_TKc 295aa 5e-73 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• Changed! pfam Pkinase 294aa 1e-74 in ref transcript
  • Protein kinase domain.
• PTZ PTZ00024 288aa 1e-45 in ref transcript
  • cyclin-dependent protein kinase; Provisional.
• Changed! smart S_TKc 284aa 1e-74 in modified transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.

CRTC1

• rs.CRTC1.F1 rs.CRTC1.R1 186 234
• NCBIGene 36.3 23373
• Single exon skipping, size difference: 48
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001098482

CSHL1

• rs.CSHL1.F1 rs.CSHL1.R1 129 305
• NCBIGene 36.3 1444
• Exon skipping and alternative 3-prime or 5-prime, size difference: 176
• Inclusion in the protein causing a frameshift, Exclusion in the protein (no frameshift)
• Reference transcript: NM_022579

• Changed! pfam Hormone_1 190aa 1e-35 in ref transcript
  • Somatotropin hormone family.

CSHL1

• rs.CSHL1.F2 rs.CSHL1.R2 187 256
• NCBIGene 36.3 1444
• Alternative 3-prime, size difference: 69
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_022579

• Changed! pfam Hormone_1 190aa 1e-35 in ref transcript
  • Somatotropin hormone family.
• Changed! pfam Hormone_1 167aa 5e-31 in modified transcript

CSN1S1

• rs.CSN1S1.F1 rs.CSN1S1.R1 98 122
• NCBIGene 36.3 1446
• Single exon skipping, size difference: 24
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001890

CSN1S1

• rs.CSN1S1.F2 rs.CSN1S1.R2 243 270
• NCBIGene 36.3 1446
• Single exon skipping, size difference: 24
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001890

CSPP1

• rs.CSPP1.F1 rs.CSPP1.R1 163 268
• NCBIGene 36.3 79848
• Multiple exon skipping, size difference: 105
• Exclusion in the protein (no frameshift), Exclusion in the protein (no frameshift)
• Reference transcript: NM_001077204

CTDP1

• rs.CTDP1.F1 rs.CTDP1.R1 210 373
• NCBIGene 36.3 9150
• Single exon skipping, size difference: 163
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_004715

• cd BRCT 81aa 1e-06 in ref transcript
  • Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks.
• cd biotinyl_domain 91aa 1e-05 in ref transcript
  • The biotinyl-domain or biotin carboxyl carrier protein (BCCP) domain is present in all biotin-dependent enzymes, such as acetyl-CoA carboxylase, pyruvate carboxylase, propionyl-CoA carboxylase, methylcrotonyl-CoA carboxylase, geranyl-CoA carboxylase, oxaloacetate decarboxylase, methylmalonyl-CoA decarboxylase, transcarboxylase and urea amidolyase. This domain functions in transferring CO2 from one subsite to another, allowing carboxylation, decarboxylation, or transcarboxylation. During this process, biotin is covalently attached to a specific lysine.
• Changed! pfam FCP1_C 246aa 2e-83 in ref transcript
  • FCP1, C-terminal. The C-terminal domain of FCP-1 is required for interaction with the carboxy terminal domain of RAP74. Interaction relies extensively on van der Waals contacts between hydrophobic residues situated within alpha-helices in both domains.
• pfam NIF 167aa 2e-68 in ref transcript
  • NLI interacting factor-like phosphatase. This family contains a number of NLI interacting factor isoforms and also an N-terminal regions of RNA polymerase II CTC phosphatase and FCP1 serine phosphatase. This region has been identified as the minimal phosphatase domain.
• smart BRCT 87aa 4e-07 in ref transcript
  • breast cancer carboxy-terminal domain.
• COG FCP1 148aa 2e-13 in ref transcript
  • TFIIF-interacting CTD phosphatases, including NLI-interacting factor [Transcription].
• PRK PRK09282 112aa 3e-05 in ref transcript
  • pyruvate carboxylase subunit B; Validated.
• Changed! pfam FCP1_C 91aa 6e-37 in modified transcript

CTH

• rs.CTH.F1 rs.CTH.R1 208 340
• NCBIGene 36.3 1491
• Single exon skipping, size difference: 132
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001902

• Changed! cd CGS_like 360aa 1e-155 in ref transcript
  • CGS_like: Cystathionine gamma-synthase is a PLP dependent enzyme and catalyzes the committed step of methionine biosynthesis. This pathway is unique to microorganisms and plants, rendering the enzyme an attractive target for the development of antimicrobials and herbicides. This subgroup also includes cystathionine gamma-lyases (CGL), O-acetylhomoserine sulfhydrylases and O-acetylhomoserine thiol lyases. CGL's are very similar to CGS's. Members of this group are widely distributed among all three forms of life.
• Changed! pfam Cys_Met_Meta_PP 377aa 1e-165 in ref transcript
  • Cys/Met metabolism PLP-dependent enzyme. This family includes enzymes involved in cysteine and methionine metabolism. The following are members: Cystathionine gamma-lyase, Cystathionine gamma-synthase, Cystathionine beta-lyase, Methionine gamma-lyase, OAH/OAS sulfhydrylase, O-succinylhomoserine sulfhydrylase All of these members participate is slightly different reactions. All these enzymes use PLP (pyridoxal-5'-phosphate) as a cofactor.
• Changed! COG MetC 386aa 1e-128 in ref transcript
  • Cystathionine beta-lyases/cystathionine gamma-synthases [Amino acid transport and metabolism].
• Changed! cd CGS_like 316aa 1e-124 in modified transcript
• Changed! pfam Cys_Met_Meta_PP 333aa 1e-134 in modified transcript
• Changed! COG MetC 342aa 1e-102 in modified transcript

CTNND1

• rs.CTNND1.F1 rs.CTNND1.R1 302 375
• NCBIGene 36.3 1500
• Alternative 5-prime, size difference: 73
• Exclusion in 5'UTR
• Reference transcript: NM_001085458

• cd ARM 119aa 1e-19 in ref transcript
  • Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model.
• cd ARM 103aa 9e-11 in ref transcript
• cd ARM 142aa 5e-05 in ref transcript
• smart ARM 42aa 5e-05 in ref transcript
  • Armadillo/beta-catenin-like repeats. Approx. 40 amino acid repeat. Tandem repeats form superhelix of helices that is proposed to mediate interaction of beta-catenin with its ligands. Involved in transducing the Wingless/Wnt signal. In plakoglobin arm repeats bind alpha-catenin and N-cadherin.
• smart ARM 41aa 1e-04 in ref transcript
• smart ARM 36aa 6e-04 in ref transcript

CTNND1

• rs.CTNND1.F2 rs.CTNND1.R2 120 183
• NCBIGene 36.3 1500
• Single exon skipping, size difference: 63
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001085458

• cd ARM 119aa 1e-19 in ref transcript
  • Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model.
• cd ARM 103aa 9e-11 in ref transcript
• cd ARM 142aa 5e-05 in ref transcript
• smart ARM 42aa 5e-05 in ref transcript
  • Armadillo/beta-catenin-like repeats. Approx. 40 amino acid repeat. Tandem repeats form superhelix of helices that is proposed to mediate interaction of beta-catenin with its ligands. Involved in transducing the Wingless/Wnt signal. In plakoglobin arm repeats bind alpha-catenin and N-cadherin.
• smart ARM 41aa 1e-04 in ref transcript
• smart ARM 36aa 6e-04 in ref transcript

CTNND1

• rs.CTNND1.F3 rs.CTNND1.R3 102 120
• NCBIGene 36.3 1500
• Single exon skipping, size difference: 18
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001085458

• cd ARM 119aa 1e-19 in ref transcript
  • Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model.
• cd ARM 103aa 9e-11 in ref transcript
• cd ARM 142aa 5e-05 in ref transcript
• smart ARM 42aa 5e-05 in ref transcript
  • Armadillo/beta-catenin-like repeats. Approx. 40 amino acid repeat. Tandem repeats form superhelix of helices that is proposed to mediate interaction of beta-catenin with its ligands. Involved in transducing the Wingless/Wnt signal. In plakoglobin arm repeats bind alpha-catenin and N-cadherin.
• smart ARM 41aa 1e-04 in ref transcript
• smart ARM 36aa 6e-04 in ref transcript

CTNND1

• rs.CTNND1.F4 rs.CTNND1.R4 235 322
• NCBIGene 36.3 1500
• Single exon skipping, size difference: 87
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001085458

• cd ARM 119aa 1e-19 in ref transcript
  • Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model.
• cd ARM 103aa 9e-11 in ref transcript
• cd ARM 142aa 5e-05 in ref transcript
• smart ARM 42aa 5e-05 in ref transcript
  • Armadillo/beta-catenin-like repeats. Approx. 40 amino acid repeat. Tandem repeats form superhelix of helices that is proposed to mediate interaction of beta-catenin with its ligands. Involved in transducing the Wingless/Wnt signal. In plakoglobin arm repeats bind alpha-catenin and N-cadherin.
• smart ARM 41aa 1e-04 in ref transcript
• smart ARM 36aa 6e-04 in ref transcript

CTNND1

• rs.CTNND1.F5 rs.CTNND1.R5 110 518
• NCBIGene 36.3 1500
• Multiple exon skipping, size difference: 408
• Exclusion in 5'UTR, Exclusion of the protein initiation site
• Reference transcript: NM_001085458

• cd ARM 119aa 1e-19 in ref transcript
  • Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model.
• cd ARM 103aa 9e-11 in ref transcript
• cd ARM 142aa 5e-05 in ref transcript
• smart ARM 42aa 5e-05 in ref transcript
  • Armadillo/beta-catenin-like repeats. Approx. 40 amino acid repeat. Tandem repeats form superhelix of helices that is proposed to mediate interaction of beta-catenin with its ligands. Involved in transducing the Wingless/Wnt signal. In plakoglobin arm repeats bind alpha-catenin and N-cadherin.
• smart ARM 41aa 1e-04 in ref transcript
• smart ARM 36aa 6e-04 in ref transcript

CTNS

• rs.CTNS.F1 rs.CTNS.R1 179 302
• NCBIGene 36.3 1497
• Alternative 5-prime, size difference: 123
• Inclusion in 5'UTR
• Reference transcript: NM_001031681

• TIGR 2A43 233aa 1e-77 in ref transcript

CTSB

• rs.CTSB.F1 rs.CTSB.R1 190 264
• NCBIGene 36.3 1508
• Single exon skipping, size difference: 74
• Exclusion in 5'UTR
• Reference transcript: NM_147780

• cd Peptidase_C1A_CathepsinB 248aa 1e-106 in ref transcript
  • Cathepsin B group; composed of cathepsin B and similar proteins, including tubulointerstitial nephritis antigen (TIN-Ag). Cathepsin B is a lysosomal papain-like cysteine peptidase which is expressed in all tissues and functions primarily as an exopeptidase through its carboxydipeptidyl activity. Together with other cathepsins, it is involved in the degradation of proteins, proenzyme activation, Ag processing, metabolism and apoptosis. Cathepsin B has been implicated in a number of human diseases such as cancer, rheumatoid arthritis, osteoporosis and Alzheimer's disease. The unique carboxydipeptidyl activity of cathepsin B is attributed to the presence of an occluding loop in its active site which favors the binding of the C-termini of substrate proteins. Some members of this group do not possess the occluding loop. TIN-Ag is an extracellular matrix basement protein which was originally identified as a target Ag involved in anti-tubular basement membrane antibody-mediated interstitial nephritis. It plays a role in renal tubulogenesis and is defective in hereditary tubulointerstitial disorders. TIN-Ag is exclusively expressed in kidney tissues.
• pfam Peptidase_C1 250aa 6e-69 in ref transcript
  • Papain family cysteine protease.
• pfam Propeptide_C1 41aa 2e-15 in ref transcript
  • Peptidase family C1 propeptide. This motif is found at the N terminal of some members of the Peptidase_C1 family (pfam00112) and is involved in activation of this peptidase.
• PTZ PTZ00200 232aa 4e-25 in ref transcript
  • cysteine proteinase precursor; Provisional.

CTSB

• rs.CTSB.F2 rs.CTSB.R2 103 191
• NCBIGene 36.3 1508
• Single exon skipping, size difference: 88
• Exclusion in 5'UTR
• Reference transcript: NM_147780

• cd Peptidase_C1A_CathepsinB 248aa 1e-106 in ref transcript
  • Cathepsin B group; composed of cathepsin B and similar proteins, including tubulointerstitial nephritis antigen (TIN-Ag). Cathepsin B is a lysosomal papain-like cysteine peptidase which is expressed in all tissues and functions primarily as an exopeptidase through its carboxydipeptidyl activity. Together with other cathepsins, it is involved in the degradation of proteins, proenzyme activation, Ag processing, metabolism and apoptosis. Cathepsin B has been implicated in a number of human diseases such as cancer, rheumatoid arthritis, osteoporosis and Alzheimer's disease. The unique carboxydipeptidyl activity of cathepsin B is attributed to the presence of an occluding loop in its active site which favors the binding of the C-termini of substrate proteins. Some members of this group do not possess the occluding loop. TIN-Ag is an extracellular matrix basement protein which was originally identified as a target Ag involved in anti-tubular basement membrane antibody-mediated interstitial nephritis. It plays a role in renal tubulogenesis and is defective in hereditary tubulointerstitial disorders. TIN-Ag is exclusively expressed in kidney tissues.
• pfam Peptidase_C1 250aa 6e-69 in ref transcript
  • Papain family cysteine protease.
• pfam Propeptide_C1 41aa 2e-15 in ref transcript
  • Peptidase family C1 propeptide. This motif is found at the N terminal of some members of the Peptidase_C1 family (pfam00112) and is involved in activation of this peptidase.
• PTZ PTZ00200 232aa 4e-25 in ref transcript
  • cysteine proteinase precursor; Provisional.

CTSB

• rs.CTSB.F3 rs.CTSB.R3 399 444
• NCBIGene 36.3 1508
• Alternative 5-prime, size difference: 45
• Exclusion in 5'UTR
• Reference transcript: NM_147781

• cd Peptidase_C1A_CathepsinB 248aa 1e-106 in ref transcript
  • Cathepsin B group; composed of cathepsin B and similar proteins, including tubulointerstitial nephritis antigen (TIN-Ag). Cathepsin B is a lysosomal papain-like cysteine peptidase which is expressed in all tissues and functions primarily as an exopeptidase through its carboxydipeptidyl activity. Together with other cathepsins, it is involved in the degradation of proteins, proenzyme activation, Ag processing, metabolism and apoptosis. Cathepsin B has been implicated in a number of human diseases such as cancer, rheumatoid arthritis, osteoporosis and Alzheimer's disease. The unique carboxydipeptidyl activity of cathepsin B is attributed to the presence of an occluding loop in its active site which favors the binding of the C-termini of substrate proteins. Some members of this group do not possess the occluding loop. TIN-Ag is an extracellular matrix basement protein which was originally identified as a target Ag involved in anti-tubular basement membrane antibody-mediated interstitial nephritis. It plays a role in renal tubulogenesis and is defective in hereditary tubulointerstitial disorders. TIN-Ag is exclusively expressed in kidney tissues.
• pfam Peptidase_C1 250aa 6e-69 in ref transcript
  • Papain family cysteine protease.
• pfam Propeptide_C1 41aa 2e-15 in ref transcript
  • Peptidase family C1 propeptide. This motif is found at the N terminal of some members of the Peptidase_C1 family (pfam00112) and is involved in activation of this peptidase.
• PTZ PTZ00200 232aa 4e-25 in ref transcript
  • cysteine proteinase precursor; Provisional.

CUGBP1

• rs.CUGBP1.F1 rs.CUGBP1.R1 104 116
• NCBIGene 36.3 10658
• Alternative 3-prime, size difference: 12
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001025596

• cd RRM 77aa 6e-17 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• cd RRM 75aa 3e-16 in ref transcript
• cd RRM 80aa 3e-14 in ref transcript
• TIGR SF-CC1 181aa 4e-18 in ref transcript
  • A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed.
• smart RRM 71aa 1e-15 in ref transcript
  • RNA recognition motif.
• COG COG0724 93aa 3e-11 in ref transcript
  • RNA-binding proteins (RRM domain) [General function prediction only].
• COG COG0724 163aa 6e-09 in ref transcript

CXXC1

• rs.CXXC1.F1 rs.CXXC1.R1 100 112
• NCBIGene 36.3 30827
• Alternative 5-prime, size difference: 12
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001101654

• pfam zf-CXXC 37aa 1e-08 in ref transcript
  • CXXC zinc finger domain. This domain contains eight conserved cysteine residues that bind to two zinc ions. The CXXC domain is found in a variety of chromatin-associated proteins. This domain binds to nonmethyl-CpG dinucleotides. The domain is characterised by two CGXCXXC repeats. The RecQ helicase has a single repeat that also binds to zinc, but this has not been included in this family. The DNA binding interface has been identified by NMR.
• pfam PHD 48aa 5e-08 in ref transcript
  • PHD-finger. PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
• COG TNG2 75aa 2e-06 in ref transcript
  • Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics].

CYFIP2

• rs.CYFIP2.F1 rs.CYFIP2.R1 115 504
• NCBIGene 36.3 26999
• Alternative 5-prime, size difference: 389
• Exclusion in 5'UTR
• Reference transcript: NM_001037332

• pfam FragX_IP 1131aa 0.0 in ref transcript
  • Cytoplasmic Fragile-X interacting family. CYFIP1/2 (Cytoplasmic fragile X mental retardation interacting protein) like proteins for a highly conserved protein family. The function of CYFIPs is unclear, but CYFIP interaction with fragile X mental retardation interacting protein (FMRP) involves the domain of FMRP which also mediating homo- and heteromerization.

CYLD

• rs.CYLD.F1 rs.CYLD.R1 243 380
• NCBIGene 36.3 1540
• Single exon skipping, size difference: 137
• Exclusion in 5'UTR
• Reference transcript: NM_015247

• cd Peptidase_C19N 272aa 3e-56 in ref transcript
  • A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
• pfam CAP_GLY 69aa 1e-13 in ref transcript
  • CAP-Gly domain. Cytoskeleton-associated proteins (CAPs) are involved in the organisation of microtubules and transportation of vesicles and organelles along the cytoskeletal network. A conserved motif, CAP-Gly, has been identified in a number of CAPs, including CLIP-170 and dynactins. The crystal structure of Caenorhabditis elegans F53F4.3 protein CAP-Gly domain was recently solved. The domain contains three beta-strands. The most conserved sequence, GKNDG, is located in two consecutive sharp turns on the surface, forming the entrance to a groove.
• pfam CAP_GLY 77aa 9e-12 in ref transcript
• pfam CAP_GLY 72aa 7e-10 in ref transcript
• COG NIP100 102aa 0.001 in ref transcript
  • Dynactin complex subunit involved in mitotic spindle partitioning in anaphase B [Cell division and chromosome partitioning].

DACH1

• rs.DACH1.F1 rs.DACH1.R1 105 549
• NCBIGene 36.3 1602
• Multiple exon skipping, size difference: 444
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift, Exclusion in the protein (no frameshift)
• Reference transcript: NM_080759

• pfam Ski_Sno 115aa 1e-44 in ref transcript
  • SKI/SNO/DAC family. This family contains a presumed domain that is about 100 amino acids long. All members of this family contain a conserved CLPQ motif. The c-ski proto-oncogene has been shown to influence proliferation, morphological transformation and myogenic differentiation. Sno, a Ski proto-oncogene homologue, is expressed in two isoforms and plays a role in the response to proliferation stimuli. Dachshund also contains this domain. It is involved in various aspects of development.

DACT1

• rs.DACT1.F1 rs.DACT1.R1 355 466
• NCBIGene 36.3 51339
• Alternative 3-prime, size difference: 111
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_016651

DBI

• rs.DBI.F1 rs.DBI.R1 172 412
• NCBIGene 36.3 1622
• Exon skipping and alternative 3-prime or 5-prime, size difference: 240
• Exclusion in 5'UTR, Exclusion of the protein initiation site
• Reference transcript: NM_020548

• Changed! cd ACBP 84aa 7e-29 in ref transcript
  • Acyl CoA binding protein (ACBP) binds thiol esters of long fatty acids and coenzyme A in a one-to-one binding mode with high specificity and affinity. Acyl-CoAs are important intermediates in fatty lipid synthesis and fatty acid degradation and play a role in regulation of intermediary metabolism and gene regulation. The suggested role of ACBP is to act as a intracellular acyl-CoA transporter and pool former. ACBPs are present in a large group of eukaryotic species and several tissue-specific isoforms have been detected.
• Changed! pfam ACBP 85aa 2e-21 in ref transcript
  • Acyl CoA binding protein.
• Changed! COG ACB 81aa 3e-21 in ref transcript
  • Acyl-CoA-binding protein [Lipid metabolism].
• Changed! cd ACBP 85aa 1e-27 in modified transcript
• Changed! pfam ACBP 85aa 1e-20 in modified transcript
• Changed! COG ACB 86aa 2e-20 in modified transcript

DBNDD2

• rs.DBNDD2.F1 rs.DBNDD2.R1 378 476
• NCBIGene 36.3 55861
• Alternative 5-prime, size difference: 98
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_001048221

• Changed! pfam Dysbindin 86aa 3e-25 in ref transcript
  • Dysbindin (Dystrobrevin binding protein 1). Dysbindin is an evolutionary conserved 40-kDa coiled-coil-containing protein that binds to alpha- and beta-dystrobrevin in muscle and brain. Dystrophin and alpha-dystrobrevin are co-immunoprecipitated with dysbindin, indicating that dysbindin is DPC-associated in muscle. Dysbindin co-localises with alpha-dystrobrevin at the sarcolemma and is up-regulated in dystrophin-deficient muscle. In the brain, dysbindin is found primarily in axon bundles and especially in certain axon terminals, notably mossy fibre synaptic terminals in the cerebellum and hippocampus. Dysbindin may have implications for the molecular pathology of Duchenne muscular dystrophy and may provide an alternative route for anchoring dystrobrevin and the DPC to the muscle membrane. Genetic variation in the human dysbindin gene is also thought to be associated with Schizophrenia.
• Changed! pfam Dysbindin 73aa 3e-23 in modified transcript

DCLRE1C

• rs.DCLRE1C.F1 rs.DCLRE1C.R1 104 426
• NCBIGene 36.3 64421
• Single exon skipping, size difference: 322
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_001033855

• Changed! pfam DRMBL 99aa 2e-16 in ref transcript
  • DNA repair metallo-beta-lactamase. The metallo-beta-lactamase fold contains five sequence motifs. The first four motifs are found in pfam00753 and are common to all metallo-beta-lactamases. The fifth motif appears to be specific to function. This entry represents the fifth motif from metallo-beta-lactamases involved in DNA repair.
• Changed! smart Lactamase_B 115aa 3e-08 in ref transcript
  • Metallo-beta-lactamase superfamily. Apart from the beta-lactamases a number of other proteins contain this domain PUBMED:7588620. These proteins include thiolesterases, members of the glyoxalase II family, that catalyse the hydrolysis of S-D-lactoyl-glutathione to form glutathione and D-lactic acid and a competence protein that is essential for natural transformation in Neisseria gonorrhoeae and could be a transporter involved in DNA uptake. Except for the competence protein these proteins bind two zinc ions per molecule as cofactor.
• Changed! COG YSH1 175aa 1e-11 in ref transcript
  • Predicted exonuclease of the beta-lactamase fold involved in RNA processing [Translation, ribosomal structure and biogenesis].
• Changed! smart Lactamase_B 71aa 2e-04 in modified transcript

DCX

• rs.DCX.F1 rs.DCX.R1 100 115
• NCBIGene 36.3 1641
• Alternative 5-prime, size difference: 15
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_000555

• cd DCX 83aa 9e-25 in ref transcript
  • DCX The ubiquitin-like DCX domain is present in tandem within the N-terminal half of the doublecortin protein. Doublecortin is expressed in migrating neurons. Mutations in the gene encoding doublecortin cause lissencephaly in males and 'double-cortex syndrome' in females.
• cd DCX 80aa 1e-19 in ref transcript
• smart DCX 91aa 5e-30 in ref transcript
  • Domain in the Doublecortin (DCX) gene product. Tandemly-repeated domain in doublin, the Doublecortin gene product. Proposed to bind tubulin. Doublecortin (DCX) is mutated in human X-linked neuronal migration defects.
• smart DCX 89aa 2e-25 in ref transcript

DDR1

• rs.DDR1.F1 rs.DDR1.R1 100 118
• NCBIGene 36.3 780
• Alternative 3-prime, size difference: 18
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_013994

• Changed! cd PTKc_DDR1 310aa 1e-174 in ref transcript
  • Catalytic Domain of the Protein Tyrosine Kinase, Discoidin Domain Receptor 1. Protein Tyrosine Kinase (PTK) family; mammalian Discoidin domain receptor 1 (DDR1) and homologs; catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. DDR1 is a member of the DDR subfamily, which are receptor tyr kinases (RTKs) containing an extracellular discoidin homology domain, a transmembrane segment, an extended juxtamembrane region, and an intracellular catalytic domain. The binding of the ligand, collagen, to DDRs results in a slow but sustained receptor activation. DDR1 binds to all collagens tested to date (types I-IV). It is widely expressed in many tissues. It is abundant in the brain and is also found in keratinocytes, colonic mucosa epithelium, lung epithelium, thyroid follicles, and the islets of Langerhans. During embryonic development, it is found in the developing neuroectoderm. DDR1 is a key regulator of cell morphogenesis, differentiation and proliferation. It is important in the development of the mammary gland, the vasculator and the kidney. DDR1 is also found in human leukocytes, where it facilitates cell adhesion, migration, maturation, and cytokine production.
• cd FA58C 117aa 9e-28 in ref transcript
  • Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes.
• Changed! smart TyrKc 302aa 8e-97 in ref transcript
  • Tyrosine kinase, catalytic domain. Phosphotransferases. Tyrosine-specific kinase subfamily.
• smart FA58C 156aa 5e-26 in ref transcript
  • Coagulation factor 5/8 C-terminal domain, discoidin domain. Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes.
• Changed! COG SPS1 297aa 9e-23 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].
• Changed! cd PTKc_DDR1 304aa 1e-176 in modified transcript
• Changed! smart TyrKc 296aa 9e-99 in modified transcript
• Changed! COG SPS1 291aa 2e-23 in modified transcript

DDR1

• rs.DDR1.F2 rs.DDR1.R2 230 341
• NCBIGene 36.3 780
• Single exon skipping, size difference: 111
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_013994

• cd PTKc_DDR1 310aa 1e-174 in ref transcript
  • Catalytic Domain of the Protein Tyrosine Kinase, Discoidin Domain Receptor 1. Protein Tyrosine Kinase (PTK) family; mammalian Discoidin domain receptor 1 (DDR1) and homologs; catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. DDR1 is a member of the DDR subfamily, which are receptor tyr kinases (RTKs) containing an extracellular discoidin homology domain, a transmembrane segment, an extended juxtamembrane region, and an intracellular catalytic domain. The binding of the ligand, collagen, to DDRs results in a slow but sustained receptor activation. DDR1 binds to all collagens tested to date (types I-IV). It is widely expressed in many tissues. It is abundant in the brain and is also found in keratinocytes, colonic mucosa epithelium, lung epithelium, thyroid follicles, and the islets of Langerhans. During embryonic development, it is found in the developing neuroectoderm. DDR1 is a key regulator of cell morphogenesis, differentiation and proliferation. It is important in the development of the mammary gland, the vasculator and the kidney. DDR1 is also found in human leukocytes, where it facilitates cell adhesion, migration, maturation, and cytokine production.
• cd FA58C 117aa 9e-28 in ref transcript
  • Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes.
• smart TyrKc 302aa 8e-97 in ref transcript
  • Tyrosine kinase, catalytic domain. Phosphotransferases. Tyrosine-specific kinase subfamily.
• smart FA58C 156aa 5e-26 in ref transcript
  • Coagulation factor 5/8 C-terminal domain, discoidin domain. Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes.
• COG SPS1 297aa 9e-23 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].

DGKG

• rs.DGKG.F1 rs.DGKG.R1 142 217
• NCBIGene 36.3 1608
• Single exon skipping, size difference: 75
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001346

• cd C1 50aa 7e-11 in ref transcript
  • Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
• cd EFh 70aa 4e-08 in ref transcript
  • EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers.
• pfam DAGK_acc 175aa 8e-87 in ref transcript
  • Diacylglycerol kinase accessory domain. Diacylglycerol (DAG) is a second messenger that acts as a protein kinase C activator. This domain is assumed to be an accessory domain: its function is unknown.
• Changed! smart DAGKc 122aa 2e-47 in ref transcript
  • Diacylglycerol kinase catalytic domain (presumed). Diacylglycerol (DAG) is a second messenger that acts as a protein kinase C activator. DAG can be produced from the hydrolysis of phosphatidylinositol 4,5-bisphosphate (PIP2) by a phosphoinositide-specific phospholipase C and by the degradation of phosphatidylcholine (PC) by a phospholipase C or the concerted actions of phospholipase D and phosphatidate phosphohydrolase. This domain is presumed to be the catalytic domain. Bacterial homologues areknown.
• pfam C1_1 50aa 1e-08 in ref transcript
  • Phorbol esters/diacylglycerol binding domain (C1 domain). This domain is also known as the Protein kinase C conserved region 1 (C1) domain.
• smart C1 41aa 4e-05 in ref transcript
  • Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
• Changed! COG LCB5 327aa 4e-10 in ref transcript
  • Sphingosine kinase and enzymes related to eukaryotic diacylglycerol kinase [Lipid metabolism / General function prediction only].
• COG FRQ1 76aa 7e-04 in ref transcript
  • Ca2+-binding protein (EF-Hand superfamily) [Signal transduction mechanisms / Cytoskeleton / Cell division and chromosome partitioning / General function prediction only].
• Changed! smart DAGKc 97aa 1e-32 in modified transcript
• Changed! COG LCB5 277aa 1e-07 in modified transcript

DGKG

• rs.DGKG.F2 rs.DGKG.R2 100 217
• NCBIGene 36.3 1608
• Single exon skipping, size difference: 117
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001346

• cd C1 50aa 7e-11 in ref transcript
  • Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
• cd EFh 70aa 4e-08 in ref transcript
  • EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers.
• pfam DAGK_acc 175aa 8e-87 in ref transcript
  • Diacylglycerol kinase accessory domain. Diacylglycerol (DAG) is a second messenger that acts as a protein kinase C activator. This domain is assumed to be an accessory domain: its function is unknown.
• smart DAGKc 122aa 2e-47 in ref transcript
  • Diacylglycerol kinase catalytic domain (presumed). Diacylglycerol (DAG) is a second messenger that acts as a protein kinase C activator. DAG can be produced from the hydrolysis of phosphatidylinositol 4,5-bisphosphate (PIP2) by a phosphoinositide-specific phospholipase C and by the degradation of phosphatidylcholine (PC) by a phospholipase C or the concerted actions of phospholipase D and phosphatidate phosphohydrolase. This domain is presumed to be the catalytic domain. Bacterial homologues areknown.
• pfam C1_1 50aa 1e-08 in ref transcript
  • Phorbol esters/diacylglycerol binding domain (C1 domain). This domain is also known as the Protein kinase C conserved region 1 (C1) domain.
• Changed! smart C1 41aa 4e-05 in ref transcript
  • Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
• COG LCB5 327aa 4e-10 in ref transcript
  • Sphingosine kinase and enzymes related to eukaryotic diacylglycerol kinase [Lipid metabolism / General function prediction only].
• COG FRQ1 76aa 7e-04 in ref transcript
  • Ca2+-binding protein (EF-Hand superfamily) [Signal transduction mechanisms / Cytoskeleton / Cell division and chromosome partitioning / General function prediction only].

DHRS2

• rs.DHRS2.F1 rs.DHRS2.R1 99 110
• NCBIGene 36.3 10202
• Alternative 5-prime, size difference: 11
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_182908

• cd NAD_bind_H4MPT_DH 53aa 2e-04 in ref transcript
  • NADP binding domain of methylene tetrahydromethanopterin dehydrogenase. Methylene Tetrahydromethanopterin Dehydrogenase (H4MPT DH) NADP binding domain. NADP-dependent H4MPT DH catalyzes the dehydrogenation of methylene- H4MPT and methylene-tetrahydrofolate (H4F) with NADP+ as cofactor. H4F and H4MPT are both cofactors that carry the one-carbon units between the formyl and methyl oxidation level. H4F and H4MPT are structurally analogous to each other with respect to the pterin moiety, but each has distinct side chain. H4MPT is present only in anaerobic methanogenic archaea and aerobic methylotrophic proteobacteria. H4MPT seems to have evolved independently from H4F and functions as a distinct carrier in C1 metabolism. Amino acid DH-like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids to keto acids with NAD(P)+ as a cofactor. The NAD(P)-binding Rossmann fold superfamily includes a wide variety of protein families including NAD(P)- binding domains of alcohol DHs, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate DH, lactate/malate DHs, formate/glycerate DHs, siroheme synthases, 6-phosphogluconate DH, amino acid DHs, repressor rex, NAD-binding potassium channel domain, CoA-binding, and ornithine cyclodeaminase-like domains. These domains have an alpha-beta-alpha configuration. NAD binding involves numerous hydrogen and van der Waals contacts.
• Changed! TIGR 3oxo_ACP_reduc 187aa 2e-30 in ref transcript
  • This model represents 3-oxoacyl-[ACP] reductase, also called 3-ketoacyl-acyl carrier protein reductase, an enzyme of fatty acid biosynthesis.
• Changed! PRK fabG 205aa 6e-43 in ref transcript
  • 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional.
• Changed! TIGR 3oxo_ACP_reduc 237aa 1e-40 in modified transcript
• Changed! PRK fabG 242aa 6e-52 in modified transcript

DIABLO

• rs.DIABLO.F1 rs.DIABLO.R1 193 222
• NCBIGene 36.3 56616
• Mutually exclusive exon skipping, size difference: 29
• Inclusion in the protein causing a new stop codon, Exclusion in the protein causing a frameshift
• Reference transcript: NM_019887

• Changed! pfam Smac_DIABLO 234aa 1e-100 in ref transcript
  • Second Mitochondria-derived Activator of Caspases. Second Mitochondria-derived Activator of Caspases promotes apoptosis by activating caspases in the cytochrome c/Apaf-1/caspase-9 pathway, and by opposing the inhibitory activity of inhibitor of apoptosis proteins (XIAP-BIR3). The protein assumes an elongated three-helix bundle structure, and forms a dimer in solution.

DIAPH1

• rs.DIAPH1.F1 rs.DIAPH1.R1 131 158
• NCBIGene 36.3 1729
• Single exon skipping, size difference: 27
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_005219

• smart FH2 438aa 1e-111 in ref transcript
  • Formin Homology 2 Domain. FH proteins control rearrangements of the actin cytoskeleton, especially in the context of cytokinesis and cell polarisation. Members of this family have been found to interact with Rho-GTPases, profilin and other actin-assoziated proteins. These interactions are mediated by the proline-rich FH1 domain, usually located in front of FH2 (but not listed in SMART). Despite this cytosolic function, vertebrate formins have been assigned functions within the nucleus. A set of Formin-Binding Proteins (FBPs) has been shown to bind FH1 with their WW domain.
• pfam Drf_GBD 186aa 3e-52 in ref transcript
  • Diaphanous GTPase-binding Domain. This domain is bound to by GTP-attached Rho proteins, leading to activation of the Drf protein.
• pfam Drf_FH3 193aa 1e-49 in ref transcript
  • Diaphanous FH3 Domain. This region is found in the Formin-like and and diaphanous proteins.
• pfam Drf_FH1 29aa 9e-08 in ref transcript
  • Formin Homology Region 1. This region is found in some of the Diaphanous related formins (Drfs). It consists of low complexity repeats of around 12 residues.

DLG1

• rs.DLG1.F1 rs.DLG1.R1 178 244
• NCBIGene 36.3 1739
• Mutually exclusive exon skipping, size difference: 66
• Inclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_004087

• cd GMPK 117aa 2e-24 in ref transcript
  • Guanosine monophosphate kinase (GMPK, EC 2.7.4.8), also known as guanylate kinase (GKase), catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to guanosine monophosphate (GMP) to yield adenosine diphosphate (ADP) and guanosine diphosphate (GDP). It plays an essential role in the biosynthesis of guanosine triphosphate (GTP). This enzyme is also important for the activation of some antiviral and anticancer agents, such as acyclovir, ganciclovir, carbovir, and thiopurines.
• cd PDZ_signaling 85aa 4e-14 in ref transcript
  • PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of PDZ domains an N-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in proteases.
• cd PDZ_signaling 87aa 1e-13 in ref transcript
• cd PDZ_signaling 81aa 2e-11 in ref transcript
• cd SH3 59aa 2e-06 in ref transcript
  • Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
• smart GuKc 179aa 2e-51 in ref transcript
  • Guanylate kinase homologues. Active enzymes catalyze ATP-dependent phosphorylation of GMP to GDP. Structure resembles that of adenylate kinase. So-called membrane-associated guanylate kinase homologues (MAGUKs) do not possess guanylate kinase activities; instead at least some possess protein-binding functions.
• pfam MAGUK_N_PEST 117aa 2e-33 in ref transcript
  • Polyubiquitination (PEST) N-terminal domain of MAGUK. The residues upstream of this domain are the probable palmitoylation sites, particularly two cysteines. The domain has a putative PEST site at the very start that seems to be responsible for poly-ubiquitination. PEST domains are polypeptide sequences enriched in proline (P), glutamic acid (E), serine (S) and threonine (T) that target proteins for rapid destruction. The whole domain, in conjunction with a C-terminal domain of the longer protein, is necessary for dimerisation of the whole protein.
• pfam L27_1 64aa 2e-28 in ref transcript
  • L27_1. The L27 domain is a protein interaction module that exists in a large family of scaffold proteins, functioning as an organisation centre of large protein assemblies required for the establishment and maintenance of cell polarity. L27 domains form specific heterotetrameric complexes, in which each domain contains three alpha-helices.
• pfam PDZ_assoc 62aa 3e-24 in ref transcript
  • PDZ-associated domain of NMDA receptors. This domain is found in higher eukaryotes between the second and third PDZ domains, pfam00595, of glutamate receptor like proteins. Its exact function is not known.
• smart PDZ 88aa 8e-17 in ref transcript
  • Domain present in PSD-95, Dlg, and ZO-1/2. Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities.
• smart PDZ 90aa 3e-16 in ref transcript
• smart PDZ 85aa 5e-14 in ref transcript
• smart SH3 59aa 3e-07 in ref transcript
  • Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.
• PRK gmk 159aa 1e-25 in ref transcript
  • guanylate kinase; Provisional.
• COG Prc 103aa 8e-05 in ref transcript
  • Periplasmic protease [Cell envelope biogenesis, outer membrane].

DLG3

• rs.DLG3.F1 rs.DLG3.R1 122 218
• NCBIGene 36.3 1741
• Mutually exclusive exon skipping, size difference: 96
• Inclusion in the protein causing a frameshift, Inclusion in the protein (no stop codon or frameshift), Exclusion in the protein causing a frameshift
• Reference transcript: NM_021120

• cd GMPK 117aa 2e-25 in ref transcript
  • Guanosine monophosphate kinase (GMPK, EC 2.7.4.8), also known as guanylate kinase (GKase), catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to guanosine monophosphate (GMP) to yield adenosine diphosphate (ADP) and guanosine diphosphate (GDP). It plays an essential role in the biosynthesis of guanosine triphosphate (GTP). This enzyme is also important for the activation of some antiviral and anticancer agents, such as acyclovir, ganciclovir, carbovir, and thiopurines.
• cd PDZ_signaling 81aa 3e-17 in ref transcript
  • PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of PDZ domains an N-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in proteases.
• cd PDZ_signaling 87aa 3e-14 in ref transcript
• cd PDZ_signaling 77aa 2e-11 in ref transcript
• cd SH3 59aa 4e-07 in ref transcript
  • Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
• smart GuKc 177aa 6e-55 in ref transcript
  • Guanylate kinase homologues. Active enzymes catalyze ATP-dependent phosphorylation of GMP to GDP. Structure resembles that of adenylate kinase. So-called membrane-associated guanylate kinase homologues (MAGUKs) do not possess guanylate kinase activities; instead at least some possess protein-binding functions.
• pfam PDZ_assoc 75aa 1e-22 in ref transcript
  • PDZ-associated domain of NMDA receptors. This domain is found in higher eukaryotes between the second and third PDZ domains, pfam00595, of glutamate receptor like proteins. Its exact function is not known.
• smart PDZ 85aa 2e-20 in ref transcript
  • Domain present in PSD-95, Dlg, and ZO-1/2. Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities.
• smart PDZ 90aa 7e-17 in ref transcript
• smart PDZ 77aa 6e-13 in ref transcript
• smart SH3 59aa 1e-08 in ref transcript
  • Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.
• pfam MAGUK_N_PEST 74aa 0.001 in ref transcript
  • Polyubiquitination (PEST) N-terminal domain of MAGUK. The residues upstream of this domain are the probable palmitoylation sites, particularly two cysteines. The domain has a putative PEST site at the very start that seems to be responsible for poly-ubiquitination. PEST domains are polypeptide sequences enriched in proline (P), glutamic acid (E), serine (S) and threonine (T) that target proteins for rapid destruction. The whole domain, in conjunction with a C-terminal domain of the longer protein, is necessary for dimerisation of the whole protein.
• PRK gmk 159aa 2e-23 in ref transcript
  • guanylate kinase; Provisional.
• COG Prc 74aa 1e-04 in ref transcript
  • Periplasmic protease [Cell envelope biogenesis, outer membrane].

DMBX1

• rs.DMBX1.F1 rs.DMBX1.R1 100 115
• NCBIGene 36.3 127343
• Alternative 5-prime and 3-prime, size difference: 15
• Inclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_147192

• cd homeodomain 54aa 8e-15 in ref transcript
  • Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
• pfam Homeobox 55aa 2e-20 in ref transcript
  • Homeobox domain.
• COG COG5576 65aa 2e-10 in ref transcript
  • Homeodomain-containing transcription factor [Transcription].

DMP1

• rs.DMP1.F1 rs.DMP1.R1 255 303
• NCBIGene 36.3 1758
• Single exon skipping, size difference: 48
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_004407

• Changed! pfam DMP1 375aa 5e-63 in ref transcript
  • Dentin matrix protein 1 (DMP1). This family consists of several mammalian dentin matrix protein 1 (DMP1) sequences. The dentin matrix acidic phosphoprotein 1 (DMP1) gene has been mapped to human chromosome 4q21. DMP1 is a bone and teeth specific protein initially identified from mineralised dentin. DMP1 is primarily localised in the nuclear compartment of undifferentiated osteoblasts. In the nucleus, DMP1 acts as a transcriptional component for activation of osteoblast-specific genes like osteocalcin. During the early phase of osteoblast maturation, Ca(2+) surges into the nucleus from the cytoplasm, triggering the phosphorylation of DMP1 by a nuclear isoform of casein kinase II. This phosphorylated DMP1 is then exported out into the extracellular matrix, where it regulates nucleation of hydroxyapatite. DMP1 is a unique molecule that initiates osteoblast differentiation by transcription in the nucleus and orchestrates mineralised matrix formation extracellularly, at later stages of osteoblast maturation. The DMP1 gene has been found to be ectopically expressed in lung cancer although the reason for this is unknown.
• pfam DMP1 35aa 1e-04 in ref transcript
• Changed! pfam DMP1 359aa 2e-61 in modified transcript

DMPK

• rs.DMPK.F1 rs.DMPK.R1 107 122
• NCBIGene 36.3 1760
• Alternative 5-prime, size difference: 15
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001081563

• Changed! cd STKc_DMPK_like 338aa 1e-170 in ref transcript
  • STKc_DMPK_like: Serine/Threonine Kinases (STKs), Myotonic Dystrophy protein kinase (DMPK)-like subfamily, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The DMPK-like subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. The DMPK-like subfamily is composed of DMPK and DMPK-related cell division control protein 42 (Cdc42) binding kinase (MRCK). Three isoforms of MRCK are known, named alpha, beta and gamma. The DMPK gene is implicated in myotonic dystrophy 1 (DM1), an inherited multisystemic disorder with symptoms that include muscle hyperexcitability, progressive muscle weakness and wasting, cataract development, testicular atrophy, and cardiac conduction defects. The genetic basis for DM1 is the mutational expansion of a CTG repeat in the 3'-UTR of DMPK. DMPK is expressed in skeletal and cardiac muscles, and in central nervous tissues. The functional role of DMPK is not fully understood. It may play a role in the signal transduction and homeostasis of calcium. MRCK is activated via interaction with the small GTPase Cdc42. MRCK/Cdc42 signaling mediates myosin-dependent cell motility. MRCKgamma is expressed in heart and skeletal muscles, unlike MRCKalpha and MRCKbeta, which are expressed ubiquitously.
• smart S_TKc 259aa 8e-69 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• pfam DMPK_coil 61aa 2e-22 in ref transcript
  • DMPK coiled coil domain like. This domain is found in the myotonic dystrophy protein kinase (DMPK) and adopts a coiled coil structure. It plays a role in dimerisation.
• Changed! smart S_TK_X 67aa 5e-08 in ref transcript
  • Extension to Ser/Thr-type protein kinases.
• PTZ PTZ00263 299aa 1e-56 in ref transcript
  • protein kinase A catalytic subunit; Provisional.
• COG Smc 63aa 0.008 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].
• Changed! cd STKc_DMPK_like 333aa 1e-171 in modified transcript
• Changed! smart S_TK_X 62aa 9e-09 in modified transcript

DNM1L

• rs.DNM1L.F1 rs.DNM1L.R1 207 285
• NCBIGene 36.3 10059
• Single exon skipping, size difference: 78
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_012062

• pfam Dynamin_M 292aa 1e-106 in ref transcript
  • Dynamin central region. This region lies between the GTPase domain, see pfam00350, and the pleckstrin homology (PH) domain, see pfam00169.
• smart DYNc 255aa 1e-90 in ref transcript
  • Dynamin, GTPase. Large GTPases that mediate vesicle trafficking. Dynamin participates in the endocytic uptake of receptors, associated ligands, and plasma membrane following an exocytic event.
• pfam GED 92aa 3e-23 in ref transcript
  • Dynamin GTPase effector domain.
• Changed! COG COG0699 414aa 2e-32 in ref transcript
  • Predicted GTPases (dynamin-related) [General function prediction only].
• Changed! COG COG0699 616aa 3e-36 in modified transcript

DNM2

• rs.DNM2.F1 rs.DNM2.R1 103 115
• NCBIGene 36.3 1785
• Single exon skipping, size difference: 12
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001005361

• cd PH_dynamin 110aa 2e-47 in ref transcript
  • Dynamin pleckstrin homology (PH) domain. Dynamin is a GTPase that regulates endocytic vesicle formation. It has an N-terminal GTPase domain, followed by a PH domain, a GTPase effector domain and a C-terminal proline arginine rich domain. Dynamin-like proteins, which are found in metazoa, plants and yeast have the same domain architecture as dynamin, but lack the PH domain. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
• smart DYNc 240aa 1e-130 in ref transcript
  • Dynamin, GTPase. Large GTPases that mediate vesicle trafficking. Dynamin participates in the endocytic uptake of receptors, associated ligands, and plasma membrane following an exocytic event.
• pfam Dynamin_M 294aa 1e-104 in ref transcript
  • Dynamin central region. This region lies between the GTPase domain, see pfam00350, and the pleckstrin homology (PH) domain, see pfam00169.
• smart GED 92aa 2e-20 in ref transcript
  • Dynamin GTPase effector domain.
• smart PH 104aa 3e-07 in ref transcript
  • Pleckstrin homology domain. Domain commonly found in eukaryotic signalling proteins. The domain family possesses multiple functions including the abilities to bind inositol phosphates, and various proteins. PH domains have been found to possess inserted domains (such as in PLC gamma, syntrophins) and to be inserted within other domains. Mutations in Brutons tyrosine kinase (Btk) within its PH domain cause X-linked agammaglobulinaemia (XLA) in patients. Point mutations cluster into the positively charged end of the molecule around the predicted binding site for phosphatidylinositol lipids.
• Changed! COG COG0699 424aa 5e-31 in ref transcript
  • Predicted GTPases (dynamin-related) [General function prediction only].
• Changed! COG COG0699 455aa 3e-31 in modified transcript

DNMT3B

• rs.DNMT3B.F1 rs.DNMT3B.R1 188 377
• NCBIGene 36.3 1789
• Multiple exon skipping, size difference: 189
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_006892

• cd Dnmt3b_related 87aa 2e-35 in ref transcript
  • The PWWP domain is an essential component of DNA methyltransferase 3 B (Dnmt3b) which is responsible for establishing DNA methylation patterns during embryogenesis and gametogenesis. In tumorigenesis, DNA methylation by Dnmt3b is known to play a role in the inactivation of tumor suppressor genes. In addition, a point mutation in the PWWP domain of Dnmt3b has been identified in patients with ICF syndrome (immunodeficiency, centromeric instability, and facial anomalies), a rare autosomal recessive disorder characterized by hypomethylation of classical satellite DNA. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
• Changed! cd Cyt_C5_DNA_methylase 271aa 4e-13 in ref transcript
  • Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the mammalian genome. These effects include transcriptional repression via inhibition of transcription factor binding or the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability.
• pfam PWWP 73aa 8e-24 in ref transcript
  • PWWP domain. The PWWP domain is named after a conserved Pro-Trp-Trp-Pro motif. The function of the domain is currently unknown.
• pfam DNA_methylase 123aa 8e-08 in ref transcript
  • C-5 cytosine-specific DNA methylase.
• COG Dcm 160aa 5e-13 in ref transcript
  • Site-specific DNA methylase [DNA replication, recombination, and repair].
• Changed! cd Cyt_C5_DNA_methylase 134aa 9e-09 in modified transcript

DNMT3B

• rs.DNMT3B.F2 rs.DNMT3B.R2 135 195
• NCBIGene 36.3 1789
• Single exon skipping, size difference: 60
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_006892

• cd Dnmt3b_related 87aa 2e-35 in ref transcript
  • The PWWP domain is an essential component of DNA methyltransferase 3 B (Dnmt3b) which is responsible for establishing DNA methylation patterns during embryogenesis and gametogenesis. In tumorigenesis, DNA methylation by Dnmt3b is known to play a role in the inactivation of tumor suppressor genes. In addition, a point mutation in the PWWP domain of Dnmt3b has been identified in patients with ICF syndrome (immunodeficiency, centromeric instability, and facial anomalies), a rare autosomal recessive disorder characterized by hypomethylation of classical satellite DNA. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
• cd Cyt_C5_DNA_methylase 271aa 4e-13 in ref transcript
  • Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the mammalian genome. These effects include transcriptional repression via inhibition of transcription factor binding or the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability.
• pfam PWWP 73aa 8e-24 in ref transcript
  • PWWP domain. The PWWP domain is named after a conserved Pro-Trp-Trp-Pro motif. The function of the domain is currently unknown.
• pfam DNA_methylase 123aa 8e-08 in ref transcript
  • C-5 cytosine-specific DNA methylase.
• COG Dcm 160aa 5e-13 in ref transcript
  • Site-specific DNA methylase [DNA replication, recombination, and repair].

DPH3

• rs.DPH3.F1 rs.DPH3.R1 260 335
• NCBIGene 36.3 285381
• Single exon skipping, size difference: 75
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_206831

• Changed! pfam zf-CSL 55aa 3e-18 in ref transcript
  • CSL zinc finger. This is a zinc binding motif which contains four cysteine residues which chelate zinc. This domain is often found associated with a pfam00226 domain. This domain is named after the conserved motif of the final cysteine.
• Changed! COG COG5216 61aa 1e-16 in ref transcript
  • Uncharacterized conserved protein [Function unknown].
• Changed! pfam zf-CSL 40aa 1e-07 in modified transcript
• Changed! COG COG5216 42aa 1e-06 in modified transcript

DPH5

• rs.DPH5.F1 rs.DPH5.R1 109 127
• NCBIGene 36.3 51611
• Alternative 5-prime, size difference: 18
• Exclusion in 5'UTR
• Reference transcript: NM_001077394

• TIGR dph5 271aa 1e-80 in ref transcript
  • This protein participates in the modification of a specific His of elongation factor 2 of eukarotes and Archaea to diphthamide. The protein was characterized in Saccharomyces cerevisiae and designated DPH5.
• PTZ PTZ00175 272aa 1e-122 in ref transcript
  • diphthine synthase; Provisional.

DSC3

• rs.DSC3.F1 rs.DSC3.R1 233 276
• NCBIGene 36.3 1825
• Single exon skipping, size difference: 43
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_001941

• cd CA 218aa 9e-36 in ref transcript
  • Cadherin repeat domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion; these domains occur as repeats in the extracellular regions which are thought to mediate cell-cell contact when bound to calcium; plays a role in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-,CNR-,proto-,and FAT-family cadherin, desmocollin, and desmoglein, exists as monomers or dimers (hetero- and homo-); two copies of the repeat are present here.
• cd CA 209aa 8e-31 in ref transcript
• cd CA 210aa 4e-24 in ref transcript
• Changed! cd CA 193aa 1e-19 in ref transcript
• pfam Cadherin_pro 87aa 5e-18 in ref transcript
  • Cadherin prodomain like. Cadherins are a family of proteins that mediate calcium dependent cell-cell adhesion. They are activated through cleavage of a prosequence in the late Golgi. This domain corresponds to the folded region of the prosequence, and is termed the prodomain. The prodomain shows structural resemblance to the cadherin domain, but lacks all the features known to be important for cadherin-cadherin interactions.
• pfam Cadherin 99aa 9e-17 in ref transcript
  • Cadherin domain.
• pfam Cadherin 103aa 2e-11 in ref transcript
• smart CA 77aa 4e-11 in ref transcript
  • Cadherin repeats. Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. Cadherin domains occur as repeats in the extracellular regions which are thought to mediate cell-cell contact when bound to calcium.
• pfam Cadherin 95aa 1e-10 in ref transcript
• Changed! pfam Cadherin_C 63aa 1e-04 in ref transcript
  • Cadherin cytoplasmic region. Cadherins are vital in cell-cell adhesion during tissue differentiation. Cadherins are linked to the cytoskeleton by catenins. Catenins bind to the cytoplasmic tail of the cadherin. Cadherins cluster to form foci of homophilic binding units. A key determinant to the strength of the binding that it is mediated by cadherins is the juxtamembrane region of the cadherin. This region induces clustering and also binds to the protein p120ctn.
• Changed! pfam Cadherin 74aa 0.009 in ref transcript
• Changed! cd CA 192aa 2e-19 in modified transcript

DTNB

• rs.DTNB.F1 rs.DTNB.R1 119 140
• NCBIGene 36.3 1838
• Single exon skipping, size difference: 21
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_021907

• cd ZZ_dystrophin 49aa 4e-18 in ref transcript
  • Zinc finger, ZZ type. Zinc finger present in dystrophin and dystrobrevin. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dystrophin attaches actin filaments to an integral membrane glycoprotein complex in muscle cells. The ZZ domain in dystrophin has been shown to be essential for binding to the membrane protein beta-dystroglycan.
• pfam efhand_1 127aa 3e-47 in ref transcript
  • EF hand. Members of this family adopt a helix-loop-helix motif, as per other EF hand domains. However, since they do not contain the canonical pattern of calcium binding residues found in many EF hand domains, they do not bind calcium ions. The main function of this domain is the provision of specificity in beta-dystroglycan recognition, though in dystrophin it serves an additional role: stabilisation of the WW domain (pfam00397), enhancing dystroglycan binding.
• pfam efhand_2 89aa 3e-37 in ref transcript
  • EF-hand. Members of this family adopt a helix-loop-helix motif, as per other EF hand domains. However, since they do not contain the canonical pattern of calcium binding residues found in many EF hand domains, they do not bind calcium ions. The main function of this domain is the provision of specificity in beta-dystroglycan recognition, though in dystrophin it serves an additional role: stabilisation of the WW domain (pfam00397), enhancing dystroglycan binding.
• smart ZnF_ZZ 45aa 3e-11 in ref transcript
  • Zinc-binding domain, present in Dystrophin, CREB-binding protein. Putative zinc-binding domain present in dystrophin-like proteins, and CREB-binding protein/p300 homologues. The ZZ in dystrophin appears to bind calmodulin. A missense mutation of one of the conserved cysteines in dystrophin results in a patient with Duchenne muscular dystrophy [3].
• Changed! TIGR SMC_prok_B 66aa 0.008 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• Changed! PRK PRK05431 65aa 0.003 in ref transcript
  • seryl-tRNA synthetase; Provisional.
• Changed! TIGR SMC_prok_A 90aa 4e-04 in modified transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent.
• Changed! PRK PRK05431 71aa 7e-05 in modified transcript

DTX2

• rs.DTX2.F1 rs.DTX2.R1 153 273
• NCBIGene 36.3 113878
• Single exon skipping, size difference: 120
• Exclusion in 5'UTR
• Reference transcript: NM_020892

• smart WWE 72aa 7e-20 in ref transcript
  • Domain in Deltex and TRIP12 homologues. Possibly involved in regulation of ubiquitin-mediated proteolysis.
• smart WWE 85aa 7e-20 in ref transcript

DTX2

• rs.DTX2.F2 rs.DTX2.R2 402 543
• NCBIGene 36.3 113878
• Single exon skipping, size difference: 141
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001102595

• smart WWE 72aa 7e-20 in ref transcript
  • Domain in Deltex and TRIP12 homologues. Possibly involved in regulation of ubiquitin-mediated proteolysis.
• smart WWE 85aa 7e-20 in ref transcript

DUSP13

• rs.DUSP13.F1 rs.DUSP13.R1 100 526
• NCBIGene 36.3 51207
• Multiple exon skipping, size difference: 426
• Exclusion in 5'UTR, Exclusion of the protein initiation site
• Reference transcript: NM_001007271

• cd DSPc 144aa 2e-32 in ref transcript
  • Dual specificity phosphatases (DSP); Ser/Thr and Tyr protein phosphatases. Structurally similar to tyrosine-specific phosphatases but with a shallower active site cleft and a distinctive active site signature motif, HCxxGxxR. Characterized as VHR- or Cdc25-like.
• smart DSPc 143aa 4e-26 in ref transcript
  • Dual specificity phosphatase, catalytic domain.
• COG CDC14 140aa 1e-07 in ref transcript
  • Predicted protein-tyrosine phosphatase [Signal transduction mechanisms].

DUSP6

• rs.DUSP6.F1 rs.DUSP6.R1 98 536
• NCBIGene 36.3 1848
• Single exon skipping, size difference: 438
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001946

• Changed! cd DSPc 138aa 7e-50 in ref transcript
  • Dual specificity phosphatases (DSP); Ser/Thr and Tyr protein phosphatases. Structurally similar to tyrosine-specific phosphatases but with a shallower active site cleft and a distinctive active site signature motif, HCxxGxxR. Characterized as VHR- or Cdc25-like.
• Changed! cd DSP_MapKP 131aa 2e-35 in ref transcript
  • N-terminal regulatory rhodanese domain of dual specificity phosphatases (DSP), such as Mapk Phosphatase. This domain is believed to determine substrate specificity by binding the substrate, such as ERK2, and activating the C-terminal catalytic domain by inducing a conformational change. This domain has homology to the Rhodanese Homology Domain.
• Changed! smart DSPc 140aa 1e-52 in ref transcript
  • Dual specificity phosphatase, catalytic domain.
• Changed! smart RHOD 114aa 7e-09 in ref transcript
  • Rhodanese Homology Domain. An alpha beta fold found duplicated in the Rhodanese protein. The the Cysteine containing enzymatically active version of the domain is also found in the CDC25 class of protein phosphatases and a variety of proteins such as sulfide dehydrogenases and stress proteins such as Senesence specific protein 1 in plants, PspE and GlpE in bacteria and cyanide and arsenate resistance proteins. Inactive versions with a loss of the cysteine are also seen in Dual specificity phosphatases, ubiquitin hydrolases from yeast and in sulfuryltransferases. These are likely to play a role in protein interactions.
• Changed! COG CDC14 169aa 2e-13 in ref transcript
  • Predicted protein-tyrosine phosphatase [Signal transduction mechanisms].
• COG SseA 96aa 0.001 in ref transcript
  • Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism].
• Changed! cd DSP_MapKP 118aa 2e-28 in modified transcript
• Changed! cd DSPc 102aa 3e-26 in modified transcript
• Changed! smart DSPc 67aa 4e-26 in modified transcript
• Changed! smart RHOD 76aa 3e-08 in modified transcript
• Changed! COG CDC14 77aa 6e-09 in modified transcript

DYNLL1

• rs.DYNLL1.F1 rs.DYNLL1.R1 112 126
• NCBIGene 36.3 8655
• Alternative 3-prime, size difference: 14
• Inclusion in 5'UTR
• Reference transcript: NM_003746

• pfam Dynein_light 89aa 2e-38 in ref transcript
  • Dynein light chain type 1.
• PTZ PTZ00059 89aa 9e-47 in ref transcript
  • dynein light chain; Provisional.

E2F6

• rs.E2F6.F1 rs.E2F6.R1 201 334
• NCBIGene 36.3 1876
• Single exon skipping, size difference: 133
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_198256

• Changed! pfam E2F_TDP 66aa 5e-22 in ref transcript
  • E2F/DP family winged-helix DNA-binding domain. This family contains the transcription factor E2F and its dimerisation partners TDP1 and TDP2, which stimulate E2F-dependent transcription. E2F binds to DNA as a homodimer or as a heterodimer in association with TDP1/2, the heterodimer having increased binding efficiency. The crystal structure of an E2F4-DP2-DNA complex shows that the DNA-binding domains of the E2F and DP proteins both have a fold related to the winged-helix DNA-binding motif. Recognition of the central c/gGCGCg/c sequence of the consensus DNA-binding site is symmetric, and amino acids that contact these bases are conserved among all known E2F and DP proteins.

E2F6

• rs.E2F6.F2 rs.E2F6.R2 128 199
• NCBIGene 36.3 1876
• Single exon skipping, size difference: 71
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_198256

• Changed! pfam E2F_TDP 66aa 5e-22 in ref transcript
  • E2F/DP family winged-helix DNA-binding domain. This family contains the transcription factor E2F and its dimerisation partners TDP1 and TDP2, which stimulate E2F-dependent transcription. E2F binds to DNA as a homodimer or as a heterodimer in association with TDP1/2, the heterodimer having increased binding efficiency. The crystal structure of an E2F4-DP2-DNA complex shows that the DNA-binding domains of the E2F and DP proteins both have a fold related to the winged-helix DNA-binding motif. Recognition of the central c/gGCGCg/c sequence of the consensus DNA-binding site is symmetric, and amino acids that contact these bases are conserved among all known E2F and DP proteins.

ECE2

• rs.ECE2.F1 rs.ECE2.R1 261 399
• NCBIGene 36.3 9718
• Alternative 5-prime, size difference: 138
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001100120

• pfam Peptidase_M13_N 386aa 1e-124 in ref transcript
  • Peptidase family M13. M13 peptidases are well-studied proteases found in a wide range of organisms including mammals and bacteria. In mammals they participate in processes such as cardiovascular development, blood-pressure regulation, nervous control of respiration, and regulation of the function of neuropeptides in the central nervous system. In bacteria they may be used for digestion of milk.
• pfam Peptidase_M13 204aa 2e-55 in ref transcript
  • Peptidase family M13. Mammalian enzymes are typically type-II membrane anchored enzymes which are known, or believed to activate or inactivate oligopeptide (pro)-hormones such as opioid peptides. The family also contains a bacterial member believed to be involved with milk protein cleavage.
• COG PepO 654aa 1e-121 in ref transcript
  • Predicted metalloendopeptidase [Posttranslational modification, protein turnover, chaperones].

ECHDC1

• rs.ECHDC1.F1 rs.ECHDC1.R1 150 203
• NCBIGene 36.3 55862
• Single exon skipping, size difference: 53
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_001002030

• Changed! cd crotonase-like 192aa 3e-42 in ref transcript
  • Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase. Many of these play important roles in fatty acid metabolism. In addition to a conserved structural core and the formation of trimers (or dimers of trimers), a common feature in this superfamily is the stabilization of an enolate anion intermediate derived from an acyl-CoA substrate. This is accomplished by two conserved backbone NH groups in active sites that form an oxyanion hole.
• Changed! pfam ECH 167aa 3e-22 in ref transcript
  • Enoyl-CoA hydratase/isomerase family. This family contains a diverse set of enzymes including: Enoyl-CoA hydratase. Napthoate synthase. Carnitate racemase. 3-hydoxybutyryl-CoA dehydratase. Dodecanoyl-CoA delta-isomerase.
• Changed! COG CaiD 244aa 2e-38 in ref transcript
  • Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism].
• Changed! cd crotonase-like 71aa 8e-14 in modified transcript
• Changed! pfam ECH 52aa 2e-05 in modified transcript
• Changed! COG CaiD 71aa 6e-11 in modified transcript

ECHDC1

• rs.ECHDC1.F2 rs.ECHDC1.R2 109 331
• NCBIGene 36.3 55862
• Single exon skipping, size difference: 222
• Exclusion of the protein initiation site
• Reference transcript: NM_001002030

• Changed! cd crotonase-like 192aa 3e-42 in ref transcript
  • Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase. Many of these play important roles in fatty acid metabolism. In addition to a conserved structural core and the formation of trimers (or dimers of trimers), a common feature in this superfamily is the stabilization of an enolate anion intermediate derived from an acyl-CoA substrate. This is accomplished by two conserved backbone NH groups in active sites that form an oxyanion hole.
• Changed! pfam ECH 167aa 3e-22 in ref transcript
  • Enoyl-CoA hydratase/isomerase family. This family contains a diverse set of enzymes including: Enoyl-CoA hydratase. Napthoate synthase. Carnitate racemase. 3-hydoxybutyryl-CoA dehydratase. Dodecanoyl-CoA delta-isomerase.
• Changed! COG CaiD 244aa 2e-38 in ref transcript
  • Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism].
• Changed! cd crotonase-like 170aa 4e-33 in modified transcript
• Changed! TIGR FadB 156aa 2e-18 in modified transcript
  • Members represent alpha subunit of multifunctional enzyme complex of the fatty acid degradation cycle. Activities include: enoyl-CoA hydratase (EC 4.2.1.17), dodecenoyl-CoA delta-isomerase activity (EC 5.3.3.8), 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35), 3-hydroxybutyryl-CoA epimerase (EC 5.1.2.3). A representative is E. coli FadB. This model excludes the FadJ family.
• Changed! COG CaiD 219aa 7e-30 in modified transcript

EDA

• rs.EDA.F1 rs.EDA.R1 168 219
• NCBIGene 36.3 1896
• Single exon skipping, size difference: 51
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_001399

• Changed! cd TNF 135aa 5e-13 in ref transcript
  • Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT (lymphotoxin-alpha, TNF-beta), CD40 ligand, Apo2L (TRAIL), Fas ligand, and osteoprotegerin (OPG) ligand. These proteins generally have an intracellular N-terminal domain, a short transmembrane segment, an extracellular stalk, and a globular TNF-like extracellular domain of about 150 residues. They initiate apoptosis by binding to related receptors, some of which have intracellular death domains. They generally form homo- or hetero- trimeric complexes.TNF cytokines bind one elongated receptor molecule along each of three clefts formed by neighboring monomers of the trimer with ligand trimerization a requiste for receptor binding.
• Changed! pfam TNF 114aa 2e-18 in ref transcript
  • TNF(Tumour Necrosis Factor) family.

EDG2

• rs.EDG2.F1 rs.EDG2.R1 313 391
• NCBIGene 36.3 1902
• Single exon skipping, size difference: 78
• Exclusion in 5'UTR
• Reference transcript: NM_057159

• pfam 7tm_1 240aa 2e-28 in ref transcript
  • 7 transmembrane receptor (rhodopsin family). This family contains, amongst other G-protein-coupled receptors (GCPRs), members of the opsin family, which have been considered to be typical members of the rhodopsin superfamily. They share several motifs, mainly the seven transmembrane helices, GCPRs of the rhodopsin superfamily. All opsins bind a chromophore, such as 11-cis-retinal. The function of most opsins other than the photoisomerases is split into two steps: light absorption and G-protein activation. Photoisomerases, on the other hand, are not coupled to G-proteins - they are thought to generate and supply the chromophore that is used by visual opsins.

EDN3

• rs.EDN3.F1 rs.EDN3.R1 121 156
• NCBIGene 36.3 1908
• Alternative 5-prime, size difference: 35
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_000114

• pfam Endothelin 30aa 4e-11 in ref transcript
  • Endothelin family.
• smart END 22aa 1e-04 in ref transcript
  • Endothelin.

EFCAB6

• rs.EFCAB6.F1 rs.EFCAB6.R1 115 473
• NCBIGene 36.3 64800
• Multiple exon skipping, size difference: 358
• Exclusion of the protein initiation site, Exclusion in the protein causing a frameshift
• Reference transcript: NM_022785

• cd EFh 60aa 8e-04 in ref transcript
  • EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers.
• cd EFh 61aa 0.001 in ref transcript
• cd EFh 59aa 0.007 in ref transcript
• pfam DUF1880 118aa 1e-60 in ref transcript
  • Domain of unknown function (DUF1880). This domain is found predominantly in DJ binding protein. It has no known function.
• Changed! PTZ PTZ00184 162aa 3e-06 in ref transcript
  • calmodulin; Provisional.
• COG FRQ1 61aa 8e-04 in ref transcript
  • Ca2+-binding protein (EF-Hand superfamily) [Signal transduction mechanisms / Cytoskeleton / Cell division and chromosome partitioning / General function prediction only].
• COG FRQ1 176aa 0.001 in ref transcript

EFTUD1

• rs.EFTUD1.F1 rs.EFTUD1.R1 251 404
• NCBIGene 36.3 79631
• Multiple exon skipping, size difference: 153
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_024580

• Changed! cd EF2 234aa 1e-108 in ref transcript
  • EF2 (for archaea and eukarya). Translocation requires hydrolysis of a molecule of GTP and is mediated by EF-G in bacteria and by eEF2 in eukaryotes. The eukaryotic elongation factor eEF2 is a GTPase involved in the translocation of the peptidyl-tRNA from the A site to the P site on the ribosome. The 95-kDa protein is highly conserved, with 60% amino acid sequence identity between the human and yeast proteins. Two major mechanisms are known to regulate protein elongation and both involve eEF2. First, eEF2 can be modulated by reversible phosphorylation. Increased levels of phosphorylated eEF2 reduce elongation rates presumably because phosphorylated eEF2 fails to bind the ribosomes. Treatment of mammalian cells with agents that raise the cytoplasmic Ca2+ and cAMP levels reduce elongation rates by activating the kinase responsible for phosphorylating eEF2. In contrast, treatment of cells with insulin increases elongation rates by promoting eEF2 dephosphorylation. Second, the protein can be post-translationally modified by ADP-ribosylation. Various bacterial toxins perform this reaction after modification of a specific histidine residue to diphthamide, but there is evidence for endogenous ADP ribosylase activity. Similar to the bacterial toxins, it is presumed that modification by the endogenous enzyme also inhibits eEF2 activity.
• cd aeEF2_snRNP_like_IV 300aa 5e-37 in ref transcript
  • This family represents domain IV of archaeal and eukaryotic elongation factor 2 (aeEF-2) and of an evolutionarily conserved U5 snRNP-specific protein. U5 snRNP is a GTP-binding factor closely related to the ribosomal translocase EF-2. In complex with GTP, EF-2 promotes the translocation step of translation. During translocation the peptidyl-tRNA is moved from the A site to the P site of the small subunit of ribosome and the mRNA is shifted one codon relative to the ribosome. It has been shown that EF-2_IV domain mimics the shape of anticodon arm of the tRNA in the structurally homologous ternary complex of Phe-tRNA, EF-1 (another transcriptional elongation factor) and GTP analog. The tip portion of this domain is found in a position that overlaps the anticodon arm of the A-site tRNA, implying that EF-2 displaces the A-site tRNA to the P-site by physical interaction with the anticodon arm.
• cd eEF2_snRNP_like_C 79aa 7e-31 in ref transcript
  • eEF2_snRNP_like_C: this family represents a C-terminal domain of eukaryotic elongation factor 2 (eEF-2) and a homologous domain of the spliceosomal human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and, its yeast counterpart Snu114p. Yeast Snu114p is essential for cell viability and for splicing in vivo. U5-116 kD binds GTP. Experiments suggest that GTP binding and probably GTP hydrolysis is important for the function of the U5-116 kD/Snu114p. In complex with GTP, EF-2 promotes the translocation step of translation. During translocation the peptidyl-tRNA is moved from the A site to the P site, the uncharged tRNA from the P site to the E-site and, the mRNA is shifted one codon relative to the ribosome.
• cd eEF2_snRNP_like_II 115aa 5e-20 in ref transcript
  • EF2_snRNP_like_II: this subfamily represents domain II of elongation factor (EF) EF-2 found eukaryotes and archaea and, the C-terminal portion of the spliceosomal human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and, its yeast counterpart Snu114p. During the process of peptide synthesis and tRNA site changes, the ribosome is moved along the mRNA a distance equal to one codon with the addition of each amino acid. This translocation step is catalyzed by EF-2_GTP, which is hydrolyzed to provide the required energy. Thus, this action releases the uncharged tRNA from the P site and transfers the newly formed peptidyl-tRNA from the A site to the P site. Yeast Snu114p is essential for cell viability and for splicing in vivo. U5-116 kD binds GTP. Experiments suggest that GTP binding and probably GTP hydrolysis is important for the function of the U5-116 kD/Snu114p.
• Changed! pfam GTP_EFTU 149aa 2e-50 in ref transcript
  • Elongation factor Tu GTP binding domain. This domain contains a P-loop motif, also found in several other families such as pfam00071, pfam00025 and pfam00063. Elongation factor Tu consists of three structural domains, this plus two C-terminal beta barrel domains.
• TIGR aEF-2 263aa 7e-19 in ref transcript
  • This model represents archaeal elongation factor 2, a protein more similar to eukaryotic EF-2 than to bacterial EF-G, both in sequence similarity and in sharing with eukaryotes the property of having a diphthamide (modified His) residue at a conserved position. The diphthamide can be ADP-ribosylated by diphtheria toxin in the presence of NAD.
• pfam EFG_C 87aa 2e-16 in ref transcript
  • Elongation factor G C-terminus. This domain includes the carboxyl terminal regions of Elongation factor G, elongation factor 2 and some tetracycline resistance proteins and adopt a ferredoxin-like fold.
• pfam EFG_IV 72aa 0.002 in ref transcript
  • Elongation factor G, domain IV. This domain is found in elongation factor G, elongation factor 2 and some tetracycline resistance proteins and adopts a ribosomal protein S5 domain 2-like fold.
• Changed! PRK PRK07560 277aa 6e-65 in ref transcript
  • elongation factor EF-2; Reviewed.
• COG FusA 206aa 6e-34 in ref transcript
  • Translation elongation factors (GTPases) [Translation, ribosomal structure and biogenesis].
• COG FusA 142aa 3e-23 in ref transcript
• Changed! cd EF2 172aa 3e-68 in modified transcript
• Changed! TIGR aEF-2 111aa 4e-30 in modified transcript
• Changed! PRK PRK07560 226aa 6e-40 in modified transcript

EIF4G2

• rs.EIF4G2.F1 rs.EIF4G2.R1 151 265
• NCBIGene 36.3 1982
• Single exon skipping, size difference: 114
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001418

• smart MA3 101aa 4e-21 in ref transcript
  • Domain in DAP-5, eIF4G, MA-3 and other proteins. Highly alpha-helical. May contain repeats and/or regions similar to MIF4G domains Ponting (TIBS) "Novel eIF4G domain homologues" in press.
• pfam MIF4G 102aa 1e-20 in ref transcript
  • MIF4G domain. MIF4G is named after Middle domain of eukaryotic initiation factor 4G (eIF4G). Also occurs in NMD2p and CBP80. The domain is rich in alpha-helices and may contain multiple alpha-helical repeats. In eIF4G, this domain binds eIF4A, eIF3, RNA and DNA.
• smart eIF5C 76aa 4e-17 in ref transcript
  • Domain at the C-termini of GCD6, eIF-2B epsilon, eIF-4 gamma and eIF-5.

ELN

• rs.ELN.F1 rs.ELN.R1 125 179
• NCBIGene 36.3 2006
• Single exon skipping, size difference: 54
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000501

ELN

• rs.ELN.F2 rs.ELN.R2 124 181
• NCBIGene 36.3 2006
• Single exon skipping, size difference: 57
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000501

ELN

• rs.ELN.F3 rs.ELN.R3 100 115
• NCBIGene 36.3 2006
• Alternative 3-prime, size difference: 15
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_000501

ELN

• rs.ELN.F4 rs.ELN.R4 254 284
• NCBIGene 36.3 2006
• Single exon skipping, size difference: 30
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000501

ELOVL7

• rs.ELOVL7.F1 rs.ELOVL7.R1 123 174
• NCBIGene 36.3 79993
• Single exon skipping, size difference: 51
• Exclusion in 5'UTR
• Reference transcript: NM_024930

• pfam ELO 240aa 9e-53 in ref transcript
  • GNS1/SUR4 family. Members of this family are involved in long chain fatty acid elongation systems that produce the 26-carbon precursors for ceramide and sphingolipid synthesis. Predicted to be integral membrane proteins, in eukaryotes they are probably located on the endoplasmic reticulum. Yeast ELO3 affects plasma membrane H+-ATPase activity, and may act on a glucose-signaling pathway that controls the expression of several genes that are transcriptionally regulated by glucose such as PMA1.
• PTZ PTZ00251 100aa 1e-04 in ref transcript
  • fatty acid elongase; Provisional.

ENPP2

• rs.ENPP2.F1 rs.ENPP2.R1 148 304
• NCBIGene 36.3 5168
• Single exon skipping, size difference: 156
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_006209

• cd NUC 259aa 6e-47 in ref transcript
  • DNA/RNA non-specific endonuclease; prokaryotic and eukaryotic double- and single-stranded DNA and RNA endonucleases also present in phosphodiesterases. They exists as monomers and homodimers.
• Changed! pfam Phosphodiest 365aa 2e-83 in ref transcript
  • Type I phosphodiesterase / nucleotide pyrophosphatase. This family consists of phosphodiesterases, including human plasma-cell membrane glycoprotein PC-1 / alkaline phosphodiesterase i / nucleotide pyrophosphatase (nppase). These enzymes catalyse the cleavage of phosphodiester and phosphosulfate bonds in NAD, deoxynucleotides and nucleotide sugars. Also in this family is ATX an autotaxin, tumour cell motility-stimulating protein which exhibits type I phosphodiesterases activity. The alignment encompasses the active site. Also present with in this family is 60-kDa Ca2+-ATPase form F. odoratum.
• smart NUC 231aa 4e-58 in ref transcript
  • DNA/RNA non-specific endonuclease. prokaryotic and eukaryotic double- and single-stranded DNA and RNA endonucleases also present in phosphodiesterases.
• pfam Somatomedin_B 44aa 3e-13 in ref transcript
  • Somatomedin B domain.
• pfam Somatomedin_B 45aa 1e-12 in ref transcript
• Changed! COG COG1524 425aa 2e-28 in ref transcript
  • Uncharacterized proteins of the AP superfamily [General function prediction only].
• COG NUC1 231aa 1e-05 in ref transcript
  • DNA/RNA endonuclease G, NUC1 [Nucleotide transport and metabolism].
• Changed! pfam Phosphodiest 313aa 8e-91 in modified transcript
• Changed! COG COG1524 373aa 5e-34 in modified transcript

ENTPD8

• rs.ENTPD8.F1 rs.ENTPD8.R1 248 359
• NCBIGene 36.3 377841
• Single exon skipping, size difference: 111
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001033113

• Changed! pfam GDA1_CD39 421aa 3e-78 in ref transcript
  • GDA1/CD39 (nucleoside phosphatase) family.
• Changed! COG COG5371 376aa 1e-12 in ref transcript
  • Golgi nucleoside diphosphatase [Carbohydrate transport and metabolism / Posttranslational modification, protein turnover, chaperones].
• Changed! pfam GDA1_CD39 384aa 2e-66 in modified transcript
• Changed! COG COG5371 304aa 6e-10 in modified transcript

EPB41

• rs.EPB41.F1 rs.EPB41.R1 355 475
• NCBIGene 36.3 2035
• Multiple exon skipping, size difference: 120
• Inclusion in the protein (no stop codon or frameshift), Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_203343

• cd FERM_C 94aa 1e-32 in ref transcript
  • The FERM_C domain is the third structural domain within the FERM domain. The FERM domain is found in the cytoskeletal-associated proteins such as ezrin, moesin, radixin, 4.1R, and merlin. These proteins provide a link between the membrane and cytoskeleton and are involved in signal transduction pathways. The FERM_C domain is also found in protein tyrosine phosphatases (PTPs) , the tryosine kinases FAKand JAK, in addition to other proteins involved in signaling. This domain is structuraly similar to the PH and PTB domains and consequently is capable of binding to both peptides and phospholipids at different sites.
• smart B41 157aa 1e-40 in ref transcript
  • Band 4.1 homologues. Also known as ezrin/radixin/moesin (ERM) protein domains. Present in myosins, ezrin, radixin, moesin, protein tyrosine phosphatases. Plasma membrane-binding domain. These proteins play structural and regulatory roles in the assembly and stabilization of specialized plasmamembrane domains. Some PDZ domain containing proteins bind one or more of this family. Now includes JAKs.
• pfam 4_1_CTD 115aa 3e-26 in ref transcript
  • 4.1 protein C-terminal domain (CTD). At the C-terminus of all known 4.1 proteins is a sequence domain unique to these proteins, known as the C-terminal domain (CTD). Mammalian CTDs are associated with a growing number of protein-protein interactions, although such activities have yet to be associated with invertebrate CTDs. Mammalian CTDs are generally defined by sequence alignment as encoded by exons 18-21. Comparison of known vertebrate 4.1 proteins with invertebrate 4.1 proteins indicates that mammalian 4.1 exon 19 represents a vertebrate adaptation that extends the sequence of the CTD with a Ser/Thr-rich sequence. The CTD was first described as a 22/24-kDa domain by chymotryptic digestion of erythrocyte 4.1 (4.1R). CTD is thought to represent an independent folding structure which has gained function since the divergence of vertebrates from invertebrates.
• pfam FERM_C 85aa 2e-20 in ref transcript
  • FERM C-terminal PH-like domain.
• Changed! pfam SAB 47aa 5e-14 in ref transcript
  • SAB domain. This presumed domain is found in proteins containing FERM domains pfam00373. This domain is found to bind to both spectrin and actin, hence the name SAB (Spectrin and Actin Binding) domain.
• pfam FA 45aa 5e-13 in ref transcript
  • FERM adjacent (FA). This region is found adjacent to Band 4.1 / FERM domains (pfam00373) in a subset of FERM containing protein. The region has been hypothesised to play a role in regulatory adaptation, based on similarity to other protein kinase substrates.
• Changed! pfam SAB 49aa 7e-15 in modified transcript

EPB41

• rs.EPB41.F2 rs.EPB41.R2 184 241
• NCBIGene 36.3 2035
• Single exon skipping, size difference: 57
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_203342

• cd FERM_C 94aa 9e-32 in ref transcript
  • The FERM_C domain is the third structural domain within the FERM domain. The FERM domain is found in the cytoskeletal-associated proteins such as ezrin, moesin, radixin, 4.1R, and merlin. These proteins provide a link between the membrane and cytoskeleton and are involved in signal transduction pathways. The FERM_C domain is also found in protein tyrosine phosphatases (PTPs) , the tryosine kinases FAKand JAK, in addition to other proteins involved in signaling. This domain is structuraly similar to the PH and PTB domains and consequently is capable of binding to both peptides and phospholipids at different sites.
• smart B41 192aa 1e-55 in ref transcript
  • Band 4.1 homologues. Also known as ezrin/radixin/moesin (ERM) protein domains. Present in myosins, ezrin, radixin, moesin, protein tyrosine phosphatases. Plasma membrane-binding domain. These proteins play structural and regulatory roles in the assembly and stabilization of specialized plasmamembrane domains. Some PDZ domain containing proteins bind one or more of this family. Now includes JAKs.
• pfam 4_1_CTD 115aa 1e-27 in ref transcript
  • 4.1 protein C-terminal domain (CTD). At the C-terminus of all known 4.1 proteins is a sequence domain unique to these proteins, known as the C-terminal domain (CTD). Mammalian CTDs are associated with a growing number of protein-protein interactions, although such activities have yet to be associated with invertebrate CTDs. Mammalian CTDs are generally defined by sequence alignment as encoded by exons 18-21. Comparison of known vertebrate 4.1 proteins with invertebrate 4.1 proteins indicates that mammalian 4.1 exon 19 represents a vertebrate adaptation that extends the sequence of the CTD with a Ser/Thr-rich sequence. The CTD was first described as a 22/24-kDa domain by chymotryptic digestion of erythrocyte 4.1 (4.1R). CTD is thought to represent an independent folding structure which has gained function since the divergence of vertebrates from invertebrates.
• pfam FERM_C 85aa 4e-20 in ref transcript
  • FERM C-terminal PH-like domain.
• pfam SAB 49aa 3e-16 in ref transcript
  • SAB domain. This presumed domain is found in proteins containing FERM domains pfam00373. This domain is found to bind to both spectrin and actin, hence the name SAB (Spectrin and Actin Binding) domain.
• pfam FA 45aa 3e-13 in ref transcript
  • FERM adjacent (FA). This region is found adjacent to Band 4.1 / FERM domains (pfam00373) in a subset of FERM containing protein. The region has been hypothesised to play a role in regulatory adaptation, based on similarity to other protein kinase substrates.

EPHA6

• rs.EPHA6.F1 rs.EPHA6.R1 137 201
• NCBIGene 36.3 285220
• Single exon skipping, size difference: 64
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_001080448

• Changed! cd PTKc_EphR_A 309aa 1e-160 in ref transcript
  • Catalytic Domain of the Protein Tyrosine Kinases, Class EphA Ephrin Receptors. Protein Tyrosine Kinase (PTK) family; Ephrin Receptor (EphR) subfamily; most class EphA receptors including EphA3, EphA4, EphA5, and EphA7, but excluding EphA1, EphA2 and EphA10; catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. EphRs comprise the largest subfamily of receptor tyr kinases (RTKs). In general, class EphA receptors bind GPI-anchored ephrin-A ligands. There are ten vertebrate EphA receptors (EphA1-10), which display promiscuous interactions with six ephrin-A ligands. One exception is EphA4, which also binds ephrins-B2/B3. EphRs contain an ephrin-binding domain and two fibronectin repeats extracellularly, a transmembrane segment, and a cytoplasmic tyr kinase domain. Binding of the ephrin ligand to EphR requires cell-cell contact since both are anchored to the plasma membrane. The resulting downstream signals occur bidirectionally in both EphR-expressing cells (forward signaling) and ephrin-expressing cells (reverse signaling). Ephrin/EphR interaction mainly results in cell-cell repulsion or adhesion, making it important in neural development and plasticity, cell morphogenesis, cell-fate determination, embryonic development, tissue patterning, and angiogenesis. EphARs and ephrin-A ligands are expressed in multiple areas of the developing brain, especially in the retina and tectum. They are part of a system controlling retinotectal mapping.
• cd FN3 92aa 1e-11 in ref transcript
  • Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.
• Changed! cd SAM 59aa 1e-07 in ref transcript
  • Sterile alpha motif.; Widespread domain in signalling and nuclear proteins. In EPH-related tyrosine kinases, appears to mediate cell-cell initiated signal transduction via the binding of SH2-containing proteins to a conserved tyrosine that is phosphorylated. In many cases mediates homodimerization.
• cd FN3 101aa 0.002 in ref transcript
• Changed! pfam Pkinase_Tyr 300aa 1e-111 in ref transcript
  • Protein tyrosine kinase.
• pfam Ephrin_lbd 173aa 7e-98 in ref transcript
  • Ephrin receptor ligand binding domain. The Eph receptors, which bind to ephrins pfam00812 are a large family of receptor tyrosine kinases. This family represents the amino terminal domain which binds the ephrin ligand.
• Changed! smart SAM 68aa 4e-12 in ref transcript
  • Sterile alpha motif. Widespread domain in signalling and nuclear proteins. In EPH-related tyrosine kinases, appears to mediate cell-cell initiated signal transduction via the binding of SH2-containing proteins to a conserved tyrosine that is phosphorylated. In many cases mediates homodimerisation.
• pfam fn3 87aa 2e-10 in ref transcript
  • Fibronectin type III domain.
• pfam fn3 96aa 3e-06 in ref transcript
• pfam GCC2_GCC3 37aa 0.002 in ref transcript
  • GCC2 and GCC3.
• Changed! COG SPS1 317aa 9e-18 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].

EPSTI1

• rs.EPSTI1.F1 rs.EPSTI1.R1 143 176
• NCBIGene 36.3 94240
• Single exon skipping, size difference: 33
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001002264

• Changed! pfam Borrelia_P83 133aa 0.007 in modified transcript
  • Borrelia P83/100 protein. This family consists of several Borrelia P83/P100 antigen proteins.
• Changed! COG TolA 169aa 0.009 in modified transcript
  • Membrane protein involved in colicin uptake [Cell envelope biogenesis, outer membrane].

ERBB4

• rs.ERBB4.F1 rs.ERBB4.R1 114 162
• NCBIGene 36.3 2066
• Single exon skipping, size difference: 48
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_005235

• cd PTKc_HER4 297aa 0.0 in ref transcript
  • Catalytic Domain of the Protein Tyrosine Kinase, HER4. Protein Tyrosine Kinase (PTK) family; HER4 (ErbB4); catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. HER4 is a member of the EGFR (HER, ErbB) subfamily of proteins, which are receptor tyr kinases (RTKs) containing an extracellular EGF-related ligand-binding region, a transmembrane helix, and a cytoplasmic region with a tyr kinase domain and a regulatory C-terminal tail. Unlike other tyr kinases, phosphorylation of the activation loop of EGFR proteins is not critical to their activation. Instead, they are activated by ligand-induced dimerization, leading to the phosphorylation of tyr residues in the C-terminal tail, which serve as binding sites for downstream signaling molecules. Ligands that bind HER4 fall into two groups, the neuregulins (or heregulins) and some EGFR (HER1) ligands including betacellulin, HBEGF, and epiregulin. All four neuregulins (NRG1-4) interact with HER4. Upon ligand binding, HER4 forms homo- or heterodimers with other HER proteins. HER4 is essential in embryonic development. It is implicated in mammary gland, cardiac, and neural development. As a postsynaptic receptor of NRG1, HER4 plays an important role in synaptic plasticity and maturation. The impairment of NRG1/HER4 signaling may contribute to schizophrenia.
• cd FU 46aa 4e-05 in ref transcript
  • Furin-like repeats. Cysteine rich region. Exact function of the domain is not known. Furin is a serine-kinase dependent proprotein processor. Other members of this family include endoproteases and cell surface receptors.
• cd FU 43aa 1e-04 in ref transcript
• pfam Pkinase_Tyr 257aa 1e-112 in ref transcript
  • Protein tyrosine kinase.
• pfam Furin-like 149aa 2e-41 in ref transcript
  • Furin-like cysteine rich region.
• pfam Recep_L_domain 113aa 7e-30 in ref transcript
  • Receptor L domain. The L domains from these receptors make up the bilobal ligand binding site. Each L domain consists of a single-stranded right hand beta-helix. This Pfam entry is missing the first 50 amino acid residues of the domain.
• pfam Recep_L_domain 121aa 4e-22 in ref transcript
• smart FU 48aa 1e-06 in ref transcript
  • Furin-like repeats.
• pfam Furin-like 101aa 2e-06 in ref transcript
• COG SPS1 230aa 4e-21 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].

ERC1

• rs.ERC1.F1 rs.ERC1.R1 108 120
• NCBIGene 36.3 23085
• Single exon skipping, size difference: 12
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_178040

• Changed! pfam Cast 829aa 1e-148 in ref transcript
  • RIM-binding protein of the cytomatrix active zone. This is a family of proteins that form part of the CAZ (cytomatrix at the active zone) complex which is involved in determining the site of synaptic vesicle fusion. The C-terminus is a PDZ-binding motif that binds directly to RIM (a small G protein Rab-3A effector). The family also contains four coiled-coil domains.
• pfam RBD-FIP 41aa 1e-07 in ref transcript
  • FIP domain. The FIP domain is the Rab11-binding domain (RBD) at the C-terminus of a family of Rab11-interacting proteins (FIPs). The Rab proteins constitute the largest family of small GTPases (>60 members in mammals). Among them Rab11 is a well characterised regulator of endocytic and recycling pathways. Rab11 associates with a broad range of post-Golgi organelles, including recycling endosomes.
• COG Smc 340aa 3e-09 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].
• Changed! COG Smc 318aa 3e-08 in ref transcript
• COG Smc 298aa 5e-06 in ref transcript
• Changed! pfam Cast 833aa 1e-149 in modified transcript
• Changed! COG Smc 264aa 6e-07 in modified transcript

ERCC8

• rs.ERCC8.F1 rs.ERCC8.R1 129 347
• NCBIGene 36.3 1161
• Single exon skipping, size difference: 218
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_000082

• Changed! cd WD40 322aa 3e-30 in ref transcript
  • WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.
• Changed! smart WD40 41aa 2e-05 in ref transcript
  • WD40 repeats. Note that these repeats are permuted with respect to the structural repeats (blades) of the beta propeller domain.
• Changed! smart WD40 32aa 0.007 in ref transcript
• Changed! COG COG2319 358aa 2e-16 in ref transcript
  • FOG: WD40 repeat [General function prediction only].

ERGIC3

• rs.ERGIC3.F1 rs.ERGIC3.R1 100 115
• NCBIGene 36.3 51614
• Single exon skipping, size difference: 15
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_198398

• Changed! pfam DUF1692 188aa 1e-70 in ref transcript
  • Protein of unknown function (DUF1692). This family contains many hypothetical proteins. It also contains proteins which are involved in transport between the ER and Golgi complex protein transport from ER to Golgi.
• Changed! pfam DUF1692 183aa 1e-72 in modified transcript

EVI1

• rs.EVI1.F1 rs.EVI1.R1 114 176
• NCBIGene 36.3 2122
• Single exon skipping, size difference: 62
• Exclusion of the protein initiation site
• Reference transcript: NM_001105077

• Changed! smart SET 57aa 1e-04 in ref transcript
  • SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain. Putative methyl transferase, based on outlier plant homologues.
• pfam zf-C2H2 23aa 0.007 in ref transcript
  • Zinc finger, C2H2 type. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter.

EXOC1

• rs.EXOC1.F1 rs.EXOC1.R1 254 299
• NCBIGene 36.3 55763
• Single exon skipping, size difference: 45
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001024924

• Changed! pfam Sec3 703aa 0.0 in ref transcript
  • Exocyst complex component Sec3. This entry is the conserved middle and C-terminus of the Sec3 protein. Sec3 binds to the C-terminal cytoplasmic domain of GLYT1 (glycine transporter protein 1). Sec3 is the exocyst component that is closest to the plasma membrane docking site and it serves as a spatial landmark in the plasma membrane for incoming secretory vesicles. Sec3 is recruited to the sites of polarised membrane growth through its interaction with Rho1p, a small GTP-binding protein.
• Changed! pfam Sec3 688aa 0.0 in modified transcript

EYA1

• rs.EYA1.F1 rs.EYA1.R1 100 115
• NCBIGene 36.3 2138
• Alternative 3-prime, size difference: 15
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000503

• TIGR EYA-cons_domain 271aa 1e-126 in ref transcript
  • This domain is common to all eyes absent (EYA) homologs. Metazoan EYA's also contain a variable N-terminal domain consisting largely of low-complexity sequences.

EYA2

• rs.EYA2.F1 rs.EYA2.R1 125 197
• NCBIGene 36.3 2139
• Alternative 5-prime and 3-prime, size difference: 72
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_172113

• TIGR EYA-cons_domain 272aa 1e-118 in ref transcript
  • This domain is common to all eyes absent (EYA) homologs. Metazoan EYA's also contain a variable N-terminal domain consisting largely of low-complexity sequences.

EZH2

• rs.EZH2.F1 rs.EZH2.R1 100 115
• NCBIGene 36.3 2146
• Alternative 5-prime, size difference: 15
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_004456

• pfam SET 124aa 3e-36 in ref transcript
  • SET domain. SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure.
• COG COG2940 208aa 4e-15 in ref transcript
  • Proteins containing SET domain [General function prediction only].

F7

• rs.F7.F1 rs.F7.R1 139 205
• NCBIGene 36.3 2155
• Single exon skipping, size difference: 66
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000131

• cd Tryp_SPc 237aa 3e-57 in ref transcript
  • Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
• cd EGF_CA 37aa 9e-06 in ref transcript
  • Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements.
• smart Tryp_SPc 235aa 1e-57 in ref transcript
  • Trypsin-like serine protease. Many of these are synthesised as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. A few, however, are active as single chain molecules, and others are inactive due to substitutions of the catalytic triad residues.
• Changed! smart GLA 63aa 1e-21 in ref transcript
  • Domain containing Gla (gamma-carboxyglutamate) residues. A hyaluronan-binding domain found in proteins associated with the extracellular matrix, cell adhesion and cell migration.
• smart EGF_CA 37aa 2e-04 in ref transcript
  • Calcium-binding EGF-like domain.
• COG COG5640 252aa 1e-14 in ref transcript
  • Secreted trypsin-like serine protease [Posttranslational modification, protein turnover, chaperones].
• Changed! smart GLA 62aa 3e-21 in modified transcript

FAM104A

• rs.FAM104A.F1 rs.FAM104A.R1 219 282
• NCBIGene 36.3 84923
• Single exon skipping, size difference: 63
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001098832

FAM107A

• rs.FAM107A.F1 rs.FAM107A.R1 294 392
• NCBIGene 36.3 11170
• Single exon skipping, size difference: 98
• Exclusion in 5'UTR
• Reference transcript: NM_007177

• pfam DUF1151 118aa 1e-24 in ref transcript
  • Protein of unknown function (DUF1151). This family consists of several hypothetical eukaryotic proteins of unknown function.

FAM123C

• rs.FAM123C.F1 rs.FAM123C.R1 239 370
• NCBIGene 36.3 205147
• Alternative 5-prime, size difference: 131
• Exclusion in 5'UTR
• Reference transcript: NM_001105193

• pfam WTX 371aa 1e-103 in ref transcript
  • WTX protein. The WTX protein is found to be inactivated in one third of Wilms tumours. The WTX protein is functionally uncharacterised.

FAM135A

• rs.FAM135A.F1 rs.FAM135A.R1 116 245
• NCBIGene 36.3 57579
• Exon skipping and alternative 3-prime or 5-prime, size difference: 129
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_001105531

• pfam DUF676 197aa 2e-59 in ref transcript
  • Putative serine esterase (DUF676). This family of proteins are probably serine esterase type enzymes with an alpha/beta hydrolase fold.

FAM135A

• rs.FAM135A.F2 rs.FAM135A.R2 101 179
• NCBIGene 36.3 57579
• Single exon skipping, size difference: 78
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_001105531

• pfam DUF676 197aa 2e-59 in ref transcript
  • Putative serine esterase (DUF676). This family of proteins are probably serine esterase type enzymes with an alpha/beta hydrolase fold.

FAM135A

• rs.FAM135A.F3 rs.FAM135A.R3 171 257
• NCBIGene 36.3 57579
• Single exon skipping, size difference: 86
• Exclusion in 5'UTR
• Reference transcript: NM_001105531

• pfam DUF676 197aa 2e-59 in ref transcript
  • Putative serine esterase (DUF676). This family of proteins are probably serine esterase type enzymes with an alpha/beta hydrolase fold.

FAM33A

• rs.FAM33A.F1 rs.FAM33A.R1 222 399
• NCBIGene 36.3 348235
• Single exon skipping, size difference: 177
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_182620

FAM33A

• rs.FAM33A.F2 rs.FAM33A.R2 202 377
• NCBIGene 36.3 348235
• Alternative 5-prime, size difference: 175
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_182620

FAM48A

• rs.FAM48A.F1 rs.FAM48A.R1 350 432
• NCBIGene 36.3 55578
• Alternative 3-prime, size difference: 3
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_001014286

FAM54A

• rs.FAM54A.F1 rs.FAM54A.R1 197 485
• NCBIGene 36.3 113115
• Alternative 5-prime, size difference: 288
• Exclusion in 5'UTR
• Reference transcript: NM_001099286

• pfam DUF729 266aa 1e-74 in ref transcript
  • Protein of unknown function (DUF729). This family consists of several uncharacterised eukaryotic proteins of unknown function.

FAM54B

• rs.FAM54B.F1 rs.FAM54B.R1 181 290
• NCBIGene 36.3 56181
• Alternative 3-prime, size difference: 109
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_001099625

• Changed! pfam DUF729 248aa 9e-51 in ref transcript
  • Protein of unknown function (DUF729). This family consists of several uncharacterised eukaryotic proteins of unknown function.
• Changed! pfam DUF729 148aa 6e-39 in modified transcript

FAM70A

• rs.FAM70A.F1 rs.FAM70A.R1 217 289
• NCBIGene 36.3 55026
• Single exon skipping, size difference: 72
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_017938

FAM72A

• rs.FAM72A.F1 rs.FAM72A.R1 237 357
• NCBIGene 36.3 729533
• Alternative 5-prime, size difference: 120
• Exclusion in the protein (no frameshift)
• Reference transcript: XM_001133365

FAM89B

• rs.FAM89B.F1 rs.FAM89B.R1 90 100
• NCBIGene 36.3 23625
• Alternative 3-prime, size difference: 10
• Inclusion in 5'UTR
• Reference transcript: NM_001098785

FAS

• rs.FAS.F1 rs.FAS.R1 187 296
• NCBIGene 36.3 355
• Single exon skipping, size difference: 109
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_000043

• Changed! cd TNFR 95aa 5e-16 in ref transcript
  • Tumor necrosis factor receptor (TNFR) domain; superfamily of TNF-like receptor domains. When bound to TNF-like cytokines, TNFRs trigger multiple signal transduction pathways, they are involved in inflammation response, apoptosis, autoimmunity and organogenesis. TNFRs domains are elongated with generally three tandem repeats of cysteine-rich domains (CRDs). They fit in the grooves between protomers within the ligand trimer. Some TNFRs, such as NGFR and HveA, bind ligands with no structural similarity to TNF and do not bind ligand trimers.
• Changed! smart DEATH 88aa 2e-16 in ref transcript
  • DEATH domain, found in proteins involved in cell death (apoptosis). Alpha-helical domain present in a variety of proteins with apoptotic functions. Some (but not all) of these domains form homotypic and heterotypic dimers.
• Changed! pfam TNFR_c6 37aa 4e-05 in ref transcript
  • TNFR/NGFR cysteine-rich region.
• Changed! cd TNFR 59aa 2e-06 in modified transcript

FAS

• rs.FAS.F2 rs.FAS.R2 104 167
• NCBIGene 36.3 355
• Single exon skipping, size difference: 63
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000043

• cd TNFR 95aa 5e-16 in ref transcript
  • Tumor necrosis factor receptor (TNFR) domain; superfamily of TNF-like receptor domains. When bound to TNF-like cytokines, TNFRs trigger multiple signal transduction pathways, they are involved in inflammation response, apoptosis, autoimmunity and organogenesis. TNFRs domains are elongated with generally three tandem repeats of cysteine-rich domains (CRDs). They fit in the grooves between protomers within the ligand trimer. Some TNFRs, such as NGFR and HveA, bind ligands with no structural similarity to TNF and do not bind ligand trimers.
• smart DEATH 88aa 2e-16 in ref transcript
  • DEATH domain, found in proteins involved in cell death (apoptosis). Alpha-helical domain present in a variety of proteins with apoptotic functions. Some (but not all) of these domains form homotypic and heterotypic dimers.
• pfam TNFR_c6 37aa 4e-05 in ref transcript
  • TNFR/NGFR cysteine-rich region.

FAS

• rs.FAS.F3 rs.FAS.R3 100 125
• NCBIGene 36.3 355
• Single exon skipping, size difference: 25
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_000043

• cd TNFR 95aa 5e-16 in ref transcript
  • Tumor necrosis factor receptor (TNFR) domain; superfamily of TNF-like receptor domains. When bound to TNF-like cytokines, TNFRs trigger multiple signal transduction pathways, they are involved in inflammation response, apoptosis, autoimmunity and organogenesis. TNFRs domains are elongated with generally three tandem repeats of cysteine-rich domains (CRDs). They fit in the grooves between protomers within the ligand trimer. Some TNFRs, such as NGFR and HveA, bind ligands with no structural similarity to TNF and do not bind ligand trimers.
• Changed! smart DEATH 88aa 2e-16 in ref transcript
  • DEATH domain, found in proteins involved in cell death (apoptosis). Alpha-helical domain present in a variety of proteins with apoptotic functions. Some (but not all) of these domains form homotypic and heterotypic dimers.
• pfam TNFR_c6 37aa 4e-05 in ref transcript
  • TNFR/NGFR cysteine-rich region.

FASTK

• rs.FASTK.F1 rs.FASTK.R1 125 548
• NCBIGene 36.3 10922
• Single exon skipping, size difference: 423
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_006712

• pfam FAST_1 67aa 1e-13 in ref transcript
  • FAST kinase-like protein, subdomain 1. This family represents a conserved region of eukaryotic Fas-activated serine/threonine (FAST) kinases (EC:2.7.1.-) that contains several conserved leucine residues. FAST kinase is rapidly activated during Fas-mediated apoptosis, when it phosphorylates TIA-1, a nuclear RNA-binding protein that has been implicated as an effector of apoptosis. Note that many family members are hypothetical proteins. This region is often found immediately N-terminal to the FAST kinase-like protein, subdomain 2.
• pfam FAST_2 92aa 8e-13 in ref transcript
  • FAST kinase-like protein, subdomain 2. This family represents a conserved region of eukaryotic Fas-activated serine/threonine (FAST) kinases (EC:2.7.1.-) that contains several conserved leucine residues. FAST kinase is rapidly activated during Fas-mediated apoptosis, when it phosphorylates TIA-1, a nuclear RNA-binding protein that has been implicated as an effector of apoptosis. Note that many family members are hypothetical proteins. This subdomain is often found associated with the FAST kinase-like protein, subdomain 2.
• pfam RAP 58aa 5e-12 in ref transcript
  • RAP domain. This domain is found in various eukaryotic species, particularly in apicomplexans such as Plasmodium falciparum, where it is found in proteins that are important in various parasite-host cell interactions. It is thought to be an RNA-binding domain.

FBXO43

• rs.FBXO43.F1 rs.FBXO43.R1 209 253
• NCBIGene 36.3 286151
• Alternative 5-prime, size difference: 44
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_001029860

• Changed! pfam IBR 43aa 0.002 in ref transcript
  • IBR domain. The IBR (In Between Ring fingers) domain is often found to occur between pairs of ring fingers (pfam00097). This domain has also been called the C6HC domain and DRIL (for double RING finger linked) domain. Proteins that contain two Ring fingers and an IBR domain (these proteins are also termed RBR family proteins) are thought to exist in all eukaryotic organisms. RBR family members play roles in protein quality control and can indirectly regulate transcription. Evidence suggests that RBR proteins are often parts of cullin-containing ubiquitin ligase complexes. The ubiquitin ligase Parkin is an RBR family protein whose mutations are involved in forms of familial Parkinson's disease.

FCGR1B

• rs.FCGR1B.F1 rs.FCGR1B.R1 108 384
• NCBIGene 36.3 2210
• Multiple exon skipping, size difference: 276
• Exclusion in the protein (no frameshift), Exclusion in the protein (no frameshift)
• Reference transcript: NM_001017986

• Changed! cd IGcam 64aa 8e-04 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• smart IGc2 59aa 4e-04 in ref transcript
  • Immunoglobulin C-2 Type.
• Changed! smart IG_like 74aa 6e-04 in ref transcript
  • Immunoglobulin like. IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.

FCGR2C

• rs.FCGR2C.F1 rs.FCGR2C.R1 103 117
• NCBIGene 36.3 9103
• Alternative 3-prime, size difference: 14
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_201563

FERMT3

• rs.FERMT3.F1 rs.FERMT3.R1 100 112
• NCBIGene 36.3 83706
• Alternative 3-prime, size difference: 12
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_178443

• Changed! cd Unc112 110aa 3e-45 in ref transcript
  • Unc-112 pleckstrin homology (PH) domain. Unc-112 and related proteins contain two FERM domains with a PH domain between them. Both the PH and FERM domains have a PH-like fold. The FERM domains are likely responsible for the role of Unc-112 in organizing beta-integrin. The specific role of the Unc-112 PH domain is not known, but it is predicted to be involved in mediating membrane interactions. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
• smart B41 90aa 2e-14 in ref transcript
  • Band 4.1 homologues. Also known as ezrin/radixin/moesin (ERM) protein domains. Present in myosins, ezrin, radixin, moesin, protein tyrosine phosphatases. Plasma membrane-binding domain. These proteins play structural and regulatory roles in the assembly and stabilization of specialized plasmamembrane domains. Some PDZ domain containing proteins bind one or more of this family. Now includes JAKs.
• pfam FERM_M 49aa 2e-10 in ref transcript
  • FERM central domain. This domain is the central structural domain of the FERM domain.
• Changed! pfam PH 95aa 2e-09 in ref transcript
  • PH domain. PH stands for pleckstrin homology.
• Changed! cd Unc112 106aa 5e-47 in modified transcript
• Changed! pfam PH 96aa 1e-09 in modified transcript

FEZ2

• rs.FEZ2.F1 rs.FEZ2.R1 241 322
• NCBIGene 36.3 9637
• Single exon skipping, size difference: 81
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001042548

• pfam FEZ 216aa 1e-70 in ref transcript
  • FEZ-like protein. This is a family of eukaryotic proteins thought to be involved in axonal outgrowth and fasciculation. The N-terminal regions of these sequences are less conserved than the C-terminal regions, and are highly acidic. The Caenorhabditis elegans homolog, UNC-76, may play structural and signalling roles in the control of axonal extension and adhesion (particularly in the presence of adjacent neuronal cells) and these roles have also been postulated for other FEZ family proteins. Certain homologs have been definitively found to interact with the N-terminal variable region (V1) of PKC-zeta, and this interaction causes cytoplasmic translocation of the FEZ family protein in mammalian neuronal cells. The C-terminal region probably participates in the association with the regulatory domain of PKC-zeta. The members of this family are predicted to form coiled-coil structures, which may interact with members of the RhoA family of signalling proteins, but are not thought to contain other characteristic protein motifs. Certain members of this family are expressed almost exclusively in the brain, whereas others (such as FEZ2) are expressed in other tissues, and are thought to perform similar but unknown functions in these tissues.

FGF8

• rs.FGF8.F2 rs.FGF8.R2 123 156
• NCBIGene 36.3 2253
• Alternative 3-prime, size difference: 33
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_033163

• cd FGF 125aa 2e-28 in ref transcript
  • Acidic and basic fibroblast growth factor family; FGFs are mitogens, which stimulate growth or differentiation of cells of mesodermal or neuroectodermal origin. The family plays essential roles in patterning and differentiation during vertebrate embryogenesis, and has neurotrophic activities. FGFs have a high affinity for heparan sulfate proteoglycans and require heparan sulfate to activate one of four cell surface FGF receptors. Upon binding to FGF, the receptors dimerize and their intracellular tyrosine kinase domains become active. FGFs have internal pseudo-threefold symmetry (beta-trefoil topology).
• pfam FGF 123aa 2e-38 in ref transcript
  • Fibroblast growth factor. Fibroblast growth factors are a family of proteins involved in growth and differentiation in a wide range of contexts. They are found in a wide range of organisms, from nematodes to humans. Most share an internal core region of high similarity, conserved residues in which are involved in binding with their receptors. On binding, they cause dimerisation of their tyrosine kinase receptors leading to intracellular signalling. There are currently four known tyrosine kinase receptors for fibroblast growth factors. These receptors can each bind several different members of this family. Members of this family have a beta trefoil structure. Most have N-terminal signal peptides and are secreted. A few lack signal sequences but are secreted anyway; still others also lack the signal peptide but are found on the cell surface and within the extracellular matrix. A third group remain intracellular. They have central roles in development, regulating cell proliferation, migration and differentiation. On the other hand, they are important in tissue repair following injury in adult organisms.

FGFR1

• rs.FGFR1.F1 rs.FGFR1.R1 107 218
• NCBIGene 36.3 2260
• Alternative 5-prime and 3-prime, size difference: 111
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_023110

• Changed! cd PTKc_FGFR1 307aa 0.0 in ref transcript
  • Catalytic Domain of the Protein Tyrosine Kinase, Fibroblast Growth Factor Receptor 1. Protein Tyrosine Kinase (PTK) family; Fibroblast Growth Factor Receptor 1 (FGFR1); catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. FGFR1 is part of the FGFR subfamily, which are receptor tyr kinases (RTKs) containing an extracellular ligand-binding region with three immunoglobulin-like domains, a transmembrane segment, and an intracellular catalytic domain. The binding of FGFRs to their ligands, the FGFs, results in receptor dimerization and activation, and intracellular signaling. The binding of FGFs to FGFRs is promiscuous, in that a receptor may be activated by several ligands and a ligand may bind to more that one type of receptor. Alternative splicing of FGFR1 transcripts produces a variety of isoforms, which are differentially expressed in cells. FGFR1 binds the ligands, FGF1 and FGF2, with high affinity and has also been reported to bind FGF4, FGF6, and FGF9. FGFR1 signaling is critical in the control of cell migration during embryo development. It promotes cell proliferation in fibroblasts. Nuclear FGFR1 plays a role in the regulation of transcription. Mutations, insertions or deletions of FGFR1 have been identified in patients with Kallman's syndrome (KS), an inherited disorder characterized by hypogonadotropic hypogonadism and loss of olfaction. Aberrant FGFR1 expression has been found in some human cancers including 8P11 myeloproliferative syndrome (EMS), breast cancer, and pancreatic adenocarcinoma.
• cd IGcam 93aa 6e-15 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• cd IGcam 103aa 2e-09 in ref transcript
• cd IGcam 55aa 0.004 in ref transcript
• Changed! pfam Pkinase_Tyr 277aa 1e-116 in ref transcript
  • Protein tyrosine kinase.
• pfam I-set 88aa 2e-13 in ref transcript
  • Immunoglobulin I-set domain.
• smart IG_like 98aa 4e-13 in ref transcript
  • Immunoglobulin like. IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
• smart IGc2 48aa 4e-07 in ref transcript
  • Immunoglobulin C-2 Type.
• Changed! COG SPS1 343aa 2e-21 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].
• Changed! cd PTKc_FGFR1 270aa 1e-158 in modified transcript
• Changed! pfam Pkinase_Tyr 236aa 2e-95 in modified transcript
• Changed! COG SPS1 238aa 4e-21 in modified transcript

FGFR1

• rs.FGFR1.F2 FGFR1.R42 228 495
• NCBIGene 36.3 2260
• Single exon skipping, size difference: 267
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_023110

• cd PTKc_FGFR1 307aa 0.0 in ref transcript
  • Catalytic Domain of the Protein Tyrosine Kinase, Fibroblast Growth Factor Receptor 1. Protein Tyrosine Kinase (PTK) family; Fibroblast Growth Factor Receptor 1 (FGFR1); catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. FGFR1 is part of the FGFR subfamily, which are receptor tyr kinases (RTKs) containing an extracellular ligand-binding region with three immunoglobulin-like domains, a transmembrane segment, and an intracellular catalytic domain. The binding of FGFRs to their ligands, the FGFs, results in receptor dimerization and activation, and intracellular signaling. The binding of FGFs to FGFRs is promiscuous, in that a receptor may be activated by several ligands and a ligand may bind to more that one type of receptor. Alternative splicing of FGFR1 transcripts produces a variety of isoforms, which are differentially expressed in cells. FGFR1 binds the ligands, FGF1 and FGF2, with high affinity and has also been reported to bind FGF4, FGF6, and FGF9. FGFR1 signaling is critical in the control of cell migration during embryo development. It promotes cell proliferation in fibroblasts. Nuclear FGFR1 plays a role in the regulation of transcription. Mutations, insertions or deletions of FGFR1 have been identified in patients with Kallman's syndrome (KS), an inherited disorder characterized by hypogonadotropic hypogonadism and loss of olfaction. Aberrant FGFR1 expression has been found in some human cancers including 8P11 myeloproliferative syndrome (EMS), breast cancer, and pancreatic adenocarcinoma.
• cd IGcam 93aa 6e-15 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• cd IGcam 103aa 2e-09 in ref transcript
• Changed! cd IGcam 55aa 0.004 in ref transcript
• pfam Pkinase_Tyr 277aa 1e-116 in ref transcript
  • Protein tyrosine kinase.
• pfam I-set 88aa 2e-13 in ref transcript
  • Immunoglobulin I-set domain.
• smart IG_like 98aa 4e-13 in ref transcript
  • Immunoglobulin like. IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
• Changed! smart IGc2 48aa 4e-07 in ref transcript
  • Immunoglobulin C-2 Type.
• COG SPS1 343aa 2e-21 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].

FGFR4

• rs.FGFR4.F1 FGFR4.R4 261 381
• NCBIGene 36.3 2264
• Exon skipping and alternative 3-prime or 5-prime, size difference: 120
• Inclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_213647

• cd PTKc_FGFR4 311aa 0.0 in ref transcript
  • Catalytic Domain of the Protein Tyrosine Kinase, Fibroblast Growth Factor Receptor 4. Protein Tyrosine Kinase (PTK) family; Fibroblast Growth Factor Receptor 4 (FGFR4); catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. FGFR4 is part of the FGFR subfamily, which are receptor tyr kinases (RTKs) containing an extracellular ligand-binding region with three immunoglobulin-like domains, a transmembrane segment, and an intracellular catalytic domain. The binding of FGFRs to their ligands, the FGFs, results in receptor dimerization and activation, and intracellular signaling. The binding of FGFs to FGFRs is promiscuous, in that a receptor may be activated by several ligands and a ligand may bind to more that one type of receptor. Unlike other FGFRs, there is only one splice form of FGFR4. It binds FGF1, FGF2, FGF6, FGF19, and FGF23. FGF19 is a selective ligand for FGFR4. Although disruption of FGFR4 in mice causes no obvious phenotype, in vivo inhibition of FGFR4 in cultured skeletal muscle cells resulted in an arrest of muscle progenitor differentiation. FGF6 and FGFR4 are uniquely expressed in myofibers and satellite cells. FGF6/FGFR4 signaling appears to play a key role in the regulation of muscle regeneration. A polymorphism in FGFR4 is found in head and neck squamous cell carcinoma.
• cd IGcam 93aa 7e-17 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• cd IGcam 101aa 2e-07 in ref transcript
• cd IGcam 67aa 0.003 in ref transcript
• pfam Pkinase_Tyr 277aa 1e-114 in ref transcript
  • Protein tyrosine kinase.
• smart IGc2 67aa 3e-15 in ref transcript
  • Immunoglobulin C-2 Type.
• smart IG_like 96aa 5e-12 in ref transcript
  • Immunoglobulin like. IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
• smart IGc2 58aa 7e-09 in ref transcript
• COG SPS1 251aa 8e-23 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].

FGFR4

• rs.FGFR4.F2 rs.FGFR4.R2 167 211
• NCBIGene 36.3 2264
• Alternative 5-prime, size difference: 44
• Exclusion in 5'UTR
• Reference transcript: NM_213647

• cd PTKc_FGFR4 311aa 0.0 in ref transcript
  • Catalytic Domain of the Protein Tyrosine Kinase, Fibroblast Growth Factor Receptor 4. Protein Tyrosine Kinase (PTK) family; Fibroblast Growth Factor Receptor 4 (FGFR4); catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. FGFR4 is part of the FGFR subfamily, which are receptor tyr kinases (RTKs) containing an extracellular ligand-binding region with three immunoglobulin-like domains, a transmembrane segment, and an intracellular catalytic domain. The binding of FGFRs to their ligands, the FGFs, results in receptor dimerization and activation, and intracellular signaling. The binding of FGFs to FGFRs is promiscuous, in that a receptor may be activated by several ligands and a ligand may bind to more that one type of receptor. Unlike other FGFRs, there is only one splice form of FGFR4. It binds FGF1, FGF2, FGF6, FGF19, and FGF23. FGF19 is a selective ligand for FGFR4. Although disruption of FGFR4 in mice causes no obvious phenotype, in vivo inhibition of FGFR4 in cultured skeletal muscle cells resulted in an arrest of muscle progenitor differentiation. FGF6 and FGFR4 are uniquely expressed in myofibers and satellite cells. FGF6/FGFR4 signaling appears to play a key role in the regulation of muscle regeneration. A polymorphism in FGFR4 is found in head and neck squamous cell carcinoma.
• cd IGcam 93aa 7e-17 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• cd IGcam 101aa 2e-07 in ref transcript
• cd IGcam 67aa 0.003 in ref transcript
• pfam Pkinase_Tyr 277aa 1e-114 in ref transcript
  • Protein tyrosine kinase.
• smart IGc2 67aa 3e-15 in ref transcript
  • Immunoglobulin C-2 Type.
• smart IG_like 96aa 5e-12 in ref transcript
  • Immunoglobulin like. IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
• smart IGc2 58aa 7e-09 in ref transcript
• COG SPS1 251aa 8e-23 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].

FKTN

• rs.FKTN.F1 rs.FKTN.R1 173 265
• NCBIGene 36.3 2218
• Single exon skipping, size difference: 92
• Exclusion in 5'UTR
• Reference transcript: NM_001079802

• pfam LicD 136aa 1e-08 in ref transcript
  • LICD Protein Family. The LICD family of proteins show high sequence similarity and are involved in phosphorylcholine metabolism. There is evidence to show that LicD2 mutants have a reduced ability to take up choline, have decreased ability to adhere to host cells and are less virulent.

FLJ11151

• rs.FLJ11151.F1 rs.FLJ11151.R1 114 540
• NCBIGene 36.3 55313
• Single exon skipping, size difference: 426
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_018340

• Changed! pfam Metallophos 172aa 3e-04 in ref transcript
  • Calcineurin-like phosphoesterase. This family includes a diverse range of phosphoesterases, including protein phosphoserine phosphatases, nucleotidases, sphingomyelin phosphodiesterases and 2'-3' cAMP phosphodiesterases as well as nucleases such as bacterial SbcD or yeast MRE11. The most conserved regions in this superfamily centre around the metal chelating residues.
• Changed! COG Icc 203aa 1e-09 in ref transcript
  • Predicted phosphohydrolases [General function prediction only].

FLJ11171

• rs.FLJ11171.F1 rs.FLJ11171.R1 181 231
• NCBIGene 36.3 55783
• Alternative 5-prime, size difference: 50
• Exclusion in 5'UTR
• Reference transcript: NM_001099642

• pfam FtsJ 209aa 2e-18 in ref transcript
  • FtsJ-like methyltransferase. This family consists of FtsJ from various bacterial and archaeal sources FtsJ is a methyltransferase, but actually has no effect on cell division. FtsJ's substrate is the 23S rRNA. The 1.5 A crystal structure of FtsJ in complex with its cofactor S-adenosylmethionine revealed that FtsJ has a methyltransferase fold. This family also includes the N terminus of flaviviral NS5 protein. It has been hypothesised that the N-terminal domain of NS5 is a methyltransferase involved in viral RNA capping.
• COG FtsJ 117aa 2e-08 in ref transcript
  • 23S rRNA methylase [Translation, ribosomal structure and biogenesis].

FLJ13611

• rs.FLJ13611.F1 rs.FLJ13611.R1 110 128
• NCBIGene 36.3 80006
• Single exon skipping, size difference: 18
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001093755

• Changed! pfam DUF974 238aa 1e-113 in ref transcript
  • Protein of unknown function (DUF974). Family of uncharacterised eukaryotic proteins.
• Changed! pfam DUF974 232aa 1e-115 in modified transcript

FLJ14154

• rs.FLJ14154.F1 rs.FLJ14154.R1 100 122
• NCBIGene 36.3 79903
• Alternative 5-prime, size difference: 22
• Exclusion in 3'UTR
• Reference transcript: NM_024845

• cd GNAT 103aa 2e-07 in ref transcript
  • GCN5-related N-acetyltransferases (GNAT) represent a large superfamily of functionally diverse enzymes that catalyze the transfer of an acetyl group from acetyl-Coenzyme A to the primary amine of a wide range of acceptor substrates. Members of this superfamily include aminoglycoside N-acetyltransferases, serotonin N-acetyltransferase, glucosamine-6-phosphate N-acetyltransferase, the histone acetyltransferases, mycothiol synthase, and the Fem family of amino acyl transferases.
• pfam Acetyltransf_1 78aa 2e-09 in ref transcript
  • Acetyltransferase (GNAT) family. This family contains proteins with N-acetyltransferase functions such as Elp3-related proteins.
• COG RimI 71aa 4e-08 in ref transcript
  • Acetyltransferases [General function prediction only].

FLJ20254

• rs.FLJ20254.F1 rs.FLJ20254.R1 175 310
• NCBIGene 36.3 54867
• Single exon skipping, size difference: 135
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_017727

• pfam DUF2359 469aa 0.0 in ref transcript
  • Uncharacterised conserved protein (DUF2359). This is a 450 amino acid region of a family of proteins conserved from insects to humans. The mouse protein, Q8BM55, is annotated as being a putative Vitamin K-dependent carboxylation gamma-carboxyglutamic (GLA) domain containing protein, but this could not be confirmed. The function is not known.

FLJ22167

• rs.FLJ22167.F1 rs.FLJ22167.R1 100 223
• NCBIGene 36.3 79583
• Alternative 3-prime, size difference: 123
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_001077416

• Changed! pfam NAcGluc_Transf 261aa 1e-100 in ref transcript
  • Carbohydrate (N-acetylglucosamine 6-O) sulfotransferase 5. Members of this family are involved in the biosynthesis of 6-Sulfo Sialyl Lewis X molecules, by catalysing the transfer of sulphate from 3'-phosphoadenosine 5'-phosphosulfate to position 6 of a non-reducing N-acetylglucosamine (GlcNAc) residue.
• Changed! pfam NAcGluc_Transf 71aa 8e-19 in modified transcript

FLJ25404

• rs.FLJ25404.F1 rs.FLJ25404.R1 200 280
• NCBIGene 36.3 146378
• Alternative 3-prime, size difference: 80
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_001109660

FLJ30428

• rs.FLJ30428.F1 rs.FLJ30428.R1 306 529
• NCBIGene 36.3 150519
• Multiple exon skipping, size difference: 223
• Exclusion in 5'UTR, Exclusion of the protein initiation site
• Reference transcript: XM_001723916

• pfam DUF1886 59aa 0.001 in ref transcript
  • Domain of unknown function (DUF1886). This domain is predominantly found in the Archaeal protein N-glycosylase/DNA lyase.

FLJ42562

• rs.FLJ42562.F1 rs.FLJ42562.R1 101 113
• NCBIGene 36.3 400954
• Alternative 5-prime, size difference: 12
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: XM_001725001

• cd WD40 306aa 8e-30 in ref transcript
  • WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.
• cd WD40 297aa 3e-29 in ref transcript
• cd WD40 351aa 5e-19 in ref transcript
• Changed! cd WD40 274aa 1e-17 in ref transcript
• cd WD40 308aa 2e-17 in ref transcript
• cd WD40 274aa 3e-17 in ref transcript
• pfam HELP 47aa 7e-08 in ref transcript
  • HELP motif. The HELP (Hydrophobic ELP) motif is found in EMAP and EMAP-like proteins (ELPs). The HELP motif contains a predicted transmembrane helix so probably does not form a globular domain. It is also not clear if these proteins localise to membranes. A preliminary study has shown that the N terminus of Sea urchin EMAP containing HELP is sufficient for microtubule binding in vitro (Eichenmuller et al In press).
• pfam HELP 29aa 3e-06 in ref transcript
• pfam HELP 41aa 2e-05 in ref transcript
• pfam WD40 34aa 0.010 in ref transcript
  • WD domain, G-beta repeat.
• Changed! COG COG2319 403aa 1e-26 in ref transcript
  • FOG: WD40 repeat [General function prediction only].
• COG COG2319 372aa 3e-21 in ref transcript
• COG COG2319 399aa 5e-19 in ref transcript
• COG COG2319 280aa 2e-14 in ref transcript
• COG COG2319 324aa 2e-10 in ref transcript
• Changed! cd WD40 278aa 6e-16 in modified transcript
• Changed! COG COG2319 407aa 8e-26 in modified transcript

FLJ42562

• rs.FLJ42562.F2 rs.FLJ42562.R2 249 345
• NCBIGene 36.3 400954
• Alternative 5-prime, size difference: 96
• Exclusion in the protein (no frameshift)
• Reference transcript: XM_001725001

• cd WD40 306aa 8e-30 in ref transcript
  • WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.
• cd WD40 297aa 3e-29 in ref transcript
• Changed! cd WD40 351aa 5e-19 in ref transcript
• cd WD40 274aa 1e-17 in ref transcript
• Changed! cd WD40 308aa 2e-17 in ref transcript
• cd WD40 274aa 3e-17 in ref transcript
• pfam HELP 47aa 7e-08 in ref transcript
  • HELP motif. The HELP (Hydrophobic ELP) motif is found in EMAP and EMAP-like proteins (ELPs). The HELP motif contains a predicted transmembrane helix so probably does not form a globular domain. It is also not clear if these proteins localise to membranes. A preliminary study has shown that the N terminus of Sea urchin EMAP containing HELP is sufficient for microtubule binding in vitro (Eichenmuller et al In press).
• pfam HELP 29aa 3e-06 in ref transcript
• pfam HELP 41aa 2e-05 in ref transcript
• pfam WD40 34aa 0.010 in ref transcript
  • WD domain, G-beta repeat.
• COG COG2319 403aa 1e-26 in ref transcript
  • FOG: WD40 repeat [General function prediction only].
• COG COG2319 372aa 3e-21 in ref transcript
• Changed! COG COG2319 399aa 5e-19 in ref transcript
• COG COG2319 280aa 2e-14 in ref transcript
• COG COG2319 324aa 2e-10 in ref transcript
• Changed! cd WD40 306aa 8e-18 in modified transcript
• Changed! cd WD40 300aa 4e-17 in modified transcript
• Changed! COG COG2319 361aa 1e-18 in modified transcript

FLJ46266

• rs.FLJ46266.F1 rs.FLJ46266.R1 144 225
• NCBIGene 36.3 399949
• Single exon skipping, size difference: 81
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_207430

FLJ77644

• rs.FLJ77644.F1 rs.FLJ77644.R1 258 399
• NCBIGene 36.3 728772
• Single exon skipping, size difference: 141
• Exclusion in the protein (no frameshift)
• Reference transcript: XM_001133074

• Changed! pfam DUF1356 241aa 1e-109 in ref transcript
  • Protein of unknown function (DUF1356). This family consists of several hypothetical mammalian proteins of around 250 residues in length. The function of this family is unknown.
• Changed! pfam DUF1356 194aa 8e-81 in modified transcript

FLJ77644

• rs.FLJ77644.F2 rs.FLJ77644.R2 134 302
• NCBIGene 36.3 728772
• Single exon skipping, size difference: 168
• Exclusion in 5'UTR
• Reference transcript: XM_001133074

• pfam DUF1356 241aa 1e-109 in ref transcript
  • Protein of unknown function (DUF1356). This family consists of several hypothetical mammalian proteins of around 250 residues in length. The function of this family is unknown.

FN1

• rs.FN1.F1 rs.FN1.R1 99 369
• NCBIGene 36.3 2335
• Single exon skipping, size difference: 270
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_212482

• cd FN2 48aa 2e-16 in ref transcript
  • Fibronectin Type II domain: FN2 is one of three types of internal repeats which combine to form larger domains within fibronectin. Fibronectin, a plasma protein that binds cell surfaces and various compounds including collagen, fibrin, heparin, DNA, and actin, usually exists as a dimer in plasma and as an insoluble multimer in extracellular matrices. Dimers of nearly identical subunits are linked by a disulfide bond close to their C-terminus. Fibronectin is composed of 3 types of modules, FN1,FN2 and FN3. The collagen binding domain contains four FN1 and two FN2 repeats.
• cd FN2 48aa 3e-16 in ref transcript
• cd FN3 83aa 4e-10 in ref transcript
  • Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.
• cd FN1 44aa 4e-09 in ref transcript
  • Fibronectin type 1 domain, approximately 40 residue long with two conserved disulfide bridges. FN1 is one of three types of internal repeats which combine to form larger domains within fibronectin. Fibronectin, a plasma protein that binds cell surfaces and various compounds including collagen, fibrin, heparin, DNA, and actin, usually exists as a dimer in plasma and as an insoluble multimer in extracellular matrices. Dimers of nearly identical subunits are linked by a disulfide bond close to their C-terminus. FN1 domains also found in coagulation factor XII, HGF activator, and tissue-type plasminogen activator. In tissue plasminogen activator, FN1 domains may form functional fibrin-binding units with EGF-like domains C-terminal to FN1.
• cd FN3 81aa 8e-09 in ref transcript
• cd FN3 80aa 1e-08 in ref transcript
• cd FN1 40aa 4e-08 in ref transcript
• cd FN1 42aa 5e-08 in ref transcript
• cd FN1 45aa 8e-08 in ref transcript
• cd FN3 88aa 1e-07 in ref transcript
• cd FN3 88aa 2e-07 in ref transcript
• cd FN1 44aa 2e-07 in ref transcript
• cd FN3 87aa 3e-07 in ref transcript
• cd FN1 38aa 4e-07 in ref transcript
• Changed! cd FN3 81aa 9e-07 in ref transcript
• cd FN3 82aa 1e-06 in ref transcript
• Changed! cd FN3 88aa 1e-06 in ref transcript
• cd FN1 41aa 1e-06 in ref transcript
• cd FN3 93aa 2e-06 in ref transcript
• cd FN1 45aa 2e-06 in ref transcript
• cd FN1 42aa 2e-06 in ref transcript
• cd FN3 81aa 6e-06 in ref transcript
• cd FN3 90aa 8e-06 in ref transcript
• cd FN3 73aa 9e-06 in ref transcript
• cd FN1 44aa 1e-05 in ref transcript
• cd FN1 43aa 3e-05 in ref transcript
• cd FN1 39aa 0.003 in ref transcript
• cd FN3 73aa 0.006 in ref transcript
• smart FN2 49aa 9e-20 in ref transcript
  • Fibronectin type 2 domain. One of three types of internal repeat within the plasma protein, fibronectin. Also occurs in coagulation factor XII, 2 type IV collagenases, PDC-109, and cation-independent mannose-6-phosphate and secretory phospholipase A2 receptors. In fibronectin, PDC-109, and the collagenases, this domain contributes to collagen-binding function.
• smart FN2 49aa 4e-19 in ref transcript
• pfam fn3 82aa 8e-17 in ref transcript
  • Fibronectin type III domain.
• smart FN1 45aa 6e-13 in ref transcript
  • Fibronectin type 1 domain. One of three types of internal repeat within the plasma protein, fibronectin. Found also in coagulation factor XII, HGF activator and tissue-type plasminogen activator. In t-PA and fibronectin, this domain type contributes to fibrin-binding.
• Changed! pfam fn1 39aa 1e-12 in ref transcript
  • Fibronectin type I domain.
• pfam fn3 81aa 3e-12 in ref transcript
• pfam fn3 81aa 3e-12 in ref transcript
• smart FN1 45aa 3e-12 in ref transcript
• smart FN1 42aa 3e-12 in ref transcript
• smart FN1 45aa 5e-12 in ref transcript
• smart FN1 39aa 2e-11 in ref transcript
• pfam fn3 81aa 4e-11 in ref transcript
• pfam fn3 83aa 5e-11 in ref transcript
• pfam fn3 67aa 8e-11 in ref transcript
• pfam fn1 39aa 8e-11 in ref transcript
• pfam fn3 81aa 1e-10 in ref transcript
• pfam fn3 80aa 1e-10 in ref transcript
• smart FN1 43aa 2e-10 in ref transcript
• pfam fn3 80aa 5e-10 in ref transcript
• smart FN1 44aa 7e-10 in ref transcript
• pfam fn3 81aa 8e-09 in ref transcript
• pfam fn3 85aa 9e-09 in ref transcript
• pfam fn3 70aa 1e-08 in ref transcript
• pfam fn3 65aa 2e-08 in ref transcript
• smart FN1 41aa 3e-08 in ref transcript
• Changed! pfam fn3 81aa 3e-07 in ref transcript
• smart FN1 41aa 5e-07 in ref transcript
• pfam fn3 54aa 5e-05 in ref transcript
• pfam fn1 31aa 9e-05 in ref transcript
• Changed! cd FN3 89aa 3e-07 in modified transcript
• Changed! smart FN1 44aa 2e-12 in modified transcript

FN1

• rs.FN1.F2 rs.FN1.R2 156 231
• NCBIGene 36.3 2335
• Alternative 3-prime, size difference: 75
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_212482

• cd FN2 48aa 2e-16 in ref transcript
  • Fibronectin Type II domain: FN2 is one of three types of internal repeats which combine to form larger domains within fibronectin. Fibronectin, a plasma protein that binds cell surfaces and various compounds including collagen, fibrin, heparin, DNA, and actin, usually exists as a dimer in plasma and as an insoluble multimer in extracellular matrices. Dimers of nearly identical subunits are linked by a disulfide bond close to their C-terminus. Fibronectin is composed of 3 types of modules, FN1,FN2 and FN3. The collagen binding domain contains four FN1 and two FN2 repeats.
• cd FN2 48aa 3e-16 in ref transcript
• cd FN3 83aa 4e-10 in ref transcript
  • Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.
• cd FN1 44aa 4e-09 in ref transcript
  • Fibronectin type 1 domain, approximately 40 residue long with two conserved disulfide bridges. FN1 is one of three types of internal repeats which combine to form larger domains within fibronectin. Fibronectin, a plasma protein that binds cell surfaces and various compounds including collagen, fibrin, heparin, DNA, and actin, usually exists as a dimer in plasma and as an insoluble multimer in extracellular matrices. Dimers of nearly identical subunits are linked by a disulfide bond close to their C-terminus. FN1 domains also found in coagulation factor XII, HGF activator, and tissue-type plasminogen activator. In tissue plasminogen activator, FN1 domains may form functional fibrin-binding units with EGF-like domains C-terminal to FN1.
• cd FN3 81aa 8e-09 in ref transcript
• cd FN3 80aa 1e-08 in ref transcript
• cd FN1 40aa 4e-08 in ref transcript
• cd FN1 42aa 5e-08 in ref transcript
• cd FN1 45aa 8e-08 in ref transcript
• cd FN3 88aa 1e-07 in ref transcript
• cd FN3 88aa 2e-07 in ref transcript
• cd FN1 44aa 2e-07 in ref transcript
• cd FN3 87aa 3e-07 in ref transcript
• cd FN1 38aa 4e-07 in ref transcript
• cd FN3 81aa 9e-07 in ref transcript
• cd FN3 82aa 1e-06 in ref transcript
• cd FN3 88aa 1e-06 in ref transcript
• cd FN1 41aa 1e-06 in ref transcript
• cd FN3 93aa 2e-06 in ref transcript
• cd FN1 45aa 2e-06 in ref transcript
• cd FN1 42aa 2e-06 in ref transcript
• cd FN3 81aa 6e-06 in ref transcript
• cd FN3 90aa 8e-06 in ref transcript
• cd FN3 73aa 9e-06 in ref transcript
• cd FN1 44aa 1e-05 in ref transcript
• cd FN1 43aa 3e-05 in ref transcript
• cd FN1 39aa 0.003 in ref transcript
• cd FN3 73aa 0.006 in ref transcript
• smart FN2 49aa 9e-20 in ref transcript
  • Fibronectin type 2 domain. One of three types of internal repeat within the plasma protein, fibronectin. Also occurs in coagulation factor XII, 2 type IV collagenases, PDC-109, and cation-independent mannose-6-phosphate and secretory phospholipase A2 receptors. In fibronectin, PDC-109, and the collagenases, this domain contributes to collagen-binding function.
• smart FN2 49aa 4e-19 in ref transcript
• pfam fn3 82aa 8e-17 in ref transcript
  • Fibronectin type III domain.
• smart FN1 45aa 6e-13 in ref transcript
  • Fibronectin type 1 domain. One of three types of internal repeat within the plasma protein, fibronectin. Found also in coagulation factor XII, HGF activator and tissue-type plasminogen activator. In t-PA and fibronectin, this domain type contributes to fibrin-binding.
• pfam fn1 39aa 1e-12 in ref transcript
  • Fibronectin type I domain.
• pfam fn3 81aa 3e-12 in ref transcript
• pfam fn3 81aa 3e-12 in ref transcript
• smart FN1 45aa 3e-12 in ref transcript
• smart FN1 42aa 3e-12 in ref transcript
• smart FN1 45aa 5e-12 in ref transcript
• smart FN1 39aa 2e-11 in ref transcript
• pfam fn3 81aa 4e-11 in ref transcript
• pfam fn3 83aa 5e-11 in ref transcript
• pfam fn3 67aa 8e-11 in ref transcript
• pfam fn1 39aa 8e-11 in ref transcript
• pfam fn3 81aa 1e-10 in ref transcript
• pfam fn3 80aa 1e-10 in ref transcript
• smart FN1 43aa 2e-10 in ref transcript
• pfam fn3 80aa 5e-10 in ref transcript
• smart FN1 44aa 7e-10 in ref transcript
• pfam fn3 81aa 8e-09 in ref transcript
• pfam fn3 85aa 9e-09 in ref transcript
• pfam fn3 70aa 1e-08 in ref transcript
• pfam fn3 65aa 2e-08 in ref transcript
• smart FN1 41aa 3e-08 in ref transcript
• pfam fn3 81aa 3e-07 in ref transcript
• smart FN1 41aa 5e-07 in ref transcript
• pfam fn3 54aa 5e-05 in ref transcript
• pfam fn1 31aa 9e-05 in ref transcript

FNTA

• rs.FNTA.F1 rs.FNTA.R1 297 383
• NCBIGene 36.3 2339
• Single exon skipping, size difference: 86
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_002027

• Changed! pfam PPTA 30aa 1e-05 in ref transcript
  • Protein prenyltransferase alpha subunit repeat. Both farnesyltransferase (FT) and geranylgeranyltransferase 1 (GGT1) recognise a CaaX motif on their substrates where 'a' stands for preferably aliphatic residues, whereas GGT2 recognises a completely different motif. Important substrates for FT include, amongst others, many members of the Ras superfamily. GGT1 substrates include some of the other small GTPases and GGT2 substrates include the Rab family.
• Changed! pfam PPTA 30aa 2e-05 in ref transcript
• Changed! pfam PPTA 30aa 0.002 in ref transcript
• Changed! pfam PPTA 29aa 0.003 in ref transcript
• Changed! COG BET4 211aa 1e-31 in ref transcript
  • Protein prenyltransferase, alpha subunit [Posttranslational modification, protein turnover, chaperones].

FOXN3

• rs.FOXN3.F1 rs.FOXN3.R1 129 195
• NCBIGene 36.3 1112
• Single exon skipping, size difference: 66
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001085471

• cd FH 79aa 1e-31 in ref transcript
  • Forkhead (FH), also known as a "winged helix". FH is named for the Drosophila fork head protein, a transcription factor which promotes terminal rather than segmental development. This family of transcription factor domains, which bind to B-DNA as monomers, are also found in the Hepatocyte nuclear factor (HNF) proteins, which provide tissue-specific gene regulation. The structure contains 2 flexible loops or "wings" in the C-terminal region, hence the term winged helix.
• smart FH 88aa 4e-34 in ref transcript
  • FORKHEAD. FORKHEAD, also known as a "winged helix".
• COG COG5025 106aa 5e-15 in ref transcript
  • Transcription factor of the Forkhead/HNF3 family [Transcription].

FOXP4

• rs.FOXP4.F1 rs.FOXP4.R1 175 211
• NCBIGene 36.3 116113
• Alternative 3-prime, size difference: 36
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001012426

• cd FH 73aa 8e-26 in ref transcript
  • Forkhead (FH), also known as a "winged helix". FH is named for the Drosophila fork head protein, a transcription factor which promotes terminal rather than segmental development. This family of transcription factor domains, which bind to B-DNA as monomers, are also found in the Hepatocyte nuclear factor (HNF) proteins, which provide tissue-specific gene regulation. The structure contains 2 flexible loops or "wings" in the C-terminal region, hence the term winged helix.
• smart FH 73aa 5e-29 in ref transcript
  • FORKHEAD. FORKHEAD, also known as a "winged helix".
• Changed! COG COG5025 197aa 5e-12 in ref transcript
  • Transcription factor of the Forkhead/HNF3 family [Transcription].
• Changed! COG COG5025 98aa 2e-10 in modified transcript
• Changed! COG COG5025 234aa 2e-08 in modified transcript

FOXRED2

• rs.FOXRED2.F1 rs.FOXRED2.R1 255 352
• NCBIGene 36.3 80020
• Alternative 5-prime, size difference: 97
• Exclusion in 5'UTR
• Reference transcript: NM_024955

• pfam HI0933_like 154aa 4e-07 in ref transcript
  • HI0933-like protein.
• TIGR TRX_reduct 86aa 0.005 in ref transcript
  • This model describes thioredoxin-disulfide reductase, a member of the pyridine nucleotide-disulphide oxidoreductases (pfam00070).
• COG TrkA 219aa 6e-18 in ref transcript
  • Predicted flavoprotein involved in K+ transport [Inorganic ion transport and metabolism].

FRS2

• rs.FRS2.F1 rs.FRS2.R1 117 185
• NCBIGene 36.3 10818
• Single exon skipping, size difference: 68
• Exclusion in 5'UTR
• Reference transcript: NM_006654

• cd FRS2 97aa 4e-43 in ref transcript
  • Fibroblast growth factor receptor substrate 2 (FRS2/SNT1) Phosphotyrosine-binding domain (IRS1-like). FRS2 mediates signaling downstream of the FGF receptor. It has an N-terminal PTBi domain, which has a PH-like fold and is similiar to the PTB domain that is found in insulin receptor substrate molecules. This PTBi domain is shorter than the PTB domain which is found in SHC, Numb and other proteins. The PTBi domain binds to phosphotyrosines which are in NPXpY motifs.
• smart PTBI 91aa 1e-24 in ref transcript
  • Phosphotyrosine-binding domain (IRS1-like).

FRS2

• rs.FRS2.F2 rs.FRS2.R2 226 287
• NCBIGene 36.3 10818
• Single exon skipping, size difference: 61
• Exclusion in 5'UTR
• Reference transcript: NM_001042555

• cd FRS2 97aa 4e-43 in ref transcript
  • Fibroblast growth factor receptor substrate 2 (FRS2/SNT1) Phosphotyrosine-binding domain (IRS1-like). FRS2 mediates signaling downstream of the FGF receptor. It has an N-terminal PTBi domain, which has a PH-like fold and is similiar to the PTB domain that is found in insulin receptor substrate molecules. This PTBi domain is shorter than the PTB domain which is found in SHC, Numb and other proteins. The PTBi domain binds to phosphotyrosines which are in NPXpY motifs.
• smart PTBI 91aa 1e-24 in ref transcript
  • Phosphotyrosine-binding domain (IRS1-like).

FSCN2

• rs.FSCN2.F1 rs.FSCN2.R1 141 213
• NCBIGene 36.3 25794
• Alternative 3-prime, size difference: 72
• Inclusion in 3'UTR
• Reference transcript: NM_012418

• cd Fascin 121aa 2e-24 in ref transcript
  • Fascin-like domain; members include actin-bundling/crosslinking proteins facsin, histoactophilin and singed; identified in sea urchin, Drosophila, Xenopus, rodents, and humans; The fascin-like domain adopts a beta-trefoil topology and contains an internal threefold repeat; the fascin subgroup contains four copies of the domain; Structurally similar to fibroblast growth factor (FGF).
• cd Fascin 117aa 3e-20 in ref transcript
• pfam Fascin 113aa 4e-30 in ref transcript
  • Fascin domain. This family consists of several eukaryotic fascin or singed proteins. The fascins are a structurally unique and evolutionarily conserved group of actin cross-linking proteins. Fascins function in the organisation of two major forms of actin-based structures: dynamic, cortical cell protrusions and cytoplasmic microfilament bundles. The cortical structures, which include filopodia, spikes, lamellipodial ribs, oocyte microvilli and the dendrites of dendritic cells, have roles in cell-matrix adhesion, cell interactions and cell migration, whereas the cytoplasmic actin bundles appear to participate in cell architecture. Dictyostelium hisactophilin, another actin-binding protein, is a submembranous pH sensor that signals slight changes of the H+ concentration to actin by inducing actin polymerisation and binding to microfilaments only at pH values below seven. Members of this family are histidine rich, typically contain the repeated motif of HHXH.
• pfam Fascin 114aa 8e-22 in ref transcript

FSHR

• rs.FSHR.F1 rs.FSHR.R1 210 396
• NCBIGene 36.3 2492
• Single exon skipping, size difference: 186
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000145

• pfam 7tm_1 242aa 1e-30 in ref transcript
  • 7 transmembrane receptor (rhodopsin family). This family contains, amongst other G-protein-coupled receptors (GCPRs), members of the opsin family, which have been considered to be typical members of the rhodopsin superfamily. They share several motifs, mainly the seven transmembrane helices, GCPRs of the rhodopsin superfamily. All opsins bind a chromophore, such as 11-cis-retinal. The function of most opsins other than the photoisomerases is split into two steps: light absorption and G-protein activation. Photoisomerases, on the other hand, are not coupled to G-proteins - they are thought to generate and supply the chromophore that is used by visual opsins.
• pfam LRRNT 26aa 0.001 in ref transcript
  • Leucine rich repeat N-terminal domain. Leucine Rich Repeats pfam00560 are short sequence motifs present in a number of proteins with diverse functions and cellular locations. Leucine Rich Repeats are often flanked by cysteine rich domains. This domain is often found at the N-terminus of tandem leucine rich repeats.
• Changed! COG COG4886 86aa 0.009 in modified transcript
  • Leucine-rich repeat (LRR) protein [Function unknown].

FUT2

• rs.FUT2.F1 rs.FUT2.R1 90 100
• NCBIGene 36.3 2524
• Alternative 5-prime, size difference: 10
• Exclusion in 5'UTR
• Reference transcript: NM_000511

• pfam Glyco_transf_11 314aa 1e-133 in ref transcript
  • Glycosyl transferase family 11. This family contains several fucosyl transferase enzymes.

FUT3

• rs.FUT3.F1 rs.FUT3.R1 112 460
• NCBIGene 36.3 2525
• Alternative 3-prime, size difference: 348
• Inclusion in 5'UTR
• Reference transcript: NM_001097639

• pfam Glyco_transf_10 291aa 1e-102 in ref transcript
  • Glycosyltransferase family 10 (fucosyltransferase). This family of Fucosyltransferases are the enzymes transferring fucose from GDP-Fucose to GlcNAc in an alpha1,3 linkage. This family is know as glycosyltransferase family 10.

FUT6

• rs.FUT6.F1 rs.FUT6.R1 187 315
• NCBIGene 36.3 2528
• Single exon skipping, size difference: 128
• Exclusion in 5'UTR
• Reference transcript: NM_000150

• pfam Glyco_transf_10 354aa 1e-113 in ref transcript
  • Glycosyltransferase family 10 (fucosyltransferase). This family of Fucosyltransferases are the enzymes transferring fucose from GDP-Fucose to GlcNAc in an alpha1,3 linkage. This family is know as glycosyltransferase family 10.

FUT8

• rs.FUT8.F1 rs.FUT8.R1 120 544
• NCBIGene 36.3 2530
• Multiple exon skipping, size difference: 424
• Exclusion in the protein causing a frameshift, Exclusion in the protein (no frameshift)
• Reference transcript: NM_178155

• Changed! cd SH3 53aa 5e-05 in ref transcript
  • Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
• Changed! smart SH3 54aa 1e-06 in ref transcript
  • Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.

FUT8

• rs.FUT8.F2 rs.FUT8.R2 116 546
• NCBIGene 36.3 2530
• Single exon skipping, size difference: 430
• Exclusion of the protein initiation site
• Reference transcript: NM_178155

• cd SH3 53aa 5e-05 in ref transcript
  • Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
• smart SH3 54aa 1e-06 in ref transcript
  • Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.

G3BP2

• rs.G3BP2.F1 rs.G3BP2.R1 149 248
• NCBIGene 36.3 9908
• Single exon skipping, size difference: 99
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_203505

• cd NTF2 129aa 4e-31 in ref transcript
  • Nuclear transport factor 2 (NTF2) domain plays an important role in the trafficking of macromolecules, ions and small molecules between the cytoplasm and nucleus. This bi-directional transport of macromolecules across the nuclear envelope requires many soluble factors that includes GDP-binding protein Ran (RanGDP). RanGDP is required for both import and export of proteins and poly(A) RNA. RanGDP also has been implicated in cell cycle control, specifically in mitotic spindle assembly. In interphase cells, RanGDP is predominately nuclear and thought to be GTP bound, but it is also present in the cytoplasm, probably in the GDP-bound state. NTF2 mediates the nuclear import of RanGDP. NTF2 binds to both RanGDP and FxFG repeat-containing nucleoporins.
• cd RRM 73aa 3e-10 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• pfam NTF2 123aa 1e-23 in ref transcript
  • Nuclear transport factor 2 (NTF2) domain. This family includes the NTF2-like Delta-5-3-ketosteroid isomerase proteins.
• pfam RRM_1 66aa 4e-10 in ref transcript
  • RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain). The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have a N terminus rrm which is included in the seed. There is a second region towards the C terminus that has some features of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.
• COG COG0724 71aa 4e-06 in ref transcript
  • RNA-binding proteins (RRM domain) [General function prediction only].

G6PC2

• rs.G6PC2.F1 rs.G6PC2.R1 276 392
• NCBIGene 36.3 57818
• Single exon skipping, size difference: 116
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_021176

• Changed! cd PAP2_glucose_6_phosphatase 241aa 5e-91 in ref transcript
  • PAP2_like proteins, glucose-6-phosphatase subfamily. Glucose-6-phosphatase converts glucose-6-phosphate into free glucose and is active in the lumen of the endoplasmic reticulum, where it is bound to the membrane. The generation of free glucose is an important control point in metabolism, and stands at the end of gluconeogenesis and the release of glucose from glycogen. Deficiency of glucose-6-phosphatase leads to von Gierke's disease.
• Changed! smart acidPPc 135aa 4e-14 in ref transcript
  • Acid phosphatase homologues.
• Changed! cd PAP2_glucose_6_phosphatase 103aa 8e-40 in modified transcript
• Changed! smart acidPPc 70aa 2e-08 in modified transcript

GAGE1

• rs.GAGE1.F1 rs.GAGE1.R1 255 398
• NCBIGene 36.3 2543
• Single exon skipping, size difference: 143
• Exclusion of the stop codon
• Reference transcript: NM_001468

• Changed! pfam GAGE 109aa 4e-09 in ref transcript
  • GAGE protein. This family consists of several GAGE and XAGE proteins which are found exclusively in humans. The function of this family is unknown although they have been implicated in human cancers.
• Changed! pfam GAGE 116aa 3e-08 in modified transcript

GARNL4

• rs.GARNL4.F1 rs.GARNL4.R1 218 263
• NCBIGene 36.3 23108
• Single exon skipping, size difference: 45
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_015085

• pfam Rap_GAP 188aa 3e-80 in ref transcript
  • Rap/ran-GAP.

GCC2

• rs.GCC2.F1 rs.GCC2.R1 198 283
• NCBIGene 36.3 9648
• Single exon skipping, size difference: 85
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_181453

• Changed! pfam GRIP 45aa 1e-08 in ref transcript
  • GRIP domain. The GRIP (golgin-97, RanBP2alpha,Imh1p and p230/golgin-245) domain is found in many large coiled-coil proteins. It has been shown to be sufficient for targeting to the Golgi. The GRIP domain contains a completely conserved tyrosine residue. At least some of these domains have been shown to bind to GTPase Arl1, see structures.
• Changed! TIGR SMC_prok_B 793aa 2e-07 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• Changed! TIGR SMC_prok_B 252aa 0.001 in ref transcript
• Changed! TIGR SMC_prok_B 305aa 0.001 in ref transcript
• Changed! COG Smc 299aa 5e-05 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].
• Changed! COG Smc 609aa 9e-05 in ref transcript
• Changed! COG Smc 295aa 0.006 in ref transcript

GCK

• rs.GCK.F1 rs.GCK.R1 169 293
• NCBIGene 36.3 2645
• Single exon skipping, size difference: 124
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_033507

• Changed! pfam Hexokinase_2 238aa 1e-97 in ref transcript
  • Hexokinase. Hexokinase (EC:2.7.1.1) contains two structurally similar domains represented by this family and pfam00349. Some members of the family have two copies of each of these domains.
• Changed! pfam Hexokinase_1 203aa 5e-75 in ref transcript
  • Hexokinase. Hexokinase (EC:2.7.1.1) contains two structurally similar domains represented by this family and pfam03727. Some members of the family have two copies of each of these domains.
• Changed! COG COG5026 455aa 1e-75 in ref transcript
  • Hexokinase [Carbohydrate transport and metabolism].

GCNT1

• rs.GCNT1.F1 rs.GCNT1.R1 229 347
• NCBIGene 36.3 2650
• Single exon skipping, size difference: 118
• Exclusion in 5'UTR
• Reference transcript: NM_001490

• pfam Branch 210aa 1e-69 in ref transcript
  • Core-2/I-Branching enzyme. This is a family of two different beta-1,6-N-acetylglucosaminyltransferase enzymes, I-branching enzyme and core-2 branching enzyme. I-branching enzyme is responsible for the production of the blood group I-antigen during embryonic development. Core-2 branching enzyme forms crucial side-chain branches in O-glycans.

GDAP1

• rs.GDAP1.F1 rs.GDAP1.R1 116 246
• NCBIGene 36.3 54332
• Alternative 5-prime and 3-prime, size difference: 130
• Exclusion in the protein causing a frameshift, Exclusion in the protein (no frameshift)
• Reference transcript: NM_018972

• Changed! cd GST_C_GDAP1 111aa 9e-48 in ref transcript
  • GST_C family, Ganglioside-induced differentiation-associated protein 1 (GDAP1) subfamily; GDAP1 was originally identified as a highly expressed gene at the differentiated stage of GD3 synthase-transfected cells. More recently, mutations in GDAP1 have been reported to cause both axonal and demyelinating autosomal-recessive Charcot-Marie-Tooth (CMT) type 4A neuropathy. CMT is characterized by slow and progressive weakness and atrophy of muscles. Sequence analysis of GDAP1 shows similarities and differences with GSTs; it appears to contain both N-terminal thioredoxin-fold and C-terminal alpha helical domains of GSTs, however, it also contains additional C-terminal transmembrane domains unlike GSTs. GDAP1 is mainly expressed in neuronal cells and is localized in the mitochondria through its transmembrane domains. It does not exhibit GST activity using standard substrates.
• Changed! cd GST_N_GDAP1 73aa 1e-36 in ref transcript
  • GST_N family, Ganglioside-induced differentiation-associated protein 1 (GDAP1) subfamily; GDAP1 was originally identified as a highly expressed gene at the differentiated stage of GD3 synthase-transfected cells. More recently, mutations in GDAP1 have been reported to cause both axonal and demyelinating autosomal-recessive Charcot-Marie-Tooth (CMT) type 4A neuropathy. CMT is characterized by slow and progressive weakness and atrophy of muscles. Sequence analysis of GDAP1 shows similarities and differences with GSTs; it appears to contain both N-terminal TRX-fold and C-terminal alpha helical domains of GSTs, however, it also contains additional C-terminal transmembrane domains unlike GSTs. GDAP1 is mainly expressed in neuronal cells and is localized in the mitochondria through its transmembrane domains. It does not exhibit GST activity using standard substrates.
• Changed! TIGR maiA 118aa 7e-09 in ref transcript
  • Maleylacetoacetate isomerase is an enzyme of tyrosine and phenylalanine catabolism. It requires glutathione and belongs by homology to the zeta family of glutathione S-transferases. The enzyme (EC 5.2.1.2) is described as active also on maleylpyruvate, and the example from a Ralstonia sp. catabolic plasmid is described as a maleylpyruvate isomerase involved in gentisate catabolism.
• Changed! pfam GST_C 84aa 0.001 in ref transcript
  • Glutathione S-transferase, C-terminal domain. GST conjugates reduced glutathione to a variety of targets including S-crystallin from squid, the eukaryotic elongation factor 1-gamma, the HSP26 family of stress-related proteins and auxin-regulated proteins in plants. Stringent starvation proteins in Escherichia coli are also included in the alignment but are not known to have GST activity. The glutathione molecule binds in a cleft between N and C-terminal domains. The catalytically important residues are proposed to reside in the N-terminal domain. In plants, GSTs are encoded by a large gene family (48 GST genes in Arabidopsis) and can be divided into the phi, tau, theta, zeta, and lambda classes.
• Changed! COG Gst 267aa 6e-15 in ref transcript
  • Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones].

GEMIN8

• rs.GEMIN8.F1 rs.GEMIN8.R1 116 204
• NCBIGene 36.3 54960
• Alternative 5-prime, size difference: 88
• Exclusion in 5'UTR
• Reference transcript: NM_017856

GFRA1

• rs.GFRA1.F1 rs.GFRA1.R1 100 115
• NCBIGene 36.3 2674
• Single exon skipping, size difference: 15
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_005264

• pfam GDNF 95aa 3e-16 in ref transcript
  • GDNF/GAS1 domain. This cysteine rich domain is found in multiple copies in GNDF and GAS1 proteins. GDNF and neurturin (NTN) receptors are potent survival factors for sympathetic, sensory and central nervous system neurons. GDNF and neurturin promote neuronal survival by signaling through similar multicomponent receptors that consist of a common receptor tyrosine kinase and a member of a GPI-linked family of receptors that determines ligand specificity.
• pfam GDNF 83aa 2e-11 in ref transcript
• pfam GDNF 80aa 9e-10 in ref transcript

GGNBP1

• rs.GGNBP1.F1 rs.GGNBP1.R1 107 170
• NCBIGene 36.3 449520
• Alternative 3-prime, size difference: 63
• Exclusion in the protein (no frameshift)
• Reference transcript: XM_001724455

GGT2

• rs.GGT2.F1 rs.GGT2.R1 108 123
• NCBIGene 36.3 728441
• Alternative 5-prime and 3-prime, size difference: 15
• Inclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: XM_001129377

• Changed! pfam G_glu_transpept 513aa 1e-162 in ref transcript
  • Gamma-glutamyltranspeptidase.
• Changed! COG Ggt 548aa 1e-116 in ref transcript
  • Gamma-glutamyltransferase [Amino acid transport and metabolism].
• Changed! pfam G_glu_transpept 508aa 1e-162 in modified transcript
• Changed! COG Ggt 543aa 1e-117 in modified transcript

GGTLA1

• rs.GGTLA1.F1 rs.GGTLA1.R1 205 301
• NCBIGene 36.3 2687
• Single exon skipping, size difference: 96
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001099781

• Changed! pfam G_glu_transpept 523aa 1e-143 in ref transcript
  • Gamma-glutamyltranspeptidase.
• Changed! COG Ggt 546aa 3e-86 in ref transcript
  • Gamma-glutamyltransferase [Amino acid transport and metabolism].
• Changed! pfam G_glu_transpept 491aa 1e-130 in modified transcript
• Changed! COG Ggt 514aa 2e-78 in modified transcript

GH1

• rs.GH1.F1 rs.GH1.R1 167 212
• NCBIGene 36.3 2688
• Alternative 3-prime, size difference: 45
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000515

• Changed! pfam Hormone_1 207aa 1e-48 in ref transcript
  • Somatotropin hormone family.
• Changed! pfam Hormone_1 192aa 2e-44 in modified transcript

GIPC1

• rs.GIPC1.F1 rs.GIPC1.R1 165 221
• NCBIGene 36.3 10755
• Single exon skipping, size difference: 56
• Exclusion in 5'UTR
• Reference transcript: NM_005716

• cd PDZ_signaling 79aa 8e-08 in ref transcript
  • PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of PDZ domains an N-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in proteases.
• smart PDZ 82aa 5e-09 in ref transcript
  • Domain present in PSD-95, Dlg, and ZO-1/2. Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities.

GIT1

• rs.GIT1.F1 rs.GIT1.R1 92 119
• NCBIGene 36.3 28964
• Single exon skipping, size difference: 27
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001085454

• cd ANK 98aa 6e-13 in ref transcript
  • ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats.
• smart ArfGap 119aa 3e-36 in ref transcript
  • Putative GTP-ase activating proteins for the small GTPase, ARF. Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs.
• pfam GIT_SHD 31aa 3e-07 in ref transcript
  • Spa2 homology domain (SHD) of GIT. GIT proteins are signaling integrators with GTPase-activating function which may be involved in the organisation of the cytoskeletal matrix assembled at active zones (CAZ). The function of the CAZ might be to define sites of neurotransmitter release. Mutations in the Spa2 homology domain (SHD) domain of GIT1 described here interfere with the association of GIT1 with Piccolo, beta-PIX, and focal adhesion kinase.
• pfam GIT_SHD 22aa 0.001 in ref transcript
• COG COG5347 115aa 3e-14 in ref transcript
  • GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion].
• COG Arp 185aa 1e-06 in ref transcript
  • FOG: Ankyrin repeat [General function prediction only].

GLRA3

• rs.GLRA3.F1 rs.GLRA3.R1 119 164
• NCBIGene 36.3 8001
• Single exon skipping, size difference: 45
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_006529

• Changed! TIGR LIC 440aa 1e-144 in ref transcript
  • selective while glycine receptors are anion selective).
• Changed! TIGR LIC 425aa 1e-145 in modified transcript

GLT8D3

• rs.GLT8D3.F1 rs.GLT8D3.R1 231 324
• NCBIGene 36.3 283464
• Single exon skipping, size difference: 93
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_173601

• cd GT8_like_2 302aa 1e-178 in ref transcript
  • GT8_like_2 represents a subfamily of GT8 with unknown function. A subfamily of glycosyltransferase family 8 with unknown function: Glycosyltransferase family 8 comprises enzymes with a number of known activities; lipopolysaccharide galactosyltransferase lipopolysaccharide glucosyltransferase 1, glycogenin glucosyltransferase and inositol 1-alpha-galactosyltransferase. It is classified as a retaining glycosyltransferase, based on the relative anomeric stereochemistry of the substrate and product in the reaction catalyzed.
• pfam Glyco_transf_8 165aa 2e-11 in ref transcript
  • Glycosyl transferase family 8. This family includes enzymes that transfer sugar residues to donor molecules. Members of this family are involved in lipopolysaccharide biosynthesis and glycogen synthesis. This family includes Lipopolysaccharide galactosyltransferase, lipopolysaccharide glucosyltransferase 1, and glycogenin glucosyltransferase.
• COG RfaJ 244aa 1e-09 in ref transcript
  • Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane].

GMEB1

• rs.GMEB1.F1 rs.GMEB1.R1 245 278
• NCBIGene 36.3 10691
• Alternative 3-prime, size difference: 30
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_006582

• pfam SAND 81aa 2e-30 in ref transcript
  • SAND domain. The DNA binding activity of two proteins has been mapped to the SAND domain. The conserved KDWK motif is necessary for DNA binding, and it appears to be important for dimerisation.

GNG4

• rs.GNG4.F1 rs.GNG4.R1 100 212
• NCBIGene 36.3 2786
• Single exon skipping, size difference: 112
• Exclusion in 5'UTR
• Reference transcript: NM_001098721

GOLSYN

• rs.GOLSYN.F1 rs.GOLSYN.R1 138 259
• NCBIGene 36.3 55638
• Single exon skipping, size difference: 121
• Exclusion in 5'UTR
• Reference transcript: NM_001099750

GOLSYN

• rs.GOLSYN.F2 rs.GOLSYN.R2 264 550
• NCBIGene 36.3 55638
• Multiple exon skipping, size difference: 286
• Exclusion of the protein initiation site, Exclusion in the protein causing a frameshift
• Reference transcript: NM_001099745

GOSR1

• rs.GOSR1.F1 rs.GOSR1.R1 100 122
• NCBIGene 36.3 9527
• Alternative 5-prime, size difference: 22
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_004871

• Changed! pfam V-SNARE 156aa 7e-32 in ref transcript
  • Vesicle transport v-SNARE protein. V-SNARE proteins are required for protein traffic between eukaryotic organelles. The v-SNAREs on transport vesicles interact with t-SNAREs on target membranes in order to facilitate this.

GPR172B

• rs.GPR172B.F1 rs.GPR172B.R1 148 182
• NCBIGene 36.3 55065
• Alternative 3-prime, size difference: 34
• Inclusion in 5'UTR
• Reference transcript: NM_017986

• pfam DUF1011 95aa 1e-29 in ref transcript
  • Protein of unknown function (DUF1011). Family of uncharacterised eukaryotic proteins.

GPR18

• rs.GPR18.F1 rs.GPR18.R1 100 292
• NCBIGene 36.3 2841
• Single exon skipping, size difference: 192
• Exclusion in 5'UTR
• Reference transcript: NM_005292

• pfam 7tm_1 242aa 7e-25 in ref transcript
  • 7 transmembrane receptor (rhodopsin family). This family contains, amongst other G-protein-coupled receptors (GCPRs), members of the opsin family, which have been considered to be typical members of the rhodopsin superfamily. They share several motifs, mainly the seven transmembrane helices, GCPRs of the rhodopsin superfamily. All opsins bind a chromophore, such as 11-cis-retinal. The function of most opsins other than the photoisomerases is split into two steps: light absorption and G-protein activation. Photoisomerases, on the other hand, are not coupled to G-proteins - they are thought to generate and supply the chromophore that is used by visual opsins.

GPR34

• rs.GPR34.F1 rs.GPR34.R1 256 332
• NCBIGene 36.3 2857
• Alternative 3-prime, size difference: 3
• Inclusion in 5'UTR
• Reference transcript: NM_005300

• pfam 7tm_1 251aa 6e-29 in ref transcript
  • 7 transmembrane receptor (rhodopsin family). This family contains, amongst other G-protein-coupled receptors (GCPRs), members of the opsin family, which have been considered to be typical members of the rhodopsin superfamily. They share several motifs, mainly the seven transmembrane helices, GCPRs of the rhodopsin superfamily. All opsins bind a chromophore, such as 11-cis-retinal. The function of most opsins other than the photoisomerases is split into two steps: light absorption and G-protein activation. Photoisomerases, on the other hand, are not coupled to G-proteins - they are thought to generate and supply the chromophore that is used by visual opsins.

GPR64

• rs.GPR64.F1 rs.GPR64.R1 134 176
• NCBIGene 36.3 10149
• Single exon skipping, size difference: 42
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001079858

• pfam 7tm_2 262aa 3e-62 in ref transcript
  • 7 transmembrane receptor (Secretin family). This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling.
• smart GPS 51aa 1e-10 in ref transcript
  • G-protein-coupled receptor proteolytic site domain. Present in latrophilin/CL-1, sea urchin REJ and polycystin.

GPR89A

• rs.GPR89A.F1 rs.GPR89A.R1 104 124
• NCBIGene 36.3 653519
• Alternative 3-prime, size difference: 20
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_001097612

GPR98

• rs.GPR98.F1 rs.GPR98.R1 132 215
• NCBIGene 36.3 84059
• Alternative 5-prime, size difference: 83
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_032119

• cd PTX 156aa 5e-06 in ref transcript
  • Pentraxins are plasma proteins characterized by their pentameric discoid assembly and their Ca2+ dependent ligand binding, such as Serum amyloid P component (SAP) and C-reactive Protein (CRP), which are cytokine-inducible acute-phase proteins implicated in innate immunity. CRP binds to ligands containing phosphocholine, SAP binds to amyloid fibrils, DNA, chromatin, fibronectin, C4-binding proteins and glycosaminoglycans. "Long" pentraxins have N-terminal extensions to the common pentraxin domain; one group, the neuronal pentraxins, may be involved in synapse formation and remodeling, and they may also be able to form heteromultimers.
• Changed! TIGR caca 203aa 1e-17 in ref transcript
  • This Hmm is specific for the eukaryotic sodium ion/calcium ion exchangers of the Caca family.
• TIGR caca 219aa 2e-15 in ref transcript
• TIGR caca 183aa 3e-13 in ref transcript
• TIGR caca 208aa 1e-12 in ref transcript
• Changed! TIGR caca 213aa 2e-12 in ref transcript
• TIGR caca 207aa 1e-11 in ref transcript
• TIGR caca 184aa 1e-11 in ref transcript
• TIGR caca 167aa 2e-11 in ref transcript
• Changed! TIGR caca 161aa 3e-11 in ref transcript
• Changed! TIGR caca 184aa 7e-11 in ref transcript
• Changed! TIGR caca 162aa 1e-10 in ref transcript
• Changed! TIGR caca 142aa 1e-10 in ref transcript
• Changed! pfam 7tm_2 245aa 2e-10 in ref transcript
  • 7 transmembrane receptor (Secretin family). This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling.
• Changed! TIGR caca 213aa 5e-10 in ref transcript
• TIGR caca 234aa 2e-07 in ref transcript
• TIGR caca 191aa 2e-07 in ref transcript
• Changed! TIGR caca 137aa 2e-05 in ref transcript
• Changed! pfam Calx-beta 94aa 5e-05 in ref transcript
  • Calx-beta domain.
• Changed! TIGR caca 184aa 1e-04 in ref transcript
• Changed! TIGR caca 169aa 2e-04 in ref transcript
• Changed! TIGR caca 95aa 2e-04 in ref transcript
• TIGR caca 158aa 2e-04 in ref transcript
• smart LamGL 137aa 7e-04 in ref transcript
  • LamG-like jellyroll fold domain.
• Changed! pfam EPTP 44aa 9e-04 in ref transcript
  • EPTP domain. Mutations in the LGI/Epitempin gene can result in a special form of epilepsy, autosomal dominant lateral temporal epilepsy. The Epitempin protein contains a large repeat in its C terminal section. The architecture and structural features of this repeat make it a likely member 7-bladed beta-propeller fold.
• Changed! pfam GPS 43aa 0.002 in ref transcript
  • Latrophilin/CL-1-like GPS domain. Domain present in latrophilin/CL-1, sea urchin REJ and polycystin.
• TIGR caca 223aa 0.004 in ref transcript
• Changed! TIGR caca 145aa 3e-09 in modified transcript

GPRASP1

• rs.GPRASP1.F1 rs.GPRASP1.R1 162 253
• NCBIGene 36.3 9737
• Single exon skipping, size difference: 91
• Exclusion in 5'UTR
• Reference transcript: NM_014710

• pfam DUF634 224aa 1e-58 in ref transcript
  • Protein of unknown function (DUF634). Mammalian protein of unknown function.

GPS1

• rs.GPS1.F1 rs.GPS1.R1 100 112
• NCBIGene 36.3 2873
• Alternative 3-prime, size difference: 12
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_212492

• pfam RPN7 183aa 2e-54 in ref transcript
  • 26S proteasome subunit RPN7. RPN7 (known as the non ATPase regulatory subunit 6 in higher eukaryotes) is one of the lid subunits of the 26S proteasome and has been shown in Saccharomyces cerevisiae to be required for structural integrity. The 26S proteasome is is involved in the ATP-dependent degradation of ubiquitinated proteins.
• pfam PCI 105aa 7e-19 in ref transcript
  • PCI domain. This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15).
• COG RPN7 300aa 5e-16 in ref transcript
  • 26S proteasome regulatory complex component, contains PCI domain [Posttranslational modification, protein turnover, chaperones].

GRIA2

• rs.GRIA2.F1 rs.GRIA2.R1 100 505
• NCBIGene 36.3 2891
• Alternative 5-prime, size difference: 405
• Exclusion of the protein initiation site
• Reference transcript: NM_001083619

• Changed! cd PBP1_iGluR_AMPA_GluR2 370aa 0.0 in ref transcript
  • N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR2 subunit of the AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptor. The AMPA receptor is a member of the glutamate-receptor ion channels (iGluRs) which are the major mediators of excitatory synaptic transmission in the central nervous system. AMPA receptors are composed of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important role in mediating the rapid excitatory synaptic current. Furthermore, this N-terminal domain of the iGluRs has homology with LIVBP, a bacterial periplasmic biding protein, as well as with the structurally related glutamate-binding domain of the G-protein-coupled metabotropic receptors (mGluRs).
• cd PBPb 112aa 3e-13 in ref transcript
  • Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD.
• cd PBPb 137aa 1e-04 in ref transcript
• pfam Lig_chan 275aa 3e-98 in ref transcript
  • Ligand-gated ion channel. This family includes the four transmembrane regions of the ionotropic glutamate receptors and NMDA receptors.
• pfam ANF_receptor 324aa 2e-39 in ref transcript
  • Receptor family ligand binding region. This family includes extracellular ligand binding domains of a wide range of receptors. This family also includes the bacterial amino acid binding proteins of known structure.
• pfam Lig_chan-Glu_bd 66aa 6e-25 in ref transcript
  • Ligated ion channel L-glutamate- and glycine-binding site. This region, sometimes called the S1 domain, is the luminal domain just upstream of the first, M1, transmembrane region of transmembrane ion-channel proteins, and it binds L-glutamate and glycine. It is found in association with Lig_chan, pfam00060.
• COG HisJ 96aa 5e-07 in ref transcript
  • ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms].
• PRK glnH 45aa 7e-04 in ref transcript
  • glutamine ABC transporter periplasmic protein; Reviewed.
• COG LivK 306aa 0.002 in ref transcript
  • ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism].
• Changed! cd PBP1_iGluR_AMPA_GluR2 350aa 0.0 in modified transcript

GRIA4

• rs.GRIA4.F1 rs.GRIA4.R1 357 470
• NCBIGene 36.3 2893
• Alternative 5-prime, size difference: 113
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_000829

• cd PBP1_iGluR_AMPA_GluR4 371aa 0.0 in ref transcript
  • N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR4 subunit of the AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptor. The AMPA receptor is a member of the glutamate-receptor ion channels (iGluRs) which are the major mediators of excitatory synaptic transmission in the central nervous system. AMPA receptors are composed of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important role in mediating the rapid excitatory synaptic current. Furthermore, this N-terminal domain of the iGluRs has homology with LIVBP, a bacterial periplasmic biding protein, as well as with the structurally related glutamate-binding domain of the G-protein-coupled metabotropic receptors (mGluRs).
• cd PBPb 118aa 6e-13 in ref transcript
  • Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD.
• pfam Lig_chan 275aa 1e-99 in ref transcript
  • Ligand-gated ion channel. This family includes the four transmembrane regions of the ionotropic glutamate receptors and NMDA receptors.
• pfam ANF_receptor 338aa 5e-50 in ref transcript
  • Receptor family ligand binding region. This family includes extracellular ligand binding domains of a wide range of receptors. This family also includes the bacterial amino acid binding proteins of known structure.
• pfam Lig_chan-Glu_bd 66aa 1e-24 in ref transcript
  • Ligated ion channel L-glutamate- and glycine-binding site. This region, sometimes called the S1 domain, is the luminal domain just upstream of the first, M1, transmembrane region of transmembrane ion-channel proteins, and it binds L-glutamate and glycine. It is found in association with Lig_chan, pfam00060.
• COG HisJ 126aa 6e-08 in ref transcript
  • ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms].
• COG LivK 329aa 6e-07 in ref transcript
  • ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism].
• PRK glnH 45aa 0.001 in ref transcript
  • glutamine ABC transporter periplasmic protein; Reviewed.

GRSF1

• rs.GRSF1.F1 rs.GRSF1.R1 112 355
• NCBIGene 36.3 2926
• Alternative 5-prime, size difference: 243
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_002092

• cd RRM 73aa 6e-09 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• cd RRM 69aa 1e-07 in ref transcript
• cd RRM 71aa 2e-05 in ref transcript
• smart RRM 68aa 6e-08 in ref transcript
  • RNA recognition motif.
• smart RRM 69aa 6e-06 in ref transcript
• smart RRM_2 69aa 7e-06 in ref transcript
  • RNA recognition motif.
• TIGR PABP-1234 120aa 6e-04 in ref transcript
  • There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, and of unknown tissue range.

GSDML

• rs.GSDML.F1 rs.GSDML.R1 115 142
• NCBIGene 36.3 55876
• Single exon skipping, size difference: 27
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001042471

• Changed! pfam Gasdermin 369aa 1e-101 in ref transcript
  • Gasdermin family. The precise function of this protein is unknown. A deletion/insertion mutation is associated with an autosomal dominant non-syndromic hearing impairment form. In addition, this protein has also been found to contribute to acquired etoposide resistance in melanoma cells. This family also includes the gasdermin protein.
• Changed! pfam Gasdermin 360aa 1e-101 in modified transcript

GSTCD

• rs.GSTCD.F1 rs.GSTCD.R1 164 425
• NCBIGene 36.3 79807
• Alternative 5-prime, size difference: 261
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001031720

• cd GST_C_family 72aa 4e-05 in ref transcript
  • Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins and stringent starvation protein A.
• TIGR RF_mod_HemK 69aa 6e-05 in ref transcript
  • Members of this protein family are HemK, a protein once thought to be involved in heme biosynthesis but now recognized to be a protein-glutamine methyltransferase that modifies the peptide chain release factors. All members of the seed alignment are encoded next to the release factor 1 gene (prfA) and confirmed by phylogenetic analysis. However, the family is diverse enough that even many members of the seed alignment do not score above the seed alignment, which was set high enough to exclude all instances of PrmB.
• COG UbiE 65aa 9e-06 in ref transcript
  • Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism].

GSTM1

• rs.GSTM1.F1 rs.GSTM1.R1 243 354
• NCBIGene 36.3 2944
• Single exon skipping, size difference: 111
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000561

• Changed! cd GST_C_Mu 121aa 3e-41 in ref transcript
  • GST_C family, Class Mu subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins, and products of oxidative stress. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. The class Mu subfamily is composed of eukaryotic GSTs. In rats, at least six distinct class Mu subunits have been identified, with homologous genes in humans for five of these subunits. Class Mu GSTs can form homodimers and heterodimers, giving a large number of possible isoenzymes that can be formed, all with overlapping activities but different substrate specificities. They are the most abundant GSTs in human liver, skeletal muscle and brain, and are believed to provide protection against diseases including cancer and neurodegenerative disorders. Some isoenzymes have additional specific functions. Human GST M1-1 acts as an endogenous inhibitor of ASK1 (apoptosis signal-regulating kinase 1) thereby suppressing ASK1-mediated cell death. Human GSTM2-2 and 3-3 have been identified as prostaglandin E2 synthases in the brain and may play crucial roles in temperature and sleep-wake regulation.
• cd GST_N_Mu 82aa 3e-38 in ref transcript
  • GST_N family, Class Mu subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. The GST fold contains an N-terminal TRX-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. The class Mu subfamily is composed of eukaryotic GSTs. In rats, at least six distinct class Mu subunits have been identified, with homologous genes in humans for five of these subunits. Class Mu GSTs can form homodimers and heterodimers, giving a large number of possible isoenzymes that can be formed, all with overlapping activities but different substrate specificities. They are the most abundant GSTs in human liver, skeletal muscle and brain, and are believed to provide protection against diseases including cancer and neurodegenerative disorders. Some isoenzymes have additional specific functions. Human GST M1-1 acts as an endogenous inhibitor of ASK1 (apoptosis signal-regulating kinase 1), thereby suppressing ASK1-mediated cell death. Human GSTM2-2 and 3-3 have been identified as prostaglandin E2 synthases in the brain and may play crucial roles in temperature and sleep-wake regulation.
• pfam GST_N 80aa 1e-17 in ref transcript
  • Glutathione S-transferase, N-terminal domain. Function: conjugation of reduced glutathione to a variety of targets. Also included in the alignment, but are not GSTs: * S-crystallins from squid. Similarity to GST previously noted. * Eukaryotic elongation factors 1-gamma. Not known to have GST activity; similarity not previously recognised. * HSP26 family of stress-related proteins. including auxin-regulated proteins in plants and stringent starvation proteins in Escherichia coli. Not known to have GST activity. Similarity not previously recognised. The glutathione molecule binds in a cleft between N and C-terminal domains - the catalytically important residues are proposed to reside in the N-terminal domain.
• Changed! pfam GST_C 51aa 5e-10 in ref transcript
  • Glutathione S-transferase, C-terminal domain. GST conjugates reduced glutathione to a variety of targets including S-crystallin from squid, the eukaryotic elongation factor 1-gamma, the HSP26 family of stress-related proteins and auxin-regulated proteins in plants. Stringent starvation proteins in Escherichia coli are also included in the alignment but are not known to have GST activity. The glutathione molecule binds in a cleft between N and C-terminal domains. The catalytically important residues are proposed to reside in the N-terminal domain. In plants, GSTs are encoded by a large gene family (48 GST genes in Arabidopsis) and can be divided into the phi, tau, theta, zeta, and lambda classes.
• Changed! PTZ PTZ00057 201aa 3e-09 in ref transcript
  • glutathione s-transferase; Provisional.
• Changed! cd GST_C_Mu 84aa 4e-16 in modified transcript
• Changed! PTZ PTZ00057 109aa 8e-07 in modified transcript

GTF2I

• rs.GTF2I.F1 rs.GTF2I.R1 110 170
• NCBIGene 36.3 2969
• Single exon skipping, size difference: 60
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_032999

• pfam GTF2I 73aa 6e-31 in ref transcript
  • GTF2I-like repeat. This region of sequence similarity is found up to six times in a variety of proteins including GTF2I. It has been suggested that this may be a DNA binding domain.
• pfam GTF2I 73aa 1e-30 in ref transcript
• pfam GTF2I 73aa 4e-30 in ref transcript
• pfam GTF2I 73aa 1e-29 in ref transcript
• pfam GTF2I 73aa 3e-26 in ref transcript
• pfam GTF2I 73aa 3e-26 in ref transcript

GTPBP10

• rs.GTPBP10.F1 rs.GTPBP10.R1 127 364
• NCBIGene 36.3 85865
• Multiple exon skipping, size difference: 237
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_033107

• Changed! cd Obg 195aa 2e-58 in ref transcript
  • Obg subfamily. The Obg nucleotide binding protein subfamily has been implicated in stress response, chromosome partitioning, replication initiation, mycelium development, and sporulation. Obg proteins are among a large group of GTP binding proteins conserved from bacteria to humans. The E. coli homolog, ObgE is believed to function in ribosomal biogenesis. Members of the subfamily contain two equally and highly conserved domains, a C-terminal GTP binding domain and an N-terminal glycine-rich domain.
• Changed! TIGR Obg_CgtA 330aa 5e-73 in ref transcript
  • This model describes a univeral, mostly one-gene-per-genome GTP-binding protein that associates with ribosomal subunits and appears to play a role in ribosomal RNA maturation. This GTPase, related to the nucleolar protein Obg, is designated CgtA in bacteria. Mutations in this gene are pleiotropic, but it appears that effects on cellular functions such as chromosome partition may be secondary to the effect on ribosome structure. Recent work done in Vibrio cholerae shows an essential role in the stringent response, in which RelA-dependent ability to synthesize the alarmone ppGpp is required for deletion of this GTPase to be lethal.
• Changed! PRK obgE 335aa 1e-72 in ref transcript
  • GTPase ObgE; Reviewed.
• Changed! cd Obg 188aa 3e-54 in modified transcript
• Changed! TIGR Obg_CgtA 242aa 3e-46 in modified transcript
• Changed! PRK obgE 247aa 1e-47 in modified transcript

GYG2

• rs.GYG2.F1 rs.GYG2.R1 307 400
• NCBIGene 36.3 8908
• Single exon skipping, size difference: 93
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_003918

• cd GT8_Glycogenin 252aa 2e-87 in ref transcript
  • Glycogenin belongs the GT 8 family and initiates the biosynthesis of glycogen. Glycogenin initiates the biosynthesis of glycogen by incorporating glucose residues through a self-glucosylation reaction at a Tyr residue, and then acts as substrate for chain elongation by glycogen synthase and branching enzyme. It contains a conserved DxD motif and an N-terminal beta-alpha-beta Rossmann-like fold that are common to the nucleotide-binding domains of most glycosyltransferases. The DxD motif is essential for coordination of the catalytic divalent cation, most commonly Mn2+. Glycogenin can be classified as a retaining glycosyltransferase, based on the relative anomeric stereochemistry of the substrate and product in the reaction catalyzed. It is placed in glycosyltransferase family 8 which includes lipopolysaccharide glucose and galactose transferases and galactinol synthases.
• pfam Glyco_transf_8 217aa 2e-51 in ref transcript
  • Glycosyl transferase family 8. This family includes enzymes that transfer sugar residues to donor molecules. Members of this family are involved in lipopolysaccharide biosynthesis and glycogen synthesis. This family includes Lipopolysaccharide galactosyltransferase, lipopolysaccharide glucosyltransferase 1, and glycogenin glucosyltransferase.
• COG COG5597 175aa 1e-11 in ref transcript
  • Alpha-N-acetylglucosamine transferase [Cell envelope biogenesis, outer membrane].

Gcom1

• rs.Gcom1.F1 rs.Gcom1.R1 135 340
• NCBIGene 36.3 145781
• Single exon skipping, size difference: 205
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_001018090

• TIGR SMC_prok_B 250aa 2e-08 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• COG Smc 266aa 4e-05 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].

HAP1

• rs.HAP1.F1 rs.HAP1.R1 102 126
• NCBIGene 36.3 9001
• Alternative 5-prime, size difference: 24
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_003949

• Changed! pfam HAP1_N 354aa 1e-71 in ref transcript
  • HAP1 N-terminal conserved region. This family represents an N-terminal conserved region found in several huntingtin-associated protein 1 (HAP1) homologues. HAP1 binds to huntingtin in a polyglutamine repeat-length-dependent manner. However, its possible role in the pathogenesis of Huntington's disease is unclear. This family also includes a similar N-terminal conserved region from hypothetical protein products of ALS2CR3 genes found in the human juvenile amyotrophic lateral sclerosis critical region 2q33-2q34.
• COG Smc 148aa 4e-07 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].
• Changed! pfam HAP1_N 362aa 3e-71 in modified transcript

HEY1

• rs.HEY1.F1 rs.HEY1.R1 103 115
• NCBIGene 36.3 23462
• Alternative 5-prime, size difference: 12
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001040708

• Changed! cd HLH 46aa 9e-06 in ref transcript
  • Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins.
• smart ORANGE 47aa 5e-09 in ref transcript
  • Orange domain. This domain confers specificity among members of the Hairy/E(SPL) family.
• Changed! pfam HLH 44aa 6e-07 in ref transcript
  • Helix-loop-helix DNA-binding domain.
• Changed! cd HLH 42aa 3e-06 in modified transcript
• Changed! pfam HLH 40aa 2e-07 in modified transcript

HGF

• rs.HGF.F1 rs.HGF.R1 110 125
• NCBIGene 36.3 3082
• Alternative 3-prime, size difference: 15
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000601

• cd Tryp_SPc 225aa 2e-51 in ref transcript
  • Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
• Changed! cd KR 82aa 6e-28 in ref transcript
  • Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides.
• cd KR 82aa 9e-28 in ref transcript
• cd KR 83aa 9e-27 in ref transcript
• cd KR 83aa 5e-25 in ref transcript
• cd PAN_APPLE 84aa 8e-20 in ref transcript
  • PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins, plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions.
• smart Tryp_SPc 223aa 3e-56 in ref transcript
  • Trypsin-like serine protease. Many of these are synthesised as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. A few, however, are active as single chain molecules, and others are inactive due to substitutions of the catalytic triad residues.
• pfam Kringle 78aa 2e-32 in ref transcript
  • Kringle domain. Kringle domains have been found in plasminogen, hepatocyte growth factors, prothrombin, and apolipoprotein A. Structure is disulfide-rich, nearly all-beta.
• pfam Kringle 79aa 6e-31 in ref transcript
• Changed! smart KR 83aa 1e-30 in ref transcript
  • Kringle domain. Named after a Danish pastry. Found in several serine proteases and in ROR-like receptors. Can occur in up to 38 copies (in apolipoprotein(a)). Plasminogen-like kringles possess affinity for free lysine and lysine- containing peptides.
• pfam Kringle 79aa 2e-26 in ref transcript
• smart PAN_AP 86aa 4e-07 in ref transcript
  • divergent subfamily of APPLE domains. Apple-like domains present in Plasminogen, C. elegans hypothetical ORFs and the extracellular portion of plant receptor-like protein kinases. Predicted to possess protein- and/or carbohydrate-binding functions.
• COG COG5640 234aa 3e-10 in ref transcript
  • Secreted trypsin-like serine protease [Posttranslational modification, protein turnover, chaperones].
• Changed! cd KR 77aa 7e-25 in modified transcript
• Changed! smart KR 78aa 2e-27 in modified transcript

HIF1A

• rs.HIF1A.F1 rs.HIF1A.R1 262 389
• NCBIGene 36.3 3091
• Single exon skipping, size difference: 127
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_001530

• cd PAS 100aa 1e-12 in ref transcript
  • PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.
• cd PAS 55aa 4e-07 in ref transcript
• pfam PAS_3 86aa 1e-15 in ref transcript
  • PAS fold. The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs. The PAS fold appears in archaea, eubacteria and eukarya.
• Changed! pfam HIF-1a_CTAD 40aa 1e-14 in ref transcript
  • HIF-1 alpha C terminal transactivation domain. Hypoxia inducible factor-1 alpha (HIF-1 alpha) is the regulatory subunit of the heterodimeric transcription factor HIF-1. It plays a key role in cellular response to low oxygen tension. This region corresponds to the C terminal transactivation domain.
• smart PAS 56aa 8e-08 in ref transcript
  • PAS domain. PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels ([1]; Ponting & Aravind, in press).

HIG2

• rs.HIG2.F1 rs.HIG2.R1 252 366
• NCBIGene 36.3 29923
• Alternative 5-prime, size difference: 114
• Exclusion in 5'UTR
• Reference transcript: NM_013332

HIPK3

• rs.HIPK3.F1 rs.HIPK3.R1 180 243
• NCBIGene 36.3 10114
• Single exon skipping, size difference: 63
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_005734

• cd S_TKc 224aa 3e-51 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• cd S_TKc 63aa 0.007 in ref transcript
• smart S_TKc 202aa 3e-52 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• smart S_TKc 30aa 0.007 in ref transcript
• PTZ PTZ00284 310aa 8e-34 in ref transcript
  • protein kinase; Provisional.

HLA-F

• rs.HLA-F.F1 rs.HLA-F.R1 137 413
• NCBIGene 36.3 3134
• Single exon skipping, size difference: 276
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001098479

• Changed! cd IGc 92aa 2e-19 in ref transcript
  • Immunoglobulin domain constant region subfamily; members of the IGc subfamily are components of immunoglobulins, T-cell receptors, CD1 cell surface glycoproteins, secretory glycoproteins A/C, and Major Histocompatibility Complex (MHC) class I/II molecules. In immunoglobulins, each chain is composed of one variable domain (IGv) and one or more constant domains (IGc); these names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. T-cell receptors form heterodimers, pairing two chains (alpha/beta or gamma/delta), each with a IGv and IGc domain. MHCs form heterodimers pairing two chains (alpha/beta or delta/epsilon), each with a MHC and IGc domain. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• pfam MHC_I 178aa 9e-84 in ref transcript
  • Class I Histocompatibility antigen, domains alpha 1 and 2.
• Changed! pfam C1-set 81aa 3e-22 in ref transcript
  • Immunoglobulin C1-set domain.

HMGA1

• rs.HMGA1.F1 rs.HMGA1.R1 145 178
• NCBIGene 36.3 3159
• Alternative 5-prime, size difference: 33
• Exclusion in 5'UTR
• Reference transcript: NM_145899

HMGA1

• rs.HMGA1.F2 rs.HMGA1.R2 194 308
• NCBIGene 36.3 3159
• Single exon skipping, size difference: 114
• Exclusion in 5'UTR
• Reference transcript: NM_002131

HMGCLL1

• rs.HMGCLL1.F1 rs.HMGCLL1.R1 319 409
• NCBIGene 36.3 54511
• Single exon skipping, size difference: 90
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_019036

• pfam HMGL-like 271aa 3e-58 in ref transcript
  • HMGL-like. This family contains a diverse set of enzymes. These include various aldolases and a region of pyruvate carboxylase.
• PRK PRK05692 286aa 1e-132 in ref transcript
  • hydroxymethylglutaryl-CoA lyase; Provisional.

HMGCS1

• rs.HMGCS1.F1 rs.HMGCS1.R1 328 387
• NCBIGene 36.3 3157
• Single exon skipping, size difference: 59
• Exclusion in 5'UTR
• Reference transcript: NM_001098272

• cd init_cond_enzymes 371aa 9e-63 in ref transcript
  • "initiating" condensing enzymes are a subclass of decarboxylating condensing enzymes, including beta-ketoacyl [ACP] synthase, type III and polyketide synthases, type III, which include chalcone synthase and related enzymes. They are characterized by the utlization of CoA substrate primers, as well as the nature of their active site residues.
• TIGR HMG-CoA-S_euk 457aa 0.0 in ref transcript
  • Hydroxymethylglutaryl(HMG)-CoA synthase is the first step of isopentenyl pyrophosphate (IPP) biosynthesis via the mevalonate pathway. This pathway is found mainly in eukaryotes, but also in archaea and some bacteria. This model is specific for eukaryotes.
• COG PksG 452aa 2e-75 in ref transcript
  • 3-hydroxy-3-methylglutaryl CoA synthase [Lipid metabolism].

HMMR

• rs.HMMR.F1 rs.HMMR.R1 138 183
• NCBIGene 36.3 3161
• Single exon skipping, size difference: 45
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_012484

• pfam SMC_N 239aa 3e-05 in ref transcript
  • RecF/RecN/SMC N terminal domain. This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.
• Changed! TIGR SMC_prok_A 213aa 9e-05 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent.
• COG Smc 236aa 4e-05 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].
• PRK PRK05771 196aa 0.002 in ref transcript
  • V-type ATP synthase subunit I; Validated.
• Changed! TIGR SMC_prok_A 223aa 3e-04 in modified transcript

HN1

• rs.HN1.F1 rs.HN1.R1 124 143
• NCBIGene 36.3 51155
• Single exon skipping, size difference: 19
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_001002032

HNF4A

• rs.HNF4A.F1 rs.HNF4A.R1 123 153
• NCBIGene 36.3 3172
• Alternative 5-prime, size difference: 30
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000457

• cd NR_LBD_HNF4_like 223aa 1e-120 in ref transcript
  • The ligand binding domain of heptocyte nuclear factor 4, which is explosively expanded in nematodes. The ligand binding domain of hepatocyte nuclear factor 4 (HNF4) like proteins: HNF4 is a member of the nuclear receptor superfamily. HNF4 plays a key role in establishing and maintenance of hepatocyte differentiation in the liver. It is also expressed in gut, kidney, and pancreatic beta cells. HNF4 was originally classified as an orphan receptor, but later it is found that HNF4 binds with very high affinity to a variety of fatty acids. However, unlike other nuclear receptors, the ligands do not act as a molecular switch for HNF4. They seem to constantly bind to the receptor, which is constitutively active as a transcription activator. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, HNF4 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). The LBD domain is also responsible for recruiting co-activator proteins. More than 280 nuclear receptors are found in C. ele gans, most of which are originated from an explosive burst of duplications of HNF4.
• pfam Hormone_recep 182aa 2e-41 in ref transcript
  • Ligand-binding domain of nuclear hormone receptor. This all helical domain is involved in binding the hormone in these receptors.
• pfam zf-C4 75aa 2e-38 in ref transcript
  • Zinc finger, C4 type (two domains). In nearly all cases, this is the DNA binding domain of a nuclear hormone receptor. The alignment contains two Zinc finger domains that are too dissimilar to be aligned with each other.

HNRNPC

• rs.HNRNPC.F1 rs.HNRNPC.R1 168 207
• NCBIGene 36.3 3183
• Alternative 5-prime, size difference: 39
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_031314

• cd RRM 68aa 1e-09 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• smart RRM_2 67aa 5e-10 in ref transcript
  • RNA recognition motif.

HNRNPC

• rs.HNRNPC.F2 rs.HNRNPC.R2 144 170
• NCBIGene 36.3 3183
• Single exon skipping, size difference: 26
• Exclusion in 5'UTR
• Reference transcript: NM_031314

• cd RRM 68aa 1e-09 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• smart RRM_2 67aa 5e-10 in ref transcript
  • RNA recognition motif.

HNRNPR

• rs.HNRNPR.F1 rs.HNRNPR.R1 147 313
• NCBIGene 36.3 10236
• Single exon skipping, size difference: 166
• Exclusion of the protein initiation site
• Reference transcript: NM_001102398

• cd RRM 73aa 1e-11 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• cd RRM 56aa 1e-11 in ref transcript
• cd RRM 82aa 2e-08 in ref transcript
• TIGR hnRNP-R-Q 313aa 1e-156 in ref transcript
  • Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.
• TIGR hnRNP-R-Q 30aa 3e-05 in ref transcript
• COG COG0724 65aa 3e-06 in ref transcript
  • RNA-binding proteins (RRM domain) [General function prediction only].
• COG COG0724 138aa 7e-06 in ref transcript

HNRPF

• rs.HNRPF.F1 rs.HNRPF.R1 232 273
• NCBIGene 36.3 3185
• Alternative 5-prime, size difference: 41
• Exclusion in 5'UTR
• Reference transcript: NM_004966

• cd RRM 73aa 3e-09 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• cd RRM 72aa 1e-08 in ref transcript
• cd RRM 76aa 3e-06 in ref transcript
• pfam zf-RNPHF 36aa 7e-14 in ref transcript
  • RNPHF zinc finger. This domain is a putative zinc-binding domain (CHHC motif) in RNP H and F. The domain is often associated with pfam00076.
• smart RRM_2 70aa 7e-10 in ref transcript
  • RNA recognition motif.
• smart RRM_2 71aa 9e-10 in ref transcript
• smart RRM_2 73aa 6e-04 in ref transcript
• TIGR SF-CC1 121aa 0.007 in ref transcript
  • A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed.
• COG COG0724 159aa 5e-04 in ref transcript
  • RNA-binding proteins (RRM domain) [General function prediction only].
• COG COG0724 57aa 0.002 in ref transcript

HNRPH2

• rs.HNRPH2.F1 rs.HNRPH2.R1 101 113
• NCBIGene 36.3 3188
• Alternative 5-prime, size difference: 12
• Exclusion in 5'UTR
• Reference transcript: NM_019597

• cd RRM 73aa 4e-09 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• cd RRM 72aa 5e-08 in ref transcript
• pfam zf-RNPHF 34aa 4e-13 in ref transcript
  • RNPHF zinc finger. This domain is a putative zinc-binding domain (CHHC motif) in RNP H and F. The domain is often associated with pfam00076.
• smart RRM_2 71aa 7e-10 in ref transcript
  • RNA recognition motif.
• smart RRM_2 70aa 3e-09 in ref transcript

HRAS

• rs.HRAS.F1 rs.HRAS.R1 176 258
• NCBIGene 36.3 3265
• Single exon skipping, size difference: 82
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_005343

• Changed! cd H_N_K_Ras_like 162aa 8e-91 in ref transcript
  • H-Ras/N-Ras/K-Ras subfamily. H-Ras, N-Ras, and K-Ras4A/4B are the prototypical members of the Ras family. These isoforms generate distinct signal outputs despite interacting with a common set of activators and effectors, and are strongly associated with oncogenic progression in tumor initiation. Mutated versions of Ras that are insensitive to GAP stimulation (and are therefore constitutively active) are found in a significant fraction of human cancers. Many Ras guanine nucleotide exchange factors (GEFs) have been identified. They are sequestered in the cytosol until activation by growth factors triggers recruitment to the plasma membrane or Golgi, where the GEF colocalizes with Ras. Active (GTP-bound) Ras interacts with several effector proteins that stimulate a variety of diverse cytoplasmic signaling activities. Some are known to positively mediate the oncogenic properties of Ras, including Raf, phosphatidylinositol 3-kinase (PI3K), RalGEFs, and Tiam1. Others are proposed to play negative regulatory roles in oncogenesis, including RASSF and NORE/MST1. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.
• Changed! smart RAS 163aa 6e-80 in ref transcript
  • Ras subfamily of RAS small GTPases. Similar in fold and function to the bacterial EF-Tu GTPase. p21Ras couples receptor Tyr kinases and G protein receptors to protein kinase cascades.
• Changed! COG COG1100 165aa 2e-19 in ref transcript
  • GTPase SAR1 and related small G proteins [General function prediction only].
• Changed! cd H_N_K_Ras_like 148aa 1e-81 in modified transcript
• Changed! smart RAS 147aa 2e-72 in modified transcript
• Changed! COG COG1100 147aa 2e-17 in modified transcript

HS6ST2

• rs.HS6ST2.F1 rs.HS6ST2.R1 200 320
• NCBIGene 36.3 90161
• Multiple exon skipping, size difference: 120
• Exclusion in the protein (no frameshift), Exclusion in the protein (no frameshift)
• Reference transcript: NM_001077188

• Changed! pfam HS6ST 353aa 1e-177 in ref transcript
  • Heparan sulfate 6-sulfotransferase (HS6ST). This family consists of several heparan sulfate 6-sulfotransferase (HS6ST) proteins. Heparan sulphate 6- O -sulphotransferase (HS6ST) catalyses the transfer of sulphate from adenosine 3'-phosphate, 5'-phosphosulphate to the 6th position of the N -sulphoglucosamine residue in heparan sulphate.
• Changed! pfam HS6ST 313aa 0.0 in modified transcript

HSF4

• rs.HSF4.F1 rs.HSF4.R1 100 114
• NCBIGene 36.3 3299
• Alternative 3-prime, size difference: 14
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_001040667

• pfam HSF_DNA-bind 194aa 1e-59 in ref transcript
  • HSF-type DNA-binding.
• COG HSF1 182aa 1e-29 in ref transcript
  • Heat shock transcription factor [Transcription].

HSF4

• rs.HSF4.F2 rs.HSF4.R2 111 215
• NCBIGene 36.3 3299
• Alternative 3-prime, size difference: 104
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_001040667

• pfam HSF_DNA-bind 194aa 1e-59 in ref transcript
  • HSF-type DNA-binding.
• COG HSF1 182aa 1e-29 in ref transcript
  • Heat shock transcription factor [Transcription].

HSPA8

• rs.HSPA8.F1 rs.HSPA8.R1 91 550
• NCBIGene 36.3 3312
• Exon skipping and alternative 3-prime or 5-prime, size difference: 459
• Exclusion in the protein (no frameshift), Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_006597

• Changed! pfam HSP70 607aa 0.0 in ref transcript
  • Hsp70 protein. Hsp70 chaperones help to fold many proteins. Hsp70 assisted folding involves repeated cycles of substrate binding and release. Hsp70 activity is ATP dependent. Hsp70 proteins are made up of two regions: the amino terminus is the ATPase domain and the carboxyl terminus is the substrate binding region.
• Changed! PTZ PTZ00009 612aa 0.0 in ref transcript
  • heat shock 70 kDa protein; Provisional.
• Changed! pfam HSP70 457aa 0.0 in modified transcript
• Changed! PTZ PTZ00009 462aa 0.0 in modified transcript

HTATIP2

• rs.HTATIP2.F1 rs.HTATIP2.R1 189 303
• NCBIGene 36.3 10553
• Alternative 5-prime, size difference: 114
• Exclusion of the protein initiation site
• Reference transcript: NM_001098520

• Changed! TIGR hemA 97aa 0.004 in ref transcript
  • This enzyme, together with glutamate-1-semialdehyde-2,1-aminomutase (TIGR00713), leads to the production of delta-amino-levulinic acid from Glu-tRNA.
• COG COG0702 173aa 2e-08 in ref transcript
  • Predicted nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism].
• Changed! TIGR hemA 78aa 0.006 in modified transcript

IARS

• rs.IARS.F1 rs.IARS.R1 127 300
• NCBIGene 36.3 3376
• Alternative 5-prime, size difference: 173
• Exclusion of the protein initiation site
• Reference transcript: NM_013417

• cd IleRS_core 235aa 5e-89 in ref transcript
  • This is the catalytic core domain of isoleucine amino-acyl tRNA synthetases (IleRS) . This class I enzyme is a monomer, which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. IleRS has an insertion in the core domain, which is subject to both deletions and rearrangements. This editing region hydrolyzes mischarged cognate tRNAs and thus prevents the incorporation of chemically similar amino acids.
• cd IleRS_core 143aa 2e-68 in ref transcript
• TIGR ileS 860aa 0.0 in ref transcript
  • The isoleucyl tRNA synthetase (IleS) is a class I amino acyl-tRNA ligase and is particularly closely related to the valyl tRNA synthetase. This model may recognize IleS from every species, including eukaryotic cytosolic and mitochondrial forms.
• PRK ileS 1029aa 0.0 in ref transcript
  • isoleucyl-tRNA synthetase; Reviewed.

ICA1L

• rs.ICA1L.F1 rs.ICA1L.R1 246 316
• NCBIGene 36.3 130026
• Single exon skipping, size difference: 70
• Inclusion in 5'UTR
• Reference transcript: NM_138468

• cd Arfaptin 205aa 3e-54 in ref transcript
  • Arfaptin domain; arfaptin is a ubiquitously expressed protein implicated in mediating cross-talk between Rac, a member of the Rho family, and Arf small GTPases; Arfaptin binds to GTP-bound Arf1 and Arf6, but binds Rac.GTP and Rac.GDP with similar affinities. Structures of Arfaptin with Rac bound to either GDP or the slowly hydrolysable analogue GMPPNP show that the switch regions adopt similar conformations in both complexes. Arf1 and Arf6 are thought to bind to the same surface as Rac.
• pfam Arfaptin 206aa 3e-73 in ref transcript
  • Arfaptin-like domain. Arfaptin interacts with ARF1, a small GTPase involved in vesicle budding at the Golgi complex and immature secretory granules. The structure of arfaptin shows that upon binding to a small GTPase, arfaptin forms a an elongated, crescent-shaped dimer of three-helix coiled-coils. The N-terminal region of ICA69 is similar to arfaptin.
• pfam ICA69 229aa 5e-54 in ref transcript
  • Islet cell autoantigen ICA69, C-terminal domain. This family includes a 69 kD protein which has been identified as an islet cell autoantigen in type I diabetes mellitus. Its precise function is unknown.

ICAM2

• rs.ICAM2.F1 rs.ICAM2.R1 178 260
• NCBIGene 36.3 3384
• Single exon skipping, size difference: 82
• Exclusion in 5'UTR
• Reference transcript: NM_001099786

• pfam ICAM_N 111aa 2e-45 in ref transcript
  • Intercellular adhesion molecule (ICAM), N-terminal domain. ICAMs normally functions to promote intercellular adhesion and signalling. However, The N-terminal domain of the receptor binds to the rhinovirus 'canyon' surrounding the icosahedral 5-fold axes, during the viral attachment process. This family is a family that is part of the Ig superfamily and is therefore related to the family ig (pfam00047).

ICAM2

• rs.ICAM2.F2 rs.ICAM2.R2 112 229
• NCBIGene 36.3 3384
• Alternative 5-prime, size difference: 117
• Exclusion in 5'UTR
• Reference transcript: NM_001099786

• pfam ICAM_N 111aa 2e-45 in ref transcript
  • Intercellular adhesion molecule (ICAM), N-terminal domain. ICAMs normally functions to promote intercellular adhesion and signalling. However, The N-terminal domain of the receptor binds to the rhinovirus 'canyon' surrounding the icosahedral 5-fold axes, during the viral attachment process. This family is a family that is part of the Ig superfamily and is therefore related to the family ig (pfam00047).

IFI6

• rs.IFI6.F1 rs.IFI6.R1 100 112
• NCBIGene 36.3 2537
• Alternative 5-prime, size difference: 12
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_022873

• pfam Ifi-6-16 59aa 2e-11 in ref transcript
  • Interferon-induced 6-16 family.

IGFBP3

• rs.IGFBP3.F1 rs.IGFBP3.R1 100 118
• NCBIGene 36.3 3486
• Alternative 5-prime, size difference: 18
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001013398

• cd TY 70aa 3e-10 in ref transcript
  • Thyroglobulin type I repeats.; The N-terminal region of human thyroglobulin contains 11 type-1 repeats TY repeats are proposed to be inhibitors of cysteine proteases.
• smart IB 78aa 4e-23 in ref transcript
  • Insulin growth factor-binding protein homologues. High affinity binding partners of insulin-like growth factors.
• pfam Thyroglobulin_1 73aa 7e-15 in ref transcript
  • Thyroglobulin type-1 repeat. Thyroglobulin type 1 repeats are thought to be involved in the control of proteolytic degradation. The domain usually contains six conserved cysteines. These form three disulphide bridges. Cysteines 1 pairs with 2, 3 with 4 and 5 with 6.

IHPK1

• rs.IHPK1.F1 rs.IHPK1.R1 138 489
• NCBIGene 36.3 9807
• Single exon skipping, size difference: 351
• Exclusion of the protein initiation site
• Reference transcript: NM_153273

• Changed! pfam IPK 272aa 2e-68 in ref transcript
  • Inositol polyphosphate kinase. ArgRIII has has been demonstrated to be an inositol polyphosphate kinase.
• Changed! pfam IPK 261aa 1e-67 in modified transcript

IKZF2

• rs.IKZF2.F1 rs.IKZF2.R1 158 236
• NCBIGene 36.3 22807
• Alternative 5-prime, size difference: 78
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_016260

• Changed! COG COG5048 83aa 0.007 in ref transcript
  • FOG: Zn-finger [General function prediction only].
• Changed! COG COG5048 88aa 0.008 in modified transcript

IKZF2

• rs.IKZF2.F2 rs.IKZF2.R2 103 140
• NCBIGene 36.3 22807
• Alternative 5-prime, size difference: 37
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_016260

• Changed! COG COG5048 83aa 0.007 in ref transcript
  • FOG: Zn-finger [General function prediction only].

IL17RE

• rs.IL17RE.F1 rs.IL17RE.R1 154 290
• NCBIGene 36.3 132014
• Multiple exon skipping, size difference: 136
• Exclusion in the protein causing a frameshift, Exclusion in the protein (no frameshift)
• Reference transcript: NM_153483

• Changed! pfam SEFIR 75aa 1e-06 in ref transcript
  • SEFIR domain. This family comprises IL17 receptors (IL17Rs) and SEF proteins. The latter are feedback inhibitors of FGF signalling and are also thought to be receptors. Due to its similarity to the TIR domain (pfam01582), the SEFIR region is thought to be involved in homotypic interactions with other SEFIR/TIR-domain-containing proteins. Thus, SEFs and IL17Rs may be involved in TOLL/IL1R-like signalling pathways.

IL32

• rs.IL32.F1 rs.IL32.R1 102 125
• NCBIGene 36.3 9235
• Alternative 5-prime, size difference: 23
• Exclusion in 5'UTR
• Reference transcript: NM_001012632

ILF3

• rs.ILF3.F1 rs.ILF3.R1 100 543
• NCBIGene 36.3 3609
• Alternative 3-prime, size difference: 443
• Exclusion of the stop codon
• Reference transcript: NM_004516

• cd DSRM 64aa 9e-09 in ref transcript
  • Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, RNases H1, and dsRNA dependent adenosine deaminases.
• cd DSRM 46aa 3e-05 in ref transcript
• smart DZF 255aa 1e-102 in ref transcript
  • domain in DSRM or ZnF_C2H2 domain containing proteins.
• smart DSRM 65aa 2e-11 in ref transcript
  • Double-stranded RNA binding motif.
• smart DSRM 47aa 2e-07 in ref transcript
• PRK rnc 37aa 3e-05 in ref transcript
  • ribonuclease III; Reviewed.
• PRK rnc 32aa 0.006 in ref transcript

ILK

• rs.ILK.F1 rs.ILK.R1 145 191
• NCBIGene 36.3 3611
• Alternative 3-prime, size difference: 46
• Inclusion in 5'UTR
• Reference transcript: NM_001014794

• cd PTKc 243aa 1e-32 in ref transcript
  • Catalytic Domain of Protein Tyrosine Kinases. Protein Tyrosine Kinase (PTK) family, catalytic domain. This PTKc family is part of a larger superfamily that includes the catalytic domains of protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. They can be classified into receptor and non-receptor tyr kinases. PTKs play important roles in many cellular processes including, lymphocyte activation, epithelium growth and maintenance, metabolism control, organogenesis regulation, survival, proliferation, differentiation, migration, adhesion, motility, and morphogenesis. Receptor tyr kinases (RTKs) are integral membrane proteins which contain an extracellular ligand-binding region, a transmembrane segment, and an intracellular tyr kinase domain. RTKs are usually activated through ligand binding, which causes dimerization and autophosphorylation of the intracellular tyr kinase catalytic domain, leading to intracellular signaling. Some RTKs are orphan receptors with no known ligands. Non-receptor (or cytoplasmic) tyr kinases are distributed in different intracellular compartments and are usually multi-domain proteins containing a catalytic tyr kinase domain as well as various regulatory domains such as SH3 and SH2. PTKs are usually autoinhibited and require a mechanism for activation. In many PTKs, the phosphorylation of tyr residues in the activation loop is essential for optimal activity. Aberrant expression of PTKs is associated with many development abnormalities and cancers.
• cd ANK 113aa 2e-27 in ref transcript
  • ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats.
• pfam Pkinase_Tyr 254aa 3e-36 in ref transcript
  • Protein tyrosine kinase.
• pfam Ank 30aa 2e-06 in ref transcript
  • Ankyrin repeat. There's no clear separation between noise and signal on the HMM search Ankyrin repeats generally consist of a beta, alpha, alpha, beta order of secondary structures. The repeats associate to form a higher order structure.
• pfam Ank 33aa 4e-05 in ref transcript
• TIGR trp 115aa 0.001 in ref transcript
  • after chronic exposure to capsaicin. (McCleskey and Gold, 1999).
• COG Arp 139aa 1e-14 in ref transcript
  • FOG: Ankyrin repeat [General function prediction only].
• PTZ PTZ00283 134aa 9e-11 in ref transcript
  • serine/threonine protein kinase; Provisional.

IMMT

• rs.IMMT.F1 rs.IMMT.R1 142 175
• NCBIGene 36.3 10989
• Alternative 3-prime, size difference: 33
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_006839

• Changed! pfam Mitofilin 753aa 0.0 in ref transcript
  • Mitochondrial inner membrane protein. Mitofilin controls mitochondrial cristae morphology. Mitofilin is enriched in the narrow space between the inner boundary and the outer membranes, where it forms a homotypic interaction and assembles into a large multimeric protein complex. The first 78 amino acids contain a typical amino-terminal-cleavable mitochondrial presequence (residues 1-43) rich in positive-charged and hydroxylated residues and a membrane anchor domain (residues 47-66). In addition, it has three centrally located coiled coil domains (residues 200-240,280-310 and 400-420).
• PRK PRK02995 107aa 9e-04 in ref transcript
  • DNA-directed RNA polymerase subunit beta'; Provisional.
• Changed! pfam Mitofilin 742aa 0.0 in modified transcript

INCENP

• rs.INCENP.F1 rs.INCENP.R1 107 119
• NCBIGene 36.3 3619
• Single exon skipping, size difference: 12
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001040694

• pfam INCENP_ARK-bind 59aa 2e-19 in ref transcript
  • Inner centromere protein, ARK binding region. This region of the inner centromere protein has been found to be necessary and sufficient for binding to aurora-related kinase. This interaction has been implicated in the coordination of chromosome segregation with cell division in yeast.

INPP4B

• rs.INPP4B.F1 rs.INPP4B.R1 97 196
• NCBIGene 36.3 8821
• Single exon skipping, size difference: 99
• Exclusion in 5'UTR
• Reference transcript: NM_003866

IQCB1

• rs.IQCB1.F1 rs.IQCB1.R1 103 502
• NCBIGene 36.3 9657
• Multiple exon skipping, size difference: 399
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_001023570

• Changed! smart IQ 22aa 0.005 in modified transcript
  • Short calmodulin-binding motif containing conserved Ile and Gln residues. Calmodulin-binding motif.

IQCE

• rs.IQCE.F1 rs.IQCE.R1 255 303
• NCBIGene 36.3 23288
• Single exon skipping, size difference: 48
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_152558

• TIGR SMC_prok_A 282aa 6e-05 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent.
• COG Smc 283aa 2e-05 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].

IQCH

• rs.IQCH.F1 rs.IQCH.R1 102 375
• NCBIGene 36.3 64799
• Single exon skipping, size difference: 273
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001031715

IRAK1

• rs.IRAK1.F1 rs.IRAK1.R1 125 362
• NCBIGene 36.3 3654
• Single exon skipping, size difference: 237
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001569

• cd S_TKc 205aa 4e-35 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• pfam Pkinase 205aa 6e-36 in ref transcript
  • Protein kinase domain.
• pfam Death 75aa 3e-07 in ref transcript
  • Death domain.
• COG SPS1 206aa 6e-24 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].

IRAK1

• rs.IRAK1.F2 rs.IRAK1.R2 242 332
• NCBIGene 36.3 3654
• Alternative 3-prime, size difference: 90
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001569

• cd S_TKc 205aa 4e-35 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• pfam Pkinase 205aa 6e-36 in ref transcript
  • Protein kinase domain.
• pfam Death 75aa 3e-07 in ref transcript
  • Death domain.
• COG SPS1 206aa 6e-24 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].

IRF2BP2

• rs.IRF2BP2.F1 rs.IRF2BP2.R1 221 269
• NCBIGene 36.3 359948
• Alternative 5-prime, size difference: 48
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_182972

ITGA6

• rs.ITGA6.F1 rs.ITGA6.R1 102 232
• NCBIGene 36.3 3655
• Single exon skipping, size difference: 130
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_001079818

• pfam Integrin_alpha2 476aa 1e-110 in ref transcript
  • Integrin alpha. This domain is found in integrin alpha and integrin alpha precursors to the C terminus of a number of pfam01839 repeats and to the N-terminus of the pfam00357 cytoplasmic region.
• smart Int_alpha 52aa 1e-11 in ref transcript
  • Integrin alpha (beta-propellor repeats). Integrins are cell adhesion molecules that mediate cell-extracellular matrix and cell-cell interactions. They contain both alpha and beta subunits. Alpha integrins are proposed to contain a domain containing a 7-fold repeat that adopts a beta-propellor fold. Some of these domains contain an inserted von Willebrand factor type-A domain. Some repeats contain putative calcium-binding sites. The 7-fold repeat domain is homologous to a similar domain in phosphatidylinositol-glycan-specific phospholipase D.
• smart Int_alpha 55aa 1e-07 in ref transcript
• smart Int_alpha 62aa 2e-05 in ref transcript

ITGB1

• rs.ITGB1.F1 rs.ITGB1.R1 113 131
• NCBIGene 36.3 3688
• Alternative 3-prime, size difference: 18
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_033667

• pfam Integrin_beta 431aa 0.0 in ref transcript
  • Integrin, beta chain. Integrins have been found in animals and their homologues have also been found in cyanobacteria, probably due to horizontal gene transfer. The sequences repeats have been trimmed due to an overlap with EGF.
• pfam Integrin_B_tail 89aa 4e-24 in ref transcript
  • Integrin beta tail domain. This is the beta tail domain of the Integrin protein. Integrins are receptors which are involved in cell-cell and cell-extracellular matrix interactions.
• Changed! pfam Integrin_b_cyt 21aa 5e-06 in ref transcript
  • Integrin beta cytoplasmic domain. Integrins are a group of transmembrane proteins which function as extracellular matrix receptors and in cell adhesion. Integrins are ubiquitously expressed and are heterodimeric, each composed of an alpha and beta subunit. Several variations of the the alpha and beta subunits exist, and association of different alpha and beta subunits can have different a different binding specificity. This domain corresponds to the cytoplasmic domain of the beta subunit.
• Changed! pfam Integrin_b_cyt 20aa 7e-06 in modified transcript

ITPR1

• rs.ITPR1.F1 rs.ITPR1.R1 201 246
• NCBIGene 36.3 3708
• Single exon skipping, size difference: 45
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001099952

• pfam Ins145_P3_rec 222aa 4e-95 in ref transcript
  • Inositol 1,4,5-trisphosphate/ryanodine receptor. This domain corresponds to the ligand binding region on inositol 1,4,5-trisphosphate receptor, and the N terminal region of the ryanodine receptor. Both receptors are involved in Ca2+ release. They can couple to the activation of neurotransmitter-gated receptors and voltage-gated Ca2+ channels on the plasma membrane, thus allowing the endoplasmic reticulum discriminate between different types of neuronal activity.
• pfam RYDR_ITPR 206aa 9e-67 in ref transcript
  • RIH domain. The RIH (RyR and IP3R Homology) domain is an extracellular domain from two types of calcium channels. This region is found in the ryanodine receptor and the inositol-1,4,5- trisphosphate receptor. This domain may form a binding site for IP3.
• Changed! pfam MIR 202aa 3e-66 in ref transcript
  • MIR domain. The MIR (protein mannosyltransferase, IP3R and RyR) domain is a domain that may have a ligand transferase function.
• pfam RIH_assoc 120aa 4e-55 in ref transcript
  • RyR and IP3R Homology associated. This eukaryotic domain is found in ryanodine receptors (RyR) and inositol 1,4,5-trisphosphate receptors (IP3R) which together form a superfamily of homotetrameric ligand-gated intracellular Ca2+ channels. There seems to be no known function for this domain. Also see the IP3-binding domain pfam01365 and pfam02815.
• pfam RYDR_ITPR 180aa 8e-55 in ref transcript
• pfam Ion_trans 224aa 5e-06 in ref transcript
  • Ion transport protein. This family contains Sodium, Potassium, Calcium ion channels. This family is 6 transmembrane helices in which the last two helices flank a loop which determines ion selectivity. In some sub-families (e.g. Na channels) the domain is repeated four times, whereas in others (e.g. K channels) the protein forms as a tetramer in the membrane. A bacterial structure of the protein is known for the last two helices but is not the Pfam family due to it lacking the first four helices.
• COG PMT1 142aa 0.004 in ref transcript
  • Dolichyl-phosphate-mannose--protein O-mannosyl transferase [Posttranslational modification, protein turnover, chaperones].
• Changed! pfam MIR 187aa 5e-68 in modified transcript

ITSN2

• rs.ITSN2.F1 rs.ITSN2.R1 426 507
• NCBIGene 36.3 50618
• Single exon skipping, size difference: 81
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_006277

• cd RhoGEF 184aa 2e-35 in ref transcript
  • Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.
• cd C2 89aa 2e-18 in ref transcript
  • Protein kinase C conserved region 2 (CalB); Ca2+-binding motif present in phospholipases, protein kinases C, and synaptotagmins (among others). Some do not appear to contain Ca2+-binding sites. Particular C2s appear to bind phospholipids, inositol polyphosphates,and intracellular proteins. Synaptotagmin and PLC C2s are permuted in sequence with respect to N- and C-terminal beta strands.
• cd EH 67aa 3e-17 in ref transcript
  • Eps15 homology domain; found in proteins implicated in endocytosis, vesicle transport, and signal transduction. The alignment contains a pair of EF-hand motifs, typically one of them is canonical and binds to Ca2+, while the other may not bind to Ca2+. A hydrophobic binding pocket is formed by residues from both EF-hand motifs. The EH domain binds to proteins containing NPF (class I), [WF]W or SWG (class II), or H[TS]F (class III) sequence motifs.
• cd EH 58aa 2e-14 in ref transcript
• cd SH3 52aa 4e-14 in ref transcript
  • Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
• cd SH3 54aa 2e-11 in ref transcript
• cd SH3 51aa 5e-11 in ref transcript
• cd SH3 52aa 6e-10 in ref transcript
• cd SH3 58aa 9e-08 in ref transcript
• cd PH 106aa 7e-04 in ref transcript
  • Pleckstrin homology (PH) domain. PH domains are only found in eukaryotes. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes.
• smart RhoGEF 181aa 2e-40 in ref transcript
  • Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases. Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains. Improved coverage.
• smart EH 93aa 4e-22 in ref transcript
  • Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
• smart EH 80aa 6e-22 in ref transcript
• smart C2 97aa 1e-20 in ref transcript
  • Protein kinase C conserved region 2 (CalB). Ca2+-binding motif present in phospholipases, protein kinases C, and synaptotamins (among others). Some do not appear to contain Ca2+-binding sites. Particular C2s appear to bind phospholipids, inositol polyphosphates, and intracellular proteins. Unusual occurrence in perforin. Synaptotagmin and PLC C2s are permuted in sequence with respect to N- and C-terminal beta strands. SMART detects C2 domains using one or both of two profiles.
• smart SH3 55aa 2e-16 in ref transcript
  • Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.
• smart SH3 55aa 4e-13 in ref transcript
• smart SH3 56aa 1e-12 in ref transcript
• smart SH3 53aa 3e-12 in ref transcript
• smart SH3 61aa 5e-09 in ref transcript
• Changed! pfam SMC_N 227aa 3e-05 in ref transcript
  • RecF/RecN/SMC N terminal domain. This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.
• smart PH 109aa 7e-05 in ref transcript
  • Pleckstrin homology domain. Domain commonly found in eukaryotic signalling proteins. The domain family possesses multiple functions including the abilities to bind inositol phosphates, and various proteins. PH domains have been found to possess inserted domains (such as in PLC gamma, syntrophins) and to be inserted within other domains. Mutations in Brutons tyrosine kinase (Btk) within its PH domain cause X-linked agammaglobulinaemia (XLA) in patients. Point mutations cluster into the positively charged end of the molecule around the predicted binding site for phosphatidylinositol lipids.
• COG ROM1 255aa 6e-11 in ref transcript
  • RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms].
• COG COG5038 96aa 3e-08 in ref transcript
  • Ca2+-dependent lipid-binding protein, contains C2 domain [General function prediction only].
• Changed! COG Smc 227aa 1e-05 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].
• Changed! TIGR SMC_prok_B 200aa 5e-08 in modified transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• Changed! COG Smc 200aa 2e-08 in modified transcript

JARID1A

• rs.JARID1A.F1 rs.JARID1A.R1 241 323
• NCBIGene 36.3 5927
• Single exon skipping, size difference: 82
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_001042603

• cd BAH_plant_2 30aa 0.003 in ref transcript
  • BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
• pfam PLU-1 333aa 1e-106 in ref transcript
  • PLU-1-like protein. Sequences in this family bear similarity to the central region of PLU-1. This is a nuclear protein that may have a role in DNA-binding and transcription, and is closely associated with the malignant phenotype of breast cancer. This region is found in various other Jumonji/ARID domain-containing proteins (see pfam02373, pfam01388).
• pfam JmjC 117aa 2e-47 in ref transcript
  • JmjC domain. The JmjC domain belongs to the Cupin superfamily. JmjC-domain proteins may be protein hydroxylases that catalyse a novel histone modification.
• pfam ARID 109aa 2e-33 in ref transcript
  • ARID/BRIGHT DNA binding domain. This domain is know as ARID for AT-Rich Interaction Domain, and also known as the BRIGHT domain.
• pfam zf-C5HC2 54aa 1e-19 in ref transcript
  • C5HC2 zinc finger. Predicted zinc finger with eight potential zinc ligand binding residues. This domain is found in Jumonji. This domain may have a DNA binding function.
• pfam PHD 49aa 1e-11 in ref transcript
  • PHD-finger. PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
• smart JmjN 35aa 2e-09 in ref transcript
  • Small domain found in the jumonji family of transcription factors. To date, this domain always co-occurs with the JmjC domain (although the reverse is not true).
• Changed! pfam PHD 47aa 3e-06 in ref transcript
• smart PHD 52aa 4e-05 in ref transcript
  • PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RI NG finger and the FYV E finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BR OMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RI NG fingers misidentified as PHD fingers.

JARID1A

• rs.JARID1A.F2 rs.JARID1A.R2 100 115
• NCBIGene 36.3 5927
• Alternative 5-prime and 3-prime, size difference: 15
• Inclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_001042603

• cd BAH_plant_2 30aa 0.003 in ref transcript
  • BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
• pfam PLU-1 333aa 1e-106 in ref transcript
  • PLU-1-like protein. Sequences in this family bear similarity to the central region of PLU-1. This is a nuclear protein that may have a role in DNA-binding and transcription, and is closely associated with the malignant phenotype of breast cancer. This region is found in various other Jumonji/ARID domain-containing proteins (see pfam02373, pfam01388).
• pfam JmjC 117aa 2e-47 in ref transcript
  • JmjC domain. The JmjC domain belongs to the Cupin superfamily. JmjC-domain proteins may be protein hydroxylases that catalyse a novel histone modification.
• pfam ARID 109aa 2e-33 in ref transcript
  • ARID/BRIGHT DNA binding domain. This domain is know as ARID for AT-Rich Interaction Domain, and also known as the BRIGHT domain.
• pfam zf-C5HC2 54aa 1e-19 in ref transcript
  • C5HC2 zinc finger. Predicted zinc finger with eight potential zinc ligand binding residues. This domain is found in Jumonji. This domain may have a DNA binding function.
• pfam PHD 49aa 1e-11 in ref transcript
  • PHD-finger. PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
• smart JmjN 35aa 2e-09 in ref transcript
  • Small domain found in the jumonji family of transcription factors. To date, this domain always co-occurs with the JmjC domain (although the reverse is not true).
• pfam PHD 47aa 3e-06 in ref transcript
• smart PHD 52aa 4e-05 in ref transcript
  • PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RI NG finger and the FYV E finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BR OMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RI NG fingers misidentified as PHD fingers.

JMJD1C

• rs.JMJD1C.F1 rs.JMJD1C.R1 260 314
• NCBIGene 36.3 221037
• Alternative 3-prime, size difference: 54
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_032776

• pfam JmjC 93aa 6e-08 in ref transcript
  • JmjC domain. The JmjC domain belongs to the Cupin superfamily. JmjC-domain proteins may be protein hydroxylases that catalyse a novel histone modification.

KCNG1

• rs.KCNG1.F1 rs.KCNG1.R1 103 377
• NCBIGene 36.3 3755
• Exon skipping and alternative 3-prime or 5-prime, size difference: 274
• Inclusion in 5'UTR, Inclusion in 5'UTR
• Reference transcript: NM_002237

• pfam K_tetra 97aa 6e-27 in ref transcript
  • K+ channel tetramerisation domain. The N-terminal, cytoplasmic tetramerisation domain (T1) of voltage-gated K+ channels encodes molecular determinants for subfamily-specific assembly of alpha-subunits into functional tetrameric channels. It is distantly related to the BTB/POZ domain pfam00651.
• pfam Ion_trans 190aa 7e-13 in ref transcript
  • Ion transport protein. This family contains Sodium, Potassium, Calcium ion channels. This family is 6 transmembrane helices in which the last two helices flank a loop which determines ion selectivity. In some sub-families (e.g. Na channels) the domain is repeated four times, whereas in others (e.g. K channels) the protein forms as a tetramer in the membrane. A bacterial structure of the protein is known for the last two helices but is not the Pfam family due to it lacking the first four helices.
• PRK PRK10537 91aa 1e-09 in ref transcript
  • voltage-gated potassium channel; Provisional.

KCNIP2

• rs.KCNIP2.F1 rs.KCNIP2.R1 102 147
• NCBIGene 36.3 30819
• Alternative 3-prime, size difference: 45
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_014591

• cd EFh 63aa 6e-08 in ref transcript
  • EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers.
• cd EFh 72aa 1e-07 in ref transcript
• smart EH 87aa 7e-04 in ref transcript
  • Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
• COG FRQ1 167aa 3e-18 in ref transcript
  • Ca2+-binding protein (EF-Hand superfamily) [Signal transduction mechanisms / Cytoskeleton / Cell division and chromosome partitioning / General function prediction only].

KCNIP2

• rs.KCNIP2.F2 rs.KCNIP2.R2 119 140
• NCBIGene 36.3 30819
• Alternative 3-prime, size difference: 21
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_014591

• cd EFh 63aa 6e-08 in ref transcript
  • EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers.
• cd EFh 72aa 1e-07 in ref transcript
• smart EH 87aa 7e-04 in ref transcript
  • Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
• Changed! COG FRQ1 167aa 3e-18 in ref transcript
  • Ca2+-binding protein (EF-Hand superfamily) [Signal transduction mechanisms / Cytoskeleton / Cell division and chromosome partitioning / General function prediction only].
• Changed! COG FRQ1 174aa 1e-17 in modified transcript

KCNJ16

• rs.KCNJ16.F1 rs.KCNJ16.R1 159 240
• NCBIGene 36.3 3773
• Exon skipping and alternative 3-prime or 5-prime, size difference: 81
• Inclusion in 5'UTR, Exclusion in 5'UTR
• Reference transcript: NM_018658

• pfam IRK 315aa 1e-152 in ref transcript
  • Inward rectifier potassium channel.

KCNK2

• rs.KCNK2.F1 rs.KCNK2.R1 149 273
• NCBIGene 36.3 3776
• Alternative 5-prime, size difference: 124
• Exclusion of the protein initiation site
• Reference transcript: NM_001017425

• pfam Ion_trans_2 52aa 2e-13 in ref transcript
  • Ion channel. This family includes the two membrane helix type ion channels found in bacteria.
• pfam Ion_trans_2 60aa 7e-09 in ref transcript

KCNMA1

• rs.KCNMA1.F1 rs.KCNMA1.R1 100 112
• NCBIGene 36.3 3778
• Single exon skipping, size difference: 12
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001014797

• pfam BK_channel_a 99aa 5e-29 in ref transcript
  • Calcium-activated BK potassium channel alpha subunit.
• pfam Ion_trans 172aa 8e-14 in ref transcript
  • Ion transport protein. This family contains Sodium, Potassium, Calcium ion channels. This family is 6 transmembrane helices in which the last two helices flank a loop which determines ion selectivity. In some sub-families (e.g. Na channels) the domain is repeated four times, whereas in others (e.g. K channels) the protein forms as a tetramer in the membrane. A bacterial structure of the protein is known for the last two helices but is not the Pfam family due to it lacking the first four helices.
• pfam TrkA_N 114aa 0.004 in ref transcript
  • TrkA-N domain. This domain is found in a wide variety of proteins. These protein include potassium channels, phosphoesterases, and various other transporters. This domain binds to NAD.
• PRK PRK10537 76aa 7e-11 in ref transcript
  • voltage-gated potassium channel; Provisional.

KDELR2

• rs.KDELR2.F1 rs.KDELR2.R1 280 533
• NCBIGene 36.3 11014
• Single exon skipping, size difference: 253
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_006854

• Changed! pfam ER_lumen_recept 143aa 3e-50 in ref transcript
  • ER lumen protein retaining receptor.
• Changed! COG ERD2 212aa 3e-51 in ref transcript
  • ER lumen protein retaining receptor [Intracellular trafficking and secretion].
• Changed! pfam ER_lumen_recept 90aa 6e-30 in modified transcript
• Changed! COG ERD2 117aa 2e-24 in modified transcript

KIAA0232

• rs.KIAA0232.F1 rs.KIAA0232.R1 198 282
• NCBIGene 36.3 9778
• Single exon skipping, size difference: 84
• Exclusion in 5'UTR
• Reference transcript: NM_014743

KIAA1191

• rs.KIAA1191.F1 rs.KIAA1191.R1 195 282
• NCBIGene 36.3 57179
• Single exon skipping, size difference: 87
• Exclusion of the protein initiation site
• Reference transcript: NM_020444

KIAA1191

• rs.KIAA1191.F2 rs.KIAA1191.R2 205 313
• NCBIGene 36.3 57179
• Single exon skipping, size difference: 108
• Exclusion in 5'UTR
• Reference transcript: NM_020444

KIAA1217

• rs.KIAA1217.F1 rs.KIAA1217.R1 297 402
• NCBIGene 36.3 56243
• Single exon skipping, size difference: 105
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_019590

KIAA1543

• rs.KIAA1543.F1 rs.KIAA1543.R1 196 277
• NCBIGene 36.3 57662
• Multiple exon skipping, size difference: 81
• Exclusion in the protein (no frameshift), Exclusion in the protein (no frameshift)
• Reference transcript: NM_001080429

• pfam DUF1781 127aa 2e-68 in ref transcript
  • Protein of unknown function (DUF1781). This is a family of uncharacterised proteins. The structure of a murine hypothetical protein from RIKEN cDNA has shown it to adopt a mainly beta barrel structure with an alpha hairpin.
• TIGR PDHac_trf_mito 71aa 0.004 in ref transcript
  • This model represents one of several closely related clades of the dihydrolipoamide acetyltransferase subunit of the pyruvate dehydrogenase complex. It includes sequences from mitochondria and from alpha and beta branches of the proteobacteria, as well as from some other bacteria. Sequences from Gram-positive bacteria are not included. The non-enzymatic homolog protein X, which serves as an E3 component binding protein, falls within the clade phylogenetically but is rejected by its low score.

KIAA1833

• rs.KIAA1833.F1 rs.KIAA1833.R1 107 227
• NCBIGene 36.3 727957
• Single exon skipping, size difference: 120
• Exclusion in 5'UTR
• Reference transcript: NM_032450

KIF13A

• rs.KIF13A.F1 rs.KIF13A.R1 134 173
• NCBIGene 36.3 63971
• Single exon skipping, size difference: 39
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_022113

• cd KISc_KIF1A_KIF1B 356aa 1e-152 in ref transcript
  • Kinesin motor domain, KIF1_like proteins. KIF1A (Unc104) transports synaptic vesicles to the nerve terminal, KIF1B has been implicated in transport of mitochondria. Both proteins are expressed in neurons. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. In contrast to the majority of dimeric kinesins, most KIF1A/Unc104 kinesins are monomeric motors. A lysine-rich loop in KIF1A binds to the negatively charged C-terminus of tubulin and compensates for the lack of a second motor domain, allowing KIF1A to move processively.
• cd FHA 98aa 8e-08 in ref transcript
  • Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins localize to the nucleus, where they participate in establishing or maintaining cell cycle checkpoints, DNA repair, or transcriptional regulation. Members of the FHA family include: Dun1, Rad53, Cds1, Mek1, KAPP(kinase-associated protein phosphatase),and Ki-67 (a human nuclear protein related to cell proliferation).
• smart KISc 355aa 1e-129 in ref transcript
  • Kinesin motor, catalytic domain. ATPase. Microtubule-dependent molecular motors that play important roles in intracellular transport of organelles and in cell division.
• pfam FHA 65aa 3e-07 in ref transcript
  • FHA domain. The FHA (Forkhead-associated) domain is a phosphopeptide binding motif.
• TIGR SMC_prok_B 219aa 0.002 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• COG KIP1 359aa 1e-69 in ref transcript
  • Kinesin-like protein [Cytoskeleton].
• COG Smc 166aa 0.001 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].

KIF13A

• rs.KIF13A.F2 rs.KIF13A.R2 232 337
• NCBIGene 36.3 63971
• Single exon skipping, size difference: 105
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_022113

• cd KISc_KIF1A_KIF1B 356aa 1e-152 in ref transcript
  • Kinesin motor domain, KIF1_like proteins. KIF1A (Unc104) transports synaptic vesicles to the nerve terminal, KIF1B has been implicated in transport of mitochondria. Both proteins are expressed in neurons. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. In contrast to the majority of dimeric kinesins, most KIF1A/Unc104 kinesins are monomeric motors. A lysine-rich loop in KIF1A binds to the negatively charged C-terminus of tubulin and compensates for the lack of a second motor domain, allowing KIF1A to move processively.
• cd FHA 98aa 8e-08 in ref transcript
  • Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins localize to the nucleus, where they participate in establishing or maintaining cell cycle checkpoints, DNA repair, or transcriptional regulation. Members of the FHA family include: Dun1, Rad53, Cds1, Mek1, KAPP(kinase-associated protein phosphatase),and Ki-67 (a human nuclear protein related to cell proliferation).
• smart KISc 355aa 1e-129 in ref transcript
  • Kinesin motor, catalytic domain. ATPase. Microtubule-dependent molecular motors that play important roles in intracellular transport of organelles and in cell division.
• pfam FHA 65aa 3e-07 in ref transcript
  • FHA domain. The FHA (Forkhead-associated) domain is a phosphopeptide binding motif.
• TIGR SMC_prok_B 219aa 0.002 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• COG KIP1 359aa 1e-69 in ref transcript
  • Kinesin-like protein [Cytoskeleton].
• COG Smc 166aa 0.001 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].

KIT

• rs.KIT.F1 rs.KIT.R1 100 112
• NCBIGene 36.3 3815
• Alternative 5-prime, size difference: 12
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000222

• cd PTKc_Kit 376aa 0.0 in ref transcript
  • Catalytic Domain of the Protein Tyrosine Kinase, Kit. Protein Tyrosine Kinase (PTK) family; Kit (or c-Kit); catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Kit is a member of the Platelet Derived Growth Factor Receptor (PDGFR) subfamily of proteins, which are receptor tyr kinases (RTKs) containing an extracellular ligand-binding region with five immunoglobulin-like domains, a transmembrane segment, and an intracellular catalytic domain. The binding of Kit to its ligand, the stem-cell factor (SCF), leads to receptor dimerization, trans phosphorylation and activation, and intracellular signaling. Kit is important in the development of melanocytes, germ cells, mast cells, hematopoietic stem cells, the interstitial cells of Cajal, and the pacemaker cells of the GI tract. Kit signaling is involved in major cellular functions including cell survival, proliferation, differentiation, adhesion, and chemotaxis. Mutations in Kit, which result in constitutive ligand-independent activation, are found in human cancers such as gastrointestinal stromal tumor (GIST) and testicular germ cell tumor (TGCT). The aberrant expression of Kit and/or SCF is associated with other tumor types such as systemic mastocytosis and cancers of the breast, neurons, lung, prostate, colon, and rectum. Although the structure of the human Kit catalytic domain is known, it is excluded from this specific alignment model because it contains a deletion in its sequence.
• cd IG 75aa 6e-06 in ref transcript
  • Immunoglobulin domain family; members are components of immunoglobulins, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• pfam Pkinase_Tyr 154aa 4e-73 in ref transcript
  • Protein tyrosine kinase.
• smart STYKc 304aa 1e-30 in ref transcript
  • Protein kinase; unclassified specificity. Phosphotransferases. The specificity of this class of kinases can not be predicted. Possible dual-specificity Ser/Thr/Tyr kinase.
• smart IG_like 87aa 8e-09 in ref transcript
  • Immunoglobulin like. IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
• COG SPS1 206aa 2e-12 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].
• COG SPS1 136aa 2e-05 in ref transcript

KITLG

• rs.KITLG.F1 rs.KITLG.R1 452 536
• NCBIGene 36.3 4254
• Single exon skipping, size difference: 84
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000899

• Changed! pfam SCF 273aa 1e-134 in ref transcript
  • Stem cell factor. Stem cell factor (SCF) is a homodimer involved in hematopoiesis. SCF binds to and activates the SCF receptor (SCFR), a receptor tyrosine kinase. The crystal structure of human SCF has been resolved and a potential receptor-binding site identified.
• Changed! pfam SCF 245aa 1e-121 in modified transcript

KLK15

• rs.KLK15.F1 rs.KLK15.R1 186 323
• NCBIGene 36.3 55554
• Single exon skipping, size difference: 137
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_017509

• Changed! cd Tryp_SPc 228aa 3e-65 in ref transcript
  • Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
• Changed! smart Tryp_SPc 225aa 9e-73 in ref transcript
  • Trypsin-like serine protease. Many of these are synthesised as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. A few, however, are active as single chain molecules, and others are inactive due to substitutions of the catalytic triad residues.
• Changed! COG COG5640 235aa 4e-17 in ref transcript
  • Secreted trypsin-like serine protease [Posttranslational modification, protein turnover, chaperones].
• Changed! cd Tryp_SPc 127aa 5e-36 in modified transcript
• Changed! smart Tryp_SPc 127aa 2e-37 in modified transcript
• Changed! COG COG5640 99aa 0.001 in modified transcript

KLK2

• rs.KLK2.F1 rs.KLK2.R1 193 230
• NCBIGene 36.3 3817
• Alternative 5-prime, size difference: 37
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_005551

• Changed! cd Tryp_SPc 232aa 1e-59 in ref transcript
  • Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
• Changed! smart Tryp_SPc 230aa 2e-67 in ref transcript
  • Trypsin-like serine protease. Many of these are synthesised as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. A few, however, are active as single chain molecules, and others are inactive due to substitutions of the catalytic triad residues.
• Changed! COG COG5640 235aa 1e-12 in ref transcript
  • Secreted trypsin-like serine protease [Posttranslational modification, protein turnover, chaperones].
• Changed! cd Tryp_SPc 185aa 3e-48 in modified transcript
• Changed! smart Tryp_SPc 186aa 1e-54 in modified transcript
• Changed! COG COG5640 51aa 6e-06 in modified transcript

KLK3

• rs.KLK3.F1 rs.KLK3.R1 107 549
• NCBIGene 36.3 354
• Alternative 3-prime, size difference: 442
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_001648

• Changed! cd Tryp_SPc 232aa 3e-64 in ref transcript
  • Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
• Changed! smart Tryp_SPc 230aa 5e-71 in ref transcript
  • Trypsin-like serine protease. Many of these are synthesised as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. A few, however, are active as single chain molecules, and others are inactive due to substitutions of the catalytic triad residues.
• Changed! COG COG5640 250aa 1e-21 in ref transcript
  • Secreted trypsin-like serine protease [Posttranslational modification, protein turnover, chaperones].
• Changed! cd Tryp_SPc 186aa 8e-45 in modified transcript
• Changed! smart Tryp_SPc 186aa 9e-50 in modified transcript
• Changed! COG COG5640 205aa 2e-08 in modified transcript

KLK6

• rs.KLK6.F1 rs.KLK6.R1 150 198
• NCBIGene 36.3 5653
• Single exon skipping, size difference: 48
• Exclusion of the protein initiation site
• Reference transcript: NM_002774

• Changed! cd Tryp_SPc 218aa 6e-64 in ref transcript
  • Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
• Changed! smart Tryp_SPc 215aa 9e-72 in ref transcript
  • Trypsin-like serine protease. Many of these are synthesised as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. A few, however, are active as single chain molecules, and others are inactive due to substitutions of the catalytic triad residues.
• Changed! COG COG5640 239aa 1e-22 in ref transcript
  • Secreted trypsin-like serine protease [Posttranslational modification, protein turnover, chaperones].

KLK8

• rs.KLK8.F1 rs.KLK8.R1 264 399
• NCBIGene 36.3 11202
• Alternative 3-prime, size difference: 135
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_144505

• cd Tryp_SPc 223aa 2e-55 in ref transcript
  • Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
• smart Tryp_SPc 221aa 3e-63 in ref transcript
  • Trypsin-like serine protease. Many of these are synthesised as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. A few, however, are active as single chain molecules, and others are inactive due to substitutions of the catalytic triad residues.
• Changed! COG COG5640 236aa 4e-13 in ref transcript
  • Secreted trypsin-like serine protease [Posttranslational modification, protein turnover, chaperones].
• Changed! COG COG5640 244aa 1e-13 in modified transcript

KRAS

• rs.KRAS.F1 rs.KRAS.R1 182 306
• NCBIGene 36.3 3845
• Single exon skipping, size difference: 124
• Exclusion of the stop codon
• Reference transcript: NM_033360

• Changed! cd H_N_K_Ras_like 162aa 3e-89 in ref transcript
  • H-Ras/N-Ras/K-Ras subfamily. H-Ras, N-Ras, and K-Ras4A/4B are the prototypical members of the Ras family. These isoforms generate distinct signal outputs despite interacting with a common set of activators and effectors, and are strongly associated with oncogenic progression in tumor initiation. Mutated versions of Ras that are insensitive to GAP stimulation (and are therefore constitutively active) are found in a significant fraction of human cancers. Many Ras guanine nucleotide exchange factors (GEFs) have been identified. They are sequestered in the cytosol until activation by growth factors triggers recruitment to the plasma membrane or Golgi, where the GEF colocalizes with Ras. Active (GTP-bound) Ras interacts with several effector proteins that stimulate a variety of diverse cytoplasmic signaling activities. Some are known to positively mediate the oncogenic properties of Ras, including Raf, phosphatidylinositol 3-kinase (PI3K), RalGEFs, and Tiam1. Others are proposed to play negative regulatory roles in oncogenesis, including RASSF and NORE/MST1. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.
• Changed! smart RAS 163aa 2e-78 in ref transcript
  • Ras subfamily of RAS small GTPases. Similar in fold and function to the bacterial EF-Tu GTPase. p21Ras couples receptor Tyr kinases and G protein receptors to protein kinase cascades.
• Changed! COG COG1100 185aa 3e-18 in ref transcript
  • GTPase SAR1 and related small G proteins [General function prediction only].
• Changed! cd H_N_K_Ras_like 162aa 9e-90 in modified transcript
• Changed! smart RAS 161aa 6e-78 in modified transcript
• Changed! COG COG1100 163aa 5e-18 in modified transcript

KRT80

• rs.KRT80.F1 rs.KRT80.R1 107 142
• NCBIGene 36.3 144501
• Alternative 3-prime, size difference: 35
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_182507

• pfam Filament 312aa 1e-69 in ref transcript
  • Intermediate filament protein.
• COG Smc 253aa 2e-05 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].

KTN1

• rs.KTN1.F1 rs.KTN1.R1 121 208
• NCBIGene 36.3 3895
• Single exon skipping, size difference: 87
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001079521

• TIGR SMC_prok_B 226aa 1e-05 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• Changed! TIGR SMC_prok_B 278aa 2e-05 in ref transcript
• Changed! COG Smc 222aa 0.002 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].
• Changed! TIGR SMC_prok_B 272aa 3e-05 in modified transcript

KTN1

• rs.KTN1.F2 rs.KTN1.R2 163 247
• NCBIGene 36.3 3895
• Single exon skipping, size difference: 84
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001079521

• TIGR SMC_prok_B 226aa 1e-05 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• TIGR SMC_prok_B 278aa 2e-05 in ref transcript
• COG Smc 222aa 0.002 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].

KTN1

• rs.KTN1.F3 rs.KTN1.R3 148 204
• NCBIGene 36.3 3895
• Single exon skipping, size difference: 56
• Exclusion of the stop codon
• Reference transcript: NM_182926

• TIGR SMC_prok_B 226aa 1e-05 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• TIGR SMC_prok_B 278aa 2e-05 in ref transcript
• COG Smc 222aa 0.002 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].

KTN1

• rs.KTN1.F4 FOX.KTN1.R1 117 186
• NCBIGene 36.3 3895
• Single exon skipping, size difference: 69
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001079521

• TIGR SMC_prok_B 226aa 1e-05 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• Changed! TIGR SMC_prok_B 278aa 2e-05 in ref transcript
• Changed! COG Smc 222aa 0.002 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].
• Changed! TIGR SMC_prok_B 255aa 1e-04 in modified transcript

KTN1

• rs.KTN1.F5 rs.KTN1.R5 277 401
• NCBIGene 36.3 3895
• Single exon skipping, size difference: 124
• Exclusion in 5'UTR
• Reference transcript: NM_182926

• TIGR SMC_prok_B 226aa 1e-05 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• TIGR SMC_prok_B 278aa 2e-05 in ref transcript
• COG Smc 222aa 0.002 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].

L1CAM

• rs.L1CAM.F1 rs.L1CAM.R1 100 112
• NCBIGene 36.3 3897
• Single exon skipping, size difference: 12
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000425

• cd IGcam 85aa 4e-14 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• cd IGcam 88aa 9e-14 in ref transcript
• cd FN3 97aa 8e-12 in ref transcript
  • Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.
• cd IGcam 92aa 6e-11 in ref transcript
• cd FN3 86aa 7e-10 in ref transcript
• cd IGcam 87aa 1e-09 in ref transcript
• cd IGcam 86aa 6e-08 in ref transcript
• cd FN3 88aa 1e-06 in ref transcript
• cd FN3 82aa 7e-06 in ref transcript
• smart IGc2 64aa 1e-14 in ref transcript
  • Immunoglobulin C-2 Type.
• smart IG_like 82aa 1e-10 in ref transcript
  • Immunoglobulin like. IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
• pfam fn3 96aa 1e-10 in ref transcript
  • Fibronectin type III domain.
• smart IG_like 83aa 2e-10 in ref transcript
• pfam I-set 90aa 2e-10 in ref transcript
  • Immunoglobulin I-set domain.
• pfam fn3 90aa 9e-10 in ref transcript
• smart FN3 85aa 1e-09 in ref transcript
  • Fibronectin type 3 domain. One of three types of internal repeat within the plasma protein, fibronectin. The tenth fibronectin type III repeat contains a RGD cell recognition sequence in a flexible loop between 2 strands. Type III modules are present in both extracellular and intracellular proteins.
• pfam fn3 82aa 5e-08 in ref transcript
• smart IG_like 85aa 2e-07 in ref transcript

LAMA2

• rs.LAMA2.F1 rs.LAMA2.R1 100 112
• NCBIGene 36.3 3908
• Single exon skipping, size difference: 12
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000426

• cd LamG 150aa 1e-29 in ref transcript
  • Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules.
• cd LamG 153aa 2e-28 in ref transcript
• Changed! cd LamG 162aa 2e-25 in ref transcript
• cd LamG 163aa 4e-22 in ref transcript
• cd LamG 160aa 1e-19 in ref transcript
• cd EGF_Lam 47aa 1e-08 in ref transcript
  • Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies.
• cd EGF_Lam 45aa 1e-07 in ref transcript
• cd EGF_Lam 49aa 5e-07 in ref transcript
• cd EGF_Lam 53aa 7e-07 in ref transcript
• cd EGF_Lam 43aa 2e-06 in ref transcript
• cd EGF_Lam 50aa 3e-06 in ref transcript
• cd EGF_Lam 49aa 7e-06 in ref transcript
• cd EGF_Lam 58aa 1e-05 in ref transcript
• cd EGF_Lam 46aa 2e-05 in ref transcript
• cd EGF_Lam 53aa 1e-04 in ref transcript
• cd EGF_Lam 48aa 0.001 in ref transcript
• cd EGF_Lam 42aa 0.002 in ref transcript
• cd EGF_Lam 58aa 0.007 in ref transcript
• pfam Laminin_N 247aa 1e-88 in ref transcript
  • Laminin N-terminal (Domain VI).
• pfam Laminin_I 266aa 1e-65 in ref transcript
  • Laminin Domain I. coiled-coil structure. It has been suggested that the domains I and II from laminin A, B1 and B2 may come together to form a triple helical coiled-coil structure.
• pfam Laminin_G_1 129aa 8e-40 in ref transcript
  • Laminin G domain.
• smart LamB 133aa 5e-38 in ref transcript
  • Laminin B domain.
• smart LamB 136aa 1e-37 in ref transcript
• pfam Laminin_II 137aa 1e-36 in ref transcript
  • Laminin Domain II. It has been suggested that the domains I and II from laminin A, B1 and B2 may come together to form a triple helical coiled-coil structure.
• Changed! pfam Laminin_G_1 140aa 3e-34 in ref transcript
• pfam Laminin_G_1 141aa 4e-30 in ref transcript
• smart LamG 130aa 8e-29 in ref transcript
  • Laminin G domain.
• pfam Laminin_G_1 142aa 1e-26 in ref transcript
• TIGR SMC_prok_B 521aa 1e-14 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• smart EGF_Lam 45aa 8e-10 in ref transcript
  • Laminin-type epidermal growth factor-like domai.
• smart EGF_Lam 47aa 1e-09 in ref transcript
• smart EGF_Lam 44aa 9e-08 in ref transcript
• pfam Laminin_EGF 47aa 1e-07 in ref transcript
  • Laminin EGF-like (Domains III and V). This family is like pfam00008 but has 8 conserved cysteines instead of 6.
• smart EGF_Lam 58aa 3e-07 in ref transcript
• smart EGF_Lam 44aa 1e-06 in ref transcript
• pfam Laminin_EGF 49aa 1e-06 in ref transcript
• smart EGF_Lam 44aa 2e-06 in ref transcript
• pfam Laminin_EGF 47aa 5e-06 in ref transcript
• pfam Laminin_EGF 41aa 8e-06 in ref transcript
• smart EGF_Lam 53aa 3e-05 in ref transcript
• pfam Laminin_EGF 56aa 3e-04 in ref transcript
• pfam Laminin_EGF 56aa 9e-04 in ref transcript
• COG SbcC 608aa 2e-20 in ref transcript
  • ATPase involved in DNA repair [DNA replication, recombination, and repair].
• Changed! cd LamG 158aa 2e-26 in modified transcript
• Changed! pfam Laminin_G_1 136aa 3e-32 in modified transcript

LAMA4

• rs.LAMA4.F1 rs.LAMA4.R1 99 116
• NCBIGene 36.3 3910
• Alternative 5-prime, size difference: 17
• Inclusion in 5'UTR
• Reference transcript: NM_001105206

• cd LamG 136aa 8e-30 in ref transcript
  • Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules.
• cd LamG 151aa 7e-25 in ref transcript
• cd LamG 159aa 6e-17 in ref transcript
• cd LamG 140aa 7e-15 in ref transcript
• cd LamG 178aa 8e-13 in ref transcript
• cd EGF_Lam 52aa 3e-11 in ref transcript
  • Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies.
• cd EGF_Lam 44aa 8e-08 in ref transcript
• cd EGF_Lam 46aa 5e-07 in ref transcript
• cd SPEC 197aa 3e-04 in ref transcript
  • Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here.
• pfam Laminin_I 248aa 1e-72 in ref transcript
  • Laminin Domain I. coiled-coil structure. It has been suggested that the domains I and II from laminin A, B1 and B2 may come together to form a triple helical coiled-coil structure.
• smart LamG 134aa 5e-31 in ref transcript
  • Laminin G domain.
• pfam Laminin_II 128aa 3e-30 in ref transcript
  • Laminin Domain II. It has been suggested that the domains I and II from laminin A, B1 and B2 may come together to form a triple helical coiled-coil structure.
• smart LamG 133aa 1e-26 in ref transcript
• smart LamG 138aa 6e-19 in ref transcript
• smart LamG 155aa 6e-16 in ref transcript
• pfam Laminin_G_2 114aa 4e-13 in ref transcript
  • Laminin G domain. This family includes the Thrombospondin N-terminal-like domain, a Laminin G subfamily.
• pfam Laminin_EGF 47aa 6e-11 in ref transcript
  • Laminin EGF-like (Domains III and V). This family is like pfam00008 but has 8 conserved cysteines instead of 6.
• TIGR SMC_prok_B 556aa 2e-09 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• smart EGF_Lam 37aa 3e-07 in ref transcript
  • Laminin-type epidermal growth factor-like domai.
• pfam Laminin_EGF 41aa 8e-07 in ref transcript
• pfam VSP 201aa 8e-04 in ref transcript
  • Giardia variant-specific surface protein.
• COG Smc 304aa 1e-11 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].
• PRK PRK02224 345aa 2e-06 in ref transcript
  • chromosome segregation protein; Provisional.

LAMA4

• rs.LAMA4.F2 rs.LAMA4.R2 127 148
• NCBIGene 36.3 3910
• Alternative 5-prime, size difference: 21
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001105206

• cd LamG 136aa 8e-30 in ref transcript
  • Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules.
• cd LamG 151aa 7e-25 in ref transcript
• cd LamG 159aa 6e-17 in ref transcript
• cd LamG 140aa 7e-15 in ref transcript
• cd LamG 178aa 8e-13 in ref transcript
• cd EGF_Lam 52aa 3e-11 in ref transcript
  • Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies.
• cd EGF_Lam 44aa 8e-08 in ref transcript
• cd EGF_Lam 46aa 5e-07 in ref transcript
• cd SPEC 197aa 3e-04 in ref transcript
  • Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here.
• pfam Laminin_I 248aa 1e-72 in ref transcript
  • Laminin Domain I. coiled-coil structure. It has been suggested that the domains I and II from laminin A, B1 and B2 may come together to form a triple helical coiled-coil structure.
• smart LamG 134aa 5e-31 in ref transcript
  • Laminin G domain.
• pfam Laminin_II 128aa 3e-30 in ref transcript
  • Laminin Domain II. It has been suggested that the domains I and II from laminin A, B1 and B2 may come together to form a triple helical coiled-coil structure.
• smart LamG 133aa 1e-26 in ref transcript
• smart LamG 138aa 6e-19 in ref transcript
• smart LamG 155aa 6e-16 in ref transcript
• pfam Laminin_G_2 114aa 4e-13 in ref transcript
  • Laminin G domain. This family includes the Thrombospondin N-terminal-like domain, a Laminin G subfamily.
• pfam Laminin_EGF 47aa 6e-11 in ref transcript
  • Laminin EGF-like (Domains III and V). This family is like pfam00008 but has 8 conserved cysteines instead of 6.
• TIGR SMC_prok_B 556aa 2e-09 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• smart EGF_Lam 37aa 3e-07 in ref transcript
  • Laminin-type epidermal growth factor-like domai.
• pfam Laminin_EGF 41aa 8e-07 in ref transcript
• pfam VSP 201aa 8e-04 in ref transcript
  • Giardia variant-specific surface protein.
• COG Smc 304aa 1e-11 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].
• PRK PRK02224 345aa 2e-06 in ref transcript
  • chromosome segregation protein; Provisional.

LARP4

• rs.LARP4.F1 rs.LARP4.R1 99 117
• NCBIGene 36.3 113251
• Alternative 3-prime, size difference: 18
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_199188

• cd RRM 67aa 0.004 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• smart LA 79aa 5e-29 in ref transcript
  • Domain in the RNA-binding Lupus La protein; unknown function.

LDB3

• rs.LDB3.F1 rs.LDB3.R1 100 289
• NCBIGene 36.3 11155
• Single exon skipping, size difference: 189
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_007078

• cd PDZ_signaling 77aa 3e-16 in ref transcript
  • PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of PDZ domains an N-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in proteases.
• smart PDZ 81aa 5e-17 in ref transcript
  • Domain present in PSD-95, Dlg, and ZO-1/2. Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities.
• pfam LIM 56aa 8e-12 in ref transcript
  • LIM domain. This family represents two copies of the LIM structural domain.
• pfam LIM 53aa 9e-10 in ref transcript
• pfam LIM 56aa 2e-08 in ref transcript
• smart ZM 26aa 3e-05 in ref transcript
  • ZASP-like motif. Short motif (26 amino acids) present in an alpha-actinin-binding protein, ZASP, and similar molecules.

LDB3

• rs.LDB3.F2 rs.LDB3.R2 381 522
• NCBIGene 36.3 11155
• Mutually exclusive exon skipping, size difference: 141
• Inclusion in the protein causing a frameshift, Inclusion in the protein (no stop codon or frameshift), Exclusion in the protein causing a frameshift
• Reference transcript: NM_007078

• cd PDZ_signaling 77aa 3e-16 in ref transcript
  • PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of PDZ domains an N-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in proteases.
• smart PDZ 81aa 5e-17 in ref transcript
  • Domain present in PSD-95, Dlg, and ZO-1/2. Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities.
• pfam LIM 56aa 8e-12 in ref transcript
  • LIM domain. This family represents two copies of the LIM structural domain.
• pfam LIM 53aa 9e-10 in ref transcript
• pfam LIM 56aa 2e-08 in ref transcript
• Changed! smart ZM 26aa 3e-05 in ref transcript
  • ZASP-like motif. Short motif (26 amino acids) present in an alpha-actinin-binding protein, ZASP, and similar molecules.
• Changed! smart ZM 26aa 3e-06 in modified transcript

LGALS9

• rs.LGALS9.F1 rs.LGALS9.R1 111 207
• NCBIGene 36.3 3965
• Single exon skipping, size difference: 96
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_009587

• cd GLECT 131aa 2e-36 in ref transcript
  • Galectin/galactose-binding lectin. This domain exclusively binds beta-galactosides, such as lactose, and does not require metal ions for activity. GLECT domains occur as homodimers or tandemly repeated domains. They are developmentally regulated and may be involved in differentiation, cell-cell interaction and cellular regulation.
• cd GLECT 128aa 5e-33 in ref transcript
• smart GLECT 131aa 4e-40 in ref transcript
  • Galectin. Galectin - galactose-binding lectin.
• pfam Gal-bind_lectin 128aa 3e-35 in ref transcript
  • Galactoside-binding lectin. This family contains galactoside binding lectins. The family also includes enzymes such as human eosinophil lysophospholipase (EC:3.1.1.5).

LILRB5

• rs.LILRB5.F1 rs.LILRB5.R1 125 425
• NCBIGene 36.3 10990
• Single exon skipping, size difference: 300
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001081442

• smart IG_like 67aa 0.010 in ref transcript
  • Immunoglobulin like. IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.

LINS1

• rs.LINS1.F1 rs.LINS1.R1 199 308
• NCBIGene 36.3 55180
• Single exon skipping, size difference: 109
• Exclusion in 5'UTR
• Reference transcript: NM_018148

LOC100129583

• rs.LOC100129583.F1 rs.LOC100129583.R1 404 449
• NCBIGene 36.3 100129583
• Alternative 5-prime, size difference: 45
• Exclusion in the protein (no frameshift)
• Reference transcript: XM_001721012

LOC100129720

• rs.LOC100129720.F1 rs.LOC100129720.R1 286 391
• NCBIGene 36.3 100129720
• Alternative 3-prime, size difference: 105
• Exclusion in the protein (no frameshift)
• Reference transcript: XM_001725772

LOC100130008

• rs.LOC100130008.F1 rs.LOC100130008.R1 199 316
• NCBIGene 36.3 100130008
• Alternative 5-prime, size difference: 117
• Exclusion in 5'UTR
• Reference transcript: XM_001725170

LOC100130771

• rs.LOC100130771.F1 rs.LOC100130771.R1 131 299
• NCBIGene 36.3 100130771
• Alternative 3-prime, size difference: 168
• Exclusion of the stop codon
• Reference transcript: XM_001725809

LOC100130890

• rs.LOC100130890.F1 rs.LOC100130890.R1 180 266
• NCBIGene 36.3 100130890
• Single exon skipping, size difference: 86
• Exclusion in 5'UTR
• Reference transcript: XM_001721588

• cd RHOD_HSP67B2 67aa 9e-15 in ref transcript
  • Member of the Rhodanese Homology Domain superfamily. This CD includes the heat shock protein 67B2 of Drosophila melanogaster and other similar proteins, many of which are uncharacterized.
• pfam Rhodanese 63aa 9e-06 in ref transcript
  • Rhodanese-like domain. Rhodanese has an internal duplication. This Pfam represents a single copy of this duplicated domain. The domain is found as a single copy in other proteins, including phosphatases and ubiquitin C-terminal hydrolases.
• PRK PRK07878 58aa 4e-05 in ref transcript
  • molybdopterin biosynthesis-like protein MoeZ; Validated.

LOC100131626

• rs.LOC100131626.F1 rs.LOC100131626.R1 287 340
• NCBIGene 36.3 100131626
• Alternative 3-prime, size difference: 53
• Exclusion in the protein causing a frameshift
• Reference transcript: XM_001726222

LOC100132134

• rs.LOC100132134.F1 rs.LOC100132134.R1 112 173
• NCBIGene 36.3 100132134
• Alternative 5-prime, size difference: 61
• Exclusion in the protein causing a frameshift
• Reference transcript: XM_001719469

• Changed! pfam Glyco_hydro_2 61aa 8e-04 in ref transcript
  • Glycosyl hydrolases family 2, immunoglobulin-like beta-sandwich domain. This family contains beta-galactosidase, beta-mannosidase and beta-glucuronidase activities.

LOC100132215

• rs.LOC100132215.F1 rs.LOC100132215.R1 144 259
• NCBIGene 36.3 100132215
• Alternative 5-prime and 3-prime, size difference: 115
• Exclusion in 5'UTR, Exclusion in 5'UTR
• Reference transcript: XM_001725462

LOC100132352

• rs.LOC100132352.F1 rs.LOC100132352.R1 138 177
• NCBIGene 36.3 100132352
• Alternative 3-prime, size difference: 39
• Exclusion of the stop codon
• Reference transcript: XM_001720717

LOC100132565

• rs.LOC100132565.F1 rs.LOC100132565.R1 149 242
• NCBIGene 36.3 100132565
• Exon skipping and alternative 3-prime or 5-prime, size difference: 93
• Inclusion in the protein (no stop codon or frameshift), Inclusion in the protein (no stop codon or frameshift), Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: XM_001724162

• TIGR SMC_prok_A 151aa 0.003 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent.

LOC100132771

• rs.LOC100132771.F1 rs.LOC100132771.R1 408 487
• NCBIGene 36.3 100132771
• Alternative 3-prime, size difference: 79
• Inclusion in 3'UTR
• Reference transcript: XM_001719907

LOC116412

• rs.LOC116412.F1 rs.LOC116412.R1 158 260
• NCBIGene 36.3 116412
• Alternative 5-prime, size difference: 102
• Exclusion in 5'UTR
• Reference transcript: XM_375665

• pfam zf-C2H2 23aa 0.006 in ref transcript
  • Zinc finger, C2H2 type. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter.
• COG COG5048 156aa 5e-06 in ref transcript
  • FOG: Zn-finger [General function prediction only].
• COG COG5048 217aa 3e-05 in ref transcript

LOC26010

• rs.LOC26010.F1 rs.LOC26010.R1 175 382
• NCBIGene 36.3 26010
• Single exon skipping, size difference: 207
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_015535

• Changed! pfam DUF1387 310aa 1e-124 in ref transcript
  • Protein of unknown function (DUF1387). This family represents a conserved region approximately 300 residues long within a number of hypothetical proteins of unknown function that seem to be restricted to mammals.
• Changed! pfam DUF1387 163aa 1e-71 in modified transcript
• Changed! pfam DUF1387 90aa 2e-19 in modified transcript

LOC284701

• rs.LOC284701.F1 rs.LOC284701.R1 128 350
• NCBIGene 36.3 284701
• Alternative 5-prime, size difference: 222
• Exclusion in 5'UTR
• Reference transcript: XM_001723603

LOC391322

• rs.LOC391322.F1 rs.LOC391322.R1 227 266
• NCBIGene 36.3 391322
• Alternative 5-prime, size difference: 39
• Exclusion in the protein (no frameshift)
• Reference transcript: XM_001726974

• Changed! pfam MIF 108aa 5e-34 in ref transcript
  • Macrophage migration inhibitory factor (MIF).
• Changed! pfam MIF 95aa 8e-37 in modified transcript

LOC439992

• rs.LOC439992.F1 rs.LOC439992.R1 262 412
• NCBIGene 36.3 439992
• Alternative 5-prime and 3-prime, size difference: 150
• Inclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: XM_926528

• Changed! pfam Ribosomal_S3Ae 199aa 4e-89 in ref transcript
  • Ribosomal S3Ae family.
• Changed! COG RPS1A 217aa 2e-48 in ref transcript
  • Ribosomal protein S3AE [Translation, ribosomal structure and biogenesis].
• Changed! pfam Ribosomal_S3Ae 149aa 2e-55 in modified transcript
• Changed! COG RPS1A 167aa 6e-30 in modified transcript

LOC440434

• rs.LOC440434.F1 rs.LOC440434.R1 111 191
• NCBIGene 36.3 440434
• Single exon skipping, size difference: 80
• Inclusion in the protein causing a frameshift
• Reference transcript: XM_001725426

• Changed! pfam Peptidase_M1 285aa 3e-88 in ref transcript
  • Peptidase family M1. Members of this family are aminopeptidases. The members differ widely in specificity, hydrolysing acidic, basic or neutral N-terminal residues. This family includes leukotriene-A4 hydrolase, this enzyme also has an aminopeptidase activity.
• Changed! COG PepN 273aa 4e-44 in ref transcript
  • Aminopeptidase N [Amino acid transport and metabolism].
• Changed! pfam Peptidase_M1 93aa 5e-10 in modified transcript

LOC51149

• rs.LOC51149.F1 rs.LOC51149.R1 146 311
• NCBIGene 36.3 51149
• Multiple exon skipping, size difference: 165
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_016175

LOC642393

• rs.LOC642393.F1 rs.LOC642393.R1 212 305
• NCBIGene 36.3 642393
• Alternative 3-prime, size difference: 93
• Inclusion in the protein causing a new stop codon
• Reference transcript: XM_001724428

• Changed! TIGR rplT_bact 73aa 4e-11 in ref transcript
  • This protein binds directly to 23s ribosomal RNA and is necessary for the in vitro assembly process of the 50s ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit. GO process changed accordingly (SS 5/09/03).
• Changed! PRK rplT 69aa 1e-11 in ref transcript
  • 50S ribosomal protein L20; Provisional.
• Changed! TIGR rplT_bact 75aa 3e-12 in modified transcript
• Changed! PRK rplT 71aa 1e-12 in modified transcript

LOC642393

• rs.LOC642393.F2 rs.LOC642393.R2 144 489
• NCBIGene 36.3 642393
• Alternative 3-prime, size difference: 345
• Inclusion in the protein causing a new stop codon
• Reference transcript: XM_001724426

• Changed! TIGR rplT_bact 98aa 2e-19 in ref transcript
  • This protein binds directly to 23s ribosomal RNA and is necessary for the in vitro assembly process of the 50s ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit. GO process changed accordingly (SS 5/09/03).
• Changed! PRK rplT 97aa 2e-22 in ref transcript
  • 50S ribosomal protein L20; Provisional.
• Changed! TIGR rplT_bact 74aa 5e-12 in modified transcript
• Changed! PRK rplT 70aa 2e-12 in modified transcript

LOC643680

• rs.LOC643680.F1 rs.LOC643680.R1 227 427
• NCBIGene 36.3 643680
• Alternative 3-prime, size difference: 200
• Exclusion of the stop codon
• Reference transcript: XM_931901

• pfam CD20 40aa 2e-04 in ref transcript
  • CD20/IgE Fc receptor beta subunit family. This family includes the CD20 protein and the beta subunit of the high affinity receptor for IgE Fc. The high affinity receptor for IgE is a tetrameric structure consisting of a single IgE-binding alpha subunit, a single beta subunit, and two disulfide-linked gamma subunits. The alpha subunit of Fc epsilon RI and most Fc receptors are homologous members of the Ig superfamily. By contrast, the beta and gamma subunits from Fc epsilon RI are not homologous to the Ig superfamily. Both molecules have four putative transmembrane segments and a probably topology where both amino- and carboxy termini protrude into the cytoplasm.

LOC653117

• rs.LOC653117.F1 rs.LOC653117.R1 101 449
• NCBIGene 36.3 653117
• Single exon skipping, size difference: 348
• Exclusion in the protein (no frameshift)
• Reference transcript: XM_001722839

• smart SPRY 123aa 3e-16 in ref transcript
  • Domain in SPla and the RYanodine Receptor. Domain of unknown function. Distant homologues are domains in butyrophilin/marenostrin/pyrin homologues.
• smart PRY 50aa 2e-10 in ref transcript
  • associated with SPRY domains.
• Changed! pfam V-set 106aa 6e-07 in ref transcript
  • Immunoglobulin V-set domain. This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.

LOC653188

• rs.LOC653188.F1 rs.LOC653188.R1 250 311
• NCBIGene 36.3 653188
• Alternative 5-prime, size difference: 61
• Exclusion in the protein causing a frameshift
• Reference transcript: XM_001721330

• Changed! pfam Glyco_hydro_2 61aa 9e-05 in ref transcript
  • Glycosyl hydrolases family 2, immunoglobulin-like beta-sandwich domain. This family contains beta-galactosidase, beta-mannosidase and beta-glucuronidase activities.
• Changed! PRK PRK10150 62aa 0.006 in ref transcript
  • beta-D-glucuronidase; Provisional.

LOC653550

• rs.LOC653550.F1 rs.LOC653550.R1 191 315
• NCBIGene 36.3 653550
• Alternative 5-prime, size difference: 124
• Exclusion in the protein causing a frameshift
• Reference transcript: XM_001725815

LOC727737

• rs.LOC727737.F1 rs.LOC727737.R1 99 115
• NCBIGene 36.3 727737
• Alternative 5-prime, size difference: 16
• Exclusion in the protein causing a frameshift
• Reference transcript: XM_001126088

• pfam Peptidase_C54 301aa 1e-102 in ref transcript
  • Peptidase family C54.

LOC727761

• rs.LOC727761.F1 rs.LOC727761.R1 114 243
• NCBIGene 36.3 727761
• Exon skipping and alternative 3-prime or 5-prime, size difference: 129
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: XM_001126211

• Changed! cd TMPK 185aa 3e-23 in ref transcript
  • Thymidine monophosphate kinase (TMPK), also known as thymidylate kinase, catalyzes the phosphorylation of thymidine monophosphate (TMP) to thymidine diphosphate (TDP) utilizing ATP as its preferred phophoryl donor. TMPK represents the rate-limiting step in either de novo or salvage biosynthesis of thymidine triphosphate (TTP).
• Changed! pfam Thymidylate_kin 181aa 3e-54 in ref transcript
  • Thymidylate kinase.
• Changed! COG Tmk 188aa 2e-32 in ref transcript
  • Thymidylate kinase [Nucleotide transport and metabolism].
• Changed! cd TMPK 142aa 2e-11 in modified transcript
• Changed! pfam Thymidylate_kin 138aa 2e-31 in modified transcript
• Changed! COG Tmk 145aa 4e-16 in modified transcript

LOC727761

• rs.LOC727761.F2 rs.LOC727761.R2 111 183
• NCBIGene 36.3 727761
• Alternative 3-prime, size difference: 72
• Exclusion in the protein (no frameshift)
• Reference transcript: XM_001126211

• Changed! cd TMPK 185aa 3e-23 in ref transcript
  • Thymidine monophosphate kinase (TMPK), also known as thymidylate kinase, catalyzes the phosphorylation of thymidine monophosphate (TMP) to thymidine diphosphate (TDP) utilizing ATP as its preferred phophoryl donor. TMPK represents the rate-limiting step in either de novo or salvage biosynthesis of thymidine triphosphate (TTP).
• Changed! pfam Thymidylate_kin 181aa 3e-54 in ref transcript
  • Thymidylate kinase.
• Changed! COG Tmk 188aa 2e-32 in ref transcript
  • Thymidylate kinase [Nucleotide transport and metabolism].
• Changed! cd TMPK 161aa 4e-17 in modified transcript
• Changed! pfam Thymidylate_kin 157aa 7e-41 in modified transcript
• Changed! COG Tmk 164aa 2e-23 in modified transcript

LOC729870

• rs.LOC729870.F1 rs.LOC729870.R1 253 392
• NCBIGene 36.3 729870
• Alternative 3-prime, size difference: 139
• Inclusion in 5'UTR
• Reference transcript: XM_001725930

LOC92482

• rs.LOC92482.F1 rs.LOC92482.R1 147 304
• NCBIGene 36.3 92482
• Single exon skipping, size difference: 157
• Exclusion in the protein causing a frameshift
• Reference transcript: XM_001726024

LPHN1

• rs.LPHN1.F1 rs.LPHN1.R1 100 115
• NCBIGene 36.3 22859
• Single exon skipping, size difference: 15
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001008701

• pfam OLF 257aa 1e-105 in ref transcript
  • Olfactomedin-like domain.
• pfam Latrophilin 362aa 1e-100 in ref transcript
  • Latrophilin Cytoplasmic C-terminal region. This family consists of the cytoplasmic C-terminal region in latrophilin. Latrophilin is a synaptic Ca2+ independent alpha- latrotoxin (LTX) receptor and is a novel member of the secretin family of G-protein coupled receptors that are involved in secretion. Latrophilin mRNA is present only in neuronal tissue. Lactrophillin interacts with G-alpha O.
• pfam 7tm_2 247aa 5e-74 in ref transcript
  • 7 transmembrane receptor (Secretin family). This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling.
• pfam Gal_Lectin 81aa 2e-25 in ref transcript
  • Galactose binding lectin domain.
• smart GPS 53aa 3e-15 in ref transcript
  • G-protein-coupled receptor proteolytic site domain. Present in latrophilin/CL-1, sea urchin REJ and polycystin.
• smart HormR 64aa 7e-14 in ref transcript
  • Domain present in hormone receptors.

LRRCC1

• rs.LRRCC1.F1 rs.LRRCC1.R1 122 328
• NCBIGene 36.3 85444
• Single exon skipping, size difference: 206
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_033402

• Changed! pfam SMC_N 259aa 3e-05 in ref transcript
  • RecF/RecN/SMC N terminal domain. This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.
• Changed! TIGR SMC_prok_B 251aa 0.002 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• Changed! COG Smc 351aa 0.002 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].

LRRFIP2

• rs.LRRFIP2.F1 rs.LRRFIP2.R1 142 337
• NCBIGene 36.3 9209
• Multiple exon skipping, size difference: 195
• Exclusion in the protein (no frameshift), Exclusion in the protein (no frameshift)
• Reference transcript: NM_006309

• Changed! pfam DUF2051 354aa 1e-54 in ref transcript
  • Double stranded RNA binding protein (DUF2051). This is a novel protein identified as interacting with the leucine-rich repeat domain of human flightless-I, FliI protein.
• Changed! COG SbcC 333aa 3e-07 in ref transcript
  • ATPase involved in DNA repair [DNA replication, recombination, and repair].
• Changed! pfam DUF2051 289aa 1e-80 in modified transcript
• Changed! COG Smc 255aa 2e-06 in modified transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].

LRRN3

• rs.LRRN3.F1 rs.LRRN3.R1 267 374
• NCBIGene 36.3 54674
• Single exon skipping, size difference: 107
• Exclusion in 5'UTR
• Reference transcript: NM_001099660

• cd IGcam 89aa 2e-10 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• cd FN3 68aa 0.006 in ref transcript
  • Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.
• pfam I-set 88aa 9e-11 in ref transcript
  • Immunoglobulin I-set domain.
• pfam fn3 68aa 2e-05 in ref transcript
  • Fibronectin type III domain.
• smart LRRCT 52aa 2e-04 in ref transcript
  • Leucine rich repeat C-terminal domain.
• smart LRRNT 45aa 0.009 in ref transcript
  • Leucine rich repeat N-terminal domain.
• COG COG4886 201aa 4e-05 in ref transcript
  • Leucine-rich repeat (LRR) protein [Function unknown].

LSP1

• rs.LSP1.F1 rs.LSP1.R1 111 550
• NCBIGene 36.3 4046
• Alternative 5-prime, size difference: 439
• Exclusion in 5'UTR
• Reference transcript: NM_001013254

• pfam Caldesmon 92aa 4e-04 in ref transcript
  • Caldesmon.

LTBP4

• rs.LTBP4.F1 rs.LTBP4.R1 100 119
• NCBIGene 36.3 8425
• Alternative 3-prime, size difference: 19
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_001042544

• Changed! cd EGF_CA 34aa 0.003 in ref transcript
  • Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements.
• Changed! cd EGF_CA 33aa 0.007 in ref transcript
• Changed! smart EGF_CA 37aa 7e-05 in ref transcript
  • Calcium-binding EGF-like domain.
• Changed! smart EGF_CA 34aa 1e-04 in ref transcript
• Changed! smart EGF_CA 36aa 4e-04 in ref transcript
• Changed! pfam TB 41aa 6e-04 in ref transcript
  • TB domain. This domain is also known as the 8 cysteine domain. This family includes the hybrid domains. This cysteine rich repeat is found in TGF binding protein and fibrillin.
• Changed! smart EGF_CA 31aa 0.001 in ref transcript
• Changed! smart EGF_CA 38aa 0.004 in ref transcript
• Changed! pfam EGF_CA 41aa 0.004 in ref transcript
  • Calcium binding EGF domain.
• Changed! smart EGF_CA 37aa 0.008 in ref transcript

MAGEA6

• rs.MAGEA6.F1 rs.MAGEA6.R1 123 187
• NCBIGene 36.3 4105
• Alternative 3-prime, size difference: 64
• Inclusion in 5'UTR
• Reference transcript: NM_005363

• pfam MAGE 171aa 5e-69 in ref transcript
  • MAGE family. The MAGE (melanoma antigen-encoding gene) family are expressed in a wide variety of tumours but not in normal cells, with the exception of the male germ cells, placenta, and, possibly, cells of the developing embryo. The cellular function of this family is unknown. This family also contains the yeast protein, Nse3. The Nse3 protein is part of the Smc5-6 complex. Nse3 has been demonstrated to be important for meiosis.

MAGEC3

• rs.MAGEC3.F1 rs.MAGEC3.R1 143 536
• NCBIGene 36.3 139081
• Exon skipping and alternative 3-prime or 5-prime, size difference: 393
• Inclusion in the protein causing a new stop codon, Inclusion in the protein causing a frameshift, Inclusion in the protein (no stop codon or frameshift), Exclusion in the protein (no frameshift)
• Reference transcript: NM_138702

• Changed! pfam MAGE 114aa 2e-35 in ref transcript
  • MAGE family. The MAGE (melanoma antigen-encoding gene) family are expressed in a wide variety of tumours but not in normal cells, with the exception of the male germ cells, placenta, and, possibly, cells of the developing embryo. The cellular function of this family is unknown. This family also contains the yeast protein, Nse3. The Nse3 protein is part of the Smc5-6 complex. Nse3 has been demonstrated to be important for meiosis.
• pfam MAGE 113aa 4e-35 in ref transcript

MAGED4B

• rs.MAGED4B.F1 rs.MAGED4B.R1 102 114
• NCBIGene 36.3 81557
• Alternative 5-prime, size difference: 12
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_177535

• pfam MAGE 170aa 8e-75 in ref transcript
  • MAGE family. The MAGE (melanoma antigen-encoding gene) family are expressed in a wide variety of tumours but not in normal cells, with the exception of the male germ cells, placenta, and, possibly, cells of the developing embryo. The cellular function of this family is unknown. This family also contains the yeast protein, Nse3. The Nse3 protein is part of the Smc5-6 complex. Nse3 has been demonstrated to be important for meiosis.
• PRK PRK07003 168aa 0.002 in ref transcript
  • DNA polymerase III subunits gamma and tau; Validated.

MAGIX

• rs.MAGIX.F1 rs.MAGIX.R1 160 388
• NCBIGene 36.3 79917
• Single exon skipping, size difference: 228
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_024859

• Changed! cd PDZ_signaling 59aa 7e-10 in ref transcript
  • PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of PDZ domains an N-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in proteases.
• Changed! smart PDZ 56aa 2e-11 in ref transcript
  • Domain present in PSD-95, Dlg, and ZO-1/2. Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities.
• Changed! COG Prc 72aa 2e-04 in ref transcript
  • Periplasmic protease [Cell envelope biogenesis, outer membrane].
• Changed! cd PDZ_signaling 38aa 3e-06 in modified transcript
• Changed! smart PDZ 40aa 7e-08 in modified transcript

MAGIX

• rs.MAGIX.F2 rs.MAGIX.R2 129 174
• NCBIGene 36.3 79917
• Alternative 3-prime, size difference: 45
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_024859

• cd PDZ_signaling 59aa 7e-10 in ref transcript
  • PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of PDZ domains an N-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in proteases.
• smart PDZ 56aa 2e-11 in ref transcript
  • Domain present in PSD-95, Dlg, and ZO-1/2. Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities.
• COG Prc 72aa 2e-04 in ref transcript
  • Periplasmic protease [Cell envelope biogenesis, outer membrane].

MAGIX

• rs.MAGIX.F3 rs.MAGIX.R3 100 115
• NCBIGene 36.3 79917
• Alternative 3-prime, size difference: 15
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_024859

• cd PDZ_signaling 59aa 7e-10 in ref transcript
  • PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of PDZ domains an N-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in proteases.
• smart PDZ 56aa 2e-11 in ref transcript
  • Domain present in PSD-95, Dlg, and ZO-1/2. Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities.
• COG Prc 72aa 2e-04 in ref transcript
  • Periplasmic protease [Cell envelope biogenesis, outer membrane].

MAP2K5

• rs.MAP2K5.F1 rs.MAP2K5.R1 229 259
• NCBIGene 36.3 5607
• Single exon skipping, size difference: 30
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_145160

• Changed! cd PKc_MKK5 279aa 1e-172 in ref transcript
  • Protein kinases (PKs), MAP kinase kinase 5 (MKK5) subfamily, catalytic (c) domain. PKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine or tyrosine residues on protein substrates. The MKK5 subfamily is part of a larger superfamily that includes the catalytic domains of other protein serine/threonine kinases, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. The mitogen-activated protein (MAP) kinase signaling pathways are important mediators of cellular responses to extracellular signals. The pathways involve a triple kinase core cascade comprising of the MAP kinase (MAPK), which is phosphorylated and activated by a MAPK kinase (MAPKK or MKK), which itself is phosphorylated and activated by a MAPK kinase kinase (MAPKKK or MKKK). MKK5, also referred to as MEK5, is a dual-specificity PK that phosphorylates its downstream target, extracellular signal-regulated kinase 5 (ERK5), on specific threonine and tyrosine residues. MKK5 is activated by MEKK2 and MEKK3 in response to mitogenic and stress stimuli. The ERK5 cascade promotes cell proliferation, differentiation, neuronal survival, and neuroprotection. This cascade plays an essential role in heart development. Mice deficient in either ERK5 or MKK5 die around embryonic day 10 due to cardiovascular defects including underdevelopment of the myocardium. In addition, MKK5 is associated with metastasis and unfavorable prognosis in prostate cancer.
• cd PB1_Map2k5 91aa 3e-47 in ref transcript
  • PB1 domain is essential part of the mitogen-activated protein kinase kinase 5 (Map2k5, alias MEK5) one of the key member of the signaling kinases cascade which involved in angiogenesis and early cardiovascular development. The PB1 domain of Map2k5 interacts with the PB1 domain of another members of kinase cascade MEKK2 (or MEKK3). A canonical PB1-PB1 interaction, involving heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. The Map2k5 protein contains a type I PB1 domain.
• Changed! smart S_TKc 242aa 1e-62 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• pfam PB1 67aa 7e-10 in ref transcript
  • PB1 domain.
• Changed! COG SPS1 255aa 6e-32 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].
• Changed! cd PKc_MKK5 269aa 1e-163 in modified transcript
• Changed! smart S_TKc 232aa 1e-58 in modified transcript
• Changed! COG SPS1 245aa 3e-29 in modified transcript

MAP4K1

• rs.MAP4K1.F1 rs.MAP4K1.R1 154 252
• NCBIGene 36.3 11184
• Single exon skipping, size difference: 98
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_007181

• cd STKc_MAP4K3_like 260aa 1e-149 in ref transcript
  • Serine/threonine kinases (STKs), mitogen-activated protein kinase (MAPK) kinase kinase kinase 3 (MAPKKKK3 or MAP4K3)-like subfamily, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The MAP4K3-like subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. This subfamily includes MAP4K3, MAP4K1, MAP4K2, MAP4K5, and related proteins. Vertebrate members contain an N-terminal catalytic domain and a C-terminal citron homology (CNH) regulatory domain, similar to MAP4K4/6. MAP4Ks are involved in some MAPK signaling pathways that are important in mediating cellular responses to extracellular signals by activating a MAPK kinase kinase (MAPKKK or MAP3K or MKKK). Each MAPK cascade is activated either by a small GTP-binding protein or by an adaptor protein, which transmits the signal either directly to a MAP3K to start the triple kinase core cascade or indirectly through a mediator kinase, a MAP4K. MAP4K1, also called haematopoietic progenitor kinase 1 (HPK1), is a hematopoietic-specific STK involved in many cellular signaling cascades including MAPK, antigen receptor, apoptosis, growth factor, and cytokine signaling. It participates in the regulation of T cell receptor signaling and T cell-mediated immune responses. MAP4K2 was referred to as germinal center (GC) kinase because of its preferred location in GC B cells. MAP4K3 plays a role in the nutrient-responsive pathway of mTOR (mammalian target of rapamycin) signaling. It is required in the activation of S6 kinase by amino acids and for the phosphorylation of the mTOR-regulated inhibitor of eukaryotic initiation factor 4E. MAP4K5, also called germinal center kinase-related enzyme (GCKR), has been shown to activate the MAPK c-Jun N-terminal kinase (JNK).
• Changed! smart CNH 308aa 9e-84 in ref transcript
  • Domain found in NIK1-like kinases, mouse citron and yeast ROM1, ROM2. Unpublished observations.
• smart S_TKc 248aa 6e-69 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• COG SPS1 354aa 8e-37 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].
• Changed! smart CNH 308aa 5e-85 in modified transcript

MAPK10

• rs.MAPK10.F1 rs.MAPK10.R1 148 175
• NCBIGene 36.3 5602
• Alternative 5-prime, size difference: 27
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_138982

• Changed! cd S_TKc 297aa 1e-66 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• Changed! smart S_TKc 284aa 1e-67 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• Changed! PTZ PTZ00024 292aa 1e-34 in ref transcript
  • cyclin-dependent protein kinase; Provisional.

MAPK14

• rs.MAPK14.F1 rs.MAPK14.R1 159 238
• NCBIGene 36.3 1432
• Single exon skipping, size difference: 79
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_139012

• Changed! cd S_TKc 276aa 7e-66 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• Changed! smart S_TKc 265aa 4e-64 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• Changed! PTZ PTZ00024 269aa 5e-38 in ref transcript
  • cyclin-dependent protein kinase; Provisional.
• Changed! cd S_TKc 220aa 1e-62 in modified transcript
• Changed! smart S_TKc 209aa 2e-60 in modified transcript
• Changed! PTZ PTZ00024 213aa 3e-37 in modified transcript

MAPK14

• rs.MAPK14.F2 rs.MAPK14.R2 101 180
• NCBIGene 36.3 1432
• Single exon skipping, size difference: 79
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_139012

• Changed! cd S_TKc 276aa 7e-66 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• Changed! smart S_TKc 265aa 4e-64 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• Changed! PTZ PTZ00024 269aa 5e-38 in ref transcript
  • cyclin-dependent protein kinase; Provisional.
• Changed! cd S_TKc 220aa 1e-62 in modified transcript
• Changed! smart S_TKc 209aa 2e-60 in modified transcript
• Changed! PTZ PTZ00024 213aa 3e-37 in modified transcript

MAPK3

• rs.MAPK3.F1 rs.MAPK3.R1 155 287
• NCBIGene 36.3 5595
• Single exon skipping, size difference: 132
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_002746

• Changed! cd S_TKc 290aa 4e-68 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• Changed! smart S_TKc 279aa 1e-69 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• Changed! PTZ PTZ00024 300aa 5e-44 in ref transcript
  • cyclin-dependent protein kinase; Provisional.
• Changed! cd S_TKc 246aa 9e-68 in modified transcript
• Changed! smart S_TKc 235aa 1e-69 in modified transcript
• Changed! PTZ PTZ00024 256aa 3e-37 in modified transcript

MATK

• rs.MATK.F1 rs.MATK.R1 316 539
• NCBIGene 36.3 4145
• Single exon skipping, size difference: 223
• Exclusion of the protein initiation site
• Reference transcript: NM_139355

• cd PTKc_Chk 254aa 1e-146 in ref transcript
  • Catalytic Domain of the Protein Tyrosine Kinase, Csk homologous kinase. Protein Tyrosine Kinase (PTK) family; Csk homologous kinase (Chk); catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Csk subfamily kinases are cytoplasmic (or nonreceptor) tyr kinases containing the Src homology domains, SH3 and SH2, N-terminal to the catalytic tyr kinase domain. They negatively regulate the activity of Src kinases that are anchored to the plasma membrane. Chk is also referred to as megakaryocyte-associated tyrosine kinase (Matk). To inhibit Src kinases, Chk is translocated to the membrane via binding to specific transmembrane proteins, G-proteins, or adaptor proteins near the membrane. Chk inhibit Src kinases using a noncatalytic mechanism by simply binding to them. As a negative regulator of Src kinases, Chk may play important roles in cell proliferation, survival, and differentiation, and consequently, in cancer development and progression. Chk is expressed in brain and hematopoietic cells. Studies in mice reveal that Chk is not functionally redundant with Csk and that it plays an important role as a regulator of immune responses. Chk also plays a role in neural differentiation in a manner independent of Src by enhancing Mapk activation via Ras-mediated signaling.
• cd SH2 90aa 1e-19 in ref transcript
  • Src homology 2 domains; Signal transduction, involved in recognition of phosphorylated tyrosine (pTyr). SH2 domains typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites.
• cd SH3 43aa 0.009 in ref transcript
  • Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
• smart TyrKc 244aa 1e-99 in ref transcript
  • Tyrosine kinase, catalytic domain. Phosphotransferases. Tyrosine-specific kinase subfamily.
• smart SH2 81aa 2e-22 in ref transcript
  • Src homology 2 domains. Src homology 2 domains bind phosphotyrosine-containing polypeptides via 2 surface pockets. Specificity is provided via interaction with residues that are distinct from the phosphotyrosine. Only a single occurrence of a SH2 domain has been found in S. cerevisiae.
• smart SH3 45aa 1e-04 in ref transcript
  • Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.
• COG SPS1 218aa 4e-22 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].

MAZ

• rs.MAZ.F1 rs.MAZ.R1 299 524
• NCBIGene 36.3 4150
• Single exon skipping, size difference: 225
• Exclusion of the stop codon
• Reference transcript: NM_001042539

• COG SFP1 58aa 0.004 in ref transcript
  • Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning].

MBP

• rs.MBP.F1 rs.MBP.R1 115 148
• NCBIGene 36.3 4155
• Single exon skipping, size difference: 33
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001025101

• Changed! pfam Myelin_MBP 154aa 1e-59 in ref transcript
  • Myelin basic protein.
• Changed! pfam Myelin_MBP 143aa 8e-52 in modified transcript

MCL1

• rs.MCL1.F1 rs.MCL1.R1 133 381
• NCBIGene 36.3 4170
• Single exon skipping, size difference: 248
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_021960

• Changed! cd Bcl-2_like 144aa 7e-37 in ref transcript
  • Apoptosis regulator proteins of the Bcl-2 family, named after B-cell lymphoma 2. This alignment model spans what have been described as Bcl-2 homology regions BH1, BH2, BH3, and BH4. Many members of this family have an additional C-terminal transmembrane segment. Some homologous proteins, which are not included in this model, may miss either the BH4 (Bax, Bak) or the BH2 (Bcl-X(S)) region, and some appear to only share the BH3 region (Bik, Bim, Bad, Bid, Egl-1). This family is involved in the regulation of the outer mitochondrial membrane's permeability and in promoting or preventing the release of apoptogenic factors, which in turn may trigger apoptosis by activating caspases. Bcl-2 and the closely related Bcl-X(L) are anti-apoptotic key regulators of programmed cell death. They are assumed to function via heterodimeric protein-protein interactions, binding pro-apoptotic proteins such as Bad (BCL2-antagonist of cell death), Bid, and Bim, by specifically interacting with their BH3 regions. Interfering with this heterodimeric interaction via small-molecule inhibitors may prove effective in targeting various cancers. This family also includes the Caenorhabditis elegans Bcl-2 homolog CED-9, which binds to CED-4, the C. Elegans homolog of mammalian Apaf-1. Apaf-1, however, does not seem to be inhibited by Bcl-2 directly.
• Changed! pfam Bcl-2 100aa 5e-32 in ref transcript
  • Apoptosis regulator proteins, Bcl-2 family.
• Changed! cd Bcl-2_like 56aa 2e-04 in modified transcript

MED24

• rs.MED24.F1 rs.MED24.R1 124 146
• NCBIGene 36.3 9862
• Alternative 3-prime, size difference: 22
• Inclusion in 5'UTR
• Reference transcript: NM_014815

MED24

• rs.MED24.F2 rs.MED24.R2 108 147
• NCBIGene 36.3 9862
• Single exon skipping, size difference: 39
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_014815

MEN1

• rs.MEN1.F1 rs.MEN1.R1 103 118
• NCBIGene 36.3 4221
• Alternative 5-prime, size difference: 15
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_130803

• Changed! pfam Menin 615aa 0.0 in ref transcript
  • Menin. MEN1, the gene responsible for multiple endocrine neoplasia type 1, is a tumour suppressor gene that encodes a protein called Menin which may be an atypical GTPase stimulated by nm23.
• Changed! pfam Menin 610aa 0.0 in modified transcript

MGC13057

• rs.MGC13057.F1 rs.MGC13057.R1 139 158
• NCBIGene 36.3 84281
• Alternative 5-prime, size difference: 19
• Exclusion in 5'UTR
• Reference transcript: NM_032321

MGC45438

• rs.MGC45438.F1 rs.MGC45438.R1 102 460
• NCBIGene 36.3 146556
• Alternative 3-prime, size difference: 358
• Exclusion of the stop codon
• Reference transcript: NM_152459

MID1IP1

• rs.MID1IP1.F1 rs.MID1IP1.R1 143 247
• NCBIGene 36.3 58526
• Single exon skipping, size difference: 104
• Exclusion in 5'UTR
• Reference transcript: NM_001098790

• pfam Spot_14 182aa 9e-66 in ref transcript
  • Thyroid hormone-inducible hepatic protein Spot 14. This family consists of several thyroid hormone-inducible hepatic protein (Spot 14 or S14) sequences. Mainly expressed in tissues that synthesise triglycerides, the mRNA coding for Spot 14 has been shown to be increased in rat liver by insulin, dietary carbohydrates, glucose in hepatocyte culture medium, as well as thyroid hormone. In contrast, dietary fats and polyunsaturated fatty acids, have been shown to decrease the amount of Spot 14 mRNA, while an elevated level of cAMP acts as a dominant negative factor. In addition, liver-specific factors or chromatin organisation of the gene have been shown to contribute to the regulation of its expression. Spot 14 protein is thought to be required for induction of hepatic lipogenesis.

MIER1

• rs.MIER1.F1 rs.MIER1.R1 115 189
• NCBIGene 36.3 57708
• Single exon skipping, size difference: 74
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_001077700

• Changed! cd SANT 44aa 7e-04 in ref transcript
  • 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
• Changed! pfam ELM2 54aa 2e-09 in ref transcript
  • ELM2 domain. The ELM2 (Egl-27 and MTA1 homology 2) domain is a small domain of unknown function. It is found in the MTA1 protein that is part of the NuRD complex. The domain is usually found to the N terminus of a myb-like DNA binding domain pfam00249. ELM2 is also found associated with an ARID DNA binding domain pfam01388 in a protein from Arabidopsis thaliana. This suggests that ELM2 may also be involved in DNA binding, or perhaps is a protein-protein interaction domain.
• Changed! smart SANT 46aa 6e-05 in ref transcript
  • SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.

MITF

• rs.MITF.F1 rs.MITF.R1 97 115
• NCBIGene 36.3 4286
• Alternative 3-prime, size difference: 18
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_198159

• cd HLH 61aa 4e-11 in ref transcript
  • Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins.
• pfam HLH 54aa 3e-11 in ref transcript
  • Helix-loop-helix DNA-binding domain.

MIZF

• rs.MIZF.F1 rs.MIZF.R1 336 453
• NCBIGene 36.3 25988
• Single exon skipping, size difference: 117
• Exclusion in 5'UTR
• Reference transcript: NM_015517

• COG COG5236 133aa 0.002 in ref transcript
  • Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only].

MLLT4

• rs.MLLT4.F1 rs.MLLT4.R1 187 226
• NCBIGene 36.3 4301
• Exon skipping and alternative 3-prime or 5-prime, size difference: 39
• Exclusion in the protein (no frameshift), Exclusion in the protein (no frameshift)
• Reference transcript: NM_001040001

• cd AF6_RA_repeat1 112aa 3e-53 in ref transcript
  • The AF-6 protein (also known as afadin and canoe) is a multidomain cell junction protein that contains two N-terminal Ras-associating (RA) domains in addition to FHA (forkhead-associated), DIL (class V myosin homology region), and PDZ domains and a proline-rich region. AF6 acts downstream of the Egfr (Epidermal Growth Factor-receptor)/Ras signalling pathway and provides a link from Egfr to cytoskeletal elements.
• cd AF6_RA_repeat2 100aa 2e-42 in ref transcript
  • The AF-6 protein (also known as afadin and canoe) is a multidomain cell junction protein that contains two N-terminal Ras-associating (RA) domains in addition to FHA (forkhead-associated), DIL (class V myosin homology region), and PDZ domains and a proline-rich region. AF6 acts downstream of the Egfr (Epidermal Growth Factor-receptor)/Ras signalling pathway and provides a link from Egfr to cytoskeletal elements.
• cd PDZ_signaling 84aa 3e-12 in ref transcript
  • PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of PDZ domains an N-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in proteases.
• cd FHA 90aa 2e-05 in ref transcript
  • Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins localize to the nucleus, where they participate in establishing or maintaining cell cycle checkpoints, DNA repair, or transcriptional regulation. Members of the FHA family include: Dun1, Rad53, Cds1, Mek1, KAPP(kinase-associated protein phosphatase),and Ki-67 (a human nuclear protein related to cell proliferation).
• pfam DIL 107aa 5e-26 in ref transcript
  • DIL domain. The DIL domain has no known function.
• smart RA 94aa 7e-17 in ref transcript
  • Ras association (RalGDS/AF-6) domain. RasGTP effectors (in cases of AF6, canoe and RalGDS); putative RasGTP effectors in other cases. Kalhammer et al. have shown that not all RA domains bind RasGTP. Predicted structure similar to that determined, and that of the RasGTP-binding domain of Raf kinase. Predicted RA domains in PLC210 and nore1 found to bind RasGTP. Included outliers (Grb7, Grb14, adenylyl cyclases etc.).
• smart PDZ 88aa 4e-14 in ref transcript
  • Domain present in PSD-95, Dlg, and ZO-1/2. Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities.
• smart RA 100aa 2e-13 in ref transcript
• smart FHA 52aa 4e-08 in ref transcript
  • Forkhead associated domain. Found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain.
• COG Prc 133aa 0.001 in ref transcript
  • Periplasmic protease [Cell envelope biogenesis, outer membrane].

MLPH

• rs.MLPH.F1 rs.MLPH.R1 121 205
• NCBIGene 36.3 79083
• Single exon skipping, size difference: 84
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_024101

• pfam MOBP 68aa 2e-20 in ref transcript
  • Myelin-associated oligodendrocytic basic protein (MOBP). MOBP is abundantly expressed in central nervous system myelin, and shares several characteristics with myelin basic protein (MBP), in terms of regional distribution and function. MOBP has been shown to be essential for normal arrangement of the radial component in central nervous system myelin.

MMD2

• rs.MMD2.F1 rs.MMD2.R1 109 181
• NCBIGene 36.3 221938
• Alternative 3-prime, size difference: 72
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001100600

• Changed! TIGR hlyIII 225aa 1e-47 in ref transcript
  • This family includes proteins from pathogenic and non-pathogenic bacteria, Homo sapiens and Drosophila. In Bacillus cereus, a pathogen, it has been show to function as a channel-forming cytolysin. The human protein is expressed preferentially in mature macrophages, consistent with a role cytolytic role.
• Changed! COG COG1272 243aa 8e-22 in ref transcript
  • Predicted membrane protein, hemolysin III homolog [General function prediction only].
• Changed! TIGR hlyIII 201aa 2e-50 in modified transcript
• Changed! COG COG1272 219aa 6e-24 in modified transcript

MOBKL3

• rs.MOBKL3.F1 rs.MOBKL3.R1 123 186
• NCBIGene 36.3 25843
• Single exon skipping, size difference: 63
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_015387

• pfam Mob1_phocein 167aa 3e-61 in ref transcript
  • Mob1/phocein family. Mob1 is an essential Saccharomyces cerevisiae protein, identified from a two-hybrid screen, that binds Mps1p, a protein kinase essential for spindle pole body duplication and mitotic checkpoint regulation. Mob1 contains no known structural motifs; however MOB1 is a member of a conserved gene family and shares sequence similarity with a nonessential yeast gene, MOB2. Mob1 is a phosphoprotein in vivo and a substrate for the Mps1p kinase in vitro. Conditional alleles of MOB1 cause a late nuclear division arrest at restrictive temperature. This family also includes phocein, a rat protein that by yeast two hybrid interacts with striatin.

MOCS1

• rs.MOCS1.F1 rs.MOCS1.R1 100 115
• NCBIGene 36.3 4337
• Alternative 5-prime, size difference: 15
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_005942

• Changed! cd MoaC_PE 140aa 2e-40 in ref transcript
  • MoaC family, prokaryotic and eukaryotic. Members of this family are involved in molybdenum cofactor (Moco) biosynthesis, an essential cofactor of a diverse group of redox enzymes. MoaC, a small hexameric protein, converts, together with MoaA, a guanosine derivative to the precursor Z by inserting the carbon-8 of the purine between the 2' and 3' ribose carbon atoms, which is the first of three phases of Moco biosynthesis.
• cd Radical_SAM 198aa 2e-19 in ref transcript
  • Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster. Mechanistically, they share the transfer of a single electron from the iron-sulfur cluster to SAM, which leads to its reductive cleavage to methionine and a 5'-deoxyadenosyl radical, which, in turn, abstracts a hydrogen from the appropriately positioned carbon atom. Depending on the enzyme, SAM is consumed during this process or it is restored and reused. Radical SAM enzymes catalyze steps in metabolism, DNA repair, the biosynthesis of vitamins and coenzymes, and the biosynthesis of many antibiotics. Examples are biotin synthase (BioB), lipoyl synthase (LipA), pyruvate formate-lyase (PFL), coproporphyrinogen oxidase (HemN), lysine 2,3-aminomutase (LAM), anaerobic ribonucleotide reductase (ARR), and MoaA, an enzyme of the biosynthesis of molybdopterin.
• Changed! TIGR moaA 306aa 1e-114 in ref transcript
  • The model for this family describes molybdenum cofactor biosynthesis protein A, or MoaA, as found in bacteria. It does not include the family of probable functional equivalent proteins from the archaea. MoaA works together with MoaC to synthesize precursor Z from guanine.
• Changed! pfam MoaC 136aa 2e-43 in ref transcript
  • MoaC family. Members of this family are involved in molybdenum cofactor biosynthesis. However their molecular function is not known.
• Changed! PRK moaA 327aa 1e-116 in ref transcript
  • molybdenum cofactor biosynthesis protein A; Reviewed.
• Changed! PRK moaC 157aa 5e-48 in ref transcript
  • molybdenum cofactor biosynthesis protein C; Provisional.
• Changed! TIGR moaA 325aa 1e-114 in modified transcript
• Changed! PRK moaA 332aa 1e-117 in modified transcript

MORC4

• rs.MORC4.F1 rs.MORC4.R1 200 238
• NCBIGene 36.3 79710
• Alternative 5-prime, size difference: 38
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_024657

• cd HATPase_c 99aa 3e-04 in ref transcript
  • Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins.
• pfam zf-CW 46aa 3e-17 in ref transcript
  • CW-type Zinc Finger. This domain appears to be a zinc finger. The alignment shows four conserved cysteine residues and a conserved tryptophan. It was first identified by, and is predicted to be a "highly specialised mononuclear four-cysteine zinc finger...that plays a role in DNA binding and/or promoting protein-protein interactions in complicated eukaryotic processes including...chromatin methylation status and early embryonic development." Weak homology to pfam00628 further evidences these predictions (personal obs: C Yeats). Twelve different CW-domain-containing protein subfamilies are described, with different subfamilies being characteristic of vertebrates, higher plants and other animals in which these domain is found.
• pfam HATPase_c 101aa 3e-06 in ref transcript
  • Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase. This family represents the structurally related ATPase domains of histidine kinase, DNA gyrase B and HSP90.
• COG MutL 63aa 0.001 in ref transcript
  • DNA mismatch repair enzyme (predicted ATPase) [DNA replication, recombination, and repair].

MPP3

• rs.MPP3.F1 rs.MPP3.R1 99 120
• NCBIGene 36.3 4356
• Single exon skipping, size difference: 21
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001932

• Changed! cd GMPK 119aa 1e-24 in ref transcript
  • Guanosine monophosphate kinase (GMPK, EC 2.7.4.8), also known as guanylate kinase (GKase), catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to guanosine monophosphate (GMP) to yield adenosine diphosphate (ADP) and guanosine diphosphate (GDP). It plays an essential role in the biosynthesis of guanosine triphosphate (GTP). This enzyme is also important for the activation of some antiviral and anticancer agents, such as acyclovir, ganciclovir, carbovir, and thiopurines.
• cd PDZ_signaling 81aa 1e-11 in ref transcript
  • PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of PDZ domains an N-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in proteases.
• cd SH3 59aa 2e-05 in ref transcript
  • Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
• Changed! smart GuKc 188aa 4e-51 in ref transcript
  • Guanylate kinase homologues. Active enzymes catalyze ATP-dependent phosphorylation of GMP to GDP. Structure resembles that of adenylate kinase. So-called membrane-associated guanylate kinase homologues (MAGUKs) do not possess guanylate kinase activities; instead at least some possess protein-binding functions.
• smart PDZ 82aa 2e-12 in ref transcript
  • Domain present in PSD-95, Dlg, and ZO-1/2. Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities.
• smart L27 54aa 1e-09 in ref transcript
  • domain in receptor targeting proteins Lin-2 and Lin-7.
• pfam L27 51aa 1e-06 in ref transcript
  • L27 domain. The L27 domain is found in receptor targeting proteins Lin-2 and Lin-7.
• smart SH3 62aa 1e-05 in ref transcript
  • Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.
• Changed! COG Gmk 187aa 9e-22 in ref transcript
  • Guanylate kinase [Nucleotide transport and metabolism].
• COG Prc 77aa 6e-05 in ref transcript
  • Periplasmic protease [Cell envelope biogenesis, outer membrane].

MRE11A

• rs.MRE11A.F1 rs.MRE11A.R1 136 220
• NCBIGene 36.3 4361
• Single exon skipping, size difference: 84
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_005591

• TIGR mre11 393aa 1e-140 in ref transcript
  • All proteins in this family for which functions are known are subunits of a nuclease complex made up of multiple proteins including MRE11 and RAD50 homologs. The functions of this nuclease complex include recombinational repair and non-homolgous end joining. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). The proteins in this family are distantly related to proteins in the SbcCD complex of bacteria.
• COG SbcD 309aa 2e-20 in ref transcript
  • DNA repair exonuclease [DNA replication, recombination, and repair].

MRGPRF

• rs.MRGPRF.F1 rs.MRGPRF.R1 99 110
• NCBIGene 36.3 219928
• Alternative 5-prime and 3-prime, size difference: 11
• Inclusion in 5'UTR, Exclusion in 5'UTR
• Reference transcript: NM_145015

• pfam 7tm_1 225aa 2e-11 in ref transcript
  • 7 transmembrane receptor (rhodopsin family). This family contains, amongst other G-protein-coupled receptors (GCPRs), members of the opsin family, which have been considered to be typical members of the rhodopsin superfamily. They share several motifs, mainly the seven transmembrane helices, GCPRs of the rhodopsin superfamily. All opsins bind a chromophore, such as 11-cis-retinal. The function of most opsins other than the photoisomerases is split into two steps: light absorption and G-protein activation. Photoisomerases, on the other hand, are not coupled to G-proteins - they are thought to generate and supply the chromophore that is used by visual opsins.

MRPL21

• rs.MRPL21.F1 rs.MRPL21.R1 109 122
• NCBIGene 36.3 219927
• Alternative 5-prime, size difference: 13
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_181514

• Changed! pfam Ribosomal_L21p 73aa 1e-15 in ref transcript
  • Ribosomal prokaryotic L21 protein.
• Changed! COG RplU 68aa 2e-06 in ref transcript
  • Ribosomal protein L21 [Translation, ribosomal structure and biogenesis].

MRPL39

• rs.MRPL39.F1 rs.MRPL39.R1 101 190
• NCBIGene 36.3 54148
• Single exon skipping, size difference: 89
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_080794

• cd TGS_ThrRS_N 55aa 1e-13 in ref transcript
  • TGS _ThrRS_N: ThrRS (threonyl-tRNA Synthetase) is a class II tRNA synthetase that couples threonine to its cognate tRNA. In addition to its catalytic and anticodon-binding domains, ThrRS has an N-terminal TGS domain, named after the ThrRS, GTPase, and SpoT proteins where it occurs. The TGS domain is thought to interact with the tRNA acceptor arm along with an adjacent N-terminal domain. The specific function of TGS is not well understood.
• TIGR thrS 133aa 2e-05 in ref transcript
  • This model represents the threonyl-tRNA synthetase found in most organisms. This protein is a class II tRNA synthetase, and is recognized by the pfam HMM tRNA-synt_2b. Note that B. subtilis has closely related isozymes thrS and thrZ. The N-terminal regions are quite dissimilar between archaeal and eubacterial forms, while some eukaryotic forms are missing sequence there altogether.
• PRK thrS 197aa 2e-12 in ref transcript
  • threonyl-tRNA synthetase; Reviewed.

MRPL42

• rs.MRPL42.F1 rs.MRPL42.R1 115 135
• NCBIGene 36.3 28977
• Single exon skipping, size difference: 20
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_172178

• Changed! pfam MRP-S32 99aa 3e-42 in ref transcript
  • Mitochondrial 28S ribosomal protein S32. This entry is of a family of short, approximately 100 amino acid residues, proteins which are mitochondrial 28S ribosomal proteins named as MRP-S32. Their exact function could not be confirmed.

MRPL55

• rs.MRPL55.F1 rs.MRPL55.R1 104 216
• NCBIGene 36.3 128308
• Alternative 5-prime, size difference: 112
• Exclusion in 5'UTR
• Reference transcript: NM_181462

• pfam Mitoc_L55 118aa 1e-32 in ref transcript
  • Mitochondrial ribosomal protein L55. Members of this family are involved in mitochondrial biogenesis and G2/M phase cell cycle progression. They form a component of the mitochondrial ribosome large subunit (39S) which comprises a 16S rRNA and about 50 distinct proteins.

MRPS11

• rs.MRPS11.F1 rs.MRPS11.R1 265 364
• NCBIGene 36.3 64963
• Single exon skipping, size difference: 99
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_022839

• Changed! TIGR bact_S11 106aa 3e-18 in ref transcript
  • This model describes the bacterial 30S ribosomal protein S11. Cutoffs are set such that the model excludes archaeal and eukaryotic ribosomal proteins, but many chloroplast and mitochondrial equivalents of S11 are detected.
• Changed! PRK PRK05309 109aa 2e-19 in ref transcript
  • 30S ribosomal protein S11; Validated.
• Changed! TIGR bact_S11 84aa 3e-13 in modified transcript
• Changed! PRK PRK05309 87aa 5e-14 in modified transcript

MRVI1

• rs.MRVI1.F1 rs.MRVI1.R1 239 293
• NCBIGene 36.3 10335
• Mutually exclusive exon skipping, size difference: 54
• Inclusion in 5'UTR, Exclusion in 5'UTR
• Reference transcript: NM_001100163

• pfam MRVI1 593aa 1e-141 in ref transcript
  • MRVI1 protein. This family consists of mammalian MRVI1 proteins which are related to the lymphoid-restricted membrane protein (JAW1) and the IP3 receptor associated cGMP kinase substrates A and B (IRAGA and IRAGB). The function of MRVI1 is unknown although mutations in the Mrvi1 gene induces myeloid leukaemia by altering the expression of a gene important for myeloid cell growth and/or differentiation so it has been speculated that Mrvi1 is a tumour suppressor gene. IRAG is very similar in sequence to MRVI1 and is an essential NO/cGKI-dependent regulator of IP3-induced calcium release. Activation of cGKI decreases IP3-stimulated elevations in intracellular calcium, induces smooth muscle relaxation and contributes to the antiproliferative and pro-apoptotic effects of NO/cGMP. Jaw1 is a member of a class of proteins with COOH-terminal hydrophobic membrane anchors and is structurally similar to proteins involved in vesicle targeting and fusion. This suggests that the function and/or the structure of the ER in lymphocytes may be modified by lymphoid-restricted resident ER proteins.

MRVI1

• rs.MRVI1.F2 rs.MRVI1.R2 257 362
• NCBIGene 36.3 10335
• Single exon skipping, size difference: 105
• Exclusion in 5'UTR
• Reference transcript: NM_001100163

• pfam MRVI1 593aa 1e-141 in ref transcript
  • MRVI1 protein. This family consists of mammalian MRVI1 proteins which are related to the lymphoid-restricted membrane protein (JAW1) and the IP3 receptor associated cGMP kinase substrates A and B (IRAGA and IRAGB). The function of MRVI1 is unknown although mutations in the Mrvi1 gene induces myeloid leukaemia by altering the expression of a gene important for myeloid cell growth and/or differentiation so it has been speculated that Mrvi1 is a tumour suppressor gene. IRAG is very similar in sequence to MRVI1 and is an essential NO/cGKI-dependent regulator of IP3-induced calcium release. Activation of cGKI decreases IP3-stimulated elevations in intracellular calcium, induces smooth muscle relaxation and contributes to the antiproliferative and pro-apoptotic effects of NO/cGMP. Jaw1 is a member of a class of proteins with COOH-terminal hydrophobic membrane anchors and is structurally similar to proteins involved in vesicle targeting and fusion. This suggests that the function and/or the structure of the ER in lymphocytes may be modified by lymphoid-restricted resident ER proteins.

MRVI1

• rs.MRVI1.F3 rs.MRVI1.R3 414 518
• NCBIGene 36.3 10335
• Single exon skipping, size difference: 104
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_001098579

• Changed! pfam MRVI1 593aa 1e-144 in ref transcript
  • MRVI1 protein. This family consists of mammalian MRVI1 proteins which are related to the lymphoid-restricted membrane protein (JAW1) and the IP3 receptor associated cGMP kinase substrates A and B (IRAGA and IRAGB). The function of MRVI1 is unknown although mutations in the Mrvi1 gene induces myeloid leukaemia by altering the expression of a gene important for myeloid cell growth and/or differentiation so it has been speculated that Mrvi1 is a tumour suppressor gene. IRAG is very similar in sequence to MRVI1 and is an essential NO/cGKI-dependent regulator of IP3-induced calcium release. Activation of cGKI decreases IP3-stimulated elevations in intracellular calcium, induces smooth muscle relaxation and contributes to the antiproliferative and pro-apoptotic effects of NO/cGMP. Jaw1 is a member of a class of proteins with COOH-terminal hydrophobic membrane anchors and is structurally similar to proteins involved in vesicle targeting and fusion. This suggests that the function and/or the structure of the ER in lymphocytes may be modified by lymphoid-restricted resident ER proteins.

MS4A13

• rs.MS4A13.F1 rs.MS4A13.R1 108 228
• NCBIGene 36.3 503497
• Single exon skipping, size difference: 120
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001012417

• Changed! pfam CD20 139aa 7e-14 in ref transcript
  • CD20/IgE Fc receptor beta subunit family. This family includes the CD20 protein and the beta subunit of the high affinity receptor for IgE Fc. The high affinity receptor for IgE is a tetrameric structure consisting of a single IgE-binding alpha subunit, a single beta subunit, and two disulfide-linked gamma subunits. The alpha subunit of Fc epsilon RI and most Fc receptors are homologous members of the Ig superfamily. By contrast, the beta and gamma subunits from Fc epsilon RI are not homologous to the Ig superfamily. Both molecules have four putative transmembrane segments and a probably topology where both amino- and carboxy termini protrude into the cytoplasm.
• Changed! pfam CD20 99aa 2e-09 in modified transcript

MS4A15

• rs.MS4A15.F1 rs.MS4A15.R1 149 436
• NCBIGene 36.3 219995
• Exon skipping and alternative 3-prime or 5-prime, size difference: 287
• Exclusion of the protein initiation site, Exclusion in the protein causing a frameshift
• Reference transcript: NM_001098835

• Changed! pfam CD20 118aa 3e-30 in ref transcript
  • CD20/IgE Fc receptor beta subunit family. This family includes the CD20 protein and the beta subunit of the high affinity receptor for IgE Fc. The high affinity receptor for IgE is a tetrameric structure consisting of a single IgE-binding alpha subunit, a single beta subunit, and two disulfide-linked gamma subunits. The alpha subunit of Fc epsilon RI and most Fc receptors are homologous members of the Ig superfamily. By contrast, the beta and gamma subunits from Fc epsilon RI are not homologous to the Ig superfamily. Both molecules have four putative transmembrane segments and a probably topology where both amino- and carboxy termini protrude into the cytoplasm.

MSLN

• rs.MSLN.F1 rs.MSLN.R1 118 142
• NCBIGene 36.3 10232
• Alternative 3-prime, size difference: 24
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_013404

• Changed! pfam Mesothelin 606aa 0.0 in ref transcript
  • Pre-pro-megakaryocyte potentiating factor precursor (Mesothelin). This family consists of several mammalian pre-pro-megakaryocyte potentiating factor precursor (MPF) or mesothelin proteins. Mesothelin is a glycosylphosphatidylinositol-linked glycoprotein highly expressed in mesothelial cells, mesotheliomas, and ovarian cancer, but the biological function of the protein is not known.
• Changed! pfam Mesothelin 598aa 0.0 in modified transcript

MSR1

• rs.MSR1.F1 rs.MSR1.R1 142 331
• NCBIGene 36.3 4481
• Single exon skipping, size difference: 189
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_138715

• Changed! smart SR 101aa 1e-39 in ref transcript
  • Scavenger receptor Cys-rich. The sea ucrhin egg peptide speract contains 4 repeats of SR domains that contain 6 conserved cysteines. May bind bacterial antigens in the protein MARCO.
• pfam Macscav_rec 49aa 3e-18 in ref transcript
  • Macrophage scavenger receptor.
• pfam Collagen 63aa 3e-13 in ref transcript
  • Collagen triple helix repeat (20 copies). Members of this family belong to the collagen superfamily. Collagens are generally extracellular structural proteins involved in formation of connective tissue structure. The alignment contains 20 copies of the G-X-Y repeat that forms a triple helix. The first position of the repeat is glycine, the second and third positions can be any residue but are frequently proline and hydroxyproline. Collagens are post translationally modified by proline hydroxylase to form the hydroxyproline residues. Defective hydroxylation is the cause of scurvy. Some members of the collagen superfamily are not involved in connective tissue structure but share the same triple helical structure.
• Changed! pfam SMC_N 83aa 0.007 in ref transcript
  • RecF/RecN/SMC N terminal domain. This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.
• Changed! pfam SMC_N 173aa 0.009 in ref transcript
• Changed! smart SR 42aa 3e-12 in modified transcript

MST4

• rs.MST4.F1 rs.MST4.R1 102 333
• NCBIGene 36.3 51765
• Single exon skipping, size difference: 231
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_016542

• Changed! cd STKc_MST4 277aa 1e-146 in ref transcript
  • Serine/threonine kinases (STKs), mammalian Ste20-like protein kinase 4 (MST4) subfamily, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The MST4 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. MST4 is sometimes referred to as MASK (MST3 and SOK1-related kinase). It plays a role in mitogen-activated protein kinase (MAPK) signaling during cytoskeletal rearrangement, morphogenesis, and apoptosis. It influences cell growth and transformation by modulating the extracellular signal-regulated kinase (ERK) pathway. MST4 may also play a role in tumor formation and progression. It localizes in the Golgi apparatus by interacting with the Golgi matrix protein GM130 and may play a role in cell migration.
• Changed! smart S_TKc 241aa 4e-70 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• Changed! COG SPS1 266aa 3e-32 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].
• Changed! cd STKc_MST3_like 204aa 1e-119 in modified transcript
  • Serine/threonine kinases (STKs), mammalian Ste20-like protein kinase 3 (MST3)-like subfamily, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The MST3-like subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. This subfamily is composed of MST3, MST4, STK25, Schizosaccharomyces pombe Nak1 and Sid1, Saccharomyces cerevisiae sporulation-specific protein 1 (SPS1), and related proteins. Nak1 is required by fission yeast for polarizing the tips of actin cytoskeleton and is involved in cell growth, cell separation, cell morphology and cell-cycle progression. Sid1 is a component in the septation initiation network (SIN) signaling pathway, and plays a role in cytokinesis. SPS1 plays a role in regulating proteins required for spore wall formation. MST4 plays a role in mitogen-activated protein kinase (MAPK) signaling during cytoskeletal rearrangement, morphogenesis, and apoptosis. MST3 phosphorylates the STK NDR and may play a role in cell cycle progression and cell morphology. STK25 may play a role in the regulation of cell migration and polarization.
• Changed! smart S_TKc 182aa 1e-60 in modified transcript
• Changed! COG SPS1 201aa 2e-27 in modified transcript

MST4

• rs.MST4.F2 rs.MST4.R2 325 511
• NCBIGene 36.3 51765
• Single exon skipping, size difference: 186
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_016542

• Changed! cd STKc_MST4 277aa 1e-146 in ref transcript
  • Serine/threonine kinases (STKs), mammalian Ste20-like protein kinase 4 (MST4) subfamily, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The MST4 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. MST4 is sometimes referred to as MASK (MST3 and SOK1-related kinase). It plays a role in mitogen-activated protein kinase (MAPK) signaling during cytoskeletal rearrangement, morphogenesis, and apoptosis. It influences cell growth and transformation by modulating the extracellular signal-regulated kinase (ERK) pathway. MST4 may also play a role in tumor formation and progression. It localizes in the Golgi apparatus by interacting with the Golgi matrix protein GM130 and may play a role in cell migration.
• Changed! smart S_TKc 241aa 4e-70 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• Changed! COG SPS1 266aa 3e-32 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].
• Changed! cd STKc_MST3_like 212aa 6e-90 in modified transcript
  • Serine/threonine kinases (STKs), mammalian Ste20-like protein kinase 3 (MST3)-like subfamily, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The MST3-like subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. This subfamily is composed of MST3, MST4, STK25, Schizosaccharomyces pombe Nak1 and Sid1, Saccharomyces cerevisiae sporulation-specific protein 1 (SPS1), and related proteins. Nak1 is required by fission yeast for polarizing the tips of actin cytoskeleton and is involved in cell growth, cell separation, cell morphology and cell-cycle progression. Sid1 is a component in the septation initiation network (SIN) signaling pathway, and plays a role in cytokinesis. SPS1 plays a role in regulating proteins required for spore wall formation. MST4 plays a role in mitogen-activated protein kinase (MAPK) signaling during cytoskeletal rearrangement, morphogenesis, and apoptosis. MST3 phosphorylates the STK NDR and may play a role in cell cycle progression and cell morphology. STK25 may play a role in the regulation of cell migration and polarization.
• Changed! smart S_TKc 166aa 5e-47 in modified transcript
• Changed! COG SPS1 208aa 2e-21 in modified transcript

MTERFD3

• rs.MTERFD3.F1 rs.MTERFD3.R1 90 100
• NCBIGene 36.3 80298
• Alternative 3-prime, size difference: 10
• Inclusion in 5'UTR
• Reference transcript: NM_025198

• pfam mTERF 282aa 3e-10 in ref transcript
  • mTERF. This family contains one sequence of known function Human mitochondrial transcription termination factor (mTERF) the rest of the family consists of hypothetical proteins none of which have any functional information. mTERF is a multizipper protein possessing three putative leucine zippers one of which is bipartite. The protein binds DNA as a monomer. The leucine zippers are not implicated in a dimerisation role as in other leucine zippers.

MTMR14

• rs.MTMR14.F1 rs.MTMR14.R1 267 423
• NCBIGene 36.3 64419
• Single exon skipping, size difference: 156
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001077525

MTUS1

• rs.MTUS1.F1 rs.MTUS1.R1 287 449
• NCBIGene 36.3 57509
• Single exon skipping, size difference: 162
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001001924

• TIGR SMC_prok_B 297aa 3e-14 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• COG Smc 320aa 2e-11 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].

MUC1

• rs.MUC1.F1 rs.MUC1.R1 101 128
• NCBIGene 36.3 4582
• Alternative 3-prime, size difference: 27
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_002456

• smart SEA 116aa 2e-31 in ref transcript
  • Domain found in sea urchin sperm protein, enterokinase, agrin. Proposed function of regulating or binding carbohydrate sidechains.

MUC1

• rs.MUC1.F3 rs.MUC1.R3 137 191
• NCBIGene 36.3 4582
• Alternative 3-prime, size difference: 54
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_002456

• Changed! smart SEA 116aa 2e-31 in ref transcript
  • Domain found in sea urchin sperm protein, enterokinase, agrin. Proposed function of regulating or binding carbohydrate sidechains.
• Changed! smart SEA 117aa 1e-26 in modified transcript

MVP

• rs.MVP.F1 rs.MVP.R1 130 171
• NCBIGene 36.3 9961
• Alternative 3-prime, size difference: 41
• Inclusion in 5'UTR
• Reference transcript: NM_005115

• pfam Vault 53aa 8e-12 in ref transcript
  • Major Vault Protein repeat. The vault is a ubiquitous and highly conserved ribonucleoprotein particle of approximately 13 mDa of unknown function. This family corresponds to a repeat found in the amino terminal half of the major vault protein.
• pfam Vault 53aa 2e-09 in ref transcript
• pfam Vault 58aa 9e-09 in ref transcript
• pfam Vault 49aa 9e-08 in ref transcript
• pfam Vault 62aa 3e-06 in ref transcript
• pfam Vault 48aa 6e-05 in ref transcript

MYH14

• rs.MYH14.F1 rs.MYH14.R1 124 148
• NCBIGene 36.3 79784
• Single exon skipping, size difference: 24
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001077186

• Changed! cd MYSc_type_II 707aa 0.0 in ref transcript
  • Myosin motor domain, type II myosins. Myosin II mediates cortical contraction in cell motility, and is the motor in smooth and skeletal muscle. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle.
• Changed! smart MYSc 709aa 0.0 in ref transcript
  • Myosin. Large ATPases. ATPase; molecular motor. Muscle contraction consists of a cyclical interaction between myosin and actin. The core of the myosin structure is similar in fold to that of kinesin.
• pfam Myosin_tail_1 499aa 1e-30 in ref transcript
  • Myosin tail. The myosin molecule is a multi-subunit complex made up of two heavy chains and four light chains it is a fundamental contractile protein found in all eukaryote cell types. This family consists of the coiled-coil myosin heavy chain tail region. The coiled-coil is composed of the tail from two molecules of myosin. These can then assemble into the macromolecular thick filament. The coiled-coil region provides the structural backbone the thick filament.
• pfam Myosin_tail_1 238aa 4e-14 in ref transcript
• Changed! COG COG5022 780aa 0.0 in ref transcript
  • Myosin heavy chain [Cytoskeleton].
• Changed! cd MYSc_type_II 699aa 0.0 in modified transcript
• Changed! smart MYSc 701aa 0.0 in modified transcript
• Changed! COG COG5022 772aa 0.0 in modified transcript

MYO3B

• rs.MYO3B.F1 rs.MYO3B.R1 134 215
• NCBIGene 36.3 140469
• Single exon skipping, size difference: 81
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_138995

• cd MYSc_type_III 699aa 0.0 in ref transcript
  • Myosin motor domain, type III myosins. Myosin III has been shown to play a role in the vision process in insects and in hearing in mammals. Myosin III, an unconventional myosin, does not form dimers. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle.
• cd STKc_myosinIIIB 291aa 0.0 in ref transcript
  • Serine/threonine kinases (STKs), class IIIB myosin subfamily, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The class III myosin subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. Class III myosins are motor proteins containing an N-terminal kinase catalytic domain and a C-terminal actin-binding domain. Class III myosins may play an important role in maintaining the structural integrity of photoreceptor cell microvilli. They may also function as cargo carriers during light-dependent translocation, in photoreceptor cells, of proteins such as transducin and arrestin. Class IIIB myosin is expressed highly in retina. It is also present in the brain and testis. The human class IIIB myosin gene maps to a region that overlaps the locus for Bardet-Biedl syndrome, which is characterized by dysmorphic extremities, retinal dystrophy, obesity, male hypogenitalism, and renal abnormalities.
• smart MYSc 696aa 0.0 in ref transcript
  • Myosin. Large ATPases. ATPase; molecular motor. Muscle contraction consists of a cyclical interaction between myosin and actin. The core of the myosin structure is similar in fold to that of kinesin.
• smart S_TKc 257aa 2e-67 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• Changed! COG COG5022 755aa 1e-168 in ref transcript
  • Myosin heavy chain [Cytoskeleton].
• COG SPS1 268aa 3e-33 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].
• Changed! COG COG5022 688aa 1e-168 in modified transcript

MYOM1

• rs.MYOM1.F1 rs.MYOM1.R1 102 390
• NCBIGene 36.3 8736
• Single exon skipping, size difference: 288
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_003803

• cd FN3 94aa 2e-15 in ref transcript
  • Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.
• cd FN3 90aa 8e-14 in ref transcript
• cd FN3 94aa 9e-14 in ref transcript
• cd IGcam 92aa 9e-14 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• cd FN3 91aa 1e-12 in ref transcript
• cd FN3 95aa 3e-12 in ref transcript
• cd IGcam 89aa 2e-11 in ref transcript
• cd IGcam 80aa 1e-05 in ref transcript
• cd IGcam 78aa 0.005 in ref transcript
• pfam I-set 85aa 4e-21 in ref transcript
  • Immunoglobulin I-set domain.
• pfam fn3 89aa 1e-12 in ref transcript
  • Fibronectin type III domain.
• smart FN3 84aa 4e-12 in ref transcript
  • Fibronectin type 3 domain. One of three types of internal repeat within the plasma protein, fibronectin. The tenth fibronectin type III repeat contains a RGD cell recognition sequence in a flexible loop between 2 strands. Type III modules are present in both extracellular and intracellular proteins.
• Changed! smart IG_like 88aa 9e-12 in ref transcript
  • Immunoglobulin like. IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
• pfam fn3 87aa 2e-11 in ref transcript
• pfam fn3 90aa 2e-10 in ref transcript
• pfam I-set 69aa 5e-10 in ref transcript
• pfam fn3 85aa 2e-09 in ref transcript
• pfam I-set 70aa 2e-05 in ref transcript
• pfam I-set 70aa 3e-04 in ref transcript
• Changed! pfam I-set 93aa 9e-12 in modified transcript

MYST3

• rs.MYST3.F1 rs.MYST3.R1 255 299
• NCBIGene 36.3 7994
• Alternative 5-prime, size difference: 44
• Exclusion in 5'UTR
• Reference transcript: NM_001099412

• cd BAH_plant_2 34aa 8e-05 in ref transcript
  • BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
• pfam MOZ_SAS 188aa 1e-101 in ref transcript
  • MOZ/SAS family. This region of these proteins has been suggested to be homologous to acetyltransferases.
• pfam PHD 52aa 3e-10 in ref transcript
  • PHD-finger. PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
• pfam PHD 58aa 7e-06 in ref transcript
• smart H15 78aa 8e-06 in ref transcript
  • Domain in histone families 1 and 5.
• COG SAS2 331aa 3e-90 in ref transcript
  • Histone acetyltransferase (MYST family) [Chromatin structure and dynamics].

NAE1

• rs.NAE1.F1 rs.NAE1.R1 190 288
• NCBIGene 36.3 8883
• Single exon skipping, size difference: 98
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_003905

• Changed! cd APPBP1_RUB 389aa 1e-178 in ref transcript
  • Ubiquitin activating enzyme (E1) subunit APPBP1. APPBP1 is part of the heterodimeric activating enzyme (E1), specific for the Rub family of ubiquitin-like proteins (Ubls). E1 enzymes are part of a conjugation cascade to attach Ub or Ubls, covalently to substrate proteins consisting of activating (E1), conjugating (E2), and/or ligating (E3) enzymes. E1 activates ubiquitin(-like) by C-terminal adenylation, and subsequently forms a highly reactive thioester bond between its catalytic cysteine and Ubls C-terminus. E1 also associates with E2 and promotes ubiquitin transfer to the E2's catalytic cysteine. Post-translational modification by Rub family of ubiquitin-like proteins (Ublps) activates SCF ubiquitin ligases and is involved in cell cycle control, signaling and embryogenesis. ABPP1 contains part of the adenylation domain.
• Changed! cd APPBP1_RUB 84aa 3e-17 in ref transcript
• Changed! TIGR Ube1 141aa 4e-16 in ref transcript
  • This model represents the full length, over a thousand amino acids, of a multicopy family of eukaryotic proteins, many of which are designated ubiquitin-activating enzyme E1. Members have two copies of the ThiF family domain (pfam00899), a repeat found in ubiquitin-activating proteins (pfam02134), and other regions.
• Changed! TIGR Ube1 104aa 7e-07 in ref transcript
• Changed! COG ThiF 185aa 4e-22 in ref transcript
  • Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 2 [Coenzyme metabolism].

NARF

• rs.NARF.F1 rs.NARF.R1 109 247
• NCBIGene 36.3 26502
• Single exon skipping, size difference: 138
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_012336

• Changed! pfam Fe_hyd_lg_C 307aa 1e-107 in ref transcript
  • Iron only hydrogenase large subunit, C-terminal domain.
• Changed! pfam Fe_hyd_SSU 54aa 2e-06 in ref transcript
  • Iron hydrogenase small subunit. This family represents the small subunit of the Fe-only hydrogenases EC:1.18.99.1. The subunit is comprised of alternating random coil and alpha helical structures that encompasses the large subunit in a novel protein fold.
• Changed! COG COG4624 412aa 6e-50 in ref transcript
  • Iron only hydrogenase large subunit, C-terminal domain [General function prediction only].
• Changed! pfam Fe_hyd_lg_C 182aa 2e-64 in modified transcript
• Changed! COG COG4624 224aa 7e-36 in modified transcript

NARF

• rs.NARF.F2 rs.NARF.R2 102 246
• NCBIGene 36.3 26502
• Single exon skipping, size difference: 144
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_012336

• Changed! pfam Fe_hyd_lg_C 307aa 1e-107 in ref transcript
  • Iron only hydrogenase large subunit, C-terminal domain.
• pfam Fe_hyd_SSU 54aa 2e-06 in ref transcript
  • Iron hydrogenase small subunit. This family represents the small subunit of the Fe-only hydrogenases EC:1.18.99.1. The subunit is comprised of alternating random coil and alpha helical structures that encompasses the large subunit in a novel protein fold.
• Changed! COG COG4624 412aa 6e-50 in ref transcript
  • Iron only hydrogenase large subunit, C-terminal domain [General function prediction only].
• Changed! pfam Fe_hyd_lg_C 302aa 1e-106 in modified transcript
• Changed! COG COG4624 387aa 1e-43 in modified transcript

NARG1L

• rs.NARG1L.F1 rs.NARG1L.R1 108 215
• NCBIGene 36.3 79612
• Single exon skipping, size difference: 107
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_024561

• cd TPR 100aa 6e-06 in ref transcript
  • Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here.
• TIGR PEP_TPR_lipo 219aa 6e-06 in ref transcript
  • This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of tetratricopeptide repeats (TPR) suggests protein-protein interaction, possibly for the regulation of PEP-CTERM protein expression, since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator.
• COG COG4783 165aa 3e-06 in ref transcript
  • Putative Zn-dependent protease, contains TPR repeats [General function prediction only].

NARG2

• rs.NARG2.F1 rs.NARG2.R1 317 477
• NCBIGene 36.3 79664
• Alternative 3-prime, size difference: 160
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_024611

• Changed! pfam NARG2_C 214aa 3e-74 in ref transcript
  • NMDA receptor-regulated gene protein 2. The transition of neuronal cells from pre-cursor to mature state is regulated by the N-methyl-d-aspartate (NMDA) receptor, a glutamate-gated ion channel that is permeable to Ca2+. NMDA receptors probably mediate this activity by permitting expression of NARG2. NARG2 is transiently expressed, being a regulatory protein that is present in the nucleus of dividing cells and then down-regulated as progenitors exit the cell cycle and begin to differentiate. NARG2 contains repeats of (S/T)PXX, (11 in mouse, six in human), a putative DNA-binding motif that is found in many gene-regulatory proteins including Kruppel, Hunchback and Antennapedi.

NBEAL1

• rs.NBEAL1.F1 rs.NBEAL1.R1 129 336
• NCBIGene 36.3 65065
• Multiple exon skipping, size difference: 207
• Exclusion in the protein (no frameshift), Exclusion in the protein (no frameshift)
• Reference transcript: NM_001099273

• Changed! cd Beach 281aa 1e-128 in ref transcript
  • BEACH (Beige and Chediak-Higashi) domains, implicated in membrane trafficking, are present in a family of proteins conserved throughout eukaryotes. This group contains human lysosomal trafficking regulator (LYST), LPS-responsive and beige-like anchor (LRBA) and neurobeachin. Disruption of LYST leads to Chediak-Higashi syndrome, characterized by severe immunodeficiency, albinism, poor blood coagulation and neurologic problems. Neurobeachin is a candidate gene linked to autism. LBRA seems to be upregulated in several cancer types. It has been shown that the BEACH domain itself is important for the function of these proteins.
• cd WD40 274aa 2e-15 in ref transcript
  • WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.
• cd Neurobeachin 84aa 9e-11 in ref transcript
  • Neurobeachin Pleckstrin homology-like domain. This domain is found in the large multi-domain eukaryotic protein Nerubeachin, N-terminal to the BEACH domain. This PH-like domain interacts with the BEACH domain in the same manner used by other PH-like domains to bind peptides.
• Changed! pfam Beach 281aa 1e-132 in ref transcript
  • Beige/BEACH domain.
• COG COG2319 285aa 4e-08 in ref transcript
  • FOG: WD40 repeat [General function prediction only].
• Changed! cd Beach 275aa 1e-124 in modified transcript
• Changed! pfam Beach 275aa 1e-128 in modified transcript

NBN

• rs.NBN.F1 rs.NBN.R1 345 395
• NCBIGene 36.3 4683
• Single exon skipping, size difference: 50
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_002485

• Changed! cd FHA 109aa 2e-14 in ref transcript
  • Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins localize to the nucleus, where they participate in establishing or maintaining cell cycle checkpoints, DNA repair, or transcriptional regulation. Members of the FHA family include: Dun1, Rad53, Cds1, Mek1, KAPP(kinase-associated protein phosphatase),and Ki-67 (a human nuclear protein related to cell proliferation).
• Changed! cd BRCT 69aa 4e-04 in ref transcript
  • Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks.
• Changed! pfam Nbs1_C 65aa 3e-30 in ref transcript
  • DNA damage repair protein Nbs1. This C terminal region of the DNA damage repair protein Nbs1 has been identified to be necessary for the binding of Mre11 and Tel1.
• Changed! pfam FHA 77aa 2e-08 in ref transcript
  • FHA domain. The FHA (Forkhead-associated) domain is a phosphopeptide binding motif.
• Changed! pfam BRCT 67aa 0.008 in ref transcript
  • BRCA1 C Terminus (BRCT) domain. The BRCT domain is found predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage. It has been suggested that the Retinoblastoma protein contains a divergent BRCT domain, this has not been included in this family. The BRCT domain of XRCC1 forms a homodimer in the crystal structure. This suggests that pairs of BRCT domains associate as homo- or heterodimers.
• Changed! cd FHA 49aa 3e-05 in modified transcript

NCALD

• rs.NCALD.F1 rs.NCALD.R1 114 201
• NCBIGene 36.3 83988
• Single exon skipping, size difference: 87
• Exclusion in 5'UTR
• Reference transcript: NM_001040625

• cd EFh 62aa 1e-10 in ref transcript
  • EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers.
• cd EFh 75aa 4e-10 in ref transcript
• smart EFh 29aa 0.001 in ref transcript
  • EF-hand, calcium binding motif. EF-hands are calcium-binding motifs that occur at least in pairs. Links between disease states and genes encoding EF-hands, particularly the S100 subclass, are emerging. Each motif consists of a 12 residue loop flanked on either side by a 12 residue alpha-helix. EF-hands undergo a conformational change unpon binding calcium ions.
• COG FRQ1 166aa 2e-26 in ref transcript
  • Ca2+-binding protein (EF-Hand superfamily) [Signal transduction mechanisms / Cytoskeleton / Cell division and chromosome partitioning / General function prediction only].

NCAM1

• rs.NCAM1.F1 rs.NCAM1.R1 170 275
• NCBIGene 36.3 4684
• Multiple exon skipping, size difference: 105
• Inclusion in the protein (no stop codon or frameshift), Inclusion in the protein (no stop codon or frameshift), Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_181351

• cd IGcam 91aa 5e-12 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• cd IGcam 87aa 8e-10 in ref transcript
• cd IGcam 104aa 1e-09 in ref transcript
• cd IGcam 73aa 2e-09 in ref transcript
• cd FN3 98aa 5e-07 in ref transcript
  • Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.
• cd FN3 88aa 2e-04 in ref transcript
• pfam I-set 83aa 1e-15 in ref transcript
  • Immunoglobulin I-set domain.
• smart IG_like 91aa 2e-11 in ref transcript
  • Immunoglobulin like. IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
• smart IGc2 69aa 8e-10 in ref transcript
  • Immunoglobulin C-2 Type.
• smart IG_like 85aa 2e-08 in ref transcript
• pfam fn3 89aa 7e-08 in ref transcript
  • Fibronectin type III domain.
• pfam fn3 83aa 1e-06 in ref transcript

NCBP2

• rs.NCBP2.F1 rs.NCBP2.R1 227 386
• NCBIGene 36.3 22916
• Alternative 5-prime and 3-prime, size difference: 159
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_007362

• Changed! cd RRM 75aa 5e-18 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• Changed! smart RRM_2 74aa 7e-18 in ref transcript
  • RNA recognition motif.
• Changed! COG COG0724 83aa 1e-11 in ref transcript
  • RNA-binding proteins (RRM domain) [General function prediction only].

NCOA3

• rs.NCOA3.F1 rs.NCOA3.R1 108 120
• NCBIGene 36.3 8202
• Alternative 5-prime, size difference: 12
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_181659

• cd PAS 66aa 2e-08 in ref transcript
  • PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.
• cd HLH 54aa 0.002 in ref transcript
  • Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins.
• pfam Nuc_rec_co-act 48aa 2e-16 in ref transcript
  • Nuclear receptor coactivator. This region is found on eukaryotic nuclear receptor coactivators and forms an alpha helical structure.
• pfam SRC-1 87aa 6e-15 in ref transcript
  • Steroid receptor coactivator. This domain is found in steroid/nuclear receptor coactivators and contains two LXXLL motifs that are involved in receptor binding. The family includes SRC-1/NcoA-1, NcoA-2/TIF2, pCIP/ACTR/GRIP-1/AIB1.
• smart PAS 58aa 8e-10 in ref transcript
  • PAS domain. PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels ([1]; Ponting & Aravind, in press).
• pfam DUF1518 58aa 4e-08 in ref transcript
  • Domain of unknown function (DUF1518). This domain, which is usually found tandemly repeated, is found various receptor co-activating proteins.
• smart HLH 55aa 3e-06 in ref transcript
  • helix loop helix domain.

NCOR2

• rs.NCOR2.F1 rs.NCOR2.R1 102 153
• NCBIGene 36.3 9612
• Single exon skipping, size difference: 51
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_006312

• cd SANT 44aa 2e-07 in ref transcript
  • 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
• cd SANT 43aa 0.003 in ref transcript
• pfam Myb_DNA-binding 44aa 1e-09 in ref transcript
  • Myb-like DNA-binding domain. This family contains the DNA binding domains from Myb proteins, as well as the SANT domain family.
• pfam Myb_DNA-binding 43aa 6e-04 in ref transcript

NCOR2

• rs.NCOR2.F2 rs.NCOR2.R2 173 311
• NCBIGene 36.3 9612
• Alternative 5-prime, size difference: 138
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_006312

• cd SANT 44aa 2e-07 in ref transcript
  • 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
• cd SANT 43aa 0.003 in ref transcript
• pfam Myb_DNA-binding 44aa 1e-09 in ref transcript
  • Myb-like DNA-binding domain. This family contains the DNA binding domains from Myb proteins, as well as the SANT domain family.
• pfam Myb_DNA-binding 43aa 6e-04 in ref transcript

NF1

• rs.NF1.F1 rs.NF1.R1 212 275
• NCBIGene 36.3 4763
• Single exon skipping, size difference: 63
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001042492

• Changed! cd RasGAP_Neurofibromin 347aa 0.0 in ref transcript
  • Neurofibromin is the product of the neurofibromatosis type 1 gene (NF1) and shares a region of similarity with catalytic domain of the mammalian p120RasGAP protein and an extended similarity with the Saccharomyces cerevisiae RasGAP proteins Ira1 and Ira2. Neurofibromin has been shown to function as a GAP (GTPase-activating protein) which inhibits low molecular weight G proteins such as Ras by stimulating their intrinsic GTPase activity. NF1 is a common genetic disorder characterized by various symptoms ranging from predisposition for the development of tumors to learning disability or mental retardation. Loss of neurofibromin activity can be correlated to the increase in Ras-GTP concentration in neurofibromas of NF1 of patients, supporting the notion that unregulated Ras signaling may contribute to their development.
• cd SEC14 147aa 1e-09 in ref transcript
  • Sec14p-like lipid-binding domain. Found in secretory proteins, such as S. cerevisiae phosphatidylinositol transfer protein (Sec14p), and in lipid regulated proteins such as RhoGAPs, RhoGEFs and neurofibromin (NF1). SEC14 domain of Dbl is known to associate with G protein beta/gamma subunits.
• Changed! smart RasGAP 371aa 2e-95 in ref transcript
  • GTPase-activator protein for Ras-like GTPases. All alpha-helical domain that accelerates the GTPase activity of Ras, thereby "switching" it into an "off" position. Improved domain limits from structure.
• smart SEC14 141aa 1e-17 in ref transcript
  • Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p). Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) and in RhoGAPs, RhoGEFs and the RasGAP, neurofibromin (NF1). Lipid-binding domain. The SEC14 domain of Dbl is known to associate with G protein beta/gamma subunits.
• Changed! COG IQG1 219aa 2e-07 in ref transcript
  • Protein involved in regulation of cellular morphogenesis/cytokinesis [Cell division and chromosome partitioning / Signal transduction mechanisms].
• Changed! cd RasGAP_Neurofibromin 326aa 0.0 in modified transcript
• Changed! smart RasGAP 350aa 1e-98 in modified transcript
• Changed! COG IQG1 198aa 5e-08 in modified transcript

NF2

• rs.NF2.F1 rs.NF2.R1 125 140
• NCBIGene 36.3 4771
• Alternative 5-prime, size difference: 15
• Exclusion in 3'UTR
• Reference transcript: NM_181832

• cd FERM_C 93aa 1e-22 in ref transcript
  • The FERM_C domain is the third structural domain within the FERM domain. The FERM domain is found in the cytoskeletal-associated proteins such as ezrin, moesin, radixin, 4.1R, and merlin. These proteins provide a link between the membrane and cytoskeleton and are involved in signal transduction pathways. The FERM_C domain is also found in protein tyrosine phosphatases (PTPs) , the tryosine kinases FAKand JAK, in addition to other proteins involved in signaling. This domain is structuraly similar to the PH and PTB domains and consequently is capable of binding to both peptides and phospholipids at different sites.
• smart B41 204aa 3e-53 in ref transcript
  • Band 4.1 homologues. Also known as ezrin/radixin/moesin (ERM) protein domains. Present in myosins, ezrin, radixin, moesin, protein tyrosine phosphatases. Plasma membrane-binding domain. These proteins play structural and regulatory roles in the assembly and stabilization of specialized plasmamembrane domains. Some PDZ domain containing proteins bind one or more of this family. Now includes JAKs.
• pfam FERM_C 87aa 9e-33 in ref transcript
  • FERM C-terminal PH-like domain.
• pfam ERM 218aa 2e-31 in ref transcript
  • Ezrin/radixin/moesin family. This family of proteins contain a band 4.1 domain (pfam00373), at their amino terminus. This family represents the rest of these proteins.

NFKB2

• rs.NFKB2.F1 rs.NFKB2.R1 102 276
• NCBIGene 36.3 4791
• Alternative 5-prime, size difference: 174
• Exclusion in 5'UTR
• Reference transcript: NM_001077494

• cd IPT_NFkappaB 100aa 9e-45 in ref transcript
  • IPT domain of the transcription factor NFkappaB and related transcription factors. NFkappaB is considered a central regulator of stress responses, activated by different stressful conditions, including physical stress, oxidative stress, and exposure to certain chemicals. NFkappaB blocking cell apoptosis in several cell types, gives it an important role in cell proliferation and differentiation.
• cd ANK 138aa 1e-21 in ref transcript
  • ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats.
• cd ANK 132aa 1e-18 in ref transcript
• pfam RHD 181aa 4e-66 in ref transcript
  • Rel homology domain (RHD). Proteins containing the Rel homology domain (RHD) are eukaryotic transcription factors. The RHD is composed of two structural domains. This is the N-terminal domain that is similar to that found in P53. The C-terminal domain has an immunoglobulin-like fold (See pfam01833) that binds to DNA.
• smart IPT 100aa 4e-13 in ref transcript
  • ig-like, plexins, transcription factors.
• TIGR trp 177aa 3e-06 in ref transcript
  • after chronic exposure to capsaicin. (McCleskey and Gold, 1999).
• COG Arp 108aa 7e-11 in ref transcript
  • FOG: Ankyrin repeat [General function prediction only].
• COG Arp 167aa 8e-07 in ref transcript

NLRP1

• rs.NLRP1.F1 rs.NLRP1.R1 101 113
• NCBIGene 36.3 22861
• Alternative 5-prime, size difference: 12
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_033004

• cd LRR_RI 179aa 8e-30 in ref transcript
  • Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1).
• cd AAA 95aa 0.009 in ref transcript
  • The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.
• pfam NACHT 170aa 5e-45 in ref transcript
  • NACHT domain. This NTPase domain is found in apoptosis proteins as well as those involved in MHC transcription activation. This family is closely related to pfam00931.
• pfam CARD 82aa 2e-16 in ref transcript
  • Caspase recruitment domain. Motif contained in proteins involved in apoptotic signaling. Predicted to possess a DEATH (pfam00531) domain-like fold.
• pfam PAAD_DAPIN 58aa 2e-08 in ref transcript
  • PAAD/DAPIN/Pyrin domain. This domain is predicted to contain 6 alpha helices and to have the same fold as the pfam00531 domain. This similarity may mean that this is a protein-protein interaction domain.
• smart LRR_RI 28aa 0.002 in ref transcript
  • Leucine rich repeat, ribonuclease inhibitor type.
• COG RNA1 142aa 0.004 in ref transcript
  • Ran GTPase-activating protein (RanGAP) involved in mRNA processing and transport [Signal transduction mechanisms / RNA processing and modification].

NOVA1

• rs.NOVA1.F1 rs.NOVA1.R1 361 433
• NCBIGene 36.3 4857
• Single exon skipping, size difference: 72
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_002515

• Changed! cd PCBP_like_KH 66aa 1e-12 in ref transcript
  • K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
• cd PCBP_like_KH 67aa 3e-12 in ref transcript
• cd KH-I 66aa 3e-09 in ref transcript
  • K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
• pfam KH_1 64aa 2e-10 in ref transcript
  • KH domain. KH motifs can bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.
• pfam KH_1 66aa 1e-09 in ref transcript
• smart KH 70aa 3e-08 in ref transcript
  • K homology RNA-binding domain.
• Changed! COG Pnp 73aa 0.007 in ref transcript
  • Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis].
• Changed! cd PCBP_like_KH 66aa 1e-12 in modified transcript
• Changed! TIGR arCOG04150 160aa 0.005 in modified transcript
  • This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.
• Changed! COG COG1094 176aa 1e-04 in modified transcript
  • Predicted RNA-binding protein (contains KH domains) [General function prediction only].

NOXO1

• rs.NOXO1.F1 rs.NOXO1.R1 100 115
• NCBIGene 36.3 124056
• Alternative 5-prime, size difference: 15
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_172168

• Changed! cd PX_NoxO1 125aa 3e-45 in ref transcript
  • The phosphoinositide binding Phox Homology domain of Nox Organizing protein 1. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions such as cell signaling, vesicular trafficking, protein sorting, and lipid modification, among others. Nox Organizing protein 1 (NoxO1) is a critical regulator of enzyme kinetics of the nonphagocytic NADPH oxidase Nox1, which catalyzes the transfer of electrons from NADPH to molecular oxygen to form superoxide. Nox1 is expressed in colon, stomach, uterus, prostate, and vascular smooth muscle cells. NoxO1, a homolog of the p47phox subunit of phagocytic NADPH oxidase, is involved in targeting activator subunits (such as NoxA1) to Nox1. It is co-localized with Nox1 in the membranes of resting cells and directs the subcellular localization of Nox1. The PX domain is involved in targeting of proteins to PI-enriched membranes, and may also be involved in protein-protein interaction. The PX domain of NoxO1 preferentially binds phosphatidylinositol-3,5-bisphosphate [PI(3,5)P2], PI5P, and PI4P.
• cd SH3 50aa 4e-06 in ref transcript
  • Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
• cd SH3 54aa 2e-04 in ref transcript
• smart SH3 45aa 2e-06 in ref transcript
  • Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.
• Changed! smart PX 101aa 2e-04 in ref transcript
  • PhoX homologous domain, present in p47phox and p40phox. Eukaryotic domain of unknown function present in phox proteins, PLD isoforms, a PI3K isoform.
• smart SH3 33aa 0.001 in ref transcript
• Changed! cd PX_NoxO1 120aa 4e-47 in modified transcript
• Changed! smart PX 96aa 9e-06 in modified transcript

NPC1L1

• rs.NPC1L1.F1 rs.NPC1L1.R1 298 379
• NCBIGene 36.3 29881
• Single exon skipping, size difference: 81
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_013389

• Changed! TIGR 2A060601 1261aa 0.0 in ref transcript
  • The model describes Niemann-Pick C type protein in eukaryotes. The defective protein has been associated with Niemann-Pick disease which is described in humans as autosomal recessive lipidosis. It is characterized by the lysosomal accumulation of unestrified cholesterol. It is an integral membrane protein, which indicates that this protein is most likely involved in cholesterol transport or acts as some component of cholesterol homeostasis.
• COG COG1033 119aa 5e-05 in ref transcript
  • Predicted exporters of the RND superfamily [General function prediction only].
• Changed! TIGR 2A060601 1234aa 0.0 in modified transcript

NQO1

• rs.NQO1.F1 rs.NQO1.R1 104 206
• NCBIGene 36.3 1728
• Single exon skipping, size difference: 102
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000903

• Changed! pfam Flavodoxin_2 213aa 5e-56 in ref transcript
  • Flavodoxin-like fold. This family consists of a domain with a flavodoxin-like fold. The family includes bacterial and eukaryotic NAD(P)H dehydrogenase (quinone) EC:1.6.99.2. These enzymes catalyse the NAD(P)H-dependent two-electron reductions of quinones and protect cells against damage by free radicals and reactive oxygen species. This enzyme uses a FAD co-factor. The equation for this reaction is:- NAD(P)H + acceptor <=> NAD(P)(+) + reduced acceptor. This enzyme is also involved in the bioactivation of prodrugs used in chemotherapy. The family also includes acyl carrier protein phosphodiesterase EC:3.1.4.14. This enzyme converts holo-ACP to apo-ACP by hydrolytic cleavage of the phosphopantetheine residue from ACP. This family is related to pfam03358 and pfam00258.
• Changed! COG MdaB 212aa 7e-32 in ref transcript
  • Putative NADPH-quinone reductase (modulator of drug activity B) [General function prediction only].
• Changed! pfam Flavodoxin_2 179aa 2e-38 in modified transcript
• Changed! COG MdaB 178aa 2e-21 in modified transcript

NQO1

• rs.NQO1.F2 rs.NQO1.R2 110 224
• NCBIGene 36.3 1728
• Single exon skipping, size difference: 114
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000903

• Changed! pfam Flavodoxin_2 213aa 5e-56 in ref transcript
  • Flavodoxin-like fold. This family consists of a domain with a flavodoxin-like fold. The family includes bacterial and eukaryotic NAD(P)H dehydrogenase (quinone) EC:1.6.99.2. These enzymes catalyse the NAD(P)H-dependent two-electron reductions of quinones and protect cells against damage by free radicals and reactive oxygen species. This enzyme uses a FAD co-factor. The equation for this reaction is:- NAD(P)H + acceptor <=> NAD(P)(+) + reduced acceptor. This enzyme is also involved in the bioactivation of prodrugs used in chemotherapy. The family also includes acyl carrier protein phosphodiesterase EC:3.1.4.14. This enzyme converts holo-ACP to apo-ACP by hydrolytic cleavage of the phosphopantetheine residue from ACP. This family is related to pfam03358 and pfam00258.
• Changed! COG MdaB 212aa 7e-32 in ref transcript
  • Putative NADPH-quinone reductase (modulator of drug activity B) [General function prediction only].
• Changed! pfam Flavodoxin_2 175aa 2e-34 in modified transcript
• Changed! COG MdaB 174aa 2e-13 in modified transcript

NR1I3

• rs.NR1I3.F1 rs.NR1I3.R1 195 335
• NCBIGene 36.3 9970
• Single exon skipping, size difference: 140
• Exclusion of the protein initiation site
• Reference transcript: NM_001077482

• cd NR_LBD_PXR_like 250aa 9e-91 in ref transcript
  • The ligand binding domain of xenobiotic receptors:pregnane X receptor and constitutive androstane receptor. The ligand binding domain of xenobiotic receptors: This xenobiotic receptor family includes pregnane X receptor (PXR), constitutive androstane receptor (CAR) and other related nuclear receptors. They function as sensors of toxic byproducts of cell metabolism and of exogenous chemicals, to facilitate their elimination. The nuclear receptor pregnane X receptor (PXR) is a ligand-regulated transcription factor that responds to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. The ligand binding domain of PXR shows remarkable flexibility to accommodate both large and small molecules. PXR functions as a heterodimer with retinoic X receptor-alpha (RXRa) and binds to a variety of response elements in the promoter regions of a diverse set of target genes involved in the metabolism, transport, and elimination of these molecules from the cell. Constitutive androstane receptor (CAR) is a closest mammalian relative of PXR, which has also been proposed to function as a xenosensor. CAR is activated by some of the same ligands as PXR and regulates a subset of common genes. The sequence homology and functional similarity suggests that the CAR gene arose from a duplication of an ancestral PXR gene. Like other nuclear receptors, xenobiotic receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
• Changed! pfam zf-C4 71aa 2e-29 in ref transcript
  • Zinc finger, C4 type (two domains). In nearly all cases, this is the DNA binding domain of a nuclear hormone receptor. The alignment contains two Zinc finger domains that are too dissimilar to be aligned with each other.
• pfam Hormone_recep 190aa 5e-23 in ref transcript
  • Ligand-binding domain of nuclear hormone receptor. This all helical domain is involved in binding the hormone in these receptors.
• Changed! pfam zf-C4 46aa 9e-13 in modified transcript

NR1I3

• rs.NR1I3.F2 rs.NR1I3.R2 105 117
• NCBIGene 36.3 9970
• Alternative 3-prime, size difference: 12
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001077482

• Changed! cd NR_LBD_PXR_like 250aa 9e-91 in ref transcript
  • The ligand binding domain of xenobiotic receptors:pregnane X receptor and constitutive androstane receptor. The ligand binding domain of xenobiotic receptors: This xenobiotic receptor family includes pregnane X receptor (PXR), constitutive androstane receptor (CAR) and other related nuclear receptors. They function as sensors of toxic byproducts of cell metabolism and of exogenous chemicals, to facilitate their elimination. The nuclear receptor pregnane X receptor (PXR) is a ligand-regulated transcription factor that responds to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. The ligand binding domain of PXR shows remarkable flexibility to accommodate both large and small molecules. PXR functions as a heterodimer with retinoic X receptor-alpha (RXRa) and binds to a variety of response elements in the promoter regions of a diverse set of target genes involved in the metabolism, transport, and elimination of these molecules from the cell. Constitutive androstane receptor (CAR) is a closest mammalian relative of PXR, which has also been proposed to function as a xenosensor. CAR is activated by some of the same ligands as PXR and regulates a subset of common genes. The sequence homology and functional similarity suggests that the CAR gene arose from a duplication of an ancestral PXR gene. Like other nuclear receptors, xenobiotic receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
• pfam zf-C4 71aa 2e-29 in ref transcript
  • Zinc finger, C4 type (two domains). In nearly all cases, this is the DNA binding domain of a nuclear hormone receptor. The alignment contains two Zinc finger domains that are too dissimilar to be aligned with each other.
• Changed! pfam Hormone_recep 190aa 5e-23 in ref transcript
  • Ligand-binding domain of nuclear hormone receptor. This all helical domain is involved in binding the hormone in these receptors.
• Changed! cd NR_LBD_PXR_like 246aa 2e-92 in modified transcript
• Changed! pfam Hormone_recep 186aa 1e-22 in modified transcript

NR1I3

• rs.NR1I3.F3 rs.NR1I3.R3 103 257
• NCBIGene 36.3 9970
• Alternative 3-prime, size difference: 154
• Exclusion of the stop codon
• Reference transcript: NM_001077482

• Changed! cd NR_LBD_PXR_like 250aa 9e-91 in ref transcript
  • The ligand binding domain of xenobiotic receptors:pregnane X receptor and constitutive androstane receptor. The ligand binding domain of xenobiotic receptors: This xenobiotic receptor family includes pregnane X receptor (PXR), constitutive androstane receptor (CAR) and other related nuclear receptors. They function as sensors of toxic byproducts of cell metabolism and of exogenous chemicals, to facilitate their elimination. The nuclear receptor pregnane X receptor (PXR) is a ligand-regulated transcription factor that responds to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. The ligand binding domain of PXR shows remarkable flexibility to accommodate both large and small molecules. PXR functions as a heterodimer with retinoic X receptor-alpha (RXRa) and binds to a variety of response elements in the promoter regions of a diverse set of target genes involved in the metabolism, transport, and elimination of these molecules from the cell. Constitutive androstane receptor (CAR) is a closest mammalian relative of PXR, which has also been proposed to function as a xenosensor. CAR is activated by some of the same ligands as PXR and regulates a subset of common genes. The sequence homology and functional similarity suggests that the CAR gene arose from a duplication of an ancestral PXR gene. Like other nuclear receptors, xenobiotic receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
• pfam zf-C4 71aa 2e-29 in ref transcript
  • Zinc finger, C4 type (two domains). In nearly all cases, this is the DNA binding domain of a nuclear hormone receptor. The alignment contains two Zinc finger domains that are too dissimilar to be aligned with each other.
• Changed! pfam Hormone_recep 190aa 5e-23 in ref transcript
  • Ligand-binding domain of nuclear hormone receptor. This all helical domain is involved in binding the hormone in these receptors.
• Changed! cd NR_LBD_PXR_like 210aa 1e-81 in modified transcript
• Changed! pfam Hormone_recep 149aa 1e-23 in modified transcript

NR1I3

• rs.NR1I3.F4 rs.NR1I3.R4 100 115
• NCBIGene 36.3 9970
• Alternative 3-prime, size difference: 15
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001077482

• Changed! cd NR_LBD_PXR_like 250aa 9e-91 in ref transcript
  • The ligand binding domain of xenobiotic receptors:pregnane X receptor and constitutive androstane receptor. The ligand binding domain of xenobiotic receptors: This xenobiotic receptor family includes pregnane X receptor (PXR), constitutive androstane receptor (CAR) and other related nuclear receptors. They function as sensors of toxic byproducts of cell metabolism and of exogenous chemicals, to facilitate their elimination. The nuclear receptor pregnane X receptor (PXR) is a ligand-regulated transcription factor that responds to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. The ligand binding domain of PXR shows remarkable flexibility to accommodate both large and small molecules. PXR functions as a heterodimer with retinoic X receptor-alpha (RXRa) and binds to a variety of response elements in the promoter regions of a diverse set of target genes involved in the metabolism, transport, and elimination of these molecules from the cell. Constitutive androstane receptor (CAR) is a closest mammalian relative of PXR, which has also been proposed to function as a xenosensor. CAR is activated by some of the same ligands as PXR and regulates a subset of common genes. The sequence homology and functional similarity suggests that the CAR gene arose from a duplication of an ancestral PXR gene. Like other nuclear receptors, xenobiotic receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
• pfam zf-C4 71aa 2e-29 in ref transcript
  • Zinc finger, C4 type (two domains). In nearly all cases, this is the DNA binding domain of a nuclear hormone receptor. The alignment contains two Zinc finger domains that are too dissimilar to be aligned with each other.
• Changed! pfam Hormone_recep 190aa 5e-23 in ref transcript
  • Ligand-binding domain of nuclear hormone receptor. This all helical domain is involved in binding the hormone in these receptors.
• Changed! cd NR_LBD_PXR_like 245aa 1e-92 in modified transcript
• Changed! pfam Hormone_recep 185aa 9e-25 in modified transcript

NR6A1

• rs.NR6A1.F1 rs.NR6A1.R1 106 118
• NCBIGene 36.3 2649
• Alternative 3-prime, size difference: 12
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_033334

• cd NR_LBD_DHR4_like 212aa 1e-103 in ref transcript
  • The ligand binding domain of orphan nuclear receptor Ecdysone-induced receptor DHR4. The ligand binding domain of Ecdysone-induced receptor DHR4: Ecdysone-induced orphan receptor DHR4 is a member of the nuclear receptor family. DHR4 is expressed during the early Drosophila larval development and is induced by ecdysone. DHR4 coordinates growth and maturation in Drosophila by mediating endocrine response to the attainment of proper body size during larval development. Mutations in DHR4 result in shorter larval development which translates into smaller and lighter flies. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, DHR4 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
• pfam zf-C4 76aa 3e-32 in ref transcript
  • Zinc finger, C4 type (two domains). In nearly all cases, this is the DNA binding domain of a nuclear hormone receptor. The alignment contains two Zinc finger domains that are too dissimilar to be aligned with each other.
• pfam Hormone_recep 165aa 1e-26 in ref transcript
  • Ligand-binding domain of nuclear hormone receptor. This all helical domain is involved in binding the hormone in these receptors.

NRD1

• rs.NRD1.F1 rs.NRD1.R1 339 543
• NCBIGene 36.3 4898
• Multiple exon skipping, size difference: 204
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_002525

• Changed! pfam Peptidase_M16 127aa 4e-37 in ref transcript
  • Insulinase (Peptidase family M16).
• pfam Peptidase_M16_C 176aa 3e-20 in ref transcript
  • Peptidase M16 inactive domain. Peptidase M16 consists of two structurally related domains. One is the active peptidase, whereas the other is inactive. The two domains hold the substrate like a clamp.
• pfam Peptidase_M16_C 183aa 1e-08 in ref transcript
• COG Ptr 879aa 1e-148 in ref transcript
  • Secreted/periplasmic Zn-dependent peptidases, insulinase-like [Posttranslational modification, protein turnover, chaperones].
• Changed! pfam Peptidase_M16 139aa 3e-38 in modified transcript

NRG1

• rs.NRG1.F1 rs.NRG1.R1 191 293
• NCBIGene 36.3 3084
• Multiple exon skipping, size difference: 102
• Exclusion in the protein (no frameshift), Exclusion in the protein (no frameshift)
• Reference transcript: NM_013956

• cd IGcam 89aa 2e-05 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• pfam Neuregulin 396aa 1e-109 in ref transcript
  • Neuregulin family.
• smart IG_like 87aa 1e-07 in ref transcript
  • Immunoglobulin like. IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
• pfam EGF 32aa 0.006 in ref transcript
  • EGF-like domain. There is no clear separation between noise and signal. pfam00053 is very similar, but has 8 instead of 6 conserved cysteines. Includes some cytokine receptors. The EGF domain misses the N-terminus regions of the Ca2+ binding EGF domains (this is the main reason of discrepancy between Swiss-Prot domain start/end and Pfam). The family is hard to model due to many similar but different sub-types of EGF domains. Pfam certainly misses a number of EGF domains.

NRG1

• rs.NRG1.F2 rs.NRG1.R2 251 393
• NCBIGene 36.3 3084
• Single exon skipping, size difference: 142
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_013956

• cd IGcam 89aa 2e-05 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• Changed! pfam Neuregulin 396aa 1e-109 in ref transcript
  • Neuregulin family.
• smart IG_like 87aa 1e-07 in ref transcript
  • Immunoglobulin like. IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
• Changed! pfam EGF 32aa 0.006 in ref transcript
  • EGF-like domain. There is no clear separation between noise and signal. pfam00053 is very similar, but has 8 instead of 6 conserved cysteines. Includes some cytokine receptors. The EGF domain misses the N-terminus regions of the Ca2+ binding EGF domains (this is the main reason of discrepancy between Swiss-Prot domain start/end and Pfam). The family is hard to model due to many similar but different sub-types of EGF domains. Pfam certainly misses a number of EGF domains.
• Changed! pfam Neuregulin 190aa 2e-57 in modified transcript

NRG1

• rs.NRG1.F3 rs.NRG1.R3 119 143
• NCBIGene 36.3 3084
• Single exon skipping, size difference: 24
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_013956

• cd IGcam 89aa 2e-05 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• pfam Neuregulin 396aa 1e-109 in ref transcript
  • Neuregulin family.
• smart IG_like 87aa 1e-07 in ref transcript
  • Immunoglobulin like. IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
• pfam EGF 32aa 0.006 in ref transcript
  • EGF-like domain. There is no clear separation between noise and signal. pfam00053 is very similar, but has 8 instead of 6 conserved cysteines. Includes some cytokine receptors. The EGF domain misses the N-terminus regions of the Ca2+ binding EGF domains (this is the main reason of discrepancy between Swiss-Prot domain start/end and Pfam). The family is hard to model due to many similar but different sub-types of EGF domains. Pfam certainly misses a number of EGF domains.

NRG2

• rs.NRG2.F1 rs.NRG2.R1 127 151
• NCBIGene 36.3 9542
• Single exon skipping, size difference: 24
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_013982

• cd IGcam 88aa 2e-11 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• pfam Neuregulin 321aa 1e-39 in ref transcript
  • Neuregulin family.
• pfam I-set 90aa 3e-15 in ref transcript
  • Immunoglobulin I-set domain.

NRG2

• rs.NRG2.F2 rs.NRG2.R2 110 134
• NCBIGene 36.3 9542
• Single exon skipping, size difference: 24
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_013983

• cd IGcam 88aa 2e-11 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• pfam Neuregulin 321aa 8e-40 in ref transcript
  • Neuregulin family.
• pfam I-set 90aa 3e-15 in ref transcript
  • Immunoglobulin I-set domain.

NRP1

• rs.NRP1.F1 rs.NRP1.R1 112 217
• NCBIGene 36.3 8829
• Single exon skipping, size difference: 105
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_003873

• cd MAM 154aa 2e-45 in ref transcript
  • Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region.
• cd FA58C 147aa 1e-36 in ref transcript
  • Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes.
• cd CUB 114aa 5e-29 in ref transcript
  • CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.
• cd CUB 118aa 1e-26 in ref transcript
• cd FA58C 148aa 2e-23 in ref transcript
• smart MAM 160aa 2e-46 in ref transcript
  • Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others). Likely to have an adhesive function. Mutations in the meprin MAM domain affect noncovalent associations within meprin oligomers. In receptor tyrosine phosphatase mu-like molecules the MAM domain is important for homophilic cell-cell interactions.
• pfam CUB 116aa 5e-33 in ref transcript
  • CUB domain.
• smart FA58C 151aa 9e-33 in ref transcript
  • Coagulation factor 5/8 C-terminal domain, discoidin domain. Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes.
• pfam CUB 112aa 2e-31 in ref transcript
• pfam F5_F8_type_C 135aa 1e-18 in ref transcript
  • F5/8 type C domain. This domain is also known as the discoidin (DS) domain family.

NRP2

• rs.NRP2.F1 rs.NRP2.R1 100 115
• NCBIGene 36.3 8828
• Alternative 5-prime, size difference: 15
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_018534

• cd FA58C 147aa 4e-39 in ref transcript
  • Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes.
• cd MAM 148aa 3e-36 in ref transcript
  • Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region.
• cd CUB 114aa 4e-31 in ref transcript
  • CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.
• cd CUB 117aa 3e-27 in ref transcript
• cd FA58C 154aa 2e-24 in ref transcript
• smart MAM 154aa 9e-40 in ref transcript
  • Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others). Likely to have an adhesive function. Mutations in the meprin MAM domain affect noncovalent associations within meprin oligomers. In receptor tyrosine phosphatase mu-like molecules the MAM domain is important for homophilic cell-cell interactions.
• smart FA58C 151aa 4e-34 in ref transcript
  • Coagulation factor 5/8 C-terminal domain, discoidin domain. Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes.
• pfam CUB 112aa 6e-31 in ref transcript
  • CUB domain.
• pfam CUB 116aa 3e-29 in ref transcript
• pfam F5_F8_type_C 141aa 3e-21 in ref transcript
  • F5/8 type C domain. This domain is also known as the discoidin (DS) domain family.

NRP2

• rs.NRP2.F2 rs.NRP2.R2 100 115
• NCBIGene 36.3 8828
• Alternative 5-prime, size difference: 15
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_201266

• cd FA58C 147aa 2e-39 in ref transcript
  • Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes.
• cd MAM 148aa 4e-36 in ref transcript
  • Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region.
• cd CUB 114aa 5e-31 in ref transcript
  • CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.
• cd CUB 117aa 4e-27 in ref transcript
• cd FA58C 154aa 8e-25 in ref transcript
• smart MAM 154aa 8e-40 in ref transcript
  • Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others). Likely to have an adhesive function. Mutations in the meprin MAM domain affect noncovalent associations within meprin oligomers. In receptor tyrosine phosphatase mu-like molecules the MAM domain is important for homophilic cell-cell interactions.
• smart FA58C 151aa 2e-34 in ref transcript
  • Coagulation factor 5/8 C-terminal domain, discoidin domain. Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes.
• pfam CUB 112aa 7e-31 in ref transcript
  • CUB domain.
• pfam CUB 116aa 4e-29 in ref transcript
• pfam F5_F8_type_C 141aa 2e-21 in ref transcript
  • F5/8 type C domain. This domain is also known as the discoidin (DS) domain family.

NRXN3

• rs.NRXN3.F1 rs.NRXN3.R1 143 233
• NCBIGene 36.3 9369
• Single exon skipping, size difference: 90
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_004796

• cd LamG 154aa 2e-23 in ref transcript
  • Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules.
• cd LamG 170aa 2e-22 in ref transcript
• Changed! cd LamG 150aa 3e-18 in ref transcript
• cd LamG 156aa 2e-12 in ref transcript
• cd EGF_CA 34aa 3e-04 in ref transcript
  • Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements.
• smart LamG 150aa 5e-28 in ref transcript
  • Laminin G domain.
• smart LamG 137aa 2e-26 in ref transcript
• Changed! smart LamG 127aa 2e-20 in ref transcript
• smart LamG 136aa 4e-19 in ref transcript
• smart LamG 40aa 0.001 in ref transcript
• pfam EGF 33aa 0.008 in ref transcript
  • EGF-like domain. There is no clear separation between noise and signal. pfam00053 is very similar, but has 8 instead of 6 conserved cysteines. Includes some cytokine receptors. The EGF domain misses the N-terminus regions of the Ca2+ binding EGF domains (this is the main reason of discrepancy between Swiss-Prot domain start/end and Pfam). The family is hard to model due to many similar but different sub-types of EGF domains. Pfam certainly misses a number of EGF domains.
• Changed! cd LamG 120aa 3e-15 in modified transcript
• Changed! smart LamG 157aa 7e-17 in modified transcript

NSL1

• rs.NSL1.F1 rs.NSL1.R1 327 412
• NCBIGene 36.3 25936
• Single exon skipping, size difference: 85
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_015471

• Changed! pfam Mis14 145aa 5e-30 in ref transcript
  • Kinetochore protein Mis14 like. Mis14 is a kinetochore protein which is known to be recruited to kinetochores independently of CENP-A.
• Changed! pfam Mis14 100aa 1e-19 in modified transcript

NTRK1

• rs.NTRK1.F1 NTRK1.R1 100 118
• NCBIGene 36.3 4914
• Single exon skipping, size difference: 18
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_002529

• cd PTKc_TrkA 280aa 1e-164 in ref transcript
  • Catalytic Domain of the Protein Tyrosine Kinase, Tropomyosin Related Kinase A. Protein Tyrosine Kinase (PTK) family; Tropomyosin related kinase A (TrkA); catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. TrkA is a member of the Trk subfamily of proteins, which are receptor tyr kinases (RTKs) containing an extracellular region with arrays of leucine-rich motifs flanked by two cysteine-rich clusters followed by two immunoglobulin-like domains, a transmembrane segment, and an intracellular catalytic domain. Binding of TrkA to its ligand, nerve growth factor (NGF), results in receptor oligomerization and activation of the catalytic domain. TrkA is expressed mainly in neural-crest-derived sensory and sympathetic neurons of the peripheral nervous system, and in basal forebrain cholinergic neurons of the central nervous system. It is critical for neuronal growth, differentiation and survival. Alternative TrkA splicing has been implicated as a pivotal regulator of neuroblastoma (NB) behavior. Normal TrkA expression is associated with better NB prognosis, while the hypoxia-regulated TrkAIII splice variant promotes NB pathogenesis and progression. Aberrant TrkA expression has also been demonstrated in non-neural tumors including prostate, breast, lung, and pancreatic cancers.
• cd IGcam 71aa 0.002 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• pfam Pkinase_Tyr 272aa 1e-104 in ref transcript
  • Protein tyrosine kinase.
• TIGR PCC 67aa 3e-05 in ref transcript
  • Note: this model is restricted to the amino half because a full-length model is incompatible with the HMM software package.
• pfam I-set 85aa 4e-04 in ref transcript
  • Immunoglobulin I-set domain.
• pfam I-set 70aa 0.002 in ref transcript
• COG SPS1 265aa 1e-23 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].

NUMB

• rs.NUMB.F1 rs.NUMB.R1 104 137
• NCBIGene 36.3 8650
• Single exon skipping, size difference: 33
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001005743

• Changed! cd Numb 149aa 2e-72 in ref transcript
  • Numb Phosphotyrosine-binding (PTB) domain. Numb is a membrane associated adaptor protein, which is a determinant of asymmetric cell division. Numb has an N-terminal PTB domain. PTB domains have a PH-like fold and are found in various eukaryotic signaling molecules. They were initially identified based upon their ability to recognize phosphorylated tyrosine residues. In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. More recent studies have found that some types of PTB domains can bind to peptides which are not tyrosine phosphorylated or lack tyrosine residues altogether.
• Changed! pfam PID 134aa 7e-34 in ref transcript
  • Phosphotyrosine interaction domain (PTB/PID).
• pfam NumbF 82aa 8e-32 in ref transcript
  • NUMB domain. This presumed domain is found in the Numb family of proteins adjacent to the PTB domain.
• Changed! cd Numb 138aa 5e-75 in modified transcript
• Changed! pfam PID 123aa 3e-33 in modified transcript

NUP50

• rs.NUP50.F1 rs.NUP50.R1 123 313
• NCBIGene 36.3 10762
• Single exon skipping, size difference: 190
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_007172

• Changed! cd RanBD 112aa 2e-16 in ref transcript
  • Ran-binding domain; This domain of approximately 150 residues shares structural similarity to the PH domain, but lacks detectable sequence similarity. Ran is a Ras-like nuclear small GTPase, which regulates receptor-mediated transport between the nucleus and the cytoplasm. RanGTP hydrolysis is stimulated by RanGAP together with the Ran-binding domain containing acessory proteins RanBP1 and RanBP2. These accessory proteins stabilize the active GTP-bound form of Ran . The Ran-binding domain is found in multiple copies in Nuclear pore complex proteins.
• Changed! pfam NUP50 303aa 5e-71 in ref transcript
  • NUP50 (Nucleoporin 50 kDa). Nucleoporin 50 kDa (NUP50) acts as a cofactor for the importin-alpha:importin-beta heterodimer, which in turn allows for transportation of many nuclear-targeted proteins through nuclear pore complexes. The C terminus of NUP50 binds importin-beta through RAN-GTP, the N terminus binds the C terminus of importin-alpha, while a central domain binds importin-beta. NUP50:importin-alpha:importin-beta then binds cargo and can stimulate nuclear import. The N-terminal domain of NUP50 is also able to actively displace nuclear localisation signals from importin-alpha.
• Changed! pfam Ran_BP1 110aa 3e-05 in ref transcript
  • RanBP1 domain.
• Changed! pfam NUP50 23aa 1e-07 in modified transcript

NUP98

• rs.NUP98.F1 rs.NUP98.R1 143 365
• NCBIGene 36.3 4928
• Single exon skipping, size difference: 222
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_016320

• pfam Nucleoporin2 156aa 2e-63 in ref transcript
  • Nucleoporin autopeptidase.

NUP98

• rs.NUP98.F2 rs.NUP98.R2 256 307
• NCBIGene 36.3 4928
• Alternative 5-prime, size difference: 51
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_016320

• pfam Nucleoporin2 156aa 2e-63 in ref transcript
  • Nucleoporin autopeptidase.

NUPR1

• rs.NUPR1.F1 rs.NUPR1.R1 231 285
• NCBIGene 36.3 26471
• Alternative 3-prime, size difference: 54
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001042483

• pfam Phospho_p8 29aa 8e-10 in ref transcript
  • DNA-binding nuclear phosphoprotein p8. P8 is a short 80-82 amino acid protein that is conserved from nematodes to humans. It carries at least one protein kinase C domain suggesting a possible role in signal transduction and it is thought to be a phosphoprotein, but the sites of phosphorylation and the kinases involved remain to be determined.

NYD-SP21

• rs.NYD-SP21.F1 rs.NYD-SP21.R1 248 299
• NCBIGene 36.3 84689
• Single exon skipping, size difference: 51
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_032597

• Changed! pfam CD20 127aa 1e-33 in ref transcript
  • CD20/IgE Fc receptor beta subunit family. This family includes the CD20 protein and the beta subunit of the high affinity receptor for IgE Fc. The high affinity receptor for IgE is a tetrameric structure consisting of a single IgE-binding alpha subunit, a single beta subunit, and two disulfide-linked gamma subunits. The alpha subunit of Fc epsilon RI and most Fc receptors are homologous members of the Ig superfamily. By contrast, the beta and gamma subunits from Fc epsilon RI are not homologous to the Ig superfamily. Both molecules have four putative transmembrane segments and a probably topology where both amino- and carboxy termini protrude into the cytoplasm.
• Changed! pfam CD20 110aa 1e-24 in modified transcript

OCIAD1

• rs.OCIAD1.F1 rs.OCIAD1.R1 153 400
• NCBIGene 36.3 54940
• Alternative 5-prime, size difference: 247
• Exclusion in 5'UTR
• Reference transcript: NM_001079839

• pfam OCIA 108aa 4e-48 in ref transcript
  • Ovarian carcinoma immunoreactive antigen (OCIA). This family consists of several ovarian carcinoma immunoreactive antigen (OCIA) and related eukaryotic sequences. The function of this family is unknown.

OGG1

• rs.OGG1.F1 rs.OGG1.R1 98 145
• NCBIGene 36.3 4968
• Alternative 3-prime, size difference: 47
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_016828

• Changed! cd ENDO3c 179aa 3e-18 in ref transcript
  • endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases.
• TIGR ogg 306aa 1e-137 in ref transcript
  • All proteins in this family for which functions are known are 8-oxo-guanaine DNA glycosylases that function in base excision repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). This family is distantly realted to the Nth-MutY superfamily.
• COG AlkA 229aa 3e-25 in ref transcript
  • 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair].
• Changed! cd ENDO3c 179aa 2e-17 in modified transcript

OGN

• rs.OGN.F1 rs.OGN.R1 122 404
• NCBIGene 36.3 4969
• Alternative 3-prime, size difference: 282
• Inclusion in 5'UTR
• Reference transcript: NM_014057

OPA1

• rs.OPA1.F1 rs.OPA1.R1 100 208
• NCBIGene 36.3 4976
• Single exon skipping, size difference: 108
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_130837

• pfam Dynamin_N 179aa 4e-38 in ref transcript
  • Dynamin family.

OPA1

• rs.OPA1.F2 rs.OPA1.R2 105 216
• NCBIGene 36.3 4976
• Single exon skipping, size difference: 111
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_130837

• pfam Dynamin_N 179aa 4e-38 in ref transcript
  • Dynamin family.

OPTN

• rs.OPTN.F1 rs.OPTN.R1 101 116
• NCBIGene 36.3 10133
• Alternative 3-prime, size difference: 15
• Inclusion in 5'UTR
• Reference transcript: NM_001008213

• pfam SMC_N 178aa 0.001 in ref transcript
  • RecF/RecN/SMC N terminal domain. This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.
• PRK PRK05771 248aa 0.010 in ref transcript
  • V-type ATP synthase subunit I; Validated.

OSBPL2

• rs.OSBPL2.F1 rs.OSBPL2.R1 121 157
• NCBIGene 36.3 9885
• Alternative 3-prime, size difference: 36
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_144498

• pfam Oxysterol_BP 351aa 4e-64 in ref transcript
  • Oxysterol-binding protein.

OSBPL3

• rs.OSBPL3.F1 rs.OSBPL3.R1 148 256
• NCBIGene 36.3 26031
• Single exon skipping, size difference: 108
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_015550

• cd PH_oxysterol_bp 91aa 2e-18 in ref transcript
  • Oxysterol binding protein (OSBP) Pleckstrin homology (PH) domain. Oxysterol binding proteins are a multigene family that is conserved in yeast, flies, worms, mammals and plants. They all contain a C-terminal oxysterol binding domain, and most contain an N-terminal PH domain. OSBP PH domains bind to membrane phosphoinositides and thus likely play an important role in intracellular targeting. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
• pfam Oxysterol_BP 300aa 2e-56 in ref transcript
  • Oxysterol-binding protein.
• smart PH 91aa 3e-09 in ref transcript
  • Pleckstrin homology domain. Domain commonly found in eukaryotic signalling proteins. The domain family possesses multiple functions including the abilities to bind inositol phosphates, and various proteins. PH domains have been found to possess inserted domains (such as in PLC gamma, syntrophins) and to be inserted within other domains. Mutations in Brutons tyrosine kinase (Btk) within its PH domain cause X-linked agammaglobulinaemia (XLA) in patients. Point mutations cluster into the positively charged end of the molecule around the predicted binding site for phosphatidylinositol lipids.

OSBPL9

• rs.OSBPL9.F1 rs.OSBPL9.R1 102 171
• NCBIGene 36.3 114883
• Single exon skipping, size difference: 69
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_148909

• cd PH_oxysterol_bp 93aa 1e-28 in ref transcript
  • Oxysterol binding protein (OSBP) Pleckstrin homology (PH) domain. Oxysterol binding proteins are a multigene family that is conserved in yeast, flies, worms, mammals and plants. They all contain a C-terminal oxysterol binding domain, and most contain an N-terminal PH domain. OSBP PH domains bind to membrane phosphoinositides and thus likely play an important role in intracellular targeting. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
• pfam Oxysterol_BP 342aa 2e-49 in ref transcript
  • Oxysterol-binding protein.
• smart PH 95aa 6e-13 in ref transcript
  • Pleckstrin homology domain. Domain commonly found in eukaryotic signalling proteins. The domain family possesses multiple functions including the abilities to bind inositol phosphates, and various proteins. PH domains have been found to possess inserted domains (such as in PLC gamma, syntrophins) and to be inserted within other domains. Mutations in Brutons tyrosine kinase (Btk) within its PH domain cause X-linked agammaglobulinaemia (XLA) in patients. Point mutations cluster into the positively charged end of the molecule around the predicted binding site for phosphatidylinositol lipids.

OSCAR

• rs.OSCAR.F1 rs.OSCAR.R1 105 117
• NCBIGene 36.3 126014
• Single exon skipping, size difference: 12
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_206818

PACRG

• rs.PACRG.F1 rs.PACRG.R1 276 393
• NCBIGene 36.3 135138
• Single exon skipping, size difference: 117
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_152410

• Changed! pfam ParcG 223aa 2e-83 in ref transcript
  • Parkin co-regulated protein. This family of proteins is transcribed anti-sense along the DNA to the Parkin gene product and the two appear to be transcribed under the same promoter. The protein has predicted alpha-helical and beta-sheet domains which suggest its function is in the ubiquitin/proteasome system. Mutations in parkin are the genetic cause of early-onset and autosomal recessive juvenile parkinsonism.
• Changed! pfam ParcG 184aa 9e-89 in modified transcript

PACS2

• rs.PACS2.F1 rs.PACS2.R1 102 114
• NCBIGene 36.3 23241
• Alternative 5-prime, size difference: 12
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001100913

• pfam Pacs-1 213aa 3e-93 in ref transcript
  • PACS-1 cytosolic sorting protein. PACS-1 is a cytosolic sorting protein that directs the localisation of membrane proteins in the trans-Golgi network (TGN)/endosomal system. PACS-1 connects the clathrin adaptor AP-1 to acidic cluster sorting motifs contained in the cytoplasmic domain of cargo proteins such as furin, the cation-independent mannose-6-phosphate receptor and in viral proteins such as human immunodeficiency virus type 1 Nef.
• pfam Pacs-1 149aa 3e-61 in ref transcript

PAICS

• rs.PAICS.F1 rs.PAICS.R1 110 131
• NCBIGene 36.3 10606
• Single exon skipping, size difference: 21
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_006452

• Changed! cd SAICAR_synt_Ade5 252aa 1e-142 in ref transcript
  • Ade5_like 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase. Eukaryotic group of SAICAR synthetases represented by the Drosophila melanogaster, N-terminal, SAICAR synthetase domain of bifunctional Ade5. The Ade5 gene product (CAIR-SAICARs) catalyzes the sixth and seventh steps of the de novo biosynthesis of purine nucleotides (also reported as seventh and eighth steps). SAICAR synthetase converts 5-aminoimidazole-4-carboxyribonucleotide (CAIR), ATP, and L-aspartate into 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR), ADP, and phosphate.
• Changed! pfam SAICAR_synt 245aa 8e-92 in ref transcript
  • SAICAR synthetase. Also known as Phosphoribosylaminoimidazole-succinocarboxamide synthase.
• TIGR purE 154aa 1e-57 in ref transcript
  • Phosphoribosylaminoimidazole carboxylase is a fusion protein in plants and fungi, but consists of two non-interacting proteins in bacteria, PurK and PurE. This model represents PurK, an N5-CAIR mutase.
• Changed! PRK PRK09362 252aa 5e-54 in ref transcript
  • phosphoribosylaminoimidazole-succinocarboxamide synthase; Reviewed.
• COG PurE 138aa 3e-19 in ref transcript
  • Phosphoribosylcarboxyaminoimidazole (NCAIR) mutase [Nucleotide transport and metabolism].
• Changed! cd SAICAR_synt_Ade5 259aa 1e-139 in modified transcript
• Changed! pfam SAICAR_synt 252aa 5e-89 in modified transcript
• Changed! PRK PRK09362 259aa 1e-50 in modified transcript

PAK4

• rs.PAK4.F1 rs.PAK4.R1 91 550
• NCBIGene 36.3 10298
• Single exon skipping, size difference: 459
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_005884

• cd STKc_PAK_II 285aa 1e-173 in ref transcript
  • Serine/threonine kinases (STKs), p21-activated kinase (PAK) subfamily, Group II, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The PAK subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. PAKs are Rho family GTPase-regulated kinases that serve as important mediators in the function of Cdc42 (cell division cycle 42) and Rac. PAKs from higher eukaryotes are classified into two groups (I and II), according to their biochemical and structural features. Group II PAKs, also called non-conventional PAKs, include PAK4, PAK5, and PAK6. Group II PAKs contain PBD (p21-binding domain) and catalytic domains, but lack other motifs found in group I PAKs, such as an AID (autoinhibitory domain) and SH3 binding sites. Since group II PAKs do not contain an obvious AID, they may be regulated differently from group I PAKs. While group I PAKs interact with the SH3 containing proteins Nck, Grb2 and PIX, no such binding has been demonstrated for group II PAKs. Some known substrates of group II PAKs are also substrates of group I PAKs such as Raf, BAD, LIMK and GEFH1. Unique group II substrates include MARK/Par-1 and PDZ-RhoGEF. Group II PAKs play important roles in filopodia formation, neuron extension, cytoskeletal organization, and cell survival.
• cd CRIB_PAK_like 39aa 4e-11 in ref transcript
  • PAK (p21 activated kinase) Binding Domain (PBD), binds Cdc42p- and/or Rho-like small GTPases; also known as the Cdc42/Rac interactive binding (CRIB) motif; has been shown to inhibit transcriptional activation and cell transformation mediated by the Ras-Rac pathway. This subgroup of CRIB/PBD-domains is found N-terminal of Serine/Threonine kinase domains in PAK and PAK-like proteins.
• smart S_TKc 242aa 5e-76 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• pfam PBD 55aa 1e-11 in ref transcript
  • P21-Rho-binding domain. Small domains that bind Cdc42p- and/or Rho-like small GTPases. Also known as the Cdc42/Rac interactive binding (CRIB).
• COG SPS1 248aa 2e-35 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].

PAP2D

• rs.PAP2D.F1 rs.PAP2D.R1 113 128
• NCBIGene 36.3 163404
• Alternative 5-prime, size difference: 15
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001037317

• cd PAP2_wunen 150aa 4e-52 in ref transcript
  • PAP2, wunen subfamily. Most likely a family of membrane associated phosphatidic acid phosphatases. Wunen is a drosophila protein expressed in the central nervous system, which provides repellent activity towards primordial germ cells (PGCs), controls the survival of PGCs and is essential in the migration process of these cells towards the somatic gonadal precursors.
• smart acidPPc 91aa 8e-11 in ref transcript
  • Acid phosphatase homologues.

PAPSS2

• rs.PAPSS2.F1 rs.PAPSS2.R1 100 115
• NCBIGene 36.3 9060
• Single exon skipping, size difference: 15
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001015880

• Changed! cd ATPS 369aa 1e-140 in ref transcript
  • ATP-sulfurylase (ATPS), also known as sulfate adenylate transferase, catalyzes the transfer of an adenylyl group from ATP to sulfate, forming adenosine 5'-phosphosulfate (APS). This reaction is generally accompanied by a further reaction, catalyzed by APS kinase, in which APS is phosphorylated to yield 3'-phospho-APS (PAPS). In some organisms the APS kinase is a separate protein, while in others it is incorporated with ATP sulfurylase in a bifunctional enzyme that catalyzes both reactions. In bifunctional proteins, the domain that performs the kinase activity can be attached at the N-terminal end of the sulfurylase unit or at the C-terminal end, depending on the organism. While the reaction is ubiquitous among organisms, the physiological role of the reaction varies. In some organisms it is used to generate APS from sulfate and ATP, while in others it proceeds in the opposite direction to generate ATP from APS and pyrophosphate. ATP sulfurylase can be a monomer, a homodimer, or a homo-oligomer, depending on the organism. ATPS belongs to a large superfamily of nucleotidyltransferases that includes pantothenate synthetase (PanC), phosphopantetheine adenylyltransferase (PPAT), and the amino-acyl tRNA synthetases. The enzymes of this family are structurally similar and share a dinucleotide-binding domain.
• cd APSK 151aa 9e-73 in ref transcript
  • Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS). The end-product PAPS is a biologically "activated" sulfate form important for the assimilation of inorganic sulfate.
• Changed! pfam ATP-sulfurylase 324aa 1e-120 in ref transcript
  • ATP-sulfurylase. This family consists of ATP-sulfurylase or sulfate adenylyltransferase EC:2.7.7.4 some of which are part of a bifunctional polypeptide chain associated with adenosyl phosphosulphate (APS) kinase pfam01583. Both enzymes are required for PAPS (phosphoadenosine-phosphosulfate) synthesis from inorganic sulphate. ATP sulfurylase catalyses the synthesis of adenosine-phosphosulfate APS from ATP and inorganic sulphate.
• pfam APS_kinase 159aa 4e-78 in ref transcript
  • Adenylylsulphate kinase. Enzyme that catalyses the phosphorylation of adenylylsulphate to 3'-phosphoadenylylsulfate. This domain contains an ATP binding P-loop motif.
• PRK PRK05506 201aa 4e-73 in ref transcript
  • bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Provisional.
• Changed! PRK sat 389aa 4e-56 in ref transcript
  • sulfate adenylyltransferase; Reviewed.
• Changed! cd ATPS 364aa 1e-140 in modified transcript
• Changed! pfam ATP-sulfurylase 322aa 1e-119 in modified transcript
• Changed! PRK sat 384aa 1e-54 in modified transcript

PARK2

• rs.PARK2.F1 rs.PARK2.R1 183 267
• NCBIGene 36.3 5071
• Single exon skipping, size difference: 84
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_004562

• cd parkin_N 70aa 9e-31 in ref transcript
  • parkin_N parkin protein is a RING-type E3 ubiquitin ligase with an amino-terminal ubiquitin-like (Ubl) domain and an RBR signature consisting of two RING finger domains separated by an IBR/DRIL domain. Naturally occurring mutations in parkin are thought to cause the disease AR_JP (autosomal-recessive juvenile parkinsonism). Parkin binds the Rpn10 subunit of 26S proteasomes through its Ubl domain.
• pfam ubiquitin 61aa 2e-15 in ref transcript
  • Ubiquitin family. This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue), Nedd8, Elongin B, Rub1, and Parkin. A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites.
• pfam IBR 63aa 2e-06 in ref transcript
  • IBR domain. The IBR (In Between Ring fingers) domain is often found to occur between pairs of ring fingers (pfam00097). This domain has also been called the C6HC domain and DRIL (for double RING finger linked) domain. Proteins that contain two Ring fingers and an IBR domain (these proteins are also termed RBR family proteins) are thought to exist in all eukaryotic organisms. RBR family members play roles in protein quality control and can indirectly regulate transcription. Evidence suggests that RBR proteins are often parts of cullin-containing ubiquitin ligase complexes. The ubiquitin ligase Parkin is an RBR family protein whose mutations are involved in forms of familial Parkinson's disease.
• PTZ PTZ00044 54aa 7e-06 in ref transcript
  • ubiquitin; Provisional.

PARP2

• rs.PARP2.F1 rs.PARP2.R1 258 297
• NCBIGene 36.3 10038
• Alternative 5-prime, size difference: 39
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_005484

• cd parp_like 344aa 1e-129 in ref transcript
  • Poly(ADP-ribose) polymerase (parp) catalytic domain catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active. Poly(ADP-ribose)-like polymerases (PARPS 1-3, VPARP, tankyrase) catalyze the addition of up to 100 ADP_ribose units from NAD+. PARPs 1 and 2 are localized in the nucleaus, bind DNA, and are activated by DNA damage. VPARP is part of the vault ribonucleoprotein complex. Tankyrases regulates telomere length through interactions with telomere repeat binding factor 1.
• pfam PARP 213aa 1e-80 in ref transcript
  • Poly(ADP-ribose) polymerase catalytic domain. Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active.
• pfam PARP_reg 130aa 5e-30 in ref transcript
  • Poly(ADP-ribose) polymerase, regulatory domain. Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active.
• smart WGR 86aa 3e-25 in ref transcript
  • Proposed nucleic acid binding domain. This domain is named after its most conserved central motif. It is found in a variety of polyA polymerases as well as in molybdate metabolism regulators (e.g. in E.coli) and other proteins of unknown function. The domain is found in isolation in some proteins and is between 70 and 80 residues in length. It is proposed that it may be a nucleic acid binding domain.

PAX3

• rs.PAX3.F1 rs.PAX3.R1 110 133
• NCBIGene 36.3 5077
• Alternative 5-prime and 3-prime, size difference: 23
• Inclusion in the protein causing a new stop codon, Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_181459

• cd PAX 128aa 2e-61 in ref transcript
  • Paired Box domain.
• cd homeodomain 58aa 6e-18 in ref transcript
  • Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
• pfam PAX 126aa 7e-69 in ref transcript
  • 'Paired box' domain.
• pfam Homeobox 57aa 5e-24 in ref transcript
  • Homeobox domain.
• COG COG5576 76aa 5e-10 in ref transcript
  • Homeodomain-containing transcription factor [Transcription].

PC

• rs.PC.F1 rs.PC.R1 93 281
• NCBIGene 36.3 5091
• Single exon skipping, size difference: 188
• Exclusion in 5'UTR
• Reference transcript: NM_001040716

• cd biotinyl_domain 67aa 7e-20 in ref transcript
  • The biotinyl-domain or biotin carboxyl carrier protein (BCCP) domain is present in all biotin-dependent enzymes, such as acetyl-CoA carboxylase, pyruvate carboxylase, propionyl-CoA carboxylase, methylcrotonyl-CoA carboxylase, geranyl-CoA carboxylase, oxaloacetate decarboxylase, methylmalonyl-CoA decarboxylase, transcarboxylase and urea amidolyase. This domain functions in transferring CO2 from one subsite to another, allowing carboxylation, decarboxylation, or transcarboxylation. During this process, biotin is covalently attached to a specific lysine.
• TIGR pyruv_carbox 1140aa 0.0 in ref transcript
  • This enzyme plays a role in gluconeogensis but not glycolysis.
• PRK PRK12999 1146aa 0.0 in ref transcript
  • pyruvate carboxylase; Reviewed.

PCBP2

• rs.PCBP2.F1 rs.PCBP2.R1 113 206
• NCBIGene 36.3 5094
• Single exon skipping, size difference: 93
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_005016

• cd PCBP_like_KH 65aa 5e-16 in ref transcript
  • K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
• cd PCBP_like_KH 62aa 4e-14 in ref transcript
• cd KH-I 63aa 7e-12 in ref transcript
  • K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
• pfam KH_1 61aa 2e-11 in ref transcript
  • KH domain. KH motifs can bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.
• pfam KH_1 63aa 3e-11 in ref transcript
• pfam KH_1 64aa 6e-10 in ref transcript
• COG NusA 122aa 6e-04 in ref transcript
  • Transcription elongation factor [Transcription].

PCBP2

• rs.PCBP2.F2 rs.PCBP2.R2 97 109
• NCBIGene 36.3 5094
• Alternative 5-prime and 3-prime, size difference: 12
• Inclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_005016

• cd PCBP_like_KH 65aa 5e-16 in ref transcript
  • K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
• cd PCBP_like_KH 62aa 4e-14 in ref transcript
• cd KH-I 63aa 7e-12 in ref transcript
  • K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
• pfam KH_1 61aa 2e-11 in ref transcript
  • KH domain. KH motifs can bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.
• pfam KH_1 63aa 3e-11 in ref transcript
• pfam KH_1 64aa 6e-10 in ref transcript
• COG NusA 122aa 6e-04 in ref transcript
  • Transcription elongation factor [Transcription].

PCMTD2

• rs.PCMTD2.F1 rs.PCMTD2.R1 263 344
• NCBIGene 36.3 55251
• Alternative 3-prime, size difference: 81
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_018257

• cd AdoMet_MTases 110aa 6e-04 in ref transcript
  • S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.).
• Changed! pfam PCMT 209aa 4e-21 in ref transcript
  • Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT).
• Changed! COG Pcm 197aa 1e-17 in ref transcript
  • Protein-L-isoaspartate carboxylmethyltransferase [Posttranslational modification, protein turnover, chaperones].
• Changed! pfam PCMT 183aa 4e-20 in modified transcript
• Changed! COG Pcm 172aa 1e-13 in modified transcript

PCSK6

• rs.PCSK6.F1 rs.PCSK6.R1 171 210
• NCBIGene 36.3 5046
• Single exon skipping, size difference: 39
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_138320

• cd FU 51aa 6e-07 in ref transcript
  • Furin-like repeats. Cysteine rich region. Exact function of the domain is not known. Furin is a serine-kinase dependent proprotein processor. Other members of this family include endoproteases and cell surface receptors.
• cd FU 43aa 2e-06 in ref transcript
• cd FU 47aa 3e-06 in ref transcript
• cd FU 53aa 1e-05 in ref transcript
• pfam Peptidase_S8 301aa 2e-94 in ref transcript
  • Subtilase family. Subtilases are a family of serine proteases. They appear to have independently and convergently evolved an Asp/Ser/His catalytic triad, like that found in the trypsin serine proteases (see pfam00089). Structure is an alpha/beta fold containing a 7-stranded parallel beta sheet, order 2314567.
• pfam P_proprotein 91aa 4e-34 in ref transcript
  • Proprotein convertase P-domain. A unique feature of the eukaryotic subtilisin-like proprotein convertases is the presence of an additional highly conserved sequence of approximately 150 residues (P domain) located immediately downstream of the catalytic domain.
• smart FU 48aa 2e-08 in ref transcript
  • Furin-like repeats.
• smart FU 44aa 2e-08 in ref transcript
• smart FU 44aa 1e-06 in ref transcript
• pfam Furin-like 112aa 4e-06 in ref transcript
  • Furin-like cysteine rich region.
• pfam VSP 115aa 5e-04 in ref transcript
  • Giardia variant-specific surface protein.
• COG AprE 324aa 1e-20 in ref transcript
  • Subtilisin-like serine proteases [Posttranslational modification, protein turnover, chaperones].
• COG COG4935 91aa 1e-15 in ref transcript
  • Regulatory P domain of the subtilisin-like proprotein convertases and other proteases [Posttranslational modification, protein turnover, chaperones].
• COG NapH 83aa 0.009 in ref transcript
  • Polyferredoxin [Energy production and conversion].

PCSK6

• rs.PCSK6.F2 rs.PCSK6.R2 227 273
• NCBIGene 36.3 5046
• Single exon skipping, size difference: 46
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_138324

• pfam Peptidase_S8 301aa 3e-91 in ref transcript
  • Subtilase family. Subtilases are a family of serine proteases. They appear to have independently and convergently evolved an Asp/Ser/His catalytic triad, like that found in the trypsin serine proteases (see pfam00089). Structure is an alpha/beta fold containing a 7-stranded parallel beta sheet, order 2314567.
• Changed! pfam P_proprotein 84aa 2e-28 in ref transcript
  • Proprotein convertase P-domain. A unique feature of the eukaryotic subtilisin-like proprotein convertases is the presence of an additional highly conserved sequence of approximately 150 residues (P domain) located immediately downstream of the catalytic domain.
• COG AprE 324aa 4e-16 in ref transcript
  • Subtilisin-like serine proteases [Posttranslational modification, protein turnover, chaperones].
• COG COG4935 69aa 4e-12 in ref transcript
  • Regulatory P domain of the subtilisin-like proprotein convertases and other proteases [Posttranslational modification, protein turnover, chaperones].
• Changed! pfam P_proprotein 85aa 7e-29 in modified transcript

PCTK3

• rs.PCTK3.F1 rs.PCTK3.R1 282 364
• NCBIGene 36.3 5129
• Alternative 5-prime, size difference: 82
• Inclusion in 5'UTR
• Reference transcript: NM_212503

• cd S_TKc 282aa 3e-64 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• smart S_TKc 272aa 1e-68 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• PTZ PTZ00024 284aa 1e-44 in ref transcript
  • cyclin-dependent protein kinase; Provisional.

PCTP

• rs.PCTP.F1 rs.PCTP.R1 99 332
• NCBIGene 36.3 58488
• Alternative 5-prime, size difference: 233
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_021213

• Changed! cd START 204aa 4e-30 in ref transcript
  • START(STeroidogenic Acute Regulatory (STAR) related lipid Transfer) Domain. These domains are 200-210 amino acid in length and occur in proteins involved in lipid transport (phosphatidylcholine) and metabolism, signal transduction, and transcriptional regulation. The most striking feature of the START domain structure is a predominantly hydrophobic tunnel extending nearly the entire protein and used to binding a single molecule of large lipophilic compounds, like cholesterol.
• Changed! smart START 204aa 5e-40 in ref transcript
  • in StAR and phosphatidylcholine transfer protein. putative lipid-binding domain in StAR and phosphatidylcholine transfer protein.

PDE8A

• rs.PDE8A.F1 rs.PDE8A.R1 120 258
• NCBIGene 36.3 5151
• Single exon skipping, size difference: 138
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_002605

• Changed! cd PAS 99aa 3e-06 in ref transcript
  • PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.
• cd HDc 195aa 4e-05 in ref transcript
  • Metal dependent phosphohydrolases with conserved 'HD' motif.
• pfam PDEase_I 255aa 2e-55 in ref transcript
  • 3'5'-cyclic nucleotide phosphodiesterase.
• Changed! pfam PAS 106aa 2e-07 in ref transcript
  • PAS fold. The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs. The PAS fold appears in archaea, eubacteria and eukarya.
• pfam Response_reg 117aa 5e-07 in ref transcript
  • Response regulator receiver domain. This domain receives the signal from the sensor partner in bacterial two-component systems. It is usually found N-terminal to a DNA binding effector domain.
• Changed! COG AtoS 113aa 1e-04 in ref transcript
  • FOG: PAS/PAC domain [Signal transduction mechanisms].

PDE9A

• rs.PDE9A.F1 rs.PDE9A.R1 278 333
• NCBIGene 36.3 5152
• Single exon skipping, size difference: 55
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_002606

• Changed! cd HDc 174aa 6e-10 in ref transcript
  • Metal dependent phosphohydrolases with conserved 'HD' motif.
• Changed! pfam PDEase_I 223aa 8e-56 in ref transcript
  • 3'5'-cyclic nucleotide phosphodiesterase.

PDS5A

• rs.PDS5A.F1 rs.PDS5A.R1 100 471
• NCBIGene 36.3 23244
• Alternative 5-prime and 3-prime, size difference: 371
• Exclusion in 5'UTR, Exclusion of the protein initiation site
• Reference transcript: NM_001100399

PELI3

• rs.PELI3.F1 rs.PELI3.R1 338 410
• NCBIGene 36.3 246330
• Single exon skipping, size difference: 72
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_145065

• Changed! pfam Pellino 394aa 1e-175 in ref transcript
  • Pellino. Pellino is involved in Toll-like signalling pathways, and associates with the kinase domain of the Pelle Ser/Thr kinase.
• Changed! pfam Pellino 416aa 0.0 in modified transcript

PFAAP5

• rs.PFAAP5.F1 rs.PFAAP5.R1 102 152
• NCBIGene 36.3 10443
• Alternative 5-prime, size difference: 50
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_033111

PH-4

• rs.PH-4.F1 rs.PH-4.R1 142 325
• NCBIGene 36.3 54681
• Alternative 5-prime and 3-prime, size difference: 183
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_177938

• cd EFh 61aa 3e-05 in ref transcript
  • EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers.
• Changed! smart P4Hc 98aa 3e-12 in ref transcript
  • Prolyl 4-hydroxylase alpha subunit homologues. Mammalian enzymes catalyse hydroxylation of collagen, for example. Prokaryotic enzymes might catalyse hydroxylation of antibiotic peptides. These are 2-oxoglutarate-dependent dioxygenases, requiring 2-oxoglutarate and dioxygen as cosubstrates and ferrous iron as a cofactor.
• Changed! smart P4Hc 85aa 4e-07 in ref transcript
• COG FRQ1 127aa 8e-05 in ref transcript
  • Ca2+-binding protein (EF-Hand superfamily) [Signal transduction mechanisms / Cytoskeleton / Cell division and chromosome partitioning / General function prediction only].
• Changed! smart P4Hc 213aa 1e-23 in modified transcript

PHACTR2

• rs.PHACTR2.F1 rs.PHACTR2.R1 310 550
• NCBIGene 36.3 9749
• Single exon skipping, size difference: 240
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001100164

• pfam RPEL 26aa 0.003 in ref transcript
  • RPEL repeat. The RPEL repeat is named after four conserved amino acids it contains. The function of the RPEL repeat is unknown however it might be a DNA binding repeat based on the observation that a member from Drosophila melanogaster contains a pfam02037 domain that is also implicated in DNA binding.
• pfam RPEL 26aa 0.006 in ref transcript

PHF20L1

• rs.PHF20L1.F1 rs.PHF20L1.R1 108 337
• NCBIGene 36.3 51105
• Alternative 3-prime, size difference: 229
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_016018

• cd TUDOR 46aa 2e-06 in ref transcript
  • Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal.
• smart TUDOR 54aa 3e-06 in ref transcript
  • Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).
• smart MBT 66aa 3e-05 in ref transcript
  • Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2. Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2. These proteins are involved in transcriptional regulation.
• Changed! pfam PHD 44aa 1e-04 in ref transcript
  • PHD-finger. PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.

PHF21A

• rs.PHF21A.F1 rs.PHF21A.R1 202 343
• NCBIGene 36.3 51317
• Mutually exclusive exon skipping, size difference: 141
• Inclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_001101802

• cd BAH_plant_2 39aa 3e-04 in ref transcript
  • BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
• pfam PHD 44aa 1e-12 in ref transcript
  • PHD-finger. PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
• Changed! COG TNG2 163aa 7e-05 in ref transcript
  • Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics].

PHYHD1

• rs.PHYHD1.F1 rs.PHYHD1.R1 124 146
• NCBIGene 36.3 254295
• Single exon skipping, size difference: 22
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_174933

• Changed! pfam PhyH 204aa 5e-26 in ref transcript
  • Phytanoyl-CoA dioxygenase (PhyH). This family is made up of several eukaryotic phytanoyl-CoA dioxygenase (PhyH) proteins, ectoine hydroxylases and a number of bacterial deoxygenases. PhyH is a peroxisomal enzyme catalysing the first step of phytanic acid alpha-oxidation. PhyH deficiency causes Refsum's disease (RD) which is an inherited neurological syndrome biochemically characterised by the accumulation of phytanic acid in plasma and tissues.
• Changed! pfam PhyH 250aa 9e-47 in modified transcript
• Changed! COG COG5285 258aa 1e-11 in modified transcript
  • Protein involved in biosynthesis of mitomycin antibiotics/polyketide fumonisin [Secondary metabolites biosynthesis, transport, and catabolism].

PHYHD1

• rs.PHYHD1.F2 rs.PHYHD1.R2 124 187
• NCBIGene 36.3 254295
• Single exon skipping, size difference: 63
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001100876

• Changed! pfam PhyH 250aa 9e-47 in ref transcript
  • Phytanoyl-CoA dioxygenase (PhyH). This family is made up of several eukaryotic phytanoyl-CoA dioxygenase (PhyH) proteins, ectoine hydroxylases and a number of bacterial deoxygenases. PhyH is a peroxisomal enzyme catalysing the first step of phytanic acid alpha-oxidation. PhyH deficiency causes Refsum's disease (RD) which is an inherited neurological syndrome biochemically characterised by the accumulation of phytanic acid in plasma and tissues.
• Changed! COG COG5285 258aa 1e-11 in ref transcript
  • Protein involved in biosynthesis of mitomycin antibiotics/polyketide fumonisin [Secondary metabolites biosynthesis, transport, and catabolism].
• Changed! pfam PhyH 229aa 5e-44 in modified transcript
• Changed! COG COG5285 237aa 1e-12 in modified transcript

PHYHIP

• rs.PHYHIP.F1 rs.PHYHIP.R1 280 402
• NCBIGene 36.3 9796
• Single exon skipping, size difference: 122
• Exclusion in 5'UTR
• Reference transcript: NM_001099335

• cd FN3 108aa 7e-04 in ref transcript
  • Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.

PICALM

• rs.PICALM.F1 rs.PICALM.R1 116 266
• NCBIGene 36.3 8301
• Single exon skipping, size difference: 150
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_007166

• cd ANTH_AP180_CALM 117aa 1e-37 in ref transcript
  • ANTH domain family; composed of adaptor protein 180 (AP180), clathrin assembly lymphoid myeloid leukemia protein (CALM) and similar proteins. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to as an AP180 N-terminal homology (ANTH) domain. AP180 and CALM play important roles in clathrin-mediated endocytosis. AP180 is a brain-specific clathrin-binding protein which stimulates clathrin assembly during the recycling of synaptic vesicles. The ANTH domain is structurally similar to the VHS domain and is composed of a superhelix of eight alpha helices. ANTH domains bind both inositol phospholipids and proteins, and contribute to the nucleation and formation of clathrin coats on membranes. ANTH-bearing proteins have recently been shown to function with adaptor protein-1 and GGA adaptors at the trans-Golgi network, which suggests that the ANTH domain is a universal component of the machinery for clathrin-mediated membrane budding.
• pfam ANTH 265aa 7e-80 in ref transcript
  • ANTH domain. AP180 is an endocytotic accessory proteins that has been implicated in the formation of clathrin-coated pits. The domain is involved in phosphatidylinositol 4,5-bisphosphate binding and is a universal adaptor for nucleation of clathrin coats.

PID1

• rs.PID1.F1 rs.PID1.R1 123 334
• NCBIGene 36.3 55022
• Single exon skipping, size difference: 211
• Exclusion of the protein initiation site
• Reference transcript: NM_017933

• cd CG8312 134aa 5e-10 in ref transcript
  • CG8312 Phosphotyrosine-binding (PTB) domain. PTB domains have a PH-like fold and are found in various eukaryotic signaling molecules. They were initially identified based upon their ability to recognize phosphorylated tyrosine residues. In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. More recent studies have found that some types of PTB domains can bind to peptides which are not tyrosine phosphorylated or lack tyrosine residues altogether.

PILRB

• rs.PILRB.F1 rs.PILRB.R1 146 355
• NCBIGene 36.3 29990
• Alternative 3-prime, size difference: 209
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_178238

• Changed! pfam V-set 92aa 1e-05 in ref transcript
  • Immunoglobulin V-set domain. This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.

PIP5K3

• rs.PIP5K3.F1 rs.PIP5K3.R1 146 437
• NCBIGene 36.3 200576
• Multiple exon skipping, size difference: 291
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_015040

• cd Fab1_TCP 245aa 1e-104 in ref transcript
  • TCP-1 like domain of the eukaryotic phosphatidylinositol 3-phosphate (PtdIns3P) 5-kinase Fab1. Fab1p is important for vacuole size regulation, presumably by modulating PtdIns(3,5)P2 effector activity. In the human homolog p235/PIKfyve deletion of this domain leads to loss of catalytic activity. However no exact function this domain has been defined. In general, chaperonins are involved in productive folding of proteins.
• cd PIPKc 314aa 5e-98 in ref transcript
  • Phosphatidylinositol phosphate kinases (PIPK) catalyze the phosphorylation of phosphatidylinositol phosphate on the fourth or fifth hydroxyl of the inositol ring, to form phosphatidylinositol bisphosphate. CD alignment includes type II phosphatidylinositol phosphate kinases (PIPKII-beta), type I andII PIPK (-alpha, -beta, and -gamma) kinases and related yeast Fab1p and Mss4p kinases. Signaling by phosphorylated species of phosphatidylinositol regulates secretion, vesicular trafficking, membrane translocation, cell adhesion, chemotaxis, DNA synthesis, and cell cycling. The catalytic core domains of PIPKs are structurally similar to PI3K, PI4K, and cAMP-dependent protein kinases (PKA), the dimerization region is a unique feature of the PIPKs.
• cd DEP_PIKfyve 82aa 1e-38 in ref transcript
  • DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in fungal RhoGEF (GDP/GTP exchange factor) PIKfyve-like proteins. PIKfyve contains N-terminal Fyve finger and DEP domains, a central chaperonin-like domain and a C-terminal PIPK (phosphatidylinositol phosphate kinase) domain. PIKfyve-like proteins are important phosphatidylinositol (3)-monophosphate (PtdIns(3)P)-5-kinases, producing PtdIns(3,5)P2, which plays a major role in multivesicular body (MVB) sorting and control of retrograde traffic from the vacuole back to the endosome and/or Golgi. PIKfyve itself has been shown to be play a role in regulating early-endosome-to-trans-Golgi network (TGN) retrograde trafficking.
• Changed! cd FYVE 53aa 2e-15 in ref transcript
  • FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;.
• smart PIPKc 238aa 5e-72 in ref transcript
  • Phosphatidylinositol phosphate kinases.
• TIGR chap_CCT_gamma 224aa 8e-32 in ref transcript
  • Members of this family, all eukaryotic, are part of the group II chaperonin complex called CCT (chaperonin containing TCP-1) or TRiC. The archaeal equivalent group II chaperonin is often called the thermosome. Both are somewhat related to the group I chaperonin of bacterial, GroEL/GroES. This family consists exclusively of the CCT gamma chain (part of a paralogous family) from animals, plants, fungi, and other eukaryotes.
• Changed! pfam FYVE 60aa 9e-20 in ref transcript
  • FYVE zinc finger. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn++ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. We have included members which do not conserve these histidine residues but are clearly related.
• smart DEP 73aa 3e-17 in ref transcript
  • Domain found in Dishevelled, Egl-10, and Pleckstrin. Domain of unknown function present in signalling proteins that contain PH, rasGEF, rhoGEF, rhoGAP, RGS, PDZ domains. DEP domain in Drosophila dishevelled is essential to rescue planar polarity defects and induce JNK signalling (Cell 94, 109-118).
• smart PIPKc 56aa 6e-17 in ref transcript
• COG MSS4 288aa 9e-54 in ref transcript
  • Phosphatidylinositol-4-phosphate 5-kinase [Signal transduction mechanisms].
• COG GroL 219aa 2e-17 in ref transcript
  • Chaperonin GroEL (HSP60 family) [Posttranslational modification, protein turnover, chaperones].

PLAGL1

• rs.PLAGL1.F1 rs.PLAGL1.R1 104 161
• NCBIGene 36.3 5325
• Exon skipping and alternative 3-prime or 5-prime, size difference: 57
• Exclusion in 5'UTR, Exclusion in 5'UTR
• Reference transcript: NM_001080951

• COG SFP1 81aa 0.004 in ref transcript
  • Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning].

PLAGL1

• rs.PLAGL1.F2 rs.PLAGL1.R2 176 216
• NCBIGene 36.3 5325
• Single exon skipping, size difference: 40
• Exclusion in 5'UTR
• Reference transcript: NM_001080954

• COG SFP1 81aa 0.004 in ref transcript
  • Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning].

PLAGL1

• rs.PLAGL1.F3 rs.PLAGL1.R3 99 113
• NCBIGene 36.3 5325
• Alternative 3-prime, size difference: 14
• Inclusion in 5'UTR
• Reference transcript: NM_001080951

• COG SFP1 81aa 0.004 in ref transcript
  • Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning].

PLAT

• rs.PLAT.F1 rs.PLAT.R1 245 383
• NCBIGene 36.3 5327
• Single exon skipping, size difference: 138
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000930

• cd Tryp_SPc 249aa 6e-67 in ref transcript
  • Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
• cd KR 86aa 4e-20 in ref transcript
  • Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides.
• cd KR 85aa 5e-17 in ref transcript
• Changed! cd FN1 43aa 3e-04 in ref transcript
  • Fibronectin type 1 domain, approximately 40 residue long with two conserved disulfide bridges. FN1 is one of three types of internal repeats which combine to form larger domains within fibronectin. Fibronectin, a plasma protein that binds cell surfaces and various compounds including collagen, fibrin, heparin, DNA, and actin, usually exists as a dimer in plasma and as an insoluble multimer in extracellular matrices. Dimers of nearly identical subunits are linked by a disulfide bond close to their C-terminus. FN1 domains also found in coagulation factor XII, HGF activator, and tissue-type plasminogen activator. In tissue plasminogen activator, FN1 domains may form functional fibrin-binding units with EGF-like domains C-terminal to FN1.
• smart Tryp_SPc 247aa 1e-71 in ref transcript
  • Trypsin-like serine protease. Many of these are synthesised as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. A few, however, are active as single chain molecules, and others are inactive due to substitutions of the catalytic triad residues.
• pfam Kringle 82aa 3e-26 in ref transcript
  • Kringle domain. Kringle domains have been found in plasminogen, hepatocyte growth factors, prothrombin, and apolipoprotein A. Structure is disulfide-rich, nearly all-beta.
• pfam Kringle 82aa 4e-21 in ref transcript
• Changed! smart FN1 43aa 4e-06 in ref transcript
  • Fibronectin type 1 domain. One of three types of internal repeat within the plasma protein, fibronectin. Found also in coagulation factor XII, HGF activator and tissue-type plasminogen activator. In t-PA and fibronectin, this domain type contributes to fibrin-binding.
• COG COG5640 251aa 2e-23 in ref transcript
  • Secreted trypsin-like serine protease [Posttranslational modification, protein turnover, chaperones].

PLAUR

• rs.PLAUR.F1 rs.PLAUR.R1 206 341
• NCBIGene 36.3 5329
• Single exon skipping, size difference: 135
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_002659

• cd LU 82aa 8e-10 in ref transcript
  • Ly-6 antigen / uPA receptor -like domain; occurs singly in GPI-linked cell-surface glycoproteins (Ly-6 family,CD59, thymocyte B cell antigen, Sgp-2) or as three-fold repeated domain in urokinase-type plasminogen activator receptor. Topology of these domains is similar to that of snake venom neurotoxins.
• Changed! cd LU 87aa 1e-06 in ref transcript
• smart LU 81aa 8e-12 in ref transcript
  • Ly-6 antigen / uPA receptor -like domain. Three-fold repeated domain in urokinase-type plasminogen activator receptor; occurs singly in other GPI-linked cell-surface glycoproteins (Ly-6 family, CD59, thymocyte B cell antigen, Sgp-2). Topology of these domains is similar to that of snake venom neurotoxins.
• Changed! smart LU 85aa 4e-11 in ref transcript
• smart LU 77aa 3e-06 in ref transcript

PLCB4

• rs.PLCB4.F1 rs.PLCB4.R1 122 159
• NCBIGene 36.3 5332
• Single exon skipping, size difference: 37
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_000933

• cd PLCc 142aa 3e-41 in ref transcript
  • Phospholipase C, catalytic domain; Phosphoinositide-specific phospholipases C catalyze hydrolysis of phosphatidylinositol-4,5-bisphosphate (PIP2) to D-myo-inositol-1,4,5-trisphosphate (1,4,5-IP3) and sn-1,2-diacylglycerol (DAG). Both products function as second messengers in eukaryotic signal transduction cascades. 1,4,5-IP3 triggers inflow of calcium from intracellular stores; the membrane resident product DAG controls cellular protein phosphorylation states by activating various protein kinase C isozymes. The enzyme comprises 2 regions (X and Y) connected via a linker which may contain inserted domains, X and Y together form a TIM barrel-like structure containing the active site residues.
• cd PH_PLC 121aa 3e-26 in ref transcript
  • Phospholipase C (PLC) pleckstrin homology (PH) domain. There are several isozymes of PLC (beta, gamma, delta, epsilon. zeta). While, PLC beta, gamma and delta all have N-terminal PH domains, lipid binding specificity is not conserved between them. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
• cd PLCc 99aa 2e-17 in ref transcript
• cd C2_2 117aa 7e-14 in ref transcript
  • Protein kinase C conserved region 2, subgroup 2; C2 Ca2+-binding motif present in phospholipases, protein kinases C, and synaptotagmins (amongst others); some PKCs lack calcium dependence. Particular C2s appear to bind phospholipids, inositol polyphosphates,and intracellular proteins. Two distinct C2 topologies generated by permutation of the sequence with respect to the N- and C-terminal beta strands are seen. In this subgroup, containing phospholipases C and D( PLC-1, PLD) and specific protein kinases C (PKC) subtypes, the C-terminal beta strand occupies the position of what is the N-terminal strand in subgroup 1.
• smart PLCYc 115aa 7e-55 in ref transcript
  • Phospholipase C, catalytic domain (part); domain Y. Phosphoinositide-specific phospholipases C. These enzymes contain 2 regions (X and Y) which together form a TIM barrel-like structure containing the active site residues. Phospholipase C enzymes (PI-PLC) act as signal transducers that generate two second messengers, inositol-1,4,5-trisphosphate and diacylglycerol. The bacterial enzyme [6] appears to be a homologue of the mammalian PLCs.
• pfam PI-PLC-X 139aa 4e-51 in ref transcript
  • Phosphatidylinositol-specific phospholipase C, X domain. This associates with pfam00387 to form a single structural unit.
• pfam efhand_like 92aa 4e-23 in ref transcript
  • Phosphoinositide-specific phospholipase C, efhand-like. Members of this family are predominantly found in phosphoinositide-specific phospholipase C. They adopt a structure consisting of a core of four alpha helices, in an EF like fold, and are required for functioning of the enzyme.
• pfam DUF1154 47aa 6e-13 in ref transcript
  • Protein of unknown function (DUF1154). This family represents a small conserved region of unknown function within eukaryotic phospholipase C (EC:3.1.4.3). All members also contain pfam00387 and pfam00388.
• smart C2 98aa 1e-11 in ref transcript
  • Protein kinase C conserved region 2 (CalB). Ca2+-binding motif present in phospholipases, protein kinases C, and synaptotamins (among others). Some do not appear to contain Ca2+-binding sites. Particular C2s appear to bind phospholipids, inositol polyphosphates, and intracellular proteins. Unusual occurrence in perforin. Synaptotagmin and PLC C2s are permuted in sequence with respect to N- and C-terminal beta strands. SMART detects C2 domains using one or both of two profiles.
• Changed! pfam SMC_N 256aa 7e-06 in ref transcript
  • RecF/RecN/SMC N terminal domain. This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.
• Changed! COG Smc 258aa 5e-05 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].
• Changed! pfam SMC_N 243aa 4e-07 in modified transcript
• Changed! COG Smc 249aa 1e-04 in modified transcript

PNMA5

• rs.PNMA5.F1 rs.PNMA5.R1 100 114
• NCBIGene 36.3 114824
• Alternative 5-prime, size difference: 14
• Exclusion in 5'UTR
• Reference transcript: NM_001103151

PNMAL1

• rs.PNMAL1.F1 rs.PNMAL1.R1 106 311
• NCBIGene 36.3 55228
• Alternative 5-prime, size difference: 205
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_018215

PNPLA7

• rs.PNPLA7.F1 rs.PNPLA7.R1 332 407
• NCBIGene 36.3 375775
• Single exon skipping, size difference: 75
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001098537

• cd Pat_PNPLA6_PNPLA7 306aa 1e-176 in ref transcript
  • Patatin-like phospholipase domain containing protein 6 and protein 7. Patatin-like phospholipase domain containing protein 6 (PNPLA6) and protein 7 (PNPLA7) are 60% identical to each other. PNPLA6 is commonly known as Neuropathy Target Esterase (NTE). NTE has at least two functional domains: the N-terminal domain putatively regulatory domain and the C-terminal catalytic domain which shows esterase activity. NTE shows phospholipase activity for lysophosphatidylcholine (LPC) and phosphatidylcholine (PC). Exposure of NTE to organophosphates leads to organophosphate-induced delayed neurotoxicity (OPIDN). OPIDN is a progressive neurological condition that is characterized by weakness, paralysis, pain, and paresthesia. PNPLA7 is an insulin-regulated phospholipase that is homologous to Neuropathy Target Esterase (NTE or PNPLA6) and is also known as NTE-related esterase (NRE). Human NRE is predominantly expressed in prostate, white adipose, and pancreatic tissue. NRE hydrolyzes sn-1 esters in lysophosphatidylcholine and lysophosphatidic acid, but shows no lipase activity with substrates like triacylglycerols (TG), cholesteryl esters, retinyl esters (RE), phosphatidylcholine (PC), or monoacylglycerol (MG). This family includes PNPLA6 and PNPLA7 from Homo sapiens, YMF9 from Yeast, and Swiss Cheese protein (sws) from Drosophila melanogaster.
• cd CAP_ED 109aa 1e-15 in ref transcript
  • effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels. Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels.
• cd CAP_ED 109aa 1e-12 in ref transcript
• cd CAP_ED 122aa 6e-11 in ref transcript
• pfam Patatin 151aa 3e-28 in ref transcript
  • Patatin-like phospholipase. This family consists of various patatin glycoproteins from plants. The patatin protein accounts for up to 40% of the total soluble protein in potato tubers. Patatin is a storage protein but it also has the enzymatic activity of lipid acyl hydrolase, catalysing the cleavage of fatty acids from membrane lipids. Members of this family have been found also in vertebrates.
• pfam cNMP_binding 91aa 4e-14 in ref transcript
  • Cyclic nucleotide-binding domain.
• pfam cNMP_binding 91aa 1e-13 in ref transcript
• pfam cNMP_binding 98aa 4e-09 in ref transcript
• COG RssA 274aa 1e-35 in ref transcript
  • Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only].
• COG Crp 116aa 1e-11 in ref transcript
  • cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms].
• COG Crp 130aa 3e-11 in ref transcript
• COG Crp 143aa 2e-10 in ref transcript

PODXL

• rs.PODXL.F1 rs.PODXL.R1 305 401
• NCBIGene 36.3 5420
• Single exon skipping, size difference: 96
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001018111

• pfam CD34_antigen 201aa 2e-62 in ref transcript
  • CD34/Podocalyxin family. This family consists of several mammalian CD34 antigen proteins. The CD34 antigen is a human leukocyte membrane protein expressed specifically by lymphohematopoietic progenitor cells. CD34 is a phosphoprotein. Activation of protein kinase C (PKC) has been found to enhance CD34 phosphorylation. This family contains several eukaryotic podocalyxin proteins. Podocalyxin is a major membrane protein of the glomerular epithelium and is thought to be involved in maintenance of the architecture of the foot processes and filtration slits characteristic of this unique epithelium by virtue of its high negative charge. Podocalyxin functions as an anti-adhesin that maintains an open filtration pathway between neighbouring foot processes in the glomerular epithelium by charge repulsion.

POLR3H

• rs.POLR3H.F1 rs.POLR3H.R1 123 210
• NCBIGene 36.3 171568
• Single exon skipping, size difference: 87
• Exclusion in 5'UTR
• Reference transcript: NM_001018050

POMT1

• rs.POMT1.F1 rs.POMT1.R1 214 366
• NCBIGene 36.3 10585
• Single exon skipping, size difference: 152
• Exclusion of the protein initiation site
• Reference transcript: NM_007171

• Changed! pfam PMT 215aa 1e-58 in ref transcript
  • Dolichyl-phosphate-mannose-protein mannosyltransferase. This is a family of Dolichyl-phosphate-mannose-protein mannosyltransferase proteins EC:2.4.1.109. These proteins are responsible for O-linked glycosylation of proteins, they catalyse the reaction:- Dolichyl phosphate D-mannose + protein <=> dolichyl phosphate + O-D-mannosyl-protein. Also in this family is Drosophila rotated abdomen protein which is a putative mannosyltransferase. This family appears to be distantly related to pfam02516 (A Bateman pers. obs.).
• pfam MIR 173aa 2e-10 in ref transcript
  • MIR domain. The MIR (protein mannosyltransferase, IP3R and RyR) domain is a domain that may have a ligand transferase function.
• Changed! COG PMT1 729aa 2e-97 in ref transcript
  • Dolichyl-phosphate-mannose--protein O-mannosyl transferase [Posttranslational modification, protein turnover, chaperones].
• Changed! pfam PMT 180aa 7e-49 in modified transcript
• Changed! COG PMT1 683aa 1e-88 in modified transcript

POMT1

• rs.POMT1.F2 rs.POMT1.R2 157 223
• NCBIGene 36.3 10585
• Alternative 5-prime, size difference: 66
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_007171

• Changed! pfam PMT 215aa 1e-58 in ref transcript
  • Dolichyl-phosphate-mannose-protein mannosyltransferase. This is a family of Dolichyl-phosphate-mannose-protein mannosyltransferase proteins EC:2.4.1.109. These proteins are responsible for O-linked glycosylation of proteins, they catalyse the reaction:- Dolichyl phosphate D-mannose + protein <=> dolichyl phosphate + O-D-mannosyl-protein. Also in this family is Drosophila rotated abdomen protein which is a putative mannosyltransferase. This family appears to be distantly related to pfam02516 (A Bateman pers. obs.).
• pfam MIR 173aa 2e-10 in ref transcript
  • MIR domain. The MIR (protein mannosyltransferase, IP3R and RyR) domain is a domain that may have a ligand transferase function.
• Changed! COG PMT1 729aa 2e-97 in ref transcript
  • Dolichyl-phosphate-mannose--protein O-mannosyl transferase [Posttranslational modification, protein turnover, chaperones].
• Changed! pfam PMT 215aa 1e-57 in modified transcript
• Changed! COG PMT1 707aa 2e-98 in modified transcript

PON2

• rs.PON2.F1 rs.PON2.R1 152 188
• NCBIGene 36.3 5445
• Alternative 3-prime, size difference: 36
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000305

• pfam Arylesterase 86aa 6e-38 in ref transcript
  • Arylesterase. This family consists of arylesterases (Also known as serum paraoxonase) EC:3.1.1.2. These enzymes hydrolyse organophosphorus esters such as paraoxon and are found in the liver and blood. They confer resistance to organophosphate toxicity. Human arylesterase (PON1) is associated with HDL and may protect against LDL oxidation.
• Changed! COG COG3386 192aa 4e-09 in ref transcript
  • Gluconolactonase [Carbohydrate transport and metabolism].
• Changed! COG COG3386 138aa 1e-08 in modified transcript

POT1

• rs.POT1.F1 rs.POT1.R1 256 353
• NCBIGene 36.3 25913
• Single exon skipping, size difference: 97
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_015450

• cd hPOT1_OB2 118aa 2e-39 in ref transcript
  • hPOT1_OB2: A subfamily of OB folds similar to the second OB fold (OB2) of human protection of telomeres 1 protein (hPOT1). POT1 proteins bind to the single-stranded (ss) 3-prime ends of the telomere. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB2) which cooperate to bind telomeric ssDNA. OB1 makes more extensive contact with the ssDNA than OB2. OB2 protects the 3' end of the ssDNA. hPOT1 is implicated in telomere length regulation.
• cd hPOT1_OB1_like 133aa 2e-33 in ref transcript
  • hPOT1_OB1_like: A subfamily of OB folds similar to the first OB fold (OB1) of human protection of telomeres 1 protein (hPOT1), the single OB fold of the N-terminal domain of Schizosaccharomyces pombe POT1 (SpPOT1), and the first OB fold of the N-terminal domain of the alpha subunit (OB1Nalpha) of Oxytricha nova telomere end binding protein (OnTEBP). POT1 proteins recognize single-stranded (ss) 3-prime ends of the telomere. A 3-prime ss overhang is conserved in ciliated protozoa, yeast, and mammals. SpPOT1 is essential for telomere maintenance. It binds specifically to the ss G-rich telomeric sequence (GGTTAC) of S. pombe. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. Deletion of the S. pombe pot1+ gene results in a rapid loss of telomere sequences, chromosome mis-segregation and chromosome circularization. hPOT1 is implicated in telomere length regulation. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB2) which cooperate to bind telomeric ssDNA. OB1 makes more extensive contact with the ssDNA than OB2. OB2 protects the 3' end of the ssDNA. A second OB fold has not been predicted in S. pombe POT1. OnTEBP binds the extreme 3-prime end of telomeric DNA. It is heterodimeric and contains four OB folds - three in the alpha subunit (two in the N-terminal domain and one in the C-terminal domain) and one in the beta subunit. OB1Nalpha, together with the second OB fold of the N-terminal domain of OnTEBP alpha subunit and the beta subunit OB fold, forms a deep cleft that binds ssDNA.
• pfam Telo_bind 103aa 4e-14 in ref transcript
  • Telomere-binding protein alpha subunit, central domain. The telomere-binding protein forms a heterodimer in ciliates consisting of an alpha and a beta subunit. This complex may function as a protective cap for the single-stranded telomeric overhang. Alpha subunit consists of 3 structural domains, all with the same beta-barrel OB fold.

POT1

• rs.POT1.F2 rs.POT1.R2 107 238
• NCBIGene 36.3 25913
• Single exon skipping, size difference: 131
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_015450

• Changed! cd hPOT1_OB2 118aa 2e-39 in ref transcript
  • hPOT1_OB2: A subfamily of OB folds similar to the second OB fold (OB2) of human protection of telomeres 1 protein (hPOT1). POT1 proteins bind to the single-stranded (ss) 3-prime ends of the telomere. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB2) which cooperate to bind telomeric ssDNA. OB1 makes more extensive contact with the ssDNA than OB2. OB2 protects the 3' end of the ssDNA. hPOT1 is implicated in telomere length regulation.
• Changed! cd hPOT1_OB1_like 133aa 2e-33 in ref transcript
  • hPOT1_OB1_like: A subfamily of OB folds similar to the first OB fold (OB1) of human protection of telomeres 1 protein (hPOT1), the single OB fold of the N-terminal domain of Schizosaccharomyces pombe POT1 (SpPOT1), and the first OB fold of the N-terminal domain of the alpha subunit (OB1Nalpha) of Oxytricha nova telomere end binding protein (OnTEBP). POT1 proteins recognize single-stranded (ss) 3-prime ends of the telomere. A 3-prime ss overhang is conserved in ciliated protozoa, yeast, and mammals. SpPOT1 is essential for telomere maintenance. It binds specifically to the ss G-rich telomeric sequence (GGTTAC) of S. pombe. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. Deletion of the S. pombe pot1+ gene results in a rapid loss of telomere sequences, chromosome mis-segregation and chromosome circularization. hPOT1 is implicated in telomere length regulation. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB2) which cooperate to bind telomeric ssDNA. OB1 makes more extensive contact with the ssDNA than OB2. OB2 protects the 3' end of the ssDNA. A second OB fold has not been predicted in S. pombe POT1. OnTEBP binds the extreme 3-prime end of telomeric DNA. It is heterodimeric and contains four OB folds - three in the alpha subunit (two in the N-terminal domain and one in the C-terminal domain) and one in the beta subunit. OB1Nalpha, together with the second OB fold of the N-terminal domain of OnTEBP alpha subunit and the beta subunit OB fold, forms a deep cleft that binds ssDNA.
• Changed! pfam Telo_bind 103aa 4e-14 in ref transcript
  • Telomere-binding protein alpha subunit, central domain. The telomere-binding protein forms a heterodimer in ciliates consisting of an alpha and a beta subunit. This complex may function as a protective cap for the single-stranded telomeric overhang. Alpha subunit consists of 3 structural domains, all with the same beta-barrel OB fold.
• Changed! cd hPOT1_OB1_like 37aa 4e-06 in modified transcript

POT1

• rs.POT1.F3 rs.POT1.R3 102 191
• NCBIGene 36.3 25913
• Single exon skipping, size difference: 89
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_015450

• cd hPOT1_OB2 118aa 2e-39 in ref transcript
  • hPOT1_OB2: A subfamily of OB folds similar to the second OB fold (OB2) of human protection of telomeres 1 protein (hPOT1). POT1 proteins bind to the single-stranded (ss) 3-prime ends of the telomere. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB2) which cooperate to bind telomeric ssDNA. OB1 makes more extensive contact with the ssDNA than OB2. OB2 protects the 3' end of the ssDNA. hPOT1 is implicated in telomere length regulation.
• cd hPOT1_OB1_like 133aa 2e-33 in ref transcript
  • hPOT1_OB1_like: A subfamily of OB folds similar to the first OB fold (OB1) of human protection of telomeres 1 protein (hPOT1), the single OB fold of the N-terminal domain of Schizosaccharomyces pombe POT1 (SpPOT1), and the first OB fold of the N-terminal domain of the alpha subunit (OB1Nalpha) of Oxytricha nova telomere end binding protein (OnTEBP). POT1 proteins recognize single-stranded (ss) 3-prime ends of the telomere. A 3-prime ss overhang is conserved in ciliated protozoa, yeast, and mammals. SpPOT1 is essential for telomere maintenance. It binds specifically to the ss G-rich telomeric sequence (GGTTAC) of S. pombe. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. Deletion of the S. pombe pot1+ gene results in a rapid loss of telomere sequences, chromosome mis-segregation and chromosome circularization. hPOT1 is implicated in telomere length regulation. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB2) which cooperate to bind telomeric ssDNA. OB1 makes more extensive contact with the ssDNA than OB2. OB2 protects the 3' end of the ssDNA. A second OB fold has not been predicted in S. pombe POT1. OnTEBP binds the extreme 3-prime end of telomeric DNA. It is heterodimeric and contains four OB folds - three in the alpha subunit (two in the N-terminal domain and one in the C-terminal domain) and one in the beta subunit. OB1Nalpha, together with the second OB fold of the N-terminal domain of OnTEBP alpha subunit and the beta subunit OB fold, forms a deep cleft that binds ssDNA.
• pfam Telo_bind 103aa 4e-14 in ref transcript
  • Telomere-binding protein alpha subunit, central domain. The telomere-binding protein forms a heterodimer in ciliates consisting of an alpha and a beta subunit. This complex may function as a protective cap for the single-stranded telomeric overhang. Alpha subunit consists of 3 structural domains, all with the same beta-barrel OB fold.

POT1

• rs.POT1.F4 rs.POT1.R4 106 226
• NCBIGene 36.3 25913
• Single exon skipping, size difference: 120
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_015450

• cd hPOT1_OB2 118aa 2e-39 in ref transcript
  • hPOT1_OB2: A subfamily of OB folds similar to the second OB fold (OB2) of human protection of telomeres 1 protein (hPOT1). POT1 proteins bind to the single-stranded (ss) 3-prime ends of the telomere. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB2) which cooperate to bind telomeric ssDNA. OB1 makes more extensive contact with the ssDNA than OB2. OB2 protects the 3' end of the ssDNA. hPOT1 is implicated in telomere length regulation.
• cd hPOT1_OB1_like 133aa 2e-33 in ref transcript
  • hPOT1_OB1_like: A subfamily of OB folds similar to the first OB fold (OB1) of human protection of telomeres 1 protein (hPOT1), the single OB fold of the N-terminal domain of Schizosaccharomyces pombe POT1 (SpPOT1), and the first OB fold of the N-terminal domain of the alpha subunit (OB1Nalpha) of Oxytricha nova telomere end binding protein (OnTEBP). POT1 proteins recognize single-stranded (ss) 3-prime ends of the telomere. A 3-prime ss overhang is conserved in ciliated protozoa, yeast, and mammals. SpPOT1 is essential for telomere maintenance. It binds specifically to the ss G-rich telomeric sequence (GGTTAC) of S. pombe. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. Deletion of the S. pombe pot1+ gene results in a rapid loss of telomere sequences, chromosome mis-segregation and chromosome circularization. hPOT1 is implicated in telomere length regulation. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB2) which cooperate to bind telomeric ssDNA. OB1 makes more extensive contact with the ssDNA than OB2. OB2 protects the 3' end of the ssDNA. A second OB fold has not been predicted in S. pombe POT1. OnTEBP binds the extreme 3-prime end of telomeric DNA. It is heterodimeric and contains four OB folds - three in the alpha subunit (two in the N-terminal domain and one in the C-terminal domain) and one in the beta subunit. OB1Nalpha, together with the second OB fold of the N-terminal domain of OnTEBP alpha subunit and the beta subunit OB fold, forms a deep cleft that binds ssDNA.
• pfam Telo_bind 103aa 4e-14 in ref transcript
  • Telomere-binding protein alpha subunit, central domain. The telomere-binding protein forms a heterodimer in ciliates consisting of an alpha and a beta subunit. This complex may function as a protective cap for the single-stranded telomeric overhang. Alpha subunit consists of 3 structural domains, all with the same beta-barrel OB fold.

PPARA

• rs.PPARA.F1 rs.PPARA.R1 127 211
• NCBIGene 36.3 5465
• Single exon skipping, size difference: 84
• Exclusion in 5'UTR
• Reference transcript: NM_005036

• cd NR_LBD_PPAR 267aa 1e-108 in ref transcript
  • The ligand binding domain of peroxisome proliferator-activated receptors. The ligand binding domain (LBD) of peroxisome proliferator-activated receptors (PPAR): Peroxisome proliferator-activated receptors (PPARs) are members of the nuclear receptor superfamily of ligand-activated transcription factors. PPARs play important roles in regulating cellular differentiation, development and lipid metabolism. Activated PPAR forms a heterodimer with the retinoid X receptor (RXR) that binds to the hormone response element located upstream of the peroxisome proliferator responsive genes and interacts with co-activators. There are three subtypes of peroxisome proliferator activated receptors, alpha, beta (or delta), and gamma, each with a distinct tissue distribution. Several essential fatty acids, oxidized lipids and prostaglandin J derivatives can bind and activate PPAR. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PPAR has a central well conserved DNA binding domain (DBD), a variable N-terminal regulatory domain, a flexible hinge a nd a C-terminal ligand binding domain (LBD).
• pfam zf-C4 75aa 1e-33 in ref transcript
  • Zinc finger, C4 type (two domains). In nearly all cases, this is the DNA binding domain of a nuclear hormone receptor. The alignment contains two Zinc finger domains that are too dissimilar to be aligned with each other.
• pfam Hormone_recep 182aa 5e-29 in ref transcript
  • Ligand-binding domain of nuclear hormone receptor. This all helical domain is involved in binding the hormone in these receptors.

PPARG

• rs.PPARG.F1 rs.PPARG.R1 143 217
• NCBIGene 36.3 5468
• Single exon skipping, size difference: 74
• Exclusion in 5'UTR
• Reference transcript: NM_138712

• cd NR_LBD_PPAR 268aa 1e-111 in ref transcript
  • The ligand binding domain of peroxisome proliferator-activated receptors. The ligand binding domain (LBD) of peroxisome proliferator-activated receptors (PPAR): Peroxisome proliferator-activated receptors (PPARs) are members of the nuclear receptor superfamily of ligand-activated transcription factors. PPARs play important roles in regulating cellular differentiation, development and lipid metabolism. Activated PPAR forms a heterodimer with the retinoid X receptor (RXR) that binds to the hormone response element located upstream of the peroxisome proliferator responsive genes and interacts with co-activators. There are three subtypes of peroxisome proliferator activated receptors, alpha, beta (or delta), and gamma, each with a distinct tissue distribution. Several essential fatty acids, oxidized lipids and prostaglandin J derivatives can bind and activate PPAR. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PPAR has a central well conserved DNA binding domain (DBD), a variable N-terminal regulatory domain, a flexible hinge a nd a C-terminal ligand binding domain (LBD).
• pfam zf-C4 75aa 1e-35 in ref transcript
  • Zinc finger, C4 type (two domains). In nearly all cases, this is the DNA binding domain of a nuclear hormone receptor. The alignment contains two Zinc finger domains that are too dissimilar to be aligned with each other.
• pfam Hormone_recep 182aa 4e-27 in ref transcript
  • Ligand-binding domain of nuclear hormone receptor. This all helical domain is involved in binding the hormone in these receptors.

PPCS

• rs.PPCS.F1 rs.PPCS.R1 100 545
• NCBIGene 36.3 79717
• Alternative 5-prime, size difference: 445
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_024664

• Changed! pfam DFP 244aa 2e-54 in ref transcript
  • DNA / pantothenate metabolism flavoprotein. The DNA/pantothenate metabolism flavoprotein (EC:4.1.1.36) affects synthesis of DNA, and pantothenate metabolism.
• Changed! COG Dfp 85aa 4e-09 in ref transcript
  • Phosphopantothenoylcysteine synthetase/decarboxylase [Coenzyme metabolism].
• Changed! PRK PRK05579 63aa 1e-06 in ref transcript
  • bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated.

PPM1B

• rs.PPM1B.F1 rs.PPM1B.R1 102 522
• NCBIGene 36.3 5495
• Alternative 3-prime, size difference: 420
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_002706

• cd PP2Cc 273aa 1e-68 in ref transcript
  • Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence similarity.
• smart PP2Cc 277aa 6e-76 in ref transcript
  • Serine/threonine phosphatases, family 2C, catalytic domain. The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence similarity.
• pfam PP2C_C 81aa 3e-26 in ref transcript
  • Protein serine/threonine phosphatase 2C, C-terminal domain. Protein phosphatase 2C (PP2C) is involved in regulating cellular responses to stress in various eukaryotes. It consists of two domains: an N-terminal catalytic domain and a C-terminal domain characteristic of mammalian PP2Cs. This domain consists of three antiparallel alpha helices, one of which packs against two corresponding alpha-helices of the N-terminal domain. The C-terminal domain does not seem to play a role in catalysis, but it may provide protein substrate specificity due to the cleft that is created between it and the catalytic domain.
• PTZ PTZ00224 297aa 2e-46 in ref transcript
  • protein phosphatase 2C; Provisional.

PPP2R5D

• rs.PPP2R5D.F1 rs.PPP2R5D.R1 195 291
• NCBIGene 36.3 5528
• Alternative 5-prime and 3-prime, size difference: 96
• Exclusion in the protein (no frameshift), Exclusion in the protein (no frameshift)
• Reference transcript: NM_006245

• Changed! pfam B56 408aa 0.0 in ref transcript
  • Protein phosphatase 2A regulatory B subunit (B56 family). Protein phosphatase 2A (PP2A) is a major intracellular protein phosphatase that regulates multiple aspects of cell growth and metabolism. The ability of this widely distributed heterotrimeric enzyme to act on a diverse array of substrates is largely controlled by the nature of its regulatory B subunit. There are multiple families of B subunits (See also pfam01240), this family is called the B56 family.
• Changed! pfam B56 400aa 0.0 in modified transcript

PPP4R1

• rs.PPP4R1.F1 rs.PPP4R1.R1 254 305
• NCBIGene 36.3 9989
• Alternative 3-prime, size difference: 51
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001042388

PQBP1

• rs.PQBP1.F1 rs.PQBP1.R1 99 110
• NCBIGene 36.3 10084
• Alternative 5-prime, size difference: 11
• Exclusion in 5'UTR
• Reference transcript: NM_001032383

• pfam WW 31aa 0.004 in ref transcript
  • WW domain. The WW domain is a protein module with two highly conserved tryptophans that binds proline-rich peptide motifs in vitro.

PRDM10

• rs.PRDM10.F1 rs.PRDM10.R1 103 115
• NCBIGene 36.3 56980
• Single exon skipping, size difference: 12
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_020228

PRDM7

• rs.PRDM7.F1 rs.PRDM7.R1 100 383
• NCBIGene 36.3 11105
• Single exon skipping, size difference: 283
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_001098173

• smart KRAB 59aa 4e-08 in ref transcript
  • krueppel associated box.
• pfam SSXRD 33aa 1e-05 in ref transcript
  • SSXRD motif. SSX1 can repress transcription, and this has been attributed to a putative Kruppel associated box (KRAB) repression domain at the N-terminus. However, from the analysis of these deletion constructs further repression activity was found at the C-terminus of SSX1. Which has been called the SSXRD (SSX Repression Domain). The potent repression exerted by full-length SSX1 appears to localise to this region.
• Changed! smart SET 111aa 1e-04 in ref transcript
  • SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain. Putative methyl transferase, based on outlier plant homologues.

PRELP

• rs.PRELP.F1 rs.PRELP.R1 90 100
• NCBIGene 36.3 5549
• Alternative 5-prime, size difference: 10
• Exclusion in 5'UTR
• Reference transcript: NM_002725

• cd LRR_RI 220aa 4e-04 in ref transcript
  • Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1).
• smart LRRNT 36aa 2e-04 in ref transcript
  • Leucine rich repeat N-terminal domain.
• COG COG4886 219aa 9e-07 in ref transcript
  • Leucine-rich repeat (LRR) protein [Function unknown].

PREPL

• rs.PREPL.F1 rs.PREPL.R1 133 331
• NCBIGene 36.3 9581
• Single exon skipping, size difference: 198
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_006036

• pfam Peptidase_S9 162aa 1e-20 in ref transcript
  • Prolyl oligopeptidase family.
• Changed! pfam Peptidase_S9_N 320aa 2e-18 in ref transcript
  • Prolyl oligopeptidase, N-terminal beta-propeller domain. This unusual 7-stranded beta-propeller domain protects the catalytic triad of prolyl oligopeptidase (see pfam00326), excluding larger peptides and proteins from proteolysis in the cytosol.
• Changed! COG PtrB 551aa 7e-83 in ref transcript
  • Protease II [Amino acid transport and metabolism].
• Changed! pfam Peptidase_S9_N 255aa 4e-17 in modified transcript
• Changed! COG PtrB 213aa 3e-49 in modified transcript
• Changed! COG PtrB 273aa 3e-25 in modified transcript
• Changed! COG DAP2 451aa 6e-07 in modified transcript
  • Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism].

PREPL

• rs.PREPL.F2 rs.PREPL.R2 162 348
• NCBIGene 36.3 9581
• Single exon skipping, size difference: 186
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_006036

• pfam Peptidase_S9 162aa 1e-20 in ref transcript
  • Prolyl oligopeptidase family.
• Changed! pfam Peptidase_S9_N 320aa 2e-18 in ref transcript
  • Prolyl oligopeptidase, N-terminal beta-propeller domain. This unusual 7-stranded beta-propeller domain protects the catalytic triad of prolyl oligopeptidase (see pfam00326), excluding larger peptides and proteins from proteolysis in the cytosol.
• Changed! COG PtrB 551aa 7e-83 in ref transcript
  • Protease II [Amino acid transport and metabolism].
• Changed! pfam Peptidase_S9_N 212aa 5e-14 in modified transcript
• Changed! COG PtrB 267aa 7e-52 in modified transcript
• Changed! COG PtrB 212aa 6e-20 in modified transcript

PRF1

• rs.PRF1.F1 rs.PRF1.R1 103 129
• NCBIGene 36.3 5551
• Alternative 3-prime, size difference: 26
• Inclusion in 5'UTR
• Reference transcript: NM_005041

• cd C2 82aa 1e-11 in ref transcript
  • Protein kinase C conserved region 2 (CalB); Ca2+-binding motif present in phospholipases, protein kinases C, and synaptotagmins (among others). Some do not appear to contain Ca2+-binding sites. Particular C2s appear to bind phospholipids, inositol polyphosphates,and intracellular proteins. Synaptotagmin and PLC C2s are permuted in sequence with respect to N- and C-terminal beta strands.
• smart MACPF 203aa 4e-44 in ref transcript
  • membrane-attack complex / perforin.
• pfam C2 81aa 5e-15 in ref transcript
  • C2 domain.
• COG COG5038 97aa 6e-04 in ref transcript
  • Ca2+-dependent lipid-binding protein, contains C2 domain [General function prediction only].

PRKCD

• rs.PRKCD.F1 rs.PRKCD.R1 180 292
• NCBIGene 36.3 5580
• Single exon skipping, size difference: 112
• Exclusion in 5'UTR
• Reference transcript: NM_006254

• cd STKc_nPKC_delta 316aa 1e-179 in ref transcript
  • STKc_nPKC_delta: Serine/Threonine Kinases (STKs), Novel Protein Kinase C (nPKC), delta isoform, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The nPKC subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. PKCs are classified into three groups (classical, atypical, and novel) depending on their mode of activation and the structural characteristics of their regulatory domain. nPKCs are calcium-independent, but require DAG (1,2-diacylglycerol) and phosphatidylserine (PS) for activity. There are four nPKC isoforms, delta, epsilon, eta, and theta. PKC-delta plays a role in cell cycle regulation and programmed cell death in many cell types. It slows down cell proliferation, inducing cell cycle arrest and enhancing cell differentiation. PKC-delta is also involved in the regulation of transcription as well as immune and inflammatory responses. It plays a central role in the genotoxic stress response that leads to DNA damaged-induced apoptosis.
• cd C1 50aa 2e-13 in ref transcript
  • Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
• cd C1 50aa 8e-10 in ref transcript
• smart S_TKc 245aa 8e-73 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• pfam C1_1 53aa 6e-18 in ref transcript
  • Phorbol esters/diacylglycerol binding domain (C1 domain). This domain is also known as the Protein kinase C conserved region 1 (C1) domain.
• smart S_TK_X 64aa 2e-17 in ref transcript
  • Extension to Ser/Thr-type protein kinases.
• pfam C1_1 50aa 2e-11 in ref transcript
• PTZ PTZ00263 323aa 1e-68 in ref transcript
  • protein kinase A catalytic subunit; Provisional.

PRKDC

• rs.PRKDC.F1 rs.PRKDC.R1 305 398
• NCBIGene 36.3 5591
• Single exon skipping, size difference: 93
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_006904

• Changed! cd PIKKc_DNA-PK 297aa 1e-115 in ref transcript
  • DNA-dependent protein kinase (DNA-PK), catalytic domain; The DNA-PK catalytic domain subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and RIO kinases. DNA-PK is a member of the phosphoinositide 3-kinase-related protein kinase (PIKK) subfamily. PIKKs have intrinsic serine/threonine kinase activity and are distinguished from other PKs by their unique catalytic domain, similar to that of lipid PI3K, and their large molecular weight (240-470 kDa). DNA-PK is comprised of a regulatory subunit, containing the Ku70/80 subunit, and a catalytic subunit, which contains a NUC194 domain of unknown function, a FAT (FRAP, ATM and TRRAP) domain, a catalytic domain, and a FATC domain at the C-terminus. It is part of a multi-component system involved in non-homologous end joining (NHEJ), a process of repairing double strand breaks (DSBs) by joining together two free DNA ends of little homology. DNA-PK functions as a molecular sensor for DNA damage that enhances the signal via phosphorylation of downstream targets. It may also act as a protein scaffold that aids the localization of DNA repair proteins to the site of DNA damage. DNA-PK also plays a role in the maintenance of telomeric stability and the prevention of chromosomal end fusion.
• pfam NUC194 398aa 0.0 in ref transcript
  • NUC194 domain. This is domain B in the catalytic subunit of DNA-dependent protein kinases.
• Changed! pfam PI3_PI4_kinase 268aa 1e-57 in ref transcript
  • Phosphatidylinositol 3- and 4-kinase. Some members of this family probably do not have lipid kinase activity and are protein kinases.
• pfam FAT 448aa 2e-52 in ref transcript
  • FAT domain. The FAT domain is named after FRAP, ATM and TRRAP.
• pfam FATC 32aa 5e-05 in ref transcript
  • FATC domain. The FATC domain is named after FRAP, ATM, TRRAP C-terminal. The solution structure of the FATC domain suggests it plays a role in redox-dependent structural and cellular stability.
• Changed! COG TEL1 579aa 2e-48 in ref transcript
  • Phosphatidylinositol kinase and protein kinases of the PI-3 kinase family [Signal transduction mechanisms / Cell division and chromosome partitioning / Chromatin structure and dynamics / DNA replication, recombination, and repair / Intracellular trafficking and secretion].
• Changed! cd PIKKc_DNA-PK 266aa 1e-114 in modified transcript
• Changed! pfam PI3_PI4_kinase 237aa 1e-51 in modified transcript
• Changed! COG TEL1 548aa 7e-44 in modified transcript

PRR3

• rs.PRR3.F1 rs.PRR3.R1 194 257
• NCBIGene 36.3 80742
• Single exon skipping, size difference: 63
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_025263

PRR5

• rs.PRR5.F1 rs.PRR5.R1 128 245
• NCBIGene 36.3 55615
• Single exon skipping, size difference: 117
• Exclusion of the protein initiation site
• Reference transcript: NM_001017528

• Changed! pfam HbrB 132aa 6e-40 in ref transcript
  • HbrB-like. HbrB is involved hyphal growth and polarity.
• Changed! pfam HbrB 71aa 4e-22 in modified transcript

PSAT1

• rs.PSAT1.F1 rs.PSAT1.R1 208 346
• NCBIGene 36.3 29968
• Single exon skipping, size difference: 138
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_058179

• Changed! cd PSAT_like 359aa 1e-175 in ref transcript
  • Phosphoserine aminotransferase (PSAT) family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major group in this CD corresponds to phosphoserine aminotransferase (PSAT). PSAT is active as a dimer and catalyzes the conversion of phosphohydroxypyruvate to phosphoserine.
• Changed! TIGR serC_1 354aa 1e-174 in ref transcript
  • This model represents the common form of the phosphoserine aminotransferase SerC. The phosphoserine aminotransferase of the archaeon Methanosarcina barkeri and putative phosphoserine aminotransferase of Mycobacterium tuberculosis are represented by separate models. All are members of the class V aminotransferases (pfam00266).
• Changed! PRK PRK05355 359aa 1e-161 in ref transcript
  • phosphoserine aminotransferase; Provisional.
• Changed! cd PSAT_like 313aa 1e-148 in modified transcript
• Changed! TIGR serC_1 308aa 1e-147 in modified transcript
• Changed! PRK PRK05355 313aa 1e-137 in modified transcript

PSG11

• rs.PSG11.F1 rs.PSG11.R1 195 263
• NCBIGene 36.3 5680
• Alternative 3-prime, size difference: 68
• Inclusion in 3'UTR
• Reference transcript: NM_002785

• cd IGcam 79aa 3e-07 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• cd IGcam 81aa 3e-04 in ref transcript
• pfam V-set 93aa 3e-10 in ref transcript
  • Immunoglobulin V-set domain. This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.
• smart IG_like 74aa 1e-08 in ref transcript
  • Immunoglobulin like. IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
• smart IG_like 61aa 7e-04 in ref transcript

PSMA4

• rs.PSMA4.F1 rs.PSMA4.R1 104 180
• NCBIGene 36.3 5685
• Alternative 5-prime, size difference: 76
• Exclusion in 5'UTR
• Reference transcript: NM_002789

• cd proteasome_alpha_type_4 214aa 1e-108 in ref transcript
  • proteasome_alpha_type_4. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.
• TIGR arc_protsome_A 233aa 8e-62 in ref transcript
  • This protein family describes the archaeal proteasome alpha subunit, homologous to both the beta subunit and to the alpha and beta subunits of eukaryotic proteasome subunits. This family is universal in the first 29 complete archaeal genomes but occasionally is duplicated.
• PTZ PTZ00246 237aa 7e-86 in ref transcript
  • proteasome subunit alpha; Provisional.

PSMA4

• rs.PSMA4.F2 rs.PSMA4.R2 120 283
• NCBIGene 36.3 5685
• Single exon skipping, size difference: 163
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_001102667

• Changed! cd proteasome_alpha_type_4 214aa 1e-108 in ref transcript
  • proteasome_alpha_type_4. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.
• Changed! TIGR arc_protsome_A 233aa 8e-62 in ref transcript
  • This protein family describes the archaeal proteasome alpha subunit, homologous to both the beta subunit and to the alpha and beta subunits of eukaryotic proteasome subunits. This family is universal in the first 29 complete archaeal genomes but occasionally is duplicated.
• Changed! PTZ PTZ00246 237aa 7e-86 in ref transcript
  • proteasome subunit alpha; Provisional.
• Changed! cd proteasome_alpha_type_4 14aa 6e-04 in modified transcript
• Changed! PTZ PTZ00246 16aa 9e-05 in modified transcript

PSMD13

• rs.PSMD13.F1 rs.PSMD13.R1 217 296
• NCBIGene 36.3 5719
• Single exon skipping, size difference: 79
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_175932

• Changed! pfam PCI 105aa 5e-14 in ref transcript
  • PCI domain. This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15).

PTBP1

• rs.PTBP1.F1 rs.PTBP1.R1 103 124
• NCBIGene 36.3 5725
• Alternative 3-prime, size difference: 21
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_002819

• cd RRM 71aa 4e-10 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• cd RRM 72aa 2e-08 in ref transcript
• cd RRM 73aa 6e-07 in ref transcript
• cd RRM 71aa 7e-05 in ref transcript
• Changed! TIGR hnRNP-L_PTB 501aa 1e-180 in ref transcript
  • Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).
• COG COG0724 171aa 9e-07 in ref transcript
  • RNA-binding proteins (RRM domain) [General function prediction only].
• Changed! TIGR hnRNP-L_PTB 494aa 1e-175 in modified transcript

PTCH1

• rs.PTCH1.F1 PTCH.R5 100 117
• NCBIGene 36.3 5727
• Alternative 5-prime, size difference: 17
• Exclusion in 5'UTR
• Reference transcript: NM_001083604

• TIGR 2A060602 1055aa 0.0 in ref transcript
• COG COG1033 173aa 2e-09 in ref transcript
  • Predicted exporters of the RND superfamily [General function prediction only].
• COG COG1033 108aa 1e-04 in ref transcript

PTCH1

• rs.PTCH1.F2 rs.PTCH1.R2 216 370
• NCBIGene 36.3 5727
• Alternative 5-prime, size difference: 154
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_001083603

• Changed! TIGR 2A060602 1141aa 0.0 in ref transcript
• Changed! COG COG1033 173aa 2e-09 in ref transcript
  • Predicted exporters of the RND superfamily [General function prediction only].
• Changed! COG COG1033 108aa 1e-04 in ref transcript

PTGER3

• rs.PTGER3.F1 rs.PTGER3.R1 186 255
• NCBIGene 36.3 5733
• Mutually exclusive exon skipping, size difference: 69
• Inclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_000957

• pfam 7tm_1 252aa 1e-09 in ref transcript
  • 7 transmembrane receptor (rhodopsin family). This family contains, amongst other G-protein-coupled receptors (GCPRs), members of the opsin family, which have been considered to be typical members of the rhodopsin superfamily. They share several motifs, mainly the seven transmembrane helices, GCPRs of the rhodopsin superfamily. All opsins bind a chromophore, such as 11-cis-retinal. The function of most opsins other than the photoisomerases is split into two steps: light absorption and G-protein activation. Photoisomerases, on the other hand, are not coupled to G-proteins - they are thought to generate and supply the chromophore that is used by visual opsins.

PTGER3

• rs.PTGER3.F2 rs.PTGER3.R2 163 255
• NCBIGene 36.3 5733
• Single exon skipping, size difference: 92
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_000957

• pfam 7tm_1 252aa 1e-09 in ref transcript
  • 7 transmembrane receptor (rhodopsin family). This family contains, amongst other G-protein-coupled receptors (GCPRs), members of the opsin family, which have been considered to be typical members of the rhodopsin superfamily. They share several motifs, mainly the seven transmembrane helices, GCPRs of the rhodopsin superfamily. All opsins bind a chromophore, such as 11-cis-retinal. The function of most opsins other than the photoisomerases is split into two steps: light absorption and G-protein activation. Photoisomerases, on the other hand, are not coupled to G-proteins - they are thought to generate and supply the chromophore that is used by visual opsins.

PTGS1

• rs.PTGS1.F1 rs.PTGS1.R1 135 246
• NCBIGene 36.3 5742
• Alternative 5-prime, size difference: 111
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000962

• cd EGF_CA 38aa 0.005 in ref transcript
  • Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements.
• Changed! pfam An_peroxidase 356aa 2e-86 in ref transcript
  • Animal haem peroxidase.
• pfam EGF 31aa 0.001 in ref transcript
  • EGF-like domain. There is no clear separation between noise and signal. pfam00053 is very similar, but has 8 instead of 6 conserved cysteines. Includes some cytokine receptors. The EGF domain misses the N-terminus regions of the Ca2+ binding EGF domains (this is the main reason of discrepancy between Swiss-Prot domain start/end and Pfam). The family is hard to model due to many similar but different sub-types of EGF domains. Pfam certainly misses a number of EGF domains.
• Changed! pfam An_peroxidase 319aa 9e-78 in modified transcript

PTPN13

• rs.PTPN13.F1 PTPN13.R3 104 119
• NCBIGene 36.3 5783
• Alternative 5-prime, size difference: 15
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_080685

• cd PTPc 228aa 3e-79 in ref transcript
  • Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active.
• cd PDZ_signaling 85aa 7e-16 in ref transcript
  • PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of PDZ domains an N-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in proteases.
• cd PDZ_signaling 80aa 1e-15 in ref transcript
• Changed! cd PDZ_signaling 90aa 2e-13 in ref transcript
• cd FERM_C 94aa 2e-13 in ref transcript
  • The FERM_C domain is the third structural domain within the FERM domain. The FERM domain is found in the cytoskeletal-associated proteins such as ezrin, moesin, radixin, 4.1R, and merlin. These proteins provide a link between the membrane and cytoskeleton and are involved in signal transduction pathways. The FERM_C domain is also found in protein tyrosine phosphatases (PTPs) , the tryosine kinases FAKand JAK, in addition to other proteins involved in signaling. This domain is structuraly similar to the PH and PTB domains and consequently is capable of binding to both peptides and phospholipids at different sites.
• cd PDZ_signaling 79aa 2e-08 in ref transcript
• cd PDZ_signaling 88aa 6e-08 in ref transcript
• smart PTPc 253aa 5e-91 in ref transcript
  • Protein tyrosine phosphatase, catalytic domain.
• smart KIND 188aa 2e-42 in ref transcript
  • kinase non-catalytic C-lobe domain. It is an interaction domain identified as being similar to the C-terminal protein kinase catalytic fold (C lobe). Its presence at the N terminus of signalling proteins and the absence of the active-site residues in the catalytic and activation loops suggest that it folds independently and is likely to be non-catalytic. The occurrence of KIND only in metazoa implies that it has evolved from the catalytic protein kinase domain into an interaction domain possibly by keeping the substrate-binding features.
• smart B41 210aa 4e-40 in ref transcript
  • Band 4.1 homologues. Also known as ezrin/radixin/moesin (ERM) protein domains. Present in myosins, ezrin, radixin, moesin, protein tyrosine phosphatases. Plasma membrane-binding domain. These proteins play structural and regulatory roles in the assembly and stabilization of specialized plasmamembrane domains. Some PDZ domain containing proteins bind one or more of this family. Now includes JAKs.
• pfam FERM_C 88aa 2e-17 in ref transcript
  • FERM C-terminal PH-like domain.
• smart PDZ 90aa 1e-16 in ref transcript
  • Domain present in PSD-95, Dlg, and ZO-1/2. Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities.
• Changed! smart PDZ 92aa 2e-15 in ref transcript
• smart PDZ 83aa 1e-13 in ref transcript
• smart PDZ 92aa 2e-11 in ref transcript
• smart PDZ 84aa 9e-08 in ref transcript
• COG PTP2 267aa 1e-40 in ref transcript
  • Protein tyrosine phosphatase [Signal transduction mechanisms].
• COG Prc 80aa 9e-05 in ref transcript
  • Periplasmic protease [Cell envelope biogenesis, outer membrane].
• COG Prc 54aa 3e-04 in ref transcript
• COG Prc 76aa 3e-04 in ref transcript
• COG Prc 68aa 0.006 in ref transcript
• Changed! cd PDZ_signaling 85aa 3e-15 in modified transcript
• Changed! smart PDZ 87aa 4e-17 in modified transcript

PTPN13

• rs.PTPN13.F2 rs.PTPN13.R2 137 194
• NCBIGene 36.3 5783
• Single exon skipping, size difference: 57
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_080685

• cd PTPc 228aa 3e-79 in ref transcript
  • Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active.
• cd PDZ_signaling 85aa 7e-16 in ref transcript
  • PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of PDZ domains an N-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in proteases.
• cd PDZ_signaling 80aa 1e-15 in ref transcript
• cd PDZ_signaling 90aa 2e-13 in ref transcript
• cd FERM_C 94aa 2e-13 in ref transcript
  • The FERM_C domain is the third structural domain within the FERM domain. The FERM domain is found in the cytoskeletal-associated proteins such as ezrin, moesin, radixin, 4.1R, and merlin. These proteins provide a link between the membrane and cytoskeleton and are involved in signal transduction pathways. The FERM_C domain is also found in protein tyrosine phosphatases (PTPs) , the tryosine kinases FAKand JAK, in addition to other proteins involved in signaling. This domain is structuraly similar to the PH and PTB domains and consequently is capable of binding to both peptides and phospholipids at different sites.
• cd PDZ_signaling 79aa 2e-08 in ref transcript
• cd PDZ_signaling 88aa 6e-08 in ref transcript
• smart PTPc 253aa 5e-91 in ref transcript
  • Protein tyrosine phosphatase, catalytic domain.
• smart KIND 188aa 2e-42 in ref transcript
  • kinase non-catalytic C-lobe domain. It is an interaction domain identified as being similar to the C-terminal protein kinase catalytic fold (C lobe). Its presence at the N terminus of signalling proteins and the absence of the active-site residues in the catalytic and activation loops suggest that it folds independently and is likely to be non-catalytic. The occurrence of KIND only in metazoa implies that it has evolved from the catalytic protein kinase domain into an interaction domain possibly by keeping the substrate-binding features.
• smart B41 210aa 4e-40 in ref transcript
  • Band 4.1 homologues. Also known as ezrin/radixin/moesin (ERM) protein domains. Present in myosins, ezrin, radixin, moesin, protein tyrosine phosphatases. Plasma membrane-binding domain. These proteins play structural and regulatory roles in the assembly and stabilization of specialized plasmamembrane domains. Some PDZ domain containing proteins bind one or more of this family. Now includes JAKs.
• pfam FERM_C 88aa 2e-17 in ref transcript
  • FERM C-terminal PH-like domain.
• smart PDZ 90aa 1e-16 in ref transcript
  • Domain present in PSD-95, Dlg, and ZO-1/2. Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities.
• smart PDZ 92aa 2e-15 in ref transcript
• smart PDZ 83aa 1e-13 in ref transcript
• smart PDZ 92aa 2e-11 in ref transcript
• smart PDZ 84aa 9e-08 in ref transcript
• COG PTP2 267aa 1e-40 in ref transcript
  • Protein tyrosine phosphatase [Signal transduction mechanisms].
• COG Prc 80aa 9e-05 in ref transcript
  • Periplasmic protease [Cell envelope biogenesis, outer membrane].
• COG Prc 54aa 3e-04 in ref transcript
• COG Prc 76aa 3e-04 in ref transcript
• COG Prc 68aa 0.006 in ref transcript

PTPN20B

• rs.PTPN20A.F2 rs.PTPN20A.R2 136 293
• NCBIGene 36.3 26095
• Single exon skipping, size difference: 157
• Inclusion in 5'UTR
• Reference transcript: NM_001042363

• cd PTPc 227aa 8e-77 in ref transcript
  • Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active.
• smart PTPc 253aa 9e-87 in ref transcript
  • Protein tyrosine phosphatase, catalytic domain.
• COG PTP2 237aa 1e-45 in ref transcript
  • Protein tyrosine phosphatase [Signal transduction mechanisms].

PTPRA

• rs.PTPRA.F1 rs.PTPRA.R1 101 191
• NCBIGene 36.3 5786
• Single exon skipping, size difference: 90
• Inclusion in 5'UTR
• Reference transcript: NM_002836

• cd PTPc 231aa 3e-89 in ref transcript
  • Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active.
• cd PTPc 231aa 5e-85 in ref transcript
• smart PTPc 259aa 1e-97 in ref transcript
  • Protein tyrosine phosphatase, catalytic domain.
• smart PTPc 261aa 1e-93 in ref transcript
• COG PTP2 231aa 2e-43 in ref transcript
  • Protein tyrosine phosphatase [Signal transduction mechanisms].
• COG PTP2 241aa 3e-43 in ref transcript

PTPRD

• rs.PTPRD.F1 rs.PTPRD.R1 102 114
• NCBIGene 36.3 5789
• Single exon skipping, size difference: 12
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_002839

• cd PTPc 230aa 5e-92 in ref transcript
  • Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active.
• cd PTPc 231aa 8e-90 in ref transcript
• cd FN3 92aa 3e-13 in ref transcript
  • Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.
• cd FN3 90aa 7e-13 in ref transcript
• cd IGcam 88aa 2e-12 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• cd IGcam 91aa 4e-12 in ref transcript
• cd FN3 95aa 8e-12 in ref transcript
• cd FN3 93aa 2e-11 in ref transcript
• cd FN3 89aa 3e-11 in ref transcript
• cd FN3 107aa 4e-09 in ref transcript
• cd FN3 82aa 2e-06 in ref transcript
• cd IGcam 78aa 1e-05 in ref transcript
• smart PTPc 256aa 1e-101 in ref transcript
  • Protein tyrosine phosphatase, catalytic domain.
• smart PTPc 260aa 1e-100 in ref transcript
• pfam I-set 92aa 5e-16 in ref transcript
  • Immunoglobulin I-set domain.
• pfam fn3 85aa 8e-15 in ref transcript
  • Fibronectin type III domain.
• pfam fn3 88aa 2e-13 in ref transcript
• pfam fn3 83aa 2e-13 in ref transcript
• smart FN3 79aa 3e-12 in ref transcript
  • Fibronectin type 3 domain. One of three types of internal repeat within the plasma protein, fibronectin. The tenth fibronectin type III repeat contains a RGD cell recognition sequence in a flexible loop between 2 strands. Type III modules are present in both extracellular and intracellular proteins.
• smart IGc2 74aa 7e-11 in ref transcript
  • Immunoglobulin C-2 Type.
• smart FN3 83aa 2e-10 in ref transcript
• pfam fn3 100aa 5e-10 in ref transcript
• smart IG_like 79aa 7e-08 in ref transcript
  • Immunoglobulin like. IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
• smart FN3 81aa 4e-05 in ref transcript
• COG PTP2 268aa 1e-48 in ref transcript
  • Protein tyrosine phosphatase [Signal transduction mechanisms].
• COG PTP2 281aa 9e-45 in ref transcript

PTPRM

• rs.PTPRM.F1 rs.PTPRM.R1 326 365
• NCBIGene 36.3 5797
• Multiple exon skipping, size difference: 39
• Exclusion in the protein (no frameshift), Exclusion in the protein (no frameshift)
• Reference transcript: NM_001105244

• cd PTPc 228aa 3e-89 in ref transcript
  • Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active.
• cd PTPc 233aa 7e-68 in ref transcript
• cd MAM 156aa 8e-41 in ref transcript
  • Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region.
• cd FN3 83aa 1e-06 in ref transcript
  • Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.
• cd FN3 95aa 8e-04 in ref transcript
• cd FN3 93aa 0.004 in ref transcript
• smart PTPc 255aa 1e-102 in ref transcript
  • Protein tyrosine phosphatase, catalytic domain.
• smart PTPc 263aa 3e-74 in ref transcript
• smart MAM 160aa 2e-49 in ref transcript
  • Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others). Likely to have an adhesive function. Mutations in the meprin MAM domain affect noncovalent associations within meprin oligomers. In receptor tyrosine phosphatase mu-like molecules the MAM domain is important for homophilic cell-cell interactions.
• pfam fn3 93aa 4e-07 in ref transcript
  • Fibronectin type III domain.
• smart FN3 85aa 4e-05 in ref transcript
  • Fibronectin type 3 domain. One of three types of internal repeat within the plasma protein, fibronectin. The tenth fibronectin type III repeat contains a RGD cell recognition sequence in a flexible loop between 2 strands. Type III modules are present in both extracellular and intracellular proteins.
• smart IG_like 88aa 3e-04 in ref transcript
  • Immunoglobulin like. IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
• smart FN3 80aa 0.002 in ref transcript
• COG PTP2 228aa 3e-45 in ref transcript
  • Protein tyrosine phosphatase [Signal transduction mechanisms].
• COG PTP2 247aa 2e-23 in ref transcript

PTPRS

• rs.PTPRS.F1 rs.PTPRS.R1 101 113
• NCBIGene 36.3 5802
• Single exon skipping, size difference: 12
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_002850

• cd PTPc 230aa 5e-95 in ref transcript
  • Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active.
• cd PTPc 231aa 2e-90 in ref transcript
• cd FN3 90aa 6e-14 in ref transcript
  • Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.
• cd FN3 89aa 2e-12 in ref transcript
• cd IGcam 87aa 4e-12 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• cd FN3 93aa 4e-11 in ref transcript
• cd IGcam 91aa 5e-11 in ref transcript
• cd FN3 90aa 2e-07 in ref transcript
• cd FN3 80aa 2e-07 in ref transcript
• cd FN3 106aa 2e-07 in ref transcript
• cd IGcam 83aa 2e-06 in ref transcript
• cd FN3 83aa 6e-05 in ref transcript
• cd FN3 64aa 0.001 in ref transcript
• smart PTPc 256aa 1e-106 in ref transcript
  • Protein tyrosine phosphatase, catalytic domain.
• smart PTPc 260aa 1e-100 in ref transcript
• pfam I-set 92aa 2e-17 in ref transcript
  • Immunoglobulin I-set domain.
• smart FN3 79aa 1e-12 in ref transcript
  • Fibronectin type 3 domain. One of three types of internal repeat within the plasma protein, fibronectin. The tenth fibronectin type III repeat contains a RGD cell recognition sequence in a flexible loop between 2 strands. Type III modules are present in both extracellular and intracellular proteins.
• smart FN3 80aa 2e-12 in ref transcript
• smart FN3 83aa 5e-11 in ref transcript
• smart IGc2 74aa 1e-10 in ref transcript
  • Immunoglobulin C-2 Type.
• pfam fn3 80aa 7e-09 in ref transcript
  • Fibronectin type III domain.
• smart IG_like 79aa 7e-09 in ref transcript
  • Immunoglobulin like. IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
• pfam fn3 91aa 4e-08 in ref transcript
• pfam fn3 99aa 2e-07 in ref transcript
• smart FN3 79aa 6e-05 in ref transcript
• smart FN3 62aa 3e-04 in ref transcript
• COG PTP2 268aa 6e-51 in ref transcript
  • Protein tyrosine phosphatase [Signal transduction mechanisms].
• COG PTP2 266aa 2e-48 in ref transcript

PUS1

• rs.PUS1.F1 rs.PUS1.R1 137 529
• NCBIGene 36.3 80324
• Alternative 5-prime, size difference: 392
• Exclusion of the protein initiation site
• Reference transcript: NM_025215

• cd PseudoU_synth_PUS1_PUS2 253aa 8e-91 in ref transcript
  • PseudoU_synth_PUS1_PUS2: Pseudouridine synthase, PUS1/ PUS2 like. This group consists of eukaryotic pseudouridine synthases similar to Saccharomyces cerevisiae Pus1p, S. cerevisiae Pus2p, Caenorhabditis elegans Pus1p and human PUS1. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. S. cerevisiae Pus1p catalyzes the formation of psi34 and psi36 in the intron-containing tRNAIle, psi35 in the intron-containing tRNATyr, psi27 and/or psi28 in several yeast cytoplasmic tRNAs and, psi44 in U2 small nuclear RNA (U2 snRNA). The presence of the intron is required for the formation of psi 34, 35 and 36. In addition S. cerevisiae PUS1 makes are psi 26, 65 and 67. C. elegans Pus1p does not modify psi44 in U2 snRNA. Mouse Pus1p makes psi27/28 in pre- tRNASer , tRNAVal and tRNAIle, psi 34/36 in tRNAIle and, psi 32 and potentially 67 in tRNAVal. Psi44 in U2 snRNA and psi32 in tRNAs are highly phylogenetically conserved. Psi 26,27,28,34,35,36,65 and 67 in tRNAs are less highly conserved. Mouse Pus1p regulates nuclear receptor activity through pseudouridylation of Steroid Receptor RNA Activator. Missense mutation in human PUS1 causes mitochondrial myopathy and sideroblastic anemia (MLASA).
• TIGR hisT_truA 252aa 1e-36 in ref transcript
  • universal so far, single copy in all prokaryotes, 3 in yeast. Trusted cutoff for orthology is about 100 based on 1 match only in complete prokaryote with length > 200.
• COG TruA 280aa 2e-44 in ref transcript
  • Pseudouridylate synthase [Translation, ribosomal structure and biogenesis].

PUS7L

• rs.PUS7L.F1 rs.PUS7L.R1 122 537
• NCBIGene 36.3 83448
• Alternative 5-prime, size difference: 415
• Exclusion in 5'UTR
• Reference transcript: NM_001098615

• cd PseudoU_synth_ScPUS7 401aa 1e-111 in ref transcript
  • PseudoU_synth_ScPUS7: Pseudouridine synthase, TruD family. This group consists of eukaryotic pseudouridine synthases similar to Saccharomyces cerevisiae Pus7. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). Saccharomyces cerevisiae Pus7 makes psi35 in U2 small nuclear RNA (U2 snRNA), psi13 in cytoplasmic tRNAs and psi35 in pre-tRNATyr. Psi35 in yeast U2 snRNA and psi13 in tRNAs are highly phylogenetically conserved. Psi34 is the mammalian U2 snRNA counterpart of yeast U2 snRNA psi35.
• cd PseudoU_synth_ScPUS7 28aa 0.002 in ref transcript
• TIGR TIGR00094 400aa 1e-33 in ref transcript
  • MJ11364 is a strong partial match from 50 to 230 aa.
• COG COG0585 405aa 1e-50 in ref transcript
  • Uncharacterized conserved protein [Function unknown].

PWWP2B

• rs.PWWP2B.F1 rs.PWWP2B.R1 127 430
• NCBIGene 36.3 170394
• Alternative 5-prime, size difference: 303
• Exclusion of the stop codon
• Reference transcript: NM_138499

• Changed! cd Dnmt3b_related 87aa 5e-32 in ref transcript
  • The PWWP domain is an essential component of DNA methyltransferase 3 B (Dnmt3b) which is responsible for establishing DNA methylation patterns during embryogenesis and gametogenesis. In tumorigenesis, DNA methylation by Dnmt3b is known to play a role in the inactivation of tumor suppressor genes. In addition, a point mutation in the PWWP domain of Dnmt3b has been identified in patients with ICF syndrome (immunodeficiency, centromeric instability, and facial anomalies), a rare autosomal recessive disorder characterized by hypomethylation of classical satellite DNA. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
• Changed! pfam PWWP 71aa 4e-10 in ref transcript
  • PWWP domain. The PWWP domain is named after a conserved Pro-Trp-Trp-Pro motif. The function of the domain is currently unknown.

PXMP3

• rs.PXMP3.F1 rs.PXMP3.R1 209 241
• NCBIGene 36.3 5828
• Single exon skipping, size difference: 32
• Exclusion in 5'UTR
• Reference transcript: NM_000318

• pfam Pex2_Pex12 207aa 4e-47 in ref transcript
  • Pex2 / Pex12 amino terminal region. This region is found at the N terminal of a number of known and predicted peroxins including Pex2, Pex10 and Pex12. This conserved region is usually associated with a C terminal ring finger (pfam00097) domain.
• smart RING 40aa 0.001 in ref transcript
  • Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s).
• COG PEX10 46aa 0.002 in ref transcript
  • RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones].

PYHIN1

• rs.PYHIN1.F1 rs.PYHIN1.R1 139 166
• NCBIGene 36.3 149628
• Alternative 3-prime, size difference: 27
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_152501

• pfam HIN 159aa 3e-51 in ref transcript
  • HIN-200/IF120x domain. This domain has no know function. It is found in one or two copies per protein, and is found associated with the PAAD/DAPIN domain pfam02758.
• pfam PAAD_DAPIN 79aa 6e-17 in ref transcript
  • PAAD/DAPIN/Pyrin domain. This domain is predicted to contain 6 alpha helices and to have the same fold as the pfam00531 domain. This similarity may mean that this is a protein-protein interaction domain.

RABEP1

• rs.RABEP1.F1 rs.RABEP1.R1 283 382
• NCBIGene 36.3 9135
• Single exon skipping, size difference: 99
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_004703

• Changed! pfam Rab5-bind 196aa 3e-25 in ref transcript
  • Rab5 binding. Members of this family are predominantly found in Rabaptin and allow for binding to the GTPase Rab5. This interaction is necessary and sufficient for Rab5-dependent recruitment of Rabaptin5 to early endosomal membranes.
• pfam Rabaptin 151aa 6e-20 in ref transcript
  • Rabaptin.
• pfam Rabaptin 111aa 2e-17 in ref transcript
• TIGR SMC_prok_B 296aa 4e-06 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• Changed! COG Smc 302aa 5e-08 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].
• COG Smc 264aa 5e-04 in ref transcript
• Changed! pfam Rab5-bind 163aa 5e-20 in modified transcript
• Changed! TIGR SMC_prok_B 280aa 1e-04 in modified transcript
• Changed! COG Smc 289aa 1e-06 in modified transcript

RAC1

• rs.RAC1.F2 rs.RAC1.R2 115 172
• NCBIGene 36.3 5879
• Single exon skipping, size difference: 57
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_018890

• Changed! cd Rac1_like 192aa 1e-107 in ref transcript
  • Rac1-like subfamily. The Rac1-like subfamily consists of Rac1, Rac2, and Rac3 proteins, plus the splice variant Rac1b that contains a 19-residue insertion near switch II relative to Rac1. While Rac1 is ubiquitously expressed, Rac2 and Rac3 are largely restricted to hematopoietic and neural tissues respectively. Rac1 stimulates the formation of actin lamellipodia and membrane ruffles. It also plays a role in cell-matrix adhesion and cell anoikis. In intestinal epithelial cells, Rac1 is an important regulator of migration and mediates apoptosis. Rac1 is also essential for RhoA-regulated actin stress fiber and focal adhesion complex formation. In leukocytes, Rac1 and Rac2 have distinct roles in regulating cell morphology, migration, and invasion, but are not essential for macrophage migration or chemotaxis. Rac3 has biochemical properties that are closely related to Rac1, such as effector interaction, nucleotide binding, and hydrolysis; Rac2 has a slower nucleotide association and is more efficiently activated by the RacGEF Tiam1. Both Rac1 and Rac3 have been implicated in the regulation of cell migration and invasion in human metastatic breast cancer. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.
• Changed! smart RHO 189aa 1e-98 in ref transcript
  • Rho (Ras homology) subfamily of Ras-like small GTPases. Members of this subfamily of Ras-like small GTPases include Cdc42 and Rac, as well as Rho isoforms.
• Changed! COG COG1100 193aa 1e-27 in ref transcript
  • GTPase SAR1 and related small G proteins [General function prediction only].
• Changed! cd Rac1_like 173aa 1e-111 in modified transcript
• Changed! smart RHO 170aa 1e-102 in modified transcript
• Changed! COG COG1100 174aa 3e-31 in modified transcript

RAD17

• rs.RAD17.F1 rs.RAD17.R1 154 338
• NCBIGene 36.3 5884
• Single exon skipping, size difference: 184
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_133339

• Changed! cd AAA 37aa 0.001 in ref transcript
  • The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.
• Changed! TIGR rad24 640aa 0.0 in ref transcript
  • This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
• Changed! PRK PRK04195 423aa 1e-16 in ref transcript
  • replication factor C large subunit; Provisional.

RAD17

• rs.RAD17.F2 rs.RAD17.R2 114 372
• NCBIGene 36.3 5884
• Single exon skipping, size difference: 258
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_133343

• cd AAA 37aa 0.001 in ref transcript
  • The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.
• Changed! TIGR rad24 640aa 0.0 in ref transcript
  • This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
• Changed! PRK PRK04195 423aa 8e-17 in ref transcript
  • replication factor C large subunit; Provisional.
• Changed! TIGR rad24 553aa 0.0 in modified transcript
• Changed! PRK PRK04195 406aa 9e-12 in modified transcript

RAD17

• rs.RAD17.F3 rs.RAD17.R3 271 375
• NCBIGene 36.3 5884
• Single exon skipping, size difference: 104
• Exclusion in 5'UTR
• Reference transcript: NM_133338

• cd AAA 37aa 0.001 in ref transcript
  • The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.
• TIGR rad24 640aa 0.0 in ref transcript
  • This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
• PRK PRK04195 423aa 8e-17 in ref transcript
  • replication factor C large subunit; Provisional.

RAD51

• rs.RAD51.F1 rs.RAD51.R1 122 413
• NCBIGene 36.3 5888
• Exon skipping and alternative 3-prime or 5-prime, size difference: 291
• Inclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_002875

• Changed! cd Rad51_DMC1_radA 234aa 1e-98 in ref transcript
  • Rad51_DMC1_radA,B. This group of recombinases includes the eukaryotic proteins RAD51, RAD55/57 and the meiosis-specific protein DMC1, and the archaeal proteins radA and radB. They are closely related to the bacterial RecA group. Rad51 proteins catalyze a similiar recombination reaction as RecA, using ATP-dependent DNA binding activity and a DNA-dependent ATPase. However, this reaction is less efficient and requires accessory proteins such as RAD55/57.
• Changed! TIGR recomb_RAD51 315aa 1e-178 in ref transcript
  • This eukaryotic sequence family consists of RAD51, a protein involved in DNA homologous recombination and repair. It is similar in sequence the exclusively meiotic recombinase DMC1 (TIGR02238), to archaeal families RadA (TIGR02236) and RadB (TIGR02237), and to bacterial RecA (TIGR02012).
• Changed! PTZ PTZ00035 332aa 1e-125 in ref transcript
  • Rad51; Provisional.
• Changed! cd Rad51_DMC1_radA 168aa 1e-59 in modified transcript
• Changed! TIGR recomb_RAD51 170aa 4e-89 in modified transcript
• Changed! TIGR recomb_RAD51 56aa 2e-20 in modified transcript
• Changed! PTZ PTZ00035 173aa 3e-64 in modified transcript
• Changed! PTZ PTZ00035 67aa 1e-10 in modified transcript

RAD51L3

• rs.RAD51L3.F1 rs.RAD51L3.R1 98 434
• NCBIGene 36.3 5892
• Multiple exon skipping, size difference: 336
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift, Exclusion in the protein (no frameshift)
• Reference transcript: NM_002878

• Changed! cd Rad51_DMC1_radA 236aa 6e-43 in ref transcript
  • Rad51_DMC1_radA,B. This group of recombinases includes the eukaryotic proteins RAD51, RAD55/57 and the meiosis-specific protein DMC1, and the archaeal proteins radA and radB. They are closely related to the bacterial RecA group. Rad51 proteins catalyze a similiar recombination reaction as RecA, using ATP-dependent DNA binding activity and a DNA-dependent ATPase. However, this reaction is less efficient and requires accessory proteins such as RAD55/57.
• Changed! TIGR recomb_radA 306aa 2e-14 in ref transcript
  • This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.
• Changed! PRK radB 223aa 3e-17 in ref transcript
  • DNA repair and recombination protein RadB; Provisional.
• Changed! cd Rad51_DMC1_radA 170aa 4e-19 in modified transcript
• Changed! PRK radB 84aa 4e-04 in modified transcript

RANBP3

• rs.RANBP3.F1 rs.RANBP3.R1 111 126
• NCBIGene 36.3 8498
• Alternative 5-prime, size difference: 15
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_007322

• cd RanBD 125aa 3e-26 in ref transcript
  • Ran-binding domain; This domain of approximately 150 residues shares structural similarity to the PH domain, but lacks detectable sequence similarity. Ran is a Ras-like nuclear small GTPase, which regulates receptor-mediated transport between the nucleus and the cytoplasm. RanGTP hydrolysis is stimulated by RanGAP together with the Ran-binding domain containing acessory proteins RanBP1 and RanBP2. These accessory proteins stabilize the active GTP-bound form of Ran . The Ran-binding domain is found in multiple copies in Nuclear pore complex proteins.
• smart RanBD 111aa 3e-15 in ref transcript
  • Ran-binding domain. Domain of apporximately 150 residues that stabilises the GTP-bound form of Ran (the Ras-like nuclear small GTPase).
• COG YRB1 71aa 1e-04 in ref transcript
  • Ran GTPase-activating protein (Ran-binding protein) [Intracellular trafficking and secretion].

RAP1A

• rs.RAP1A.F1 rs.RAP1A.R1 176 270
• NCBIGene 36.3 5906
• Single exon skipping, size difference: 94
• Exclusion in 5'UTR
• Reference transcript: NM_001010935

• cd Rap_like 149aa 3e-84 in ref transcript
  • Rap-like subfamily. The Rap subfamily consists of the Rap1, Rap2, and RSR1. Rap subfamily proteins perform different cellular functions, depending on the isoform and its subcellular localization. For example, in rat salivary gland, neutrophils, and platelets, Rap1 localizes to secretory granules and is believed to regulate exocytosis or the formation of secretory granules. Rap1 has also been shown to localize in the Golgi of rat fibroblasts, zymogen granules, plasma membrane, and microsomal membrane of the pancreatic acini, as well as in the endocytic compartment of skeletal muscle cells and fibroblasts. Rap1 localizes in the nucleus of human oropharyngeal squamous cell carcinomas (SCCs) and cell lines. Rap1 plays a role in phagocytosis by controlling the binding of adhesion receptors (typically integrins) to their ligands. In yeast, Rap1 has been implicated in multiple functions, including activation and silencing of transcription and maintenance of telomeres. Rap2 is involved in multiple functions, including activation of c-Jun N-terminal kinase (JNK) to regulate the actin cytoskeleton and activation of the Wnt/beta-catenin signaling pathway in embryonic Xenopus. A number of effector proteins for Rap2 have been identified, including isoform 3 of the human mitogen-activated protein kinase kinase kinase kinase 4 (MAP4K4) and Traf2- and Nck-interacting kinase (TNIK), and the RalGEFs RalGDS, RGL, and Rlf, which also interact with Rap1 and Ras. RSR1 is the fungal homolog of Rap1 and Rap2. In budding yeasts, it is involved in selecting a site for bud growth, which directs the establishment of cell polarization. The Rho family GTPase Cdc42 and its GEF, Cdc24, then establish an axis of polarized growth. It is believed that Cdc42 interacts directly with RSR1 in vivo. In filamentous fungi such as Ashbya gossypii, RSR1 is a key regulator of polar growth in the hypha. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.
• smart RAS 151aa 8e-78 in ref transcript
  • Ras subfamily of RAS small GTPases. Similar in fold and function to the bacterial EF-Tu GTPase. p21Ras couples receptor Tyr kinases and G protein receptors to protein kinase cascades.
• COG COG1100 150aa 1e-16 in ref transcript
  • GTPase SAR1 and related small G proteins [General function prediction only].

RAP1GDS1

• rs.RAP1GDS1.F1 rs.RAP1GDS1.R1 193 340
• NCBIGene 36.3 5910
• Single exon skipping, size difference: 147
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001100426

• cd ARM 114aa 1e-08 in ref transcript
  • Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model.
• Changed! cd ARM 124aa 3e-07 in ref transcript
• pfam Arm 32aa 0.003 in ref transcript
  • Armadillo/beta-catenin-like repeat. Approx. 40 amino acid repeat. Tandem repeats form super-helix of helices that is proposed to mediate interaction of beta-catenin with its ligands. CAUTION: This family does not contain all known armadillo repeats.
• Changed! COG SRP1 57aa 0.008 in ref transcript
  • Karyopherin (importin) alpha [Intracellular trafficking and secretion].
• Changed! cd ARM 120aa 3e-09 in modified transcript
• Changed! COG SRP1 318aa 9e-04 in modified transcript

RARB

• rs.RARB.F1 rs.RARB.R1 137 494
• NCBIGene 36.3 5915
• Alternative 5-prime, size difference: 357
• Exclusion of the protein initiation site
• Reference transcript: NM_000965

• cd NR_LBD_RAR 231aa 1e-131 in ref transcript
  • The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily. The ligand binding domain (LBD) of retinoic acid receptor (RAR): Retinoic acid receptors are members of the nuclear receptor (NR) superfamily of ligand-regulated transcription factors. RARs mediate the biological effect of retinoids, including both naturally dietary vitamin A (retinol) metabolites and active synthetic analogs. Retinoids play key roles in a wide variety of essential biological processes, such as vertebrate embryonic morphogenesis and organogenesis, differentiation and apoptosis, and homeostasis. RARs function as heterodimers with retinoic X receptors by binding to specific RAR response elements (RAREs) found in the promoter regions of retinoid target genes. In the absence of ligand, the RAR-RXR heterodimer recruits the corepressor proteins NCoR or AMRT, and associated factors such as histone deacetylases or DNA-methyltransferases, leading to an inactive condensed chromatin structure, preventing transcription. Upon ligand binding, the corepressors are released, and coactivator complexes such as histone acetyltransferase or histone arginine methyltransferases are recruited to activate transcription. There are three RAR subtypes (alpha, beta, gamma), originating from three distinct genes. For each subtype, several isoforms exist that differ in their N-terminal region, allowing retinoids to exert their pleiotropic effects. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, retinoic acid receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).
• Changed! pfam zf-C4 76aa 6e-38 in ref transcript
  • Zinc finger, C4 type (two domains). In nearly all cases, this is the DNA binding domain of a nuclear hormone receptor. The alignment contains two Zinc finger domains that are too dissimilar to be aligned with each other.
• pfam Hormone_recep 181aa 5e-31 in ref transcript
  • Ligand-binding domain of nuclear hormone receptor. This all helical domain is involved in binding the hormone in these receptors.
• Changed! pfam zf-C4 42aa 8e-17 in modified transcript

RASA4

• rs.RASA4.F1 rs.RASA4.R1 141 279
• NCBIGene 36.3 10156
• Single exon skipping, size difference: 138
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_006989

• cd RasGAP_RASA4 331aa 1e-172 in ref transcript
  • Ras GTPase activating-like 4 protein (RASAL4), also known as Ca2+ -promoted Ras inactivator (CAPRI), is a member of the GAP1 family. Members of the GAP1 family are characterized by a conserved domain structure comprising N-terminal tandem C2 domains, a highly conserved central RasGAP domain, and a C-terminal pleckstrin-homology domain that is associated with a Bruton's tyrosine kinase motif. RASAL4, like RASAL, is a cytosolic protein that undergoes a rapid translocation to the plasma membrane in response to a receptor-mediated elevation in the concentration of intracellular free Ca2+ ([Ca2+]i). However, unlike RASAL, RASAL4 does not sense oscillations in [Ca2+]i.
• Changed! cd PH_RasGAP_CG9209 103aa 1e-34 in ref transcript
  • RAS_GTPase activating protein (GAP)_CG9209 pleckstrin homology (PH) domain. This protein consists of two C2 domains, followed by a RasGAP domain, a PH domain and a BTK domain. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinsases, regulators of G-proteins, endocytotic GTPAses, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes.
• cd C2_1 118aa 2e-29 in ref transcript
  • Protein kinase C conserved region 2, subgroup 1; C2 Ca2+-binding motif present in phospholipases, protein kinases C, and synaptotagmins (amongst others); some PKCs lack calcium dependence. Particular C2s appear to bind phospholipids, inositol polyphosphates,and intracellular proteins. Two distinct C2 topologies generated by permutation of the sequence with respect to the N- and C-terminal beta strands are seen. In this subgroup, containing synaptotagmins, specific protein kinases C (PKC) subtypes and other proteins, the N-terminal beta strand occupies the position of what is the C-terminal strand in subgroup 2.
• cd C2 102aa 3e-20 in ref transcript
  • Protein kinase C conserved region 2 (CalB); Ca2+-binding motif present in phospholipases, protein kinases C, and synaptotagmins (among others). Some do not appear to contain Ca2+-binding sites. Particular C2s appear to bind phospholipids, inositol polyphosphates,and intracellular proteins. Synaptotagmin and PLC C2s are permuted in sequence with respect to N- and C-terminal beta strands.
• smart RasGAP 362aa 3e-97 in ref transcript
  • GTPase-activator protein for Ras-like GTPases. All alpha-helical domain that accelerates the GTPase activity of Ras, thereby "switching" it into an "off" position. Improved domain limits from structure.
• pfam C2 82aa 2e-21 in ref transcript
  • C2 domain.
• pfam C2 82aa 8e-20 in ref transcript
• Changed! smart PH 106aa 6e-08 in ref transcript
  • Pleckstrin homology domain. Domain commonly found in eukaryotic signalling proteins. The domain family possesses multiple functions including the abilities to bind inositol phosphates, and various proteins. PH domains have been found to possess inserted domains (such as in PLC gamma, syntrophins) and to be inserted within other domains. Mutations in Brutons tyrosine kinase (Btk) within its PH domain cause X-linked agammaglobulinaemia (XLA) in patients. Point mutations cluster into the positively charged end of the molecule around the predicted binding site for phosphatidylinositol lipids.
• pfam BTK 28aa 2e-07 in ref transcript
  • BTK motif. Zinc-binding motif containing conserved cysteines and a histidine. Always found C-terminal to PH domains. The crystal structure shows this motif packs against the PH domain. The PH+Btk module pair has been called the Tec homology (TH) region.
• COG COG5038 88aa 3e-10 in ref transcript
  • Ca2+-dependent lipid-binding protein, contains C2 domain [General function prediction only].
• COG COG5038 81aa 4e-09 in ref transcript
• COG IQG1 246aa 4e-05 in ref transcript
  • Protein involved in regulation of cellular morphogenesis/cytokinesis [Cell division and chromosome partitioning / Signal transduction mechanisms].

RASSF1

• rs.RASSF1.F1 rs.RASSF1.R1 100 112
• NCBIGene 36.3 11186
• Alternative 3-prime, size difference: 12
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_170714

• cd RASSF1_RA 96aa 4e-39 in ref transcript
  • RASSF1 (also known as RASSF3 and NORE1) is a tumour suppressor protein with a C-terminal Ras-associating (RA) domain that binds Ras. RASSF1 also binds the proapoptotic protein kinase MST1 and is thus thought to regulate the proapoptotic signalling pathway. RASSF1 also associates with microtubule-associated proteins like MAP1B and regulates tubulin polymerization. RASSF1 also binds CDC20 and regulates mitosis by inhibiting the anaphase-promoting complex and preventing degradation of cyclin A and cyclin B until the spindle checkpoint becomes fully operational.
• Changed! cd C1 54aa 1e-06 in ref transcript
  • Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
• smart RA 88aa 6e-17 in ref transcript
  • Ras association (RalGDS/AF-6) domain. RasGTP effectors (in cases of AF6, canoe and RalGDS); putative RasGTP effectors in other cases. Kalhammer et al. have shown that not all RA domains bind RasGTP. Predicted structure similar to that determined, and that of the RasGTP-binding domain of Raf kinase. Predicted RA domains in PLC210 and nore1 found to bind RasGTP. Included outliers (Grb7, Grb14, adenylyl cyclases etc.).
• Changed! pfam C1_1 54aa 2e-07 in ref transcript
  • Phorbol esters/diacylglycerol binding domain (C1 domain). This domain is also known as the Protein kinase C conserved region 1 (C1) domain.
• Changed! cd C1 50aa 2e-08 in modified transcript
• Changed! pfam C1_1 50aa 2e-08 in modified transcript

RBM23

• rs.RBM23.F1 rs.RBM23.R1 107 155
• NCBIGene 36.3 55147
• Single exon skipping, size difference: 48
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001077351

• cd RRM 73aa 2e-21 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• cd RRM 73aa 9e-10 in ref transcript
• TIGR SF-CC1 292aa 3e-92 in ref transcript
  • A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed.
• COG COG0724 162aa 3e-15 in ref transcript
  • RNA-binding proteins (RRM domain) [General function prediction only].

RBM23

• rs.RBM23.F2 rs.RBM23.R2 217 271
• NCBIGene 36.3 55147
• Single exon skipping, size difference: 54
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001077351

• cd RRM 73aa 2e-21 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• cd RRM 73aa 9e-10 in ref transcript
• Changed! TIGR SF-CC1 292aa 3e-92 in ref transcript
  • A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed.
• COG COG0724 162aa 3e-15 in ref transcript
  • RNA-binding proteins (RRM domain) [General function prediction only].
• Changed! TIGR SF-CC1 286aa 1e-90 in modified transcript

RBM33

• rs.RBM33.F1 rs.RBM33.R1 173 203
• NCBIGene 36.3 155435
• Alternative 3-prime, size difference: 30
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001008408

• cd RRM 64aa 0.001 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• smart RRM_2 64aa 3e-04 in ref transcript
  • RNA recognition motif.

RBM35A

• rs.RBM35A.F1 rs.RBM35A.R1 100 112
• NCBIGene 36.3 54845
• Alternative 5-prime, size difference: 12
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_017697

• cd RRM 76aa 1e-07 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• cd RRM 75aa 3e-07 in ref transcript
• cd ERI-1_3'hExo_like 117aa 3e-07 in ref transcript
  • This subfamily is composed of Caenorhabditis elegans ERI-1, human 3' exonuclease (3'hExo), Drosophila exonuclease snipper (snp), and similar proteins from eukaryotes and bacteria. These are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ERI-1 has been implicated in the degradation of small interfering RNAs (RNAi). 3'hExo participates in the degradation of histone mRNAs. Snp is a non-essential exonuclease that efficiently degrades structured RNA and DNA substrates as long as there is a minimum of 2 nucleotides in the 3' overhang to initiate degradation. Snp is not a functional homolog of either ERI-1 or 3'hExo.
• smart RRM_2 75aa 6e-05 in ref transcript
  • RNA recognition motif.
• smart RRM_2 74aa 3e-04 in ref transcript

RBM47

• rs.RBM47.F1 rs.RBM47.R1 123 330
• NCBIGene 36.3 54502
• Single exon skipping, size difference: 207
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001098634

• cd RRM 72aa 1e-13 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• cd RRM 68aa 8e-12 in ref transcript
• cd RRM 79aa 1e-06 in ref transcript
• Changed! TIGR hnRNP-R-Q 573aa 0.0 in ref transcript
  • Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.
• COG COG0724 143aa 4e-09 in ref transcript
  • RNA-binding proteins (RRM domain) [General function prediction only].
• COG COG0724 71aa 2e-07 in ref transcript
• Changed! TIGR hnRNP-R-Q 354aa 1e-178 in modified transcript
• Changed! TIGR hnRNP-R-Q 175aa 6e-25 in modified transcript

RBMY1A1

• rs.RBMY1A1.F1 rs.RBMY1A1.R1 345 523
• NCBIGene 36.3 5940
• Single exon skipping, size difference: 178
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_005058

• Changed! cd RRM 73aa 1e-22 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• Changed! pfam RRM_1 70aa 2e-20 in ref transcript
  • RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain). The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have a N terminus rrm which is included in the seed. There is a second region towards the C terminus that has some features of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.
• Changed! pfam RBM1CTR 44aa 2e-08 in ref transcript
  • RBM1CTR (NUC064) family. This C-terminal region is found in RBM1-like RNA binding hnRNPs.
• Changed! COG COG0724 84aa 1e-09 in ref transcript
  • RNA-binding proteins (RRM domain) [General function prediction only].
• Changed! cd RRM 65aa 2e-17 in modified transcript
• Changed! pfam RRM_1 63aa 2e-16 in modified transcript
• Changed! COG COG0724 79aa 2e-08 in modified transcript

RCC1

• rs.RCC1.F1 rs.RCC1.R1 111 153
• NCBIGene 36.3 1104
• Alternative 5-prime, size difference: 42
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001048194

• pfam RCC1 50aa 5e-11 in ref transcript
  • Regulator of chromosome condensation (RCC1).
• pfam RCC1 49aa 1e-10 in ref transcript
• pfam RCC1 51aa 5e-10 in ref transcript
• pfam RCC1 52aa 8e-10 in ref transcript
• pfam RCC1 66aa 1e-08 in ref transcript
• pfam RCC1 31aa 2e-04 in ref transcript
• pfam RCC1 51aa 4e-04 in ref transcript
• Changed! COG ATS1 350aa 5e-42 in ref transcript
  • Alpha-tubulin suppressor and related RCC1 domain-containing proteins [Cell division and chromosome partitioning / Cytoskeleton].
• Changed! COG ATS1 415aa 3e-42 in modified transcript

RCP9

• rs.RCP9.F1 rs.RCP9.R1 222 321
• NCBIGene 36.3 27297
• Single exon skipping, size difference: 99
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_014478

• Changed! pfam RNA_pol_III_C17 120aa 5e-36 in ref transcript
  • RNA polymerase III subunit C17. C17 (aka CGRP-RCP) is an essential subunit of RNA polymerase III. C17 forms a subcomplex with C25 which is likely to be the counterpart of subcomplex Rpb4/7 in Pol II.
• Changed! pfam RNA_pol_III_C17 87aa 1e-22 in modified transcript

REG3A

• rs.REG3A.F1 rs.REG3A.R1 107 130
• NCBIGene 36.3 5068
• Alternative 3-prime, size difference: 23
• Inclusion in 5'UTR
• Reference transcript: NM_138937

• cd CLECT_REG-1_like 134aa 7e-41 in ref transcript
  • CLECT_REG-1_like: C-type lectin-like domain (CTLD) of the type found in Human REG-1 (lithostathine), REG-4, and avian eggshell-specific proteins: ansocalcin, structhiocalcin-1(SCA-1), and -2(SCA-2). CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. REG-1 is a proliferating factor which participates in various kinds of tissue regeneration including pancreatic beta-cell regeneration, regeneration of intestinal mucosa, regeneration of motor neurons, and perhaps in tissue regeneration of damaged heart. REG-1 may play a role on the pathophysiology of Alzheimer's disease and in the development of gastric cancers. Its expression is correlated with reduced survival from early-stage colorectal cancer. REG-1 also binds and aggregates several bacterial strains from the intestinal flora and it has been suggested that it is involved in the control of the intestinal bacterial ecosystem. Rat lithostathine has calcium carbonate crystal inhibitor activity in vitro. REG-IV is unregulated in pancreatic, gastric, hepatocellular, and prostrate adenocarcinomas. REG-IV activates the EGF receptor/Akt/AP-1 signaling pathway in colorectal carcinoma. Ansocalcin, SCA-1 and -2 are found at high concentration in the calcified egg shell layer of goose and ostrich, respectively and tend to form aggregates. Ansocalcin nucleates calcite crystal aggregates in vitro.
• smart CLECT 133aa 2e-23 in ref transcript
  • C-type lectin (CTL) or carbohydrate-recognition domain (CRD). Many of these domains function as calcium-dependent carbohydrate binding modules.

REG3G

• rs.REG3G.F1 rs.REG3G.R1 280 380
• NCBIGene 36.3 130120
• Alternative 3-prime, size difference: 100
• Inclusion in 5'UTR
• Reference transcript: NM_198448

• cd CLECT_REG-1_like 134aa 5e-38 in ref transcript
  • CLECT_REG-1_like: C-type lectin-like domain (CTLD) of the type found in Human REG-1 (lithostathine), REG-4, and avian eggshell-specific proteins: ansocalcin, structhiocalcin-1(SCA-1), and -2(SCA-2). CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. REG-1 is a proliferating factor which participates in various kinds of tissue regeneration including pancreatic beta-cell regeneration, regeneration of intestinal mucosa, regeneration of motor neurons, and perhaps in tissue regeneration of damaged heart. REG-1 may play a role on the pathophysiology of Alzheimer's disease and in the development of gastric cancers. Its expression is correlated with reduced survival from early-stage colorectal cancer. REG-1 also binds and aggregates several bacterial strains from the intestinal flora and it has been suggested that it is involved in the control of the intestinal bacterial ecosystem. Rat lithostathine has calcium carbonate crystal inhibitor activity in vitro. REG-IV is unregulated in pancreatic, gastric, hepatocellular, and prostrate adenocarcinomas. REG-IV activates the EGF receptor/Akt/AP-1 signaling pathway in colorectal carcinoma. Ansocalcin, SCA-1 and -2 are found at high concentration in the calcified egg shell layer of goose and ostrich, respectively and tend to form aggregates. Ansocalcin nucleates calcite crystal aggregates in vitro.
• smart CLECT 133aa 2e-21 in ref transcript
  • C-type lectin (CTL) or carbohydrate-recognition domain (CRD). Many of these domains function as calcium-dependent carbohydrate binding modules.

REPIN1

• rs.REPIN1.F1 rs.REPIN1.R1 274 399
• NCBIGene 36.3 29803
• Single exon skipping, size difference: 125
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_001099695

• Changed! COG COG5048 275aa 2e-06 in ref transcript
  • FOG: Zn-finger [General function prediction only].

RERE

• rs.RERE.F1 rs.RERE.R1 207 392
• NCBIGene 36.3 473
• Single exon skipping, size difference: 185
• Exclusion in 5'UTR
• Reference transcript: NM_012102

• cd BAH_MTA 206aa 4e-60 in ref transcript
  • BAH, or Bromo Adjacent Homology domain, as present in MTA1 and similar proteins. The Metastasis-associated protein MTA1 is part of the NURD (nucleosome remodeling and deacetylating) complex and plays a role in cellular transformation and metastasis. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
• cd ZnF_GATA 55aa 4e-09 in ref transcript
  • Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C.
• cd SANT 44aa 0.001 in ref transcript
  • 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
• pfam Atrophin-1 622aa 1e-154 in ref transcript
  • Atrophin-1 family. Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteristic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.
• pfam Atrophin-1 134aa 4e-20 in ref transcript
• smart ZnF_GATA 50aa 4e-11 in ref transcript
  • zinc finger binding to DNA consensus sequence [AT]GATA[AG].
• smart BAH 177aa 3e-08 in ref transcript
  • Bromo adjacent homology domain.
• pfam ELM2 53aa 2e-07 in ref transcript
  • ELM2 domain. The ELM2 (Egl-27 and MTA1 homology 2) domain is a small domain of unknown function. It is found in the MTA1 protein that is part of the NuRD complex. The domain is usually found to the N terminus of a myb-like DNA binding domain pfam00249. ELM2 is also found associated with an ARID DNA binding domain pfam01388 in a protein from Arabidopsis thaliana. This suggests that ELM2 may also be involved in DNA binding, or perhaps is a protein-protein interaction domain.
• smart SANT 46aa 2e-04 in ref transcript
  • SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.

RGR

• rs.RGR.F1 rs.RGR.R1 100 112
• NCBIGene 36.3 5995
• Alternative 3-prime, size difference: 12
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_002921

• Changed! pfam 7tm_1 229aa 7e-11 in ref transcript
  • 7 transmembrane receptor (rhodopsin family). This family contains, amongst other G-protein-coupled receptors (GCPRs), members of the opsin family, which have been considered to be typical members of the rhodopsin superfamily. They share several motifs, mainly the seven transmembrane helices, GCPRs of the rhodopsin superfamily. All opsins bind a chromophore, such as 11-cis-retinal. The function of most opsins other than the photoisomerases is split into two steps: light absorption and G-protein activation. Photoisomerases, on the other hand, are not coupled to G-proteins - they are thought to generate and supply the chromophore that is used by visual opsins.
• Changed! pfam 7tm_1 225aa 3e-12 in modified transcript

RGS11

• rs.RGS11.F1 rs.RGS11.R1 94 105
• NCBIGene 36.3 8786
• Alternative 5-prime, size difference: 11
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_183337

• Changed! cd DEP_RGS7-like 88aa 5e-25 in ref transcript
  • DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in RGS (regulator of G-protein signaling) proteins of the subfamily R7. This subgroup contains RGS7, RGS6, RGS9 and RGS11. They share a common domain architecture, containing, beside the RGS domain, a DEP domain and a GGL (G-protein gamma subunit-like ) domain. RGS proteins are GTPase-activating (GAP) proteins of heterotrimeric G proteins by increasing the rate of GTP hydrolysis of the alpha subunit. The fungal homologs, like yeast Sst2, share a related common domain architecture, containing RGS and DEP domains. Sst2 has been identified as the principal regulator of mating pheromone signaling and recently the DEP domain of Sst2 has been shown to be necessary and sufficient to mediate receptor interaction.
• Changed! cd GGL 56aa 3e-13 in ref transcript
  • G protein gamma subunit-like motifs, the alpha-helical G-gamma chain dimerizes with the G-beta propeller subunit as part of the heterotrimeric G-protein complex; involved in signal transduction via G-protein-coupled receptors.
• Changed! pfam RGS 115aa 7e-35 in ref transcript
  • Regulator of G protein signaling domain. RGS family members are GTPase-activating proteins for heterotrimeric G-protein alpha-subunits.
• Changed! smart GGL 62aa 2e-18 in ref transcript
  • G protein gamma subunit-like motifs.
• Changed! pfam DEP 80aa 1e-16 in ref transcript
  • Domain found in Dishevelled, Egl-10, and Pleckstrin. The DEP domain is responsible for mediating intracellular protein targeting and regulation of protein stability in the cell. The DEP domain is present in a number of signaling molecules, including Regulator of G protein Signaling (RGS) proteins, and has been implicated in membrane targeting. New findings in yeast, however, demonstrate a major role for a DEP domain in mediating the interaction of an RGS protein to the C-terminal tail of a GPCR, thus placing RGS in close proximity with its substrate G protein alpha subunit.

RGS8

• rs.RGS8.F1 rs.RGS8.R1 153 282
• NCBIGene 36.3 85397
• Single exon skipping, size difference: 129
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_033345

• Changed! pfam RGS 115aa 2e-38 in ref transcript
  • Regulator of G protein signaling domain. RGS family members are GTPase-activating proteins for heterotrimeric G-protein alpha-subunits.

RHBDD2

• rs.RHBDD2.F1 rs.RHBDD2.R1 295 417
• NCBIGene 36.3 57414
• Single exon skipping, size difference: 122
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_001040456

• Changed! pfam Rhomboid 146aa 6e-11 in ref transcript
  • Rhomboid family. This family contains integral membrane proteins that are related to Drosophila rhomboid protein. Members of this family are found in bacteria and eukaryotes. Rhomboid promotes the cleavage of the membrane-anchored TGF-alpha-like growth factor Spitz, allowing it to activate the Drosophila EGF receptor. Analysis has shown that Rhomboid-1 is an intramembrane serine protease (EC:3.4.21.105). Parasite-encoded rhomboid enzymes are also important for invasion of host cells by Toxoplasma and the malaria parasite.
• Changed! COG GlpG 79aa 0.005 in ref transcript
  • Uncharacterized membrane protein (homolog of Drosophila rhomboid) [General function prediction only].

RHOC

• rs.RHOC.F1 rs.RHOC.R1 293 362
• NCBIGene 36.3 389
• Single exon skipping, size difference: 69
• Exclusion in 5'UTR
• Reference transcript: NM_175744

• cd RhoA_like 175aa 1e-106 in ref transcript
  • RhoA-like subfamily. The RhoA subfamily consists of RhoA, RhoB, and RhoC. RhoA promotes the formation of stress fibers and focal adhesions, regulating cell shape, attachment, and motility. RhoA can bind to multiple effector proteins, thereby triggering different downstream responses. In many cell types, RhoA mediates local assembly of the contractile ring, which is necessary for cytokinesis. RhoA is vital for muscle contraction; in vascular smooth muscle cells, RhoA plays a key role in cell contraction, differentiation, migration, and proliferation. RhoA activities appear to be elaborately regulated in a time- and space-dependent manner to control cytoskeletal changes. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins. RhoA and RhoC are observed only in geranylgeranylated forms; however, RhoB can be present in palmitoylated, farnesylated, and geranylgeranylated forms. RhoA and RhoC are highly relevant for tumor progression and invasiveness; however, RhoB has recently been suggested to be a tumor suppressor. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.
• smart RHO 173aa 7e-99 in ref transcript
  • Rho (Ras homology) subfamily of Ras-like small GTPases. Members of this subfamily of Ras-like small GTPases include Cdc42 and Rac, as well as Rho isoforms.
• COG COG1100 184aa 6e-32 in ref transcript
  • GTPase SAR1 and related small G proteins [General function prediction only].

RIMS2

• rs.RIMS2.F1 rs.RIMS2.R1 154 220
• NCBIGene 36.3 9699
• Single exon skipping, size difference: 66
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_001100117

• cd C2_1 121aa 3e-28 in ref transcript
  • Protein kinase C conserved region 2, subgroup 1; C2 Ca2+-binding motif present in phospholipases, protein kinases C, and synaptotagmins (amongst others); some PKCs lack calcium dependence. Particular C2s appear to bind phospholipids, inositol polyphosphates,and intracellular proteins. Two distinct C2 topologies generated by permutation of the sequence with respect to the N- and C-terminal beta strands are seen. In this subgroup, containing synaptotagmins, specific protein kinases C (PKC) subtypes and other proteins, the N-terminal beta strand occupies the position of what is the C-terminal strand in subgroup 2.
• cd C2_1 124aa 2e-22 in ref transcript
• cd PDZ_signaling 82aa 2e-11 in ref transcript
  • PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of PDZ domains an N-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in proteases.
• smart C2 104aa 5e-14 in ref transcript
  • Protein kinase C conserved region 2 (CalB). Ca2+-binding motif present in phospholipases, protein kinases C, and synaptotamins (among others). Some do not appear to contain Ca2+-binding sites. Particular C2s appear to bind phospholipids, inositol polyphosphates, and intracellular proteins. Unusual occurrence in perforin. Synaptotagmin and PLC C2s are permuted in sequence with respect to N- and C-terminal beta strands. SMART detects C2 domains using one or both of two profiles.
• smart C2 108aa 2e-12 in ref transcript
• smart PDZ 91aa 3e-11 in ref transcript
  • Domain present in PSD-95, Dlg, and ZO-1/2. Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities.
• pfam RPH3A_effector 132aa 2e-08 in ref transcript
  • Rabphilin-3A effector domain. This is a family of proteins involved in protein transport in synaptic vesicles. Rabphilin-3A has been shown to contact Rab3A, a small G protein important in neurotransmitter release, in two distinct areas.
• COG Prc 81aa 0.004 in ref transcript
  • Periplasmic protease [Cell envelope biogenesis, outer membrane].

RIMS2

• rs.RIMS2.F2 rs.RIMS2.R2 177 225
• NCBIGene 36.3 9699
• Single exon skipping, size difference: 48
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001100117

• cd C2_1 121aa 3e-28 in ref transcript
  • Protein kinase C conserved region 2, subgroup 1; C2 Ca2+-binding motif present in phospholipases, protein kinases C, and synaptotagmins (amongst others); some PKCs lack calcium dependence. Particular C2s appear to bind phospholipids, inositol polyphosphates,and intracellular proteins. Two distinct C2 topologies generated by permutation of the sequence with respect to the N- and C-terminal beta strands are seen. In this subgroup, containing synaptotagmins, specific protein kinases C (PKC) subtypes and other proteins, the N-terminal beta strand occupies the position of what is the C-terminal strand in subgroup 2.
• Changed! cd C2_1 124aa 2e-22 in ref transcript
• cd PDZ_signaling 82aa 2e-11 in ref transcript
  • PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of PDZ domains an N-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in proteases.
• smart C2 104aa 5e-14 in ref transcript
  • Protein kinase C conserved region 2 (CalB). Ca2+-binding motif present in phospholipases, protein kinases C, and synaptotamins (among others). Some do not appear to contain Ca2+-binding sites. Particular C2s appear to bind phospholipids, inositol polyphosphates, and intracellular proteins. Unusual occurrence in perforin. Synaptotagmin and PLC C2s are permuted in sequence with respect to N- and C-terminal beta strands. SMART detects C2 domains using one or both of two profiles.
• smart C2 108aa 2e-12 in ref transcript
• smart PDZ 91aa 3e-11 in ref transcript
  • Domain present in PSD-95, Dlg, and ZO-1/2. Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities.
• pfam RPH3A_effector 132aa 2e-08 in ref transcript
  • Rabphilin-3A effector domain. This is a family of proteins involved in protein transport in synaptic vesicles. Rabphilin-3A has been shown to contact Rab3A, a small G protein important in neurotransmitter release, in two distinct areas.
• COG Prc 81aa 0.004 in ref transcript
  • Periplasmic protease [Cell envelope biogenesis, outer membrane].
• Changed! cd C2_1 125aa 6e-23 in modified transcript

RLN2

• rs.RLN2.F1 rs.RLN2.R1 271 372
• NCBIGene 36.3 6019
• Single exon skipping, size difference: 101
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_134441

• Changed! cd IlGF_relaxin_like 40aa 3e-10 in ref transcript
  • IlGF_like family, relaxin_like subgroup, specific to vertebrates. Members include a number of active peptides including (pro)relaxin, mammalian Leydig cell-specific insulin-like peptide (gene INSL3), early placenta insulin-like peptide (ELIP; gene INSL4), and insulin-like peptides 5 (INSL5) and 6 (INSL6). Members of this subgroup are widely expressed in testes (INSL3, INSL6), decidua, placenta, prostate, corpus luteum, brain (various relaxins), GI tract, and kidney (INSL5) where they serve a variety of functions in parturition and development. Typically, the active forms of these peptide hormones are composed of two chains (A and B) linked by two disulfide bonds; the arrangement of four cysteines is conserved in the "A" chain: Cys1 is linked by a disulfide bond to Cys3, Cys2 and Cys4 are linked by interchain disulfide bonds to cysteines in the "B" chain. This alignment contains both chains, plus the intervening linker region, arranged as found in the propeptide form. Propeptides are cleaved to yield two separate chains linked covalently by the two disulfide bonds.
• cd IlGF_relaxin_like 24aa 5e-05 in ref transcript
• Changed! pfam Insulin 50aa 3e-08 in ref transcript
  • Insulin/IGF/Relaxin family. Superfamily includes insulins; relaxins; insulin-like growth factor; and bombyxin. All are secreted regulatory hormones. Disulfide rich, all-alpha fold. Alignment includes B chain, linker (which is processed out of the final product), and A chain.
• Changed! smart IlGF 40aa 2e-06 in ref transcript
  • Insulin / insulin-like growth factor / relaxin family. Family of proteins including insulin, relaxin, and IGFs. Insulin decreases blood glucose concentration.
• Changed! smart IlGF 37aa 3e-06 in modified transcript

RNASE1

• rs.RNASE1.F1 rs.RNASE1.R1 100 112
• NCBIGene 36.3 6035
• Alternative 3-prime, size difference: 12
• Inclusion in 5'UTR
• Reference transcript: NM_198234

• cd RNase_A_canonical 120aa 1e-39 in ref transcript
  • Canonical RNase A family includes all vertebrate homologues to the bovine pancreatic ribonuclease A (RNase A) that contain the catalytic site, necessary for RNase activity. In the human genome 8 RNases , refered to as "canonical" RNases, have been identified, pancreatic RNase (RNase 1), Eosinophil Derived Neurotoxin (SEDN/RNASE 2), Eosinophil Cationic Protein (ECP/RNase 3), RNase 4, Angiogenin (RNase 5), RNase 6 or k6, the skin derived RNase (RNase 7) and RNase 8. The eight human genes are all located in a cluster on chromosome 14. Canonical RNase A enzymes have special biological activities; for example, some stimulate the development of vascular endothelial cells, dendritic cells, and neurons, are cytotoxic/anti-tumoral and/or anti-pathogenic. RNase A is involved in endonucleolytic cleavage of 3'-phosphomononucleotides and 3'-phosphooligonucleotides ending in C-P or U-P with 2',3'-cyclic phosphate intermediates. The catalytic mechanism is a transphosphorylation of P-O 5' bonds on the 3' side of pyrimidines and subsequent hydrolysis to generate 3' phosphate groups. The canonical RNase A family proteins have a conserved catalytic triad (two histidines and one lysine). They also share 6 to 8 cysteines that form three to four disulfide bonds. Two disulfide bonds that are close to the N and C termini contribute most significantly to conformational stability. Angiogenin or RNAse 5 has been implicated in tumor-associated angiogenesis. Comparative analysis in mammals and birds indicates that the whole family may have originated from a RNase 5-like gene. This hypothesis is supported by the fact that only RNase 5-like RNases have been reported outside the mammalian class. The RNase 5 group would therefore be the most ancient form of this family, and all other members would have arisen during mammalian evolution.
• smart RNAse_Pc 124aa 1e-54 in ref transcript
  • Pancreatic ribonuclease.

RNASEN

• rs.RNASEN.F1 rs.RNASEN.R1 172 248
• NCBIGene 36.3 29102
• Single exon skipping, size difference: 76
• Inclusion in 5'UTR
• Reference transcript: NM_013235

• cd RIBOc 133aa 1e-32 in ref transcript
  • RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in post-transcriptional control of mRNA stability and translational efficiency. It is involved in the processing of ribosomal RNA precursors. Prokaryotic RNAse III also plays a role in the maturation of tRNA precursors and in the processing of phage and plasmid transcripts. Eukaryotic RNase III's participate (through direct cleavage) in rRNA processing, in processing of small nucleolar RNAs (snoRNAs) and snRNA's (components of the spliceosome). In eukaryotes RNase III or RNaseIII like enzymes such as Dicer are involved in RNAi (RNA interference) and miRNA (micro-RNA) gene silencing.
• cd RIBOc 115aa 2e-29 in ref transcript
• cd DSRM 72aa 1e-11 in ref transcript
  • Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, RNases H1, and dsRNA dependent adenosine deaminases.
• TIGR RNaseIII 222aa 2e-47 in ref transcript
  • This family consists of bacterial examples of ribonuclease III. This enzyme cleaves double-stranded rRNA. It is involved in processing ribosomal RNA precursors. It is found even in minimal genones such as Mycoplasma genitalium and Buchnera aphidicola, and in some cases has been shown to be an essential gene. These bacterial proteins contain a double-stranded RNA binding motif (pfam00035) and a ribonuclease III domain (pfam00636). Eukaryotic homologs tend to be much longer proteins with additional domains, localized to the nucleus, and not included in this family.
• smart RIBOc 133aa 7e-33 in ref transcript
  • Ribonuclease III family.
• PRK rnc 229aa 1e-51 in ref transcript
  • ribonuclease III; Reviewed.
• PRK rnc 109aa 8e-27 in ref transcript

RNASEN

• rs.RNASEN.F2 rs.RNASEN.R2 131 242
• NCBIGene 36.3 29102
• Single exon skipping, size difference: 111
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_013235

• cd RIBOc 133aa 1e-32 in ref transcript
  • RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in post-transcriptional control of mRNA stability and translational efficiency. It is involved in the processing of ribosomal RNA precursors. Prokaryotic RNAse III also plays a role in the maturation of tRNA precursors and in the processing of phage and plasmid transcripts. Eukaryotic RNase III's participate (through direct cleavage) in rRNA processing, in processing of small nucleolar RNAs (snoRNAs) and snRNA's (components of the spliceosome). In eukaryotes RNase III or RNaseIII like enzymes such as Dicer are involved in RNAi (RNA interference) and miRNA (micro-RNA) gene silencing.
• cd RIBOc 115aa 2e-29 in ref transcript
• cd DSRM 72aa 1e-11 in ref transcript
  • Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, RNases H1, and dsRNA dependent adenosine deaminases.
• TIGR RNaseIII 222aa 2e-47 in ref transcript
  • This family consists of bacterial examples of ribonuclease III. This enzyme cleaves double-stranded rRNA. It is involved in processing ribosomal RNA precursors. It is found even in minimal genones such as Mycoplasma genitalium and Buchnera aphidicola, and in some cases has been shown to be an essential gene. These bacterial proteins contain a double-stranded RNA binding motif (pfam00035) and a ribonuclease III domain (pfam00636). Eukaryotic homologs tend to be much longer proteins with additional domains, localized to the nucleus, and not included in this family.
• smart RIBOc 133aa 7e-33 in ref transcript
  • Ribonuclease III family.
• PRK rnc 229aa 1e-51 in ref transcript
  • ribonuclease III; Reviewed.
• PRK rnc 109aa 8e-27 in ref transcript

RNF13

• rs.RNF13.F1 rs.RNF13.R1 90 100
• NCBIGene 36.3 11342
• Alternative 5-prime, size difference: 10
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_007282

• Changed! cd PA_C_RZF_like 158aa 8e-50 in ref transcript
  • PA_C-RZF_ like: Protease-associated (PA) domain C_RZF-like. This group includes various PA domain-containing proteins similar to C-RZF (chicken embryo RING zinc finger) protein. These proteins contain a C3H2C3 RING finger. C-RZF is expressed in embryo cells and is restricted mainly to brain and heart, it is localized to both the nucleus and endosomes. Additional C3H2C3 RING finger proteins belonging to this group, include Arabidopsis ReMembR-H2 protein and mouse sperizin. ReMembR-H2 is likely to be an integral membrane protein, and to traffic through the endosomal pathway. Sperizin is expressed in haploid germ cells and localized in the cytoplasm, it may participate in spermatogenesis. The significance of the PA domain to these proteins has not been ascertained. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate.
• Changed! cd RING 46aa 1e-10 in ref transcript
  • RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H).
• Changed! pfam PA 92aa 2e-11 in ref transcript
  • PA domain. The PA (Protease associated) domain is found as an insert domain in diverse proteases. The PA domain is also found in a plant vacuolar sorting receptor and members of the RZF family. It has been suggested that this domain forms a lid-like structure that covers the active site in active proteases, and is involved in protein recognition in vacuolar sorting receptors.
• Changed! smart RING 42aa 7e-09 in ref transcript
  • Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s).
• Changed! COG COG5540 253aa 1e-11 in ref transcript
  • RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones].
• Changed! cd PA_C_RZF_like 116aa 1e-37 in modified transcript
• Changed! pfam PA 66aa 7e-08 in modified transcript

RORA

• rs.RORA.F1 rs.RORA.R1 215 239
• NCBIGene 36.3 6095
• Mutually exclusive exon skipping, size difference: 24
• Inclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_134260

• cd NR_LBD_ROR_like 241aa 1e-127 in ref transcript
  • The ligand binding domain of Retinoid-related orphan receptors, of the nuclear receptor superfamily. The ligand binding domain (LBD) of Retinoid-related orphan receptors (RORs): Retinoid-related orphan receptors (RORs) are transcription factors belonging to the nuclear receptor superfamily. RORs are key regulators of many physiological processes during embryonic development. RORs bind as monomers to specific ROR response elements (ROREs) consisting of the consensus core motif AGGTCA preceded by a 5-bp A/T-rich sequence. Transcription regulation by RORs is mediated through certain corepressors, as well as coactivators. There are three subtypes of retinoid-related orphan receptors (RORs), alpha, beta, and gamma that differ only in N-terminal sequence and are distributed in distinct tissues. RORalpha plays a key role in the development of the cerebellum, particularly in the regulation of the maturation and survival of Purkinje cells. RORbeta expression is largely restricted to several regions of the brain, the retina, and pineal gland. RORgamma is essential for lymph node organogenesis. Recently, it has been su ggested that cholesterol or a cholesterol derivative is the natural ligand of RORalpha. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, retinoid-related orphan receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).
• pfam zf-C4 76aa 6e-39 in ref transcript
  • Zinc finger, C4 type (two domains). In nearly all cases, this is the DNA binding domain of a nuclear hormone receptor. The alignment contains two Zinc finger domains that are too dissimilar to be aligned with each other.
• pfam Hormone_recep 183aa 3e-33 in ref transcript
  • Ligand-binding domain of nuclear hormone receptor. This all helical domain is involved in binding the hormone in these receptors.

RPL14

• rs.RPL14.F1 rs.RPL14.R1 122 233
• NCBIGene 36.3 9045
• Alternative 5-prime, size difference: 111
• Exclusion of the protein initiation site
• Reference transcript: NM_001034996

• pfam Ribosomal_L14e 77aa 1e-20 in ref transcript
  • Ribosomal protein L14. This family includes the eukaryotic ribosomal protein L14.
• PTZ PTZ00065 123aa 3e-19 in ref transcript
  • 60S ribosomal protein L14; Provisional.

RPP14

• rs.RPP14.F1 rs.RPP14.R1 135 369
• NCBIGene 36.3 11102
• Alternative 5-prime, size difference: 234
• Exclusion in 5'UTR
• Reference transcript: NM_001098783

• cd R_hydratase 127aa 1e-37 in ref transcript
  • (R)-hydratase [(R)-specific enoyl-CoA hydratase] catalyzes the hydration of trans-2-enoyl CoA to (R)-3-hydroxyacyl-CoA as part of the PHA (polyhydroxyalkanoate) biosynthetic pathway. (R)-hydratase contains a hot-dog fold similar to those of thioesterase II, and beta-hydroxydecanoyl-ACP dehydratase, MaoC dehydratase, Hydratase-Dehydrogenase-Epimerase protein (HDE), and the fatty acid synthase beta subunit. The active site lies within a substrate-binding tunnel formed by the (R)-hydratase homodimer. A subset of the bacterial (R)-hydratases contain a C-terminal phosphotransacetylase (PTA) domain.
• pfam MaoC_dehydratas 108aa 2e-15 in ref transcript
  • MaoC like domain. The maoC gene is part of a operon with maoA which is involved in the synthesis of monoamine oxidase. The MaoC protein is found to share similarity with a wide variety of enzymes; estradiol 17 beta-dehydrogenase 4, peroxisomal hydratase-dehydrogenase-epimerase, fatty acid synthase beta subunit. Several bacterial proteins that are composed solely of this domain have (R)-specific enoyl-CoA hydratase activity. This domain is also present in the NodN nodulation protein N.
• PRK PRK08190 131aa 5e-28 in ref transcript
  • bifunctional enoyl-CoA hydratase/phosphate acetyltransferase; Validated.

RPP38

• rs.RPP38.F1 rs.RPP38.R1 104 461
• NCBIGene 36.3 10557
• Alternative 5-prime, size difference: 357
• Exclusion in 5'UTR
• Reference transcript: NM_183005

• pfam Ribosomal_L7Ae 79aa 0.005 in ref transcript
  • Ribosomal protein L7Ae/L30e/S12e/Gadd45 family. This family includes: Ribosomal L7A from metazoa, Ribosomal L8-A and L8-B from fungi, 30S ribosomal protein HS6 from archaebacteria, 40S ribosomal protein S12 from eukaryotes, Ribosomal protein L30 from eukaryotes and archaebacteria. Gadd45 and MyD118.

RPS15A

• rs.RPS15A.F1 rs.RPS15A.R1 474 540
• NCBIGene 36.3 6210
• Alternative 5-prime, size difference: 66
• Exclusion in 5'UTR
• Reference transcript: NM_001019

• pfam Ribosomal_S8 125aa 3e-37 in ref transcript
  • Ribosomal protein S8.
• PTZ PTZ00158 130aa 8e-68 in ref transcript
  • 40S ribosomal protein S15A; Provisional.

RPS24

• rs.RPS24.F1 rs.RPS24.R1 112 134
• NCBIGene 36.3 6229
• Single exon skipping, size difference: 22
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_001026

• pfam Ribosomal_S24e 83aa 4e-16 in ref transcript
  • Ribosomal protein S24e.
• PTZ PTZ00071 130aa 9e-29 in ref transcript
  • 40S ribosomal protein S24; Provisional.

RRBP1

• rs.RRBP1.F1 rs.RRBP1.R1 112 189
• NCBIGene 36.3 6238
• Single exon skipping, size difference: 77
• Exclusion in 5'UTR
• Reference transcript: NM_001042576

• pfam Rib_recp_KP_reg 144aa 7e-12 in ref transcript
  • Ribosome receptor lysine/proline rich region. This highly conserved region is found towards the C-terminus of the transmembrane domain. The function is unclear.
• TIGR SMC_prok_A 286aa 1e-04 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent.
• TIGR SMC_prok_B 340aa 5e-04 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• PRK PRK00409 94aa 0.003 in ref transcript
  • recombination and DNA strand exchange inhibitor protein; Reviewed.
• PRK PRK02224 456aa 0.009 in ref transcript
  • chromosome segregation protein; Provisional.

RSRC2

• rs.RSRC2.F1 rs.RSRC2.R1 100 122
• NCBIGene 36.3 65117
• Alternative 3-prime, size difference: 22
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_198261

RTKN

• rs.RTKN.F1 rs.RTKN.R1 102 529
• NCBIGene 36.3 6242
• Single exon skipping, size difference: 427
• Exclusion of the protein initiation site
• Reference transcript: NM_033046

• cd PH 99aa 5e-06 in ref transcript
  • Pleckstrin homology (PH) domain. PH domains are only found in eukaryotes. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes.
• Changed! smart Hr1 56aa 1e-08 in ref transcript
  • Rho effector or protein kinase C-related kinase homology region 1 homologues. Alpha-helical domain found in vertebrate PRK1 and yeast PKC1 protein kinases C. The HR1 in rhophilin bind RhoGTP; those in PRK1 bind RhoA and RhoB. Also called RBD - Rho-binding domain.
• smart PH 99aa 1e-07 in ref transcript
  • Pleckstrin homology domain. Domain commonly found in eukaryotic signalling proteins. The domain family possesses multiple functions including the abilities to bind inositol phosphates, and various proteins. PH domains have been found to possess inserted domains (such as in PLC gamma, syntrophins) and to be inserted within other domains. Mutations in Brutons tyrosine kinase (Btk) within its PH domain cause X-linked agammaglobulinaemia (XLA) in patients. Point mutations cluster into the positively charged end of the molecule around the predicted binding site for phosphatidylinositol lipids.
• Changed! smart Hr1 41aa 5e-04 in modified transcript

RTN2

• rs.RTN2.F1 rs.RTN2.R1 157 376
• NCBIGene 36.3 6253
• Single exon skipping, size difference: 219
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_005619

• Changed! pfam Reticulon 171aa 1e-30 in ref transcript
  • Reticulon. Reticulon, also know as neuroendocrine-specific protein (NSP), is a protein of unknown function which associates with the endoplasmic reticulum. This family represents the C-terminal domain of the three reticulon isoforms and their homologues.
• Changed! pfam Reticulon 171aa 6e-32 in modified transcript

RUFY2

• rs.RUFY2.F1 rs.RUFY2.R1 160 262
• NCBIGene 36.3 55680
• Single exon skipping, size difference: 102
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_017987

• cd FYVE 53aa 2e-19 in ref transcript
  • FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;.
• pfam FYVE 62aa 2e-24 in ref transcript
  • FYVE zinc finger. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn++ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. We have included members which do not conserve these histidine residues but are clearly related.
• TIGR SMC_prok_B 285aa 3e-13 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• Changed! COG Smc 308aa 1e-12 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].
• PTZ PTZ00303 65aa 2e-04 in ref transcript
  • phosphatidylinositol kinase; Provisional.
• Changed! COG Smc 305aa 2e-12 in modified transcript

RUNX2

• rs.RUNX2.F1 rs.RUNX2.R1 310 376
• NCBIGene 36.3 860
• Single exon skipping, size difference: 66
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001024630

• pfam Runt 134aa 9e-74 in ref transcript
  • Runt domain.
• pfam RunxI 78aa 2e-32 in ref transcript
  • Runx inhibition domain. This domain lies to the C-terminus of Runx-related transcription factors and homologous proteins (AML, CBF-alpha, PEBP2). Its function might be to interact with functional cofactors.

RUSC1

• rs.RUSC1.F1 rs.RUSC1.R1 121 439
• NCBIGene 36.3 23623
• Alternative 3-prime, size difference: 318
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001105203

• cd SH3 50aa 3e-08 in ref transcript
  • Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
• Changed! pfam RUN 137aa 5e-21 in ref transcript
  • RUN domain. This domain is present in several proteins that are linked to the functions of GTPases in the Rap and Rab families. They could hence play important roles in multiple Ras-like GTPase signalling pathways. The domain is comprises six conserved regions, which in some proteins have considerable insertions between them. The domain core is thought to take up a predominantly alpha fold, with basic amino acids in regions A and D possibly playing a functional role in interactions with Ras GTPases.
• smart SH3 53aa 6e-10 in ref transcript
  • Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.
• Changed! pfam RUN 92aa 5e-16 in modified transcript

RUSC1

• rs.RUSC1.F2 rs.RUSC1.R2 138 181
• NCBIGene 36.3 23623
• Alternative 5-prime, size difference: 43
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_001105205

• Changed! cd SH3 50aa 7e-09 in ref transcript
  • Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
• Changed! pfam RUN 137aa 1e-20 in ref transcript
  • RUN domain. This domain is present in several proteins that are linked to the functions of GTPases in the Rap and Rab families. They could hence play important roles in multiple Ras-like GTPase signalling pathways. The domain is comprises six conserved regions, which in some proteins have considerable insertions between them. The domain core is thought to take up a predominantly alpha fold, with basic amino acids in regions A and D possibly playing a functional role in interactions with Ras GTPases.
• Changed! smart SH3 53aa 1e-10 in ref transcript
  • Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.

RYR1

• rs.RYR1.F1 rs.RYR1.R1 125 140
• NCBIGene 36.3 6261
• Single exon skipping, size difference: 15
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000540

• pfam Ins145_P3_rec 199aa 1e-71 in ref transcript
  • Inositol 1,4,5-trisphosphate/ryanodine receptor. This domain corresponds to the ligand binding region on inositol 1,4,5-trisphosphate receptor, and the N terminal region of the ryanodine receptor. Both receptors are involved in Ca2+ release. They can couple to the activation of neurotransmitter-gated receptors and voltage-gated Ca2+ channels on the plasma membrane, thus allowing the endoplasmic reticulum discriminate between different types of neuronal activity.
• pfam RYDR_ITPR 204aa 1e-62 in ref transcript
  • RIH domain. The RIH (RyR and IP3R Homology) domain is an extracellular domain from two types of calcium channels. This region is found in the ryanodine receptor and the inositol-1,4,5- trisphosphate receptor. This domain may form a binding site for IP3.
• pfam MIR 179aa 3e-51 in ref transcript
  • MIR domain. The MIR (protein mannosyltransferase, IP3R and RyR) domain is a domain that may have a ligand transferase function.
• pfam RYDR_ITPR 209aa 2e-49 in ref transcript
• pfam RIH_assoc 133aa 7e-42 in ref transcript
  • RyR and IP3R Homology associated. This eukaryotic domain is found in ryanodine receptors (RyR) and inositol 1,4,5-trisphosphate receptors (IP3R) which together form a superfamily of homotetrameric ligand-gated intracellular Ca2+ channels. There seems to be no known function for this domain. Also see the IP3-binding domain pfam01365 and pfam02815.
• pfam RyR 95aa 4e-41 in ref transcript
  • RyR domain. This domain is called RyR for Ryanodine receptor. The domain is found in four copies in the ryanodine receptor. The function of this domain is unknown.
• pfam RyR 95aa 3e-39 in ref transcript
• pfam RR_TM4-6 225aa 3e-39 in ref transcript
  • Ryanodine Receptor TM 4-6. This region covers TM regions 4-6 of the ryanodine receptor 1 family.
• pfam RyR 90aa 3e-38 in ref transcript
• pfam RyR 89aa 4e-31 in ref transcript
• smart SPRY 123aa 1e-29 in ref transcript
  • Domain in SPla and the RYanodine Receptor. Domain of unknown function. Distant homologues are domains in butyrophilin/marenostrin/pyrin homologues.
• pfam SPRY 137aa 9e-24 in ref transcript
  • SPRY domain. SPRY Domain is named from SPla and the RYanodine Receptor. Domain of unknown function. Distant homologues are domains in butyrophilin/marenostrin/pyrin homologues.
• pfam SPRY 141aa 6e-23 in ref transcript

S100A4

• rs.S100A4.F1 rs.S100A4.R1 136 185
• NCBIGene 36.3 6275
• Single exon skipping, size difference: 49
• Exclusion in 5'UTR
• Reference transcript: NM_019554

• cd S-100 87aa 6e-25 in ref transcript
  • S-100: S-100 domain, which represents the largest family within the superfamily of proteins carrying the Ca-binding EF-hand motif. Note that this S-100 hierarchy contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100 proteins are expressed exclusively in vertebrates, and are implicated in intracellular and extracellular regulatory activities. Intracellularly, S100 proteins act as Ca-signaling or Ca-buffering proteins. The most unusual characteristic of certain S100 proteins is their occurrence in extracellular space, where they act in a cytokine-like manner through RAGE, the receptor for advanced glycation products. Structural data suggest that many S100 members exist within cells as homo- or heterodimers and even oligomers; oligomerization contributes to their functional diversification. Upon binding calcium, most S100 proteins change conformation to a more open structure exposing a hydrophobic cleft. This hydrophobic surface represents the interaction site of S100 proteins with their target proteins. There is experimental evidence showing that many S100 proteins have multiple binding partners with diverse mode of interaction with different targets. In addition to S100 proteins (such as S100A1,-3,-4,-6,-7,-10,-11,and -13), this group includes the ''fused'' gene family, a group of calcium binding S100-related proteins. The ''fused'' gene family includes multifunctional epidermal differentiation proteins - profilaggrin, trichohyalin, repetin, hornerin, and cornulin; functionally these proteins are associated with keratin intermediate filaments and partially crosslinked to the cell envelope. These ''fused'' gene proteins contain N-terminal sequence with two Ca-binding EF-hands motif, which may be associated with calcium signaling in epidermal cells and autoprocessing in a calcium-dependent manner. In contrast to S100 proteins, "fused" gene family proteins contain an extraordinary high number of almost perfect peptide repeats with regular array of polar and charged residues similar to many known cell envelope proteins.
• pfam S_100 44aa 2e-13 in ref transcript
  • S-100/ICaBP type calcium binding domain. The S-100 domain is a subfamily of the EF-hand calcium binding proteins.

SCARB1

• rs.SCARB1.F1 rs.SCARB1.R1 184 313
• NCBIGene 36.3 949
• Single exon skipping, size difference: 129
• Exclusion of the stop codon
• Reference transcript: NM_005505

• pfam CD36 414aa 1e-168 in ref transcript
  • CD36 family. The CD36 family is thought to be a novel class of scavenger receptors. There is also evidence suggesting a possible role in signal transduction. CD36 is involved in cell adhesion.

SCARF2

• rs.SCARF2.F1 rs.SCARF2.R1 100 115
• NCBIGene 36.3 91179
• Alternative 3-prime, size difference: 15
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_153334

SCN3A

• rs.SCN3A.F1 rs.SCN3A.R1 163 310
• NCBIGene 36.3 6328
• Alternative 5-prime, size difference: 147
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_006922

• pfam Na_trans_assoc 221aa 1e-65 in ref transcript
  • Sodium ion transport-associated. Members of this family contain a region found exclusively in eukaryotic sodium channels or their subunits, many of which are voltage-gated. Members very often also contain between one and four copies of pfam00520 and, less often, one copy of pfam00612.
• pfam Ion_trans 226aa 9e-34 in ref transcript
  • Ion transport protein. This family contains Sodium, Potassium, Calcium ion channels. This family is 6 transmembrane helices in which the last two helices flank a loop which determines ion selectivity. In some sub-families (e.g. Na channels) the domain is repeated four times, whereas in others (e.g. K channels) the protein forms as a tetramer in the membrane. A bacterial structure of the protein is known for the last two helices but is not the Pfam family due to it lacking the first four helices.
• pfam Ion_trans 159aa 5e-25 in ref transcript
• pfam Ion_trans 141aa 5e-25 in ref transcript
• pfam Ion_trans 178aa 1e-24 in ref transcript
• pfam Ion_trans 72aa 2e-13 in ref transcript

SCN5A

• rs.SCN5A.F1 SCN5A.R5 271 325
• NCBIGene 36.3 6331
• Single exon skipping, size difference: 54
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_198056

• pfam Na_trans_assoc 265aa 7e-60 in ref transcript
  • Sodium ion transport-associated. Members of this family contain a region found exclusively in eukaryotic sodium channels or their subunits, many of which are voltage-gated. Members very often also contain between one and four copies of pfam00520 and, less often, one copy of pfam00612.
• pfam Ion_trans 209aa 2e-29 in ref transcript
  • Ion transport protein. This family contains Sodium, Potassium, Calcium ion channels. This family is 6 transmembrane helices in which the last two helices flank a loop which determines ion selectivity. In some sub-families (e.g. Na channels) the domain is repeated four times, whereas in others (e.g. K channels) the protein forms as a tetramer in the membrane. A bacterial structure of the protein is known for the last two helices but is not the Pfam family due to it lacking the first four helices.
• Changed! pfam Ion_trans 229aa 8e-26 in ref transcript
• pfam Ion_trans 123aa 2e-25 in ref transcript
• pfam Ion_trans 176aa 5e-23 in ref transcript
• pfam Ion_trans 74aa 2e-13 in ref transcript
• Changed! pfam Ion_trans 211aa 9e-21 in modified transcript

SCYL1

• rs.SCYL1.F1 rs.SCYL1.R1 123 174
• NCBIGene 36.3 57410
• Alternative 3-prime, size difference: 51
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_020680

• cd S_TKc 228aa 3e-16 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• pfam Pkinase 189aa 1e-09 in ref transcript
  • Protein kinase domain.
• PTZ PTZ00267 251aa 5e-04 in ref transcript
  • NIMA-related protein kinase; Provisional.

SDCBP

• rs.SDCBP.F1 rs.SDCBP.R1 102 120
• NCBIGene 36.3 6386
• Alternative 5-prime, size difference: 18
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001007067

• cd PDZ_signaling 80aa 4e-13 in ref transcript
  • PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of PDZ domains an N-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in proteases.
• cd PDZ_signaling 74aa 3e-09 in ref transcript
• smart PDZ 83aa 2e-10 in ref transcript
  • Domain present in PSD-95, Dlg, and ZO-1/2. Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities.
• smart PDZ 76aa 1e-07 in ref transcript
• COG Prc 127aa 7e-07 in ref transcript
  • Periplasmic protease [Cell envelope biogenesis, outer membrane].

SEC24B

• rs.SEC24B.F1 FOX.SEC24B.R1 220 325
• NCBIGene 36.3 10427
• Single exon skipping, size difference: 105
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_006323

• cd Sec24-like 244aa 1e-100 in ref transcript
  • Sec24-like: Protein and membrane traffic in eukaryotes is mediated by at least in part by the budding and fusion of intracellular transport vesicles that selectively carry cargo proteins and lipids from donor to acceptor organelles. The two main classes of vesicular carriers within the endocytic and the biosynthetic pathways are COP- and clathrin-coated vesicles. Formation of COPII vesicles requires the ordered assembly of the coat built from several cytosolic components GTPase Sar1, complexes of Sec23-Sec24 and Sec13-Sec31. The process is initiated by the conversion of GDP to GTP by the GTPase Sar1 which then recruits the heterodimeric complex of Sec23 and Sec24. This heterodimeric complex generates the pre-budding complex. The final step leading to membrane deformation and budding of COPII-coated vesicles is carried by the heterodimeric complex Sec13-Sec31. The members of this CD belong to the Sec23-like family. Sec 24 is very similar to Sec23. The Sec23 and Sec24 polypeptides fold into five distinct domains: a beta-barrel, a zinc finger, a vWA or trunk, an all helical region and a carboxy Gelsolin domain. The members of this subgroup carry a partial MIDAS motif and have the overall Para-Rossmann type fold that is characteristic of this superfamily.
• pfam Sec23_trunk 240aa 5e-90 in ref transcript
  • Sec23/Sec24 trunk domain. COPII-coated vesicles carry proteins from the endoplasmic reticulum to the Golgi complex. This vesicular transport can be reconstituted by using three cytosolic components containing five proteins: the small GTPase Sar1p, the Sec23p/24p complex, and the Sec13p/Sec31p complex. This domain is known as the trunk domain and has an alpha/beta vWA fold and forms the dimer interface.
• pfam Sec23_helical 103aa 2e-29 in ref transcript
  • Sec23/Sec24 helical domain. COPII-coated vesicles carry proteins from the endoplasmic reticulum to the Golgi complex. This vesicular transport can be reconstituted by using three cytosolic components containing five proteins: the small GTPase Sar1p, the Sec23p/24p complex, and the Sec13p/Sec31p complex. This domain is composed of five alpha helices.
• pfam Sec23_BS 85aa 1e-28 in ref transcript
  • Sec23/Sec24 beta-sandwich domain.
• pfam zf-Sec23_Sec24 39aa 2e-12 in ref transcript
  • Sec23/Sec24 zinc finger. COPII-coated vesicles carry proteins from the endoplasmic reticulum to the Golgi complex. This vesicular transport can be reconstituted by using three cytosolic components containing five proteins: the small GTPase Sar1p, the Sec23p/24p complex, and the Sec13p/Sec31p complex. This domain is found to be zinc binding domain.
• pfam Gelsolin 75aa 7e-09 in ref transcript
  • Gelsolin repeat.
• COG COG5028 797aa 1e-143 in ref transcript
  • Vesicle coat complex COPII, subunit SEC24/subunit SFB2/subunit SFB3 [Intracellular trafficking and secretion].

SEC31A

• rs.SEC31A.F1 rs.SEC31A.R1 155 200
• NCBIGene 36.3 22872
• Alternative 5-prime, size difference: 45
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001077207

• cd WD40 244aa 4e-22 in ref transcript
  • WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.
• COG COG2319 306aa 6e-15 in ref transcript
  • FOG: WD40 repeat [General function prediction only].

SEMA6D

• rs.SEMA6D.F1 rs.SEMA6D.R1 152 209
• NCBIGene 36.3 80031
• Single exon skipping, size difference: 57
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_153618

• pfam Sema 418aa 1e-121 in ref transcript
  • Sema domain. The Sema domain occurs in semaphorins, which are a large family of secreted and transmembrane proteins, some of which function as repellent signals during axon guidance. Sema domains also occur in the hepatocyte growth factor receptor and the human Plexin-A3 precursor.
• pfam PSI 45aa 7e-07 in ref transcript
  • Plexin repeat. A cysteine rich repeat found in several different extracellular receptors. The function of the repeat is unknown. Three copies of the repeat are found Plexin. Two copies of the repeat are found in mahogany protein. A related Caenorhabditis elegans protein contains four copies of the repeat. The Met receptor contains a single copy of the repeat. The Pfam alignment shows 6 conserved cysteine residues that may form three conserved disulphide bridges, whereas shows 8 conserved cysteines. The pattern of conservation suggests that cysteines 5 and 7 (that are not absolutely conserved) form a disulphide bridge (Personal observation. A Bateman).
• pfam DUF1043 111aa 0.007 in ref transcript
  • Protein of unknown function (DUF1043). This family consists of several hypothetical bacterial proteins of unknown function.

SEMA6D

• rs.SEMA6D.F2 rs.SEMA6D.R2 342 475
• NCBIGene 36.3 80031
• Alternative 5-prime, size difference: 133
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_153618

• pfam Sema 418aa 1e-121 in ref transcript
  • Sema domain. The Sema domain occurs in semaphorins, which are a large family of secreted and transmembrane proteins, some of which function as repellent signals during axon guidance. Sema domains also occur in the hepatocyte growth factor receptor and the human Plexin-A3 precursor.
• pfam PSI 45aa 7e-07 in ref transcript
  • Plexin repeat. A cysteine rich repeat found in several different extracellular receptors. The function of the repeat is unknown. Three copies of the repeat are found Plexin. Two copies of the repeat are found in mahogany protein. A related Caenorhabditis elegans protein contains four copies of the repeat. The Met receptor contains a single copy of the repeat. The Pfam alignment shows 6 conserved cysteine residues that may form three conserved disulphide bridges, whereas shows 8 conserved cysteines. The pattern of conservation suggests that cysteines 5 and 7 (that are not absolutely conserved) form a disulphide bridge (Personal observation. A Bateman).
• Changed! pfam DUF1043 111aa 0.007 in ref transcript
  • Protein of unknown function (DUF1043). This family consists of several hypothetical bacterial proteins of unknown function.

SENP6

• rs.SENP6.F1 rs.SENP6.R1 121 142
• NCBIGene 36.3 26054
• Single exon skipping, size difference: 21
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_015571

• pfam Peptidase_C48 120aa 9e-10 in ref transcript
  • Ulp1 protease family, C-terminal catalytic domain. This domain contains the catalytic triad Cys-His-Asn.
• pfam Peptidase_C48 95aa 5e-08 in ref transcript
• COG ULP1 112aa 3e-18 in ref transcript
  • Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones].
• COG ULP1 91aa 2e-06 in ref transcript

SENP7

• rs.SENP7.F1 rs.SENP7.R1 191 386
• NCBIGene 36.3 57337
• Single exon skipping, size difference: 195
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_020654

• pfam Peptidase_C48 242aa 3e-20 in ref transcript
  • Ulp1 protease family, C-terminal catalytic domain. This domain contains the catalytic triad Cys-His-Asn.
• COG ULP1 114aa 7e-21 in ref transcript
  • Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones].
• COG ULP1 81aa 0.009 in ref transcript

SEPT8

• rs.SEPT8.F1 rs.SEPT8.R1 137 405
• NCBIGene 36.3 23176
• Alternative 3-prime, size difference: 268
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_001098812

• cd CDC_Septin 269aa 1e-110 in ref transcript
  • CDC/Septin. Septins are a conserved family of GTP-binding proteins associated with diverse processes in dividing and non-dividing cells. They were first discovered in the budding yeast S. cerevisiae as a set of genes (CDC3, CDC10, CDC11 and CDC12) required for normal bud morphology. Septins are also present in metazoan cells, where they are required for cytokinesis in some systems, and implicated in a variety of other processes involving organization of the cell cortex and exocytosis. In humans, 12 septin genes generate dozens of polypeptides, many of which comprise heterooligomeric complexes. Since septin mutants are commonly defective in cytokinesis and formation of the neck formation of the neck filaments/septin rings, septins have been considered to be the primary constituents of the neck filaments. Septins belong to the GTPase superfamily for their conserved GTPase motifs and enzymatic activities.
• pfam Septin 268aa 3e-84 in ref transcript
  • Septin. Members of this family include CDC3, CDC10, CDC11 and CDC12/Septin. Members of this family bind GTP. As regards the septins, these are polypeptides of 30-65kDa with three characteristic GTPase motifs (G-1, G-3 and G-4) that are similar to those of the Ras family. The G-4 motif is strictly conserved with a unique septin consensus of AKAD. Most septins are thought to have at least one coiled-coil region, which in some cases is necessary for intermolecular interactions that allow septins to polymerise to form rod-shaped complexes. In turn, these are arranged into tandem arrays to form filaments. They are multifunctional proteins, with roles in cytokinesis, sporulation, germ cell development, exocytosis and apoptosis.
• COG CDC3 322aa 6e-74 in ref transcript
  • Septin family protein [Cell division and chromosome partitioning / Cytoskeleton].

SERBP1

• rs.SERBP1.F1 rs.SERBP1.R1 103 148
• NCBIGene 36.3 26135
• Alternative 3-prime, size difference: 45
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001018067

• Changed! pfam HABP4_PAI-RBP1 125aa 2e-16 in ref transcript
  • Hyaluronan / mRNA binding family. This family includes the HABP4 family of hyaluronan-binding proteins, and the PAI-1 mRNA-binding protein, PAI-RBP1. HABP4 has been observed to bind hyaluronan (a glucosaminoglycan), but it is not known whether this is its primary role in vivo. It has also been observed to bind RNA, but with a lower affinity than that for hyaluronan. PAI-1 mRNA-binding protein specifically binds the mRNA of type-1 plasminogen activator inhibitor (PAI-1), and is thought to be involved in regulation of mRNA stability. However, in both cases, the sequence motifs predicted to be important for ligand binding are not conserved throughout the family, so it is not known whether members of this family share a common function.
• Changed! pfam HABP4_PAI-RBP1 110aa 9e-18 in modified transcript

SERPINB8

• rs.SERPINB8.F1 rs.SERPINB8.R1 100 117
• NCBIGene 36.3 5271
• Alternative 5-prime, size difference: 17
• Exclusion in 5'UTR
• Reference transcript: NM_198833

• cd PAI-2 371aa 1e-137 in ref transcript
  • Plasminogen Activator Inhibitor-2 (PAI-2). PAI-2 is a serine protease inhibitor that belongs to the ov-serpin branch of the serpin superfamily. It is is an effective inhibitor of urinary plasminogen activator (urokinase or uPA) and is involved in cell differentiation, tissue growth and regeneration.
• smart SERPIN 362aa 1e-116 in ref transcript
  • SERine Proteinase INhibitors.
• COG COG4826 372aa 1e-60 in ref transcript
  • Serine protease inhibitor [Posttranslational modification, protein turnover, chaperones].

SEZ6

• rs.SEZ6.F1 rs.SEZ6.R1 103 119
• NCBIGene 36.3 124925
• Alternative 3-prime, size difference: 16
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_178860

• cd CUB 111aa 9e-19 in ref transcript
  • CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.
• cd CUB 109aa 6e-16 in ref transcript
• cd CCP 57aa 1e-10 in ref transcript
  • Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR); The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function.
• cd CCP 59aa 2e-08 in ref transcript
• cd CCP 60aa 1e-07 in ref transcript
• cd CCP 56aa 2e-06 in ref transcript
• cd CCP 57aa 3e-04 in ref transcript
• smart CUB 99aa 1e-15 in ref transcript
  • Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. This domain is found mostly among developmentally-regulated proteins. Spermadhesins contain only this domain.
• smart CUB 100aa 1e-14 in ref transcript
• pfam Sushi 56aa 2e-12 in ref transcript
  • Sushi domain (SCR repeat).
• smart CCP 60aa 7e-08 in ref transcript
  • Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR). The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. A missense mutation in seventh CCP domain causes deficiency of the b subunit of factor XIII.
• smart CCP 58aa 7e-08 in ref transcript
• pfam Sushi 55aa 5e-07 in ref transcript
• smart CCP 56aa 4e-05 in ref transcript

SEZ6L2

• rs.SEZ6L2.F1 rs.SEZ6L2.R1 123 333
• NCBIGene 36.3 26470
• Alternative 3-prime, size difference: 210
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_201575

• cd CUB 91aa 6e-11 in ref transcript
  • CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.
• cd CUB 69aa 7e-11 in ref transcript
• cd CCP 57aa 4e-09 in ref transcript
  • Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR); The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function.
• cd CUB 113aa 3e-08 in ref transcript
• cd CCP 59aa 3e-08 in ref transcript
• cd CCP 60aa 2e-07 in ref transcript
• cd CCP 56aa 2e-06 in ref transcript
• pfam CUB 91aa 2e-08 in ref transcript
  • CUB domain.
• smart CCP 56aa 3e-08 in ref transcript
  • Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR). The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. A missense mutation in seventh CCP domain causes deficiency of the b subunit of factor XIII.
• smart CCP 56aa 5e-08 in ref transcript
• pfam Sushi 58aa 1e-07 in ref transcript
  • Sushi domain (SCR repeat).
• smart CCP 60aa 3e-07 in ref transcript
• smart CUB 59aa 3e-06 in ref transcript
  • Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. This domain is found mostly among developmentally-regulated proteins. Spermadhesins contain only this domain.
• smart CUB 102aa 5e-04 in ref transcript
• pfam Sushi 57aa 0.003 in ref transcript

SFRS12

• rs.SFRS12.F1 rs.SFRS12.R1 372 496
• NCBIGene 36.3 140890
• Single exon skipping, size difference: 124
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_001077199

• Changed! cd RRM 73aa 2e-14 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• cd RRM 74aa 2e-05 in ref transcript
• Changed! smart RRM_2 72aa 5e-14 in ref transcript
  • RNA recognition motif.
• Changed! smart RRM 71aa 1e-04 in ref transcript
  • RNA recognition motif.
• Changed! COG COG0724 106aa 7e-05 in ref transcript
  • RNA-binding proteins (RRM domain) [General function prediction only].
• Changed! pfam RRM_1 69aa 1e-05 in modified transcript
  • RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain). The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have a N terminus rrm which is included in the seed. There is a second region towards the C terminus that has some features of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.
• Changed! COG COG0724 86aa 7e-04 in modified transcript

SFRS18

• rs.SFRS18.F1 rs.SFRS18.R1 203 283
• NCBIGene 36.3 25957
• Single exon skipping, size difference: 80
• Exclusion in 5'UTR
• Reference transcript: NM_032870

SGCE

• rs.SGCE.F1 rs.SGCE.R1 163 198
• NCBIGene 36.3 8910
• Single exon skipping, size difference: 35
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_001099401

• pfam Sarcoglycan_2 389aa 1e-168 in ref transcript
  • Sarcoglycan alpha/epsilon. Sarcoglycans are a subcomplex of transmembrane proteins which are part of the dystrophin-glycoprotein complex. They are expressed in the skeletal, cardiac and smooth muscle. Although numerous studies have been conducted on the sarcoglycan subcomplex in skeletal and cardiac muscle, the manner of the distribution and localisation of these proteins along the nonjunctional sarcolemma is not clear. This family contains alpha and epsilon members.

SGCE

• rs.SGCE.F2 rs.SGCE.R2 147 222
• NCBIGene 36.3 8910
• Single exon skipping, size difference: 75
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001099401

• Changed! pfam Sarcoglycan_2 389aa 1e-168 in ref transcript
  • Sarcoglycan alpha/epsilon. Sarcoglycans are a subcomplex of transmembrane proteins which are part of the dystrophin-glycoprotein complex. They are expressed in the skeletal, cardiac and smooth muscle. Although numerous studies have been conducted on the sarcoglycan subcomplex in skeletal and cardiac muscle, the manner of the distribution and localisation of these proteins along the nonjunctional sarcolemma is not clear. This family contains alpha and epsilon members.
• Changed! pfam Sarcoglycan_2 386aa 1e-169 in modified transcript

SGCE

• rs.SGCE.F3 rs.SGCE.R3 137 164
• NCBIGene 36.3 8910
• Single exon skipping, size difference: 27
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001099401

• Changed! pfam Sarcoglycan_2 389aa 1e-168 in ref transcript
  • Sarcoglycan alpha/epsilon. Sarcoglycans are a subcomplex of transmembrane proteins which are part of the dystrophin-glycoprotein complex. They are expressed in the skeletal, cardiac and smooth muscle. Although numerous studies have been conducted on the sarcoglycan subcomplex in skeletal and cardiac muscle, the manner of the distribution and localisation of these proteins along the nonjunctional sarcolemma is not clear. This family contains alpha and epsilon members.
• Changed! pfam Sarcoglycan_2 380aa 1e-162 in modified transcript

SGSM1

• rs.SGSM1.F1 rs.SGSM1.R1 174 339
• NCBIGene 36.3 129049
• Single exon skipping, size difference: 165
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001039948

• smart TBC 145aa 2e-30 in ref transcript
  • Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs. Widespread domain present in Gyp6 and Gyp7, thereby giving rise to the notion that it performs a GTP-activator activity on Rab-like GTPases.
• pfam RUN 146aa 5e-21 in ref transcript
  • RUN domain. This domain is present in several proteins that are linked to the functions of GTPases in the Rap and Rab families. They could hence play important roles in multiple Ras-like GTPase signalling pathways. The domain is comprises six conserved regions, which in some proteins have considerable insertions between them. The domain core is thought to take up a predominantly alpha fold, with basic amino acids in regions A and D possibly playing a functional role in interactions with Ras GTPases.
• COG COG5210 212aa 2e-18 in ref transcript
  • GTPase-activating protein [General function prediction only].

SGSM2

• rs.SGSM2.F1 rs.SGSM2.R1 329 464
• NCBIGene 36.3 9905
• Single exon skipping, size difference: 135
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_014853

• smart TBC 147aa 1e-31 in ref transcript
  • Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs. Widespread domain present in Gyp6 and Gyp7, thereby giving rise to the notion that it performs a GTP-activator activity on Rab-like GTPases.
• pfam RUN 144aa 6e-25 in ref transcript
  • RUN domain. This domain is present in several proteins that are linked to the functions of GTPases in the Rap and Rab families. They could hence play important roles in multiple Ras-like GTPase signalling pathways. The domain is comprises six conserved regions, which in some proteins have considerable insertions between them. The domain core is thought to take up a predominantly alpha fold, with basic amino acids in regions A and D possibly playing a functional role in interactions with Ras GTPases.
• COG COG5210 212aa 1e-19 in ref transcript
  • GTPase-activating protein [General function prediction only].

SH2D5

• rs.SH2D5.F1 rs.SH2D5.R1 170 299
• NCBIGene 36.3 400745
• Single exon skipping, size difference: 129
• Exclusion of the protein initiation site
• Reference transcript: NM_001103161

• cd SH2 88aa 2e-09 in ref transcript
  • Src homology 2 domains; Signal transduction, involved in recognition of phosphorylated tyrosine (pTyr). SH2 domains typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites.
• Changed! cd PTB 119aa 2e-07 in ref transcript
  • Phosphotyrosine-binding (PTB) domain; PTB domains have a PH-like fold and are found in various eukaryotic signaling molecules. They were initially identified based upon their ability to recognize phosphorylated tyrosine residues. In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. The PTB domain of SHC binds to a NPXpY sequence. More recent studies have found that some types of PTB domains such as the neuronal protein X11 and in the cell-fate determinant protein Numb can bind to peptides which are not tyrosine phosphorylated; whereas, other PTB domains can bind motifs lacking tyrosine residues altogether.
• Changed! smart PTB 121aa 3e-09 in ref transcript
  • Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain. PTB/PI domain structure similar to those of pleckstrin homology (PH) and IRS-1-like PTB domains.
• smart SH2 77aa 0.002 in ref transcript
  • Src homology 2 domains. Src homology 2 domains bind phosphotyrosine-containing polypeptides via 2 surface pockets. Specificity is provided via interaction with residues that are distinct from the phosphotyrosine. Only a single occurrence of a SH2 domain has been found in S. cerevisiae.

SHMT1

• rs.SHMT1.F1 rs.SHMT1.R1 215 332
• NCBIGene 36.3 6470
• Single exon skipping, size difference: 117
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_004169

• Changed! cd SHMT 427aa 0.0 in ref transcript
  • Serine-glycine hydroxymethyltransferase (SHMT). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). SHMT carries out interconversion of serine and glycine; it catalyzes the transfer of hydroxymethyl group of N5, N10-methylene tetrahydrofolate to glycine resulting in the formation of serine and tetrahydrofolate. Both eukaryotic and prokaryotic SHMT enzymes form tight obligate homodimers; the mammalian enzyme forms a homotetramer comprising four pyridoxal phosphate-bound active sites.
• Changed! pfam SHMT 400aa 0.0 in ref transcript
  • Serine hydroxymethyltransferase.
• Changed! PTZ PTZ00094 457aa 0.0 in ref transcript
  • serine hydroxymethyltransferase; Provisional.
• Changed! cd SHMT 388aa 1e-167 in modified transcript
• Changed! pfam SHMT 361aa 1e-178 in modified transcript
• Changed! PTZ PTZ00094 418aa 0.0 in modified transcript

SHPRH

• rs.SHPRH.F1 rs.SHPRH.R1 100 447
• NCBIGene 36.3 257218
• Alternative 3-prime, size difference: 347
• Exclusion of the stop codon
• Reference transcript: NM_001042683

• cd H15 73aa 5e-11 in ref transcript
  • linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, consisting of an octamer of core histones, two full turns of DNA, a linker histone (H1 or H5) and a variable length of linker DNA; H1/H5 are chromatin-associated proteins that bind to the exterior of nucleosomes and dramatically stabilize the highly condensed states of chromatin fibers; stabilization of higher order folding occurs through electrostatic neutralization of the linker DNA segments, through a highly positively charged carboxy- terminal domain known as the AKP helix (Ala, Lys, Pro); thought to be involved in specific protein-protein and protein-DNA interactions and play a role in suppressing core histone tail domain acetylation in the chromatin fiber.
• cd HELICc 121aa 1e-08 in ref transcript
  • Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process.
• cd RING 51aa 1e-04 in ref transcript
  • RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H).
• pfam SNF2_N 217aa 2e-14 in ref transcript
  • SNF2 family N-terminal domain. This domain is found in proteins involved in a variety of processes including transcription regulation (e.g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as well as a variety of other proteins with little functional information (e.g., lodestar, ETL1).
• pfam Linker_histone 73aa 2e-08 in ref transcript
  • linker histone H1 and H5 family. Linker histone H1 is an essential component of chromatin structure. H1 links nucleosomes into higher order structures Histone H1 is replaced by histone H5 in some cell types.
• smart HELICc 81aa 7e-06 in ref transcript
  • helicase superfamily c-terminal domain.
• pfam SNF2_N 25aa 1e-04 in ref transcript
• smart RING 47aa 0.001 in ref transcript
  • Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s).
• smart PHD 32aa 0.006 in ref transcript
  • PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RI NG finger and the FYV E finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BR OMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RI NG fingers misidentified as PHD fingers.
• Changed! COG HepA 168aa 1e-16 in ref transcript
  • Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair].
• COG HepA 282aa 3e-13 in ref transcript
• COG PEX10 73aa 0.009 in ref transcript
  • RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones].
• Changed! COG HepA 138aa 2e-15 in modified transcript

SIKE

• rs.SIKE.F1 rs.SIKE.R1 100 112
• NCBIGene 36.3 80143
• Alternative 5-prime, size difference: 12
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001102396

• Changed! pfam DUF837 176aa 7e-57 in ref transcript
  • Protein of unknown function (DUF837). This family consists of several eukaryotic proteins of unknown function. One of the family members is a circulating cathodic antigen (CCA) found in Schistosoma mansoni (Blood fluke).
• Changed! pfam DUF837 172aa 8e-58 in modified transcript

SLA

• rs.SLA.F1 rs.SLA.R1 105 383
• NCBIGene 36.3 6503
• Single exon skipping, size difference: 278
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_001045557

• Changed! cd SH2 93aa 3e-20 in ref transcript
  • Src homology 2 domains; Signal transduction, involved in recognition of phosphorylated tyrosine (pTyr). SH2 domains typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites.
• Changed! smart SH2 85aa 6e-21 in ref transcript
  • Src homology 2 domains. Src homology 2 domains bind phosphotyrosine-containing polypeptides via 2 surface pockets. Specificity is provided via interaction with residues that are distinct from the phosphotyrosine. Only a single occurrence of a SH2 domain has been found in S. cerevisiae.
• Changed! smart SH3 38aa 5e-04 in ref transcript
  • Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.

SLC12A6

• rs.SLC12A6.F1 rs.SLC12A6.R1 134 179
• NCBIGene 36.3 9990
• Single exon skipping, size difference: 45
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_133647

• TIGR 2a30 1042aa 0.0 in ref transcript
• COG PotE 244aa 2e-16 in ref transcript
  • Amino acid transporters [Amino acid transport and metabolism].
• COG PotE 201aa 5e-08 in ref transcript

SLC12A6

• rs.SLC12A6.F2 rs.SLC12A6.R2 243 309
• NCBIGene 36.3 9990
• Alternative 3-prime, size difference: 66
• Exclusion of the protein initiation site
• Reference transcript: NM_001042496

• TIGR 2a30 1042aa 0.0 in ref transcript
• COG PotE 244aa 3e-16 in ref transcript
  • Amino acid transporters [Amino acid transport and metabolism].
• COG PotE 201aa 7e-08 in ref transcript

SLC17A3

• rs.SLC17A3.F1 rs.SLC17A3.R1 130 364
• NCBIGene 36.3 10786
• Single exon skipping, size difference: 234
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001098486

• Changed! cd MFS 356aa 9e-21 in ref transcript
  • The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated.
• Changed! TIGR 2A0114euk 475aa 1e-102 in ref transcript
• Changed! COG UhpC 228aa 2e-10 in ref transcript
  • Sugar phosphate permease [Carbohydrate transport and metabolism].
• Changed! cd MFS 272aa 3e-10 in modified transcript
• Changed! TIGR 2A0114euk 313aa 2e-72 in modified transcript
• Changed! TIGR 2A0114euk 50aa 6e-07 in modified transcript
• Changed! COG UhpC 166aa 4e-05 in modified transcript

SLC23A1

• rs.SLC23A1.F1 rs.SLC23A1.R1 97 109
• NCBIGene 36.3 9963
• Alternative 5-prime, size difference: 12
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_152685

• Changed! pfam Xan_ur_permease 437aa 8e-61 in ref transcript
  • Permease family. This family includes permeases for diverse substrates such as xanthine, uracil and vitamin C. However many members of this family are functionally uncharacterised and may transport other substrates. Members of this family have ten predicted transmembrane helices.
• Changed! COG UraA 499aa 2e-43 in ref transcript
  • Xanthine/uracil permeases [Nucleotide transport and metabolism].
• Changed! pfam Xan_ur_permease 433aa 1e-62 in modified transcript
• Changed! COG UraA 495aa 2e-44 in modified transcript

SLC25A45

• rs.SLC25A45.F1 rs.SLC25A45.R1 117 172
• NCBIGene 36.3 283130
• Single exon skipping, size difference: 55
• Exclusion of the protein initiation site
• Reference transcript: NM_182556

• pfam Mito_carr 92aa 5e-19 in ref transcript
  • Mitochondrial carrier protein.
• pfam Mito_carr 92aa 8e-19 in ref transcript
• Changed! pfam Mito_carr 76aa 2e-15 in ref transcript
• PTZ PTZ00169 163aa 1e-11 in ref transcript
  • ADP/ATP transporter on adenylate translocase; Provisional.
• Changed! PTZ PTZ00169 166aa 2e-11 in ref transcript

SLC35C2

• rs.SLC35C2.F1 rs.SLC35C2.R1 142 205
• NCBIGene 36.3 51006
• Alternative 3-prime, size difference: 63
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_173179

• pfam TPT 149aa 5e-16 in ref transcript
  • Triose-phosphate Transporter family. This family includes transporters with a specificity for triose phosphate.

SLC35C2

• rs.SLC35C2.F2 rs.SLC35C2.R2 108 303
• NCBIGene 36.3 51006
• Alternative 3-prime, size difference: 195
• Inclusion in 5'UTR
• Reference transcript: NM_015945

• pfam TPT 149aa 5e-16 in ref transcript
  • Triose-phosphate Transporter family. This family includes transporters with a specificity for triose phosphate.

SLC38A1

• rs.SLC38A1.F1 rs.SLC38A1.R1 191 530
• NCBIGene 36.3 81539
• Alternative 5-prime, size difference: 339
• Exclusion in 5'UTR
• Reference transcript: NM_030674

• pfam Aa_trans 386aa 2e-42 in ref transcript
  • Transmembrane amino acid transporter protein. This transmembrane region is found in many amino acid transporters including UNC-47 and MTR. UNC-47 encodes a vesicular amino butyric acid (GABA) transporter, (VGAT). UNC-47 is predicted to have 10 transmembrane domains. MTR is a N system amino acid transporter system protein involved in methyltryptophan resistance. Other members of this family include proline transporters and amino acid permeases.
• PTZ PTZ00206 364aa 6e-22 in ref transcript
  • amino acid transporter; Provisional.

SLC3A2

• rs.SLC3A2.F1 rs.SLC3A2.R1 313 403
• NCBIGene 36.3 6520
• Single exon skipping, size difference: 93
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001012661

• TIGR trehalose_treC 136aa 4e-16 in ref transcript
  • Trehalose is a glucose disaccharide that serves in many biological systems as a compatible solute for protection against hyperosmotic and thermal stress. This family describes trehalose-6-phosphate hydrolase, product of the treC (or treA) gene, which is often found together with a trehalose uptake transporter and a trehalose operon repressor.
• pfam Alpha-amylase 244aa 8e-14 in ref transcript
  • Alpha amylase, catalytic domain. Alpha amylase is classified as family 13 of the glycosyl hydrolases. The structure is an 8 stranded alpha/beta barrel containing the active site, interrupted by a ~70 a.a. calcium-binding domain protruding between beta strand 3 and alpha helix 3, and a carboxyl-terminal Greek key beta-barrel domain.
• TIGR treS_nterm 120aa 3e-08 in ref transcript
  • Trehalose synthase interconverts maltose and alpha, alpha-trehalose by transglucosylation. This is one of at least three mechanisms for biosynthesis of trehalose, an important and widespread compatible solute. However, it is not driven by phosphate activation of sugars and its physiological role may tend toward trehalose degradation. This view is accentuated by numerous examples of fusion to a probable maltokinase domain. The sequence region described by this model is found both as the whole of a trehalose synthase and as the N-terminal region of a larger fusion protein that includes trehalose synthase activity. Several of these fused trehalose synthases have a domain homologous to proteins with maltokinase activity from Actinoplanes missouriensis and Streptomyces coelicolor (PMID:15378530).
• COG AmyA 340aa 3e-18 in ref transcript
  • Glycosidases [Carbohydrate transport and metabolism].

SLC3A2

• rs.SLC3A2.F2 rs.SLC3A2.R2 231 324
• NCBIGene 36.3 6520
• Single exon skipping, size difference: 93
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001012661

• TIGR trehalose_treC 136aa 4e-16 in ref transcript
  • Trehalose is a glucose disaccharide that serves in many biological systems as a compatible solute for protection against hyperosmotic and thermal stress. This family describes trehalose-6-phosphate hydrolase, product of the treC (or treA) gene, which is often found together with a trehalose uptake transporter and a trehalose operon repressor.
• pfam Alpha-amylase 244aa 8e-14 in ref transcript
  • Alpha amylase, catalytic domain. Alpha amylase is classified as family 13 of the glycosyl hydrolases. The structure is an 8 stranded alpha/beta barrel containing the active site, interrupted by a ~70 a.a. calcium-binding domain protruding between beta strand 3 and alpha helix 3, and a carboxyl-terminal Greek key beta-barrel domain.
• TIGR treS_nterm 120aa 3e-08 in ref transcript
  • Trehalose synthase interconverts maltose and alpha, alpha-trehalose by transglucosylation. This is one of at least three mechanisms for biosynthesis of trehalose, an important and widespread compatible solute. However, it is not driven by phosphate activation of sugars and its physiological role may tend toward trehalose degradation. This view is accentuated by numerous examples of fusion to a probable maltokinase domain. The sequence region described by this model is found both as the whole of a trehalose synthase and as the N-terminal region of a larger fusion protein that includes trehalose synthase activity. Several of these fused trehalose synthases have a domain homologous to proteins with maltokinase activity from Actinoplanes missouriensis and Streptomyces coelicolor (PMID:15378530).
• COG AmyA 340aa 3e-18 in ref transcript
  • Glycosidases [Carbohydrate transport and metabolism].

SLC47A2

• rs.SLC47A2.F1 rs.SLC47A2.R1 99 207
• NCBIGene 36.3 146802
• Alternative 3-prime, size difference: 108
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_152908

• Changed! TIGR matE 373aa 6e-35 in ref transcript
  • The MATE family consists of probable efflux proteins including a functionally characterized multi drug efflux system from Vibrio parahaemolyticus, a putative ethionine resistance protein of Saccharomyces cerevisiae, and the functionally uncharacterized DNA damage-inducible protein F (DinF) of E. coli. These proteins have 12 probable TMS.
• Changed! COG NorM 471aa 3e-36 in ref transcript
  • Na+-driven multidrug efflux pump [Defense mechanisms].
• Changed! TIGR matE 337aa 6e-39 in modified transcript
• Changed! COG NorM 435aa 7e-40 in modified transcript

SLC4A3

• rs.SLC4A3.F1 rs.SLC4A3.R1 191 251
• NCBIGene 36.3 6508
• Alternative 3-prime, size difference: 60
• Inclusion in 5'UTR
• Reference transcript: NM_201574

• TIGR ae 910aa 0.0 in ref transcript
  • They preferentially catalyze anion exchange (antiport) reactions, typically acting as HCO3-:Cl- antiporters, but also transporting a range of other inorganic and organic anions. Additionally, renal Na+:HCO3- cotransporters have been found to be members of the AE family. They catalyze the reabsorption of HCO3- in the renal proximal tubule.

SLC5A10

• rs.SLC5A10.F1 rs.SLC5A10.R1 385 433
• NCBIGene 36.3 125206
• Alternative 3-prime, size difference: 48
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_152351

• Changed! pfam SSF 446aa 3e-88 in ref transcript
  • Sodium:solute symporter family.
• Changed! PRK PRK10484 592aa 5e-41 in ref transcript
  • putative symporter YidK; Provisional.
• Changed! pfam SSF 430aa 3e-90 in modified transcript
• Changed! PRK PRK10484 576aa 3e-42 in modified transcript

SLC7A3

• rs.SLC7A3.F1 rs.SLC7A3.R1 123 147
• NCBIGene 36.3 84889
• Alternative 3-prime, size difference: 24
• Inclusion in 5'UTR
• Reference transcript: NM_001048164

• TIGR 2A0303 583aa 1e-180 in ref transcript
• COG PotE 418aa 2e-34 in ref transcript
  • Amino acid transporters [Amino acid transport and metabolism].

SLC7A6

• rs.SLC7A6.F1 rs.SLC7A6.R1 270 357
• NCBIGene 36.3 9057
• Single exon skipping, size difference: 87
• Exclusion in 5'UTR
• Reference transcript: NM_001076785

• TIGR 2A0308 485aa 1e-147 in ref transcript
• COG PotE 456aa 9e-35 in ref transcript
  • Amino acid transporters [Amino acid transport and metabolism].

SLC9A6

• rs.SLC9A6.F1 rs.SLC9A6.R1 154 250
• NCBIGene 36.3 10479
• Alternative 5-prime, size difference: 96
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001042537

• Changed! TIGR b_cpa1 408aa 7e-72 in ref transcript
  • This Hmm is specific for the eukaryotic members members of this family.
• Changed! COG NhaP 359aa 7e-42 in ref transcript
  • NhaP-type Na+/H+ and K+/H+ antiporters [Inorganic ion transport and metabolism].
• Changed! TIGR b_cpa1 459aa 1e-72 in modified transcript
• Changed! COG NhaP 361aa 6e-41 in modified transcript

SLFN11

• rs.SLFN11.F1 rs.SLFN11.R1 147 255
• NCBIGene 36.3 91607
• Alternative 5-prime, size difference: 108
• Exclusion in 5'UTR
• Reference transcript: NM_001104587

• pfam AAA_4 101aa 5e-16 in ref transcript
  • Divergent AAA domain. This family is related to the pfam00004 family, and presumably has the same function (ATP-binding).
• COG COG2865 87aa 2e-06 in ref transcript
  • Predicted transcriptional regulator containing an HTH domain and an uncharacterized domain shared with the mammalian protein Schlafen [Transcription].

SLFN11

• rs.SLFN11.F2 rs.SLFN11.R2 100 162
• NCBIGene 36.3 91607
• Alternative 5-prime, size difference: 62
• Exclusion in 5'UTR
• Reference transcript: NM_001104587

• pfam AAA_4 101aa 5e-16 in ref transcript
  • Divergent AAA domain. This family is related to the pfam00004 family, and presumably has the same function (ATP-binding).
• COG COG2865 87aa 2e-06 in ref transcript
  • Predicted transcriptional regulator containing an HTH domain and an uncharacterized domain shared with the mammalian protein Schlafen [Transcription].

SLFN11

• rs.SLFN11.F3 rs.SLFN11.R3 140 300
• NCBIGene 36.3 91607
• Single exon skipping, size difference: 160
• Exclusion in 5'UTR
• Reference transcript: NM_001104587

• pfam AAA_4 101aa 5e-16 in ref transcript
  • Divergent AAA domain. This family is related to the pfam00004 family, and presumably has the same function (ATP-binding).
• COG COG2865 87aa 2e-06 in ref transcript
  • Predicted transcriptional regulator containing an HTH domain and an uncharacterized domain shared with the mammalian protein Schlafen [Transcription].

SLTM

• rs.SLTM.F1 rs.SLTM.R1 264 318
• NCBIGene 36.3 79811
• Alternative 3-prime, size difference: 54
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_024755

• cd RRM 75aa 6e-12 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• smart RRM 71aa 1e-11 in ref transcript
  • RNA recognition motif.
• smart SAP 35aa 8e-06 in ref transcript
  • Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation.
• COG COG0724 112aa 0.001 in ref transcript
  • RNA-binding proteins (RRM domain) [General function prediction only].

SMAD5

• rs.SMAD5.F1 rs.SMAD5.R1 176 260
• NCBIGene 36.3 4090
• Single exon skipping, size difference: 84
• Exclusion in 5'UTR
• Reference transcript: NM_001001419

• cd MH2 176aa 1e-73 in ref transcript
  • MH2 domain; C terminal domain of SMAD family proteins, responsible for receptor interaction, transactivation, and homo- and heterooligomerisation; also known as Domain B in dwarfin family proteins.
• cd MH1 121aa 4e-34 in ref transcript
  • MH1 is a small DNA binding domain, binding in an unusal way involving a beta hairpin structure binding to the major groove. MH1 is present in Smad proteins, an important family of proteins involved in TGF-beta signalling and frequent targets of tumorigenic mutations. Also known as Domain A in dwarfin family proteins.
• pfam MH2 176aa 1e-80 in ref transcript
  • MH2 domain. This is the MH2 (MAD homology 2) domain found at the carboxy terminus of MAD related proteins such as Smads. This domain is separated from the MH1 domain by a non-conserved linker region. The MH2 domain mediates interaction with a wide variety of proteins and provides specificity and selectivity to Smad function and also is critical for mediating interactions in Smad oligomers. Unlike MH1, MH2 does not bind DNA. The well-studied MH2 domain of Smad4 is composed of five alpha helices and three loops enclosing a beta sandwich. Smads are involved in the propagation of TGF-beta signals by direct association with the TGF-beta receptor kinase which phosphorylates the last two Ser of a conserved 'SSXS' motif located at the C-terminus of MH2.
• pfam MH1 76aa 2e-35 in ref transcript
  • MH1 domain. The MH1 (MAD homology 1) domain is found at the amino terminus of MAD related proteins such as Smads. This domain is separated from the MH2 domain by a non-conserved linker region. The crystal structure of the MH1 domain shows that a highly conserved 11 residue beta hairpin is used to bind the DNA consensus sequence GNCN in the major groove, shown to be vital for the transcriptional activation of target genes. Not all examples of MH1 can bind to DNA however. Smad2 cannot bind DNA and has a large insertion within the hairpin that presumably abolishes DNA binding. A basic helix (H2) in MH1 with the nuclear localisation signal KKLKK has been shown to be essential for Smad3 nuclear import. Smads also use the MH1 domain to interact with transcription factors such as Jun, TFE3, Sp1, and Runx.

SMAP1

• rs.SMAP1.F1 rs.SMAP1.R1 151 232
• NCBIGene 36.3 60682
• Single exon skipping, size difference: 81
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001044305

• pfam ArfGap 100aa 8e-37 in ref transcript
  • Putative GTPase activating protein for Arf. Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs.
• COG COG5347 91aa 2e-29 in ref transcript
  • GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion].

SMN1

• rs.SMN1.F1 rs.SMN1.R1 118 214
• NCBIGene 36.3 6606
• Single exon skipping, size difference: 96
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000344

• cd TUDOR 48aa 2e-08 in ref transcript
  • Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal.
• Changed! pfam SMN 166aa 3e-40 in ref transcript
  • Survival motor neuron protein (SMN). This family consists of several eukaryotic survival motor neuron (SMN) proteins. The Survival of Motor Neurons (SMN) protein, the product of the spinal muscular atrophy-determining gene, is part of a large macromolecular complex (SMN complex) that functions in the assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs). The SMN complex functions as a specificity factor essential for the efficient assembly of Sm proteins on U snRNAs and likely protects cells from illicit, and potentially deleterious, non-specific binding of Sm proteins to RNAs.
• Changed! pfam SMN 35aa 2e-11 in ref transcript
• Changed! pfam SMN 229aa 7e-52 in modified transcript

SMN2

• rs.SMN2.F1 rs.SMN2.R1 123 177
• NCBIGene 36.3 6607
• Single exon skipping, size difference: 54
• Exclusion of the stop codon
• Reference transcript: NM_017411

• cd TUDOR 48aa 2e-08 in ref transcript
  • Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal.
• pfam SMN 166aa 3e-40 in ref transcript
  • Survival motor neuron protein (SMN). This family consists of several eukaryotic survival motor neuron (SMN) proteins. The Survival of Motor Neurons (SMN) protein, the product of the spinal muscular atrophy-determining gene, is part of a large macromolecular complex (SMN complex) that functions in the assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs). The SMN complex functions as a specificity factor essential for the efficient assembly of Sm proteins on U snRNAs and likely protects cells from illicit, and potentially deleterious, non-specific binding of Sm proteins to RNAs.
• Changed! pfam SMN 35aa 2e-11 in ref transcript
• Changed! pfam SMN 27aa 2e-08 in modified transcript

SNHG3-RCC1

• rs.SNHG3-RCC1.F1 rs.SNHG3-RCC1.R1 103 246
• NCBIGene 36.3 751867
• Single exon skipping, size difference: 143
• Exclusion in 5'UTR
• Reference transcript: NM_001048197

• pfam RCC1 50aa 1e-10 in ref transcript
  • Regulator of chromosome condensation (RCC1).
• pfam RCC1 49aa 2e-10 in ref transcript
• pfam RCC1 51aa 1e-09 in ref transcript
• pfam RCC1 52aa 2e-09 in ref transcript
• pfam RCC1 66aa 3e-08 in ref transcript
• pfam RCC1 31aa 2e-04 in ref transcript
• pfam RCC1 51aa 7e-04 in ref transcript
• COG ATS1 350aa 3e-42 in ref transcript
  • Alpha-tubulin suppressor and related RCC1 domain-containing proteins [Cell division and chromosome partitioning / Cytoskeleton].

SNRK

• rs.SNRK.F1 rs.SNRK.R1 338 400
• NCBIGene 36.3 54861
• Single exon skipping, size difference: 62
• Exclusion in 5'UTR
• Reference transcript: NM_017719

• cd S_TKc 254aa 6e-82 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• smart S_TKc 243aa 3e-84 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• PTZ PTZ00263 258aa 5e-42 in ref transcript
  • protein kinase A catalytic subunit; Provisional.

SNUPN

• rs.SNUPN.F1 rs.SNUPN.R1 201 306
• NCBIGene 36.3 10073
• Alternative 5-prime, size difference: 105
• Exclusion in 5'UTR
• Reference transcript: NM_005701

SNX14

• rs.SNX14.F1 rs.SNX14.R1 161 293
• NCBIGene 36.3 57231
• Multiple exon skipping, size difference: 132
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_153816

• cd PX_SNX14 123aa 3e-50 in ref transcript
  • The phosphoinositide binding Phox Homology domain of Sorting Nexin 14. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. SNX14 may be involved in recruiting other proteins to the membrane via protein-protein and protein-ligand interaction. It is expressed in the embryonic nervous system of mice, and is co-expressed in the motoneurons and the anterior pituary with Islet-1. SNX14 shows a similar domain architecture as SNX13, containing an N-terminal PXA domain, a regulator of G protein signaling (RGS) domain, a PX domain, and a C-terminal domain that is conserved in some SNXs.
• pfam Nexin_C 106aa 5e-25 in ref transcript
  • Sorting nexin C terminal. This region is found a the C terminal of proteins belonging to the sorting nexin family. It is found on proteins which also contain pfam00787.
• Changed! smart PXA 156aa 6e-22 in ref transcript
  • Domain associated with PX domains. unpubl. observations.
• pfam PX 105aa 2e-17 in ref transcript
  • PX domain. PX domains bind to phosphoinositides.
• smart RGS 128aa 2e-07 in ref transcript
  • Regulator of G protein signalling domain. RGS family members are GTPase-activating proteins for heterotrimeric G-protein alpha-subunits.
• COG COG5391 140aa 0.002 in ref transcript
  • Phox homology (PX) domain protein [Intracellular trafficking and secretion / General function prediction only].
• Changed! smart PXA 131aa 2e-12 in modified transcript

SNX21

• rs.SNX21.F1 rs.SNX21.R1 99 110
• NCBIGene 36.3 90203
• Single exon skipping, size difference: 11
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_033421

• Changed! cd PX_SNX21 112aa 1e-55 in ref transcript
  • The phosphoinositide binding Phox Homology domain of Sorting Nexin 21. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. Some SNXs are localized in early endosome structures such as clathrin-coated pits, while others are located in late structures of the endocytic pathway. SNX21, also called SNX-L, is distinctly and highly-expressed in fetal liver and may be involved in protein sorting and degradation during embryonic liver development.
• Changed! pfam PX 106aa 8e-12 in ref transcript
  • PX domain. PX domains bind to phosphoinositides.
• Changed! COG COG5391 112aa 3e-04 in ref transcript
  • Phox homology (PX) domain protein [Intracellular trafficking and secretion / General function prediction only].
• Changed! cd PX_SNX21 19aa 1e-04 in modified transcript

SOD2

• rs.SOD2.F1 rs.SOD2.R1 283 400
• NCBIGene 36.3 6648
• Single exon skipping, size difference: 117
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001024465

• Changed! pfam Sod_Fe_C 106aa 3e-49 in ref transcript
  • Iron/manganese superoxide dismutases, C-terminal domain. superoxide dismutases (SODs) catalyse the conversion of superoxide radicals to hydrogen peroxide and molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the Mn/Fe-binding family is one. In humans, there is a cytoplasmic Cu/Zn SOD, and a mitochondrial Mn/Fe SOD. C-terminal domain is a mixed alpha/beta fold.
• Changed! pfam Sod_Fe_N 82aa 3e-34 in ref transcript
  • Iron/manganese superoxide dismutases, alpha-hairpin domain. superoxide dismutases (SODs) catalyse the conversion of superoxide radicals to hydrogen peroxide and molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the Mn/Fe-binding family is one. In humans, there is a cytoplasmic Cu/Zn SOD, and a mitochondrial Mn/Fe SOD. N-terminal domain is a long alpha antiparallel hairpin. A small fragment of YTRE_LEPBI matches well - sequencing error?.
• Changed! COG SodA 200aa 1e-69 in ref transcript
  • Superoxide dismutase [Inorganic ion transport and metabolism].
• Changed! pfam Sod_Fe_C 103aa 3e-47 in modified transcript
• Changed! pfam Sod_Fe_N 59aa 6e-21 in modified transcript
• Changed! COG SodA 161aa 3e-52 in modified transcript

SORBS1

• rs.SORBS1.F1 rs.SORBS1.R1 129 195
• NCBIGene 36.3 10580
• Mutually exclusive exon skipping, size difference: 66
• Inclusion in the protein (no stop codon or frameshift), Exclusion in the protein (no frameshift)
• Reference transcript: NM_001034954

• cd SH3 54aa 3e-12 in ref transcript
  • Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
• cd SH3 52aa 8e-11 in ref transcript
• cd SH3 52aa 6e-10 in ref transcript
• smart SH3 59aa 4e-13 in ref transcript
  • Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.
• smart SH3 53aa 3e-12 in ref transcript
• smart SH3 59aa 7e-11 in ref transcript
• pfam Sorb 41aa 4e-10 in ref transcript
  • Sorbin homologous domain.

SORBS1

• rs.SORBS1.F2 rs.SORBS1.R2 106 208
• NCBIGene 36.3 10580
• Single exon skipping, size difference: 102
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001034954

• cd SH3 54aa 3e-12 in ref transcript
  • Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
• cd SH3 52aa 8e-11 in ref transcript
• cd SH3 52aa 6e-10 in ref transcript
• smart SH3 59aa 4e-13 in ref transcript
  • Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.
• smart SH3 53aa 3e-12 in ref transcript
• smart SH3 59aa 7e-11 in ref transcript
• pfam Sorb 41aa 4e-10 in ref transcript
  • Sorbin homologous domain.

SORBS2

• rs.SORBS2.F1 rs.SORBS2.R1 156 206
• NCBIGene 36.3 8470
• Single exon skipping, size difference: 50
• Inclusion in 5'UTR
• Reference transcript: NM_021069

• cd SH3 52aa 8e-14 in ref transcript
  • Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
• cd SH3 54aa 9e-12 in ref transcript
• cd SH3 54aa 3e-11 in ref transcript
• pfam Sorb 50aa 9e-21 in ref transcript
  • Sorbin homologous domain.
• smart SH3 53aa 5e-16 in ref transcript
  • Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.
• smart SH3 59aa 2e-12 in ref transcript
• smart SH3 59aa 2e-12 in ref transcript

SP8

• rs.SP8.F1 rs.SP8.R1 128 224
• NCBIGene 36.3 221833
• Single exon skipping, size difference: 96
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_182700

SPAG11B

• rs.SPAG11B.F1 rs.SPAG11B.R1 195 271
• NCBIGene 36.3 10407
• Single exon skipping, size difference: 76
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_058207

• Changed! pfam Defensin_beta 36aa 1e-04 in ref transcript
  • Beta defensin. The beta defensins are antimicrobial peptides implicated in the resistance of epithelial surfaces to microbial colonisation.

SPAG11B

• rs.SPAG11B.F2 rs.SPAG11B.R2 117 195
• NCBIGene 36.3 10407
• Single exon skipping, size difference: 78
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_058200

• pfam Sperm_Ag_HE2 70aa 2e-28 in ref transcript
  • Sperm antigen HE2. This family consists of several variants of the human and chimpanzee sperm antigen proteins (HE2 and EP2 respectively). The EP2 gene codes for a family of androgen-dependent, epididymis-specific secretory proteins.The EP2 gene uses alternative promoters and differential splicing to produce a family of variant messages. The translated putative protein variants differ significantly from each other. Some of these putative proteins have similarity to beta-defensins, a family of antimicrobial peptides.

SPAG11B

• rs.SPAG11B.F3 rs.SPAG11B.R3 180 256
• NCBIGene 36.3 10407
• Single exon skipping, size difference: 76
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_058201

• Changed! pfam Sperm_Ag_HE2 70aa 1e-30 in ref transcript
  • Sperm antigen HE2. This family consists of several variants of the human and chimpanzee sperm antigen proteins (HE2 and EP2 respectively). The EP2 gene codes for a family of androgen-dependent, epididymis-specific secretory proteins.The EP2 gene uses alternative promoters and differential splicing to produce a family of variant messages. The translated putative protein variants differ significantly from each other. Some of these putative proteins have similarity to beta-defensins, a family of antimicrobial peptides.
• Changed! pfam Defensin_beta 36aa 2e-06 in ref transcript
  • Beta defensin. The beta defensins are antimicrobial peptides implicated in the resistance of epithelial surfaces to microbial colonisation.
• Changed! pfam Sperm_Ag_HE2 74aa 1e-29 in modified transcript

SPAG6

• rs.SPAG6.F1 rs.SPAG6.R1 131 277
• NCBIGene 36.3 9576
• Single exon skipping, size difference: 146
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_012443

• cd ARM 119aa 7e-16 in ref transcript
  • Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model.
• cd ARM 119aa 4e-14 in ref transcript
• cd ARM 119aa 6e-10 in ref transcript
• cd ARM 78aa 0.006 in ref transcript
• pfam Arm 41aa 3e-05 in ref transcript
  • Armadillo/beta-catenin-like repeat. Approx. 40 amino acid repeat. Tandem repeats form super-helix of helices that is proposed to mediate interaction of beta-catenin with its ligands. CAUTION: This family does not contain all known armadillo repeats.
• pfam Adaptin_N 359aa 0.003 in ref transcript
  • Adaptin N terminal region. This family consists of the N terminal region of various alpha, beta and gamma subunits of the AP-1, AP-2 and AP-3 adaptor protein complexes. The adaptor protein (AP) complexes are involved in the formation of clathrin-coated pits and vesicles. The N-terminal region of the various adaptor proteins (APs) is constant by comparison to the C-terminal which is variable within members of the AP-2 family; and it has been proposed that this constant region interacts with another uniform component of the coated vesicles.
• COG SRP1 312aa 1e-19 in ref transcript
  • Karyopherin (importin) alpha [Intracellular trafficking and secretion].

SPG3A

• rs.SPG3A.F1 rs.SPG3A.R1 123 138
• NCBIGene 36.3 51062
• Single exon skipping, size difference: 15
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_015915

• cd GBP 247aa 1e-55 in ref transcript
  • Guanylate-binding protein (GBP), N-terminal domain. Guanylate-binding proteins (GBPs) define a group of proteins that are synthesized after activation of the cell by interferons. The biochemical properties of GBPs are clearly different from those of Ras-like and heterotrimeric GTP-binding proteins. They bind guanine nucleotides with low affinity (micromolar range), are stable in their absence and have a high turnover GTPase. In addition to binding GDP/GTP, they have the unique ability to bind GMP with equal affinity and hydrolyze GTP not only to GDP, but also to GMP. Furthermore, two unique regions around the base and the phosphate-binding areas, the guanine and the phosphate caps, respectively, give the nucleotide-binding site a unique appearance not found in the canonical GTP-binding proteins. The phosphate cap, which constitutes the region analogous to switch I, completely shields the phosphate-binding site from solvent such that a potential GTPase-activating protein (GAP) cannot approach.
• pfam GBP 272aa 1e-101 in ref transcript
  • Guanylate-binding protein, N-terminal domain. Transcription of the anti-viral guanylate-binding protein (GBP) is induced by interferon-gamma during macrophage induction. This family contains GBP1 and GPB2, both GTPases capable of binding GTP, GDP and GMP.

SPOP

• rs.SPOP.F1 rs.SPOP.R1 193 245
• NCBIGene 36.3 8405
• Single exon skipping, size difference: 52
• Exclusion in 5'UTR
• Reference transcript: NM_001007230

• cd MATH_SPOP 139aa 8e-70 in ref transcript
  • Speckle-type POZ protein (SPOP) family, MATH domain; composed of proteins with similarity to human SPOP. SPOP was isolated as a novel antigen recognized by serum from a scleroderma patient, whose overexpression in COS cells results in a discrete speckled pattern in the nuclei. It contains an N-terminal MATH domain and a C-terminal BTB (also called POZ) domain. Together with Cul3, SPOP constitutes an ubiquitin E3 ligase which is able to ubiquitinate the PcG protein BMI1, the variant histone macroH2A1 and the death domain-associated protein Daxx. Therefore, SPOP may be involved in the regulation of these proteins and may play a role in transcriptional regulation, apoptosis and X-chromosome inactivation. Cul3 binds to the BTB domain of SPOP whereas Daxx and the macroH2A1 nonhistone region have been shown to bind to the MATH domain. Both MATH and BTB domains are necessary for the nuclear speckled accumulation of SPOP. There are many proteins, mostly uncharacterized, containing both MATH and BTB domains from C. elegans and plants which are excluded from this family.
• pfam BTB 108aa 3e-21 in ref transcript
  • BTB/POZ domain. The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN.
• smart MATH 102aa 8e-10 in ref transcript
  • meprin and TRAF homology.

SPP1

• rs.SPP1.F1 rs.SPP1.R1 250 331
• NCBIGene 36.3 6696
• Single exon skipping, size difference: 81
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001040058

• Changed! pfam Osteopontin 314aa 1e-96 in ref transcript
  • Osteopontin.
• Changed! pfam Osteopontin 287aa 2e-76 in modified transcript

SPP1

• rs.SPP1.F2 rs.SPP1.R2 373 415
• NCBIGene 36.3 6696
• Single exon skipping, size difference: 42
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001040058

• Changed! pfam Osteopontin 314aa 1e-96 in ref transcript
  • Osteopontin.
• Changed! pfam Osteopontin 300aa 9e-89 in modified transcript

SPPL2B

• rs.SPPL2B.F1 rs.SPPL2B.R1 149 212
• NCBIGene 36.3 56928
• Alternative 5-prime, size difference: 63
• Exclusion in 3'UTR
• Reference transcript: NM_001077238

• cd PA_hSPPL_like 120aa 6e-51 in ref transcript
  • PA_hSPPL_like: Protease-associated domain containing human signal peptide peptidase-like (hSPPL)-like. This group contains various PA domain-containing proteins similar to hSPPL2a and 2b. These SPPLs are GxGD aspartic proteases. SPPL2a is sorted to the late endosomes, SPPL2b to the plasma membrane. In activated dendritic cells, hSPPL2a and 2b catalyze the intramembrane proteolysis of tumor necrosis factor alpha triggering IL-12 production. hSPPL2a and 2b may have a broad substrate spectrum. The significance of the PA domain to these SPPLs has not been ascertained. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate.
• pfam PA 81aa 9e-10 in ref transcript
  • PA domain. The PA (Protease associated) domain is found as an insert domain in diverse proteases. The PA domain is also found in a plant vacuolar sorting receptor and members of the RZF family. It has been suggested that this domain forms a lid-like structure that covers the active site in active proteases, and is involved in protein recognition in vacuolar sorting receptors.
• smart PSN 58aa 0.003 in ref transcript
  • Presenilin, signal peptide peptidase, family. Presenilin 1 and presenilin 2 are polytopic membrane proteins, whose genes are mutated in some individuals with Alzheimer's disease. Distant homologues, present in eukaryotes and archaea, also contain conserved aspartic acid residues which are predicted to contribute to catalysis. At least one member of this family has been shown to possess signal peptide peptidase activity.

SPRR3

• rs.SPRR3.F1 rs.SPRR3.R1 107 191
• NCBIGene 36.3 6707
• Single exon skipping, size difference: 84
• Exclusion in 5'UTR
• Reference transcript: NM_005416

• pfam Cornifin 137aa 1e-18 in ref transcript
  • Cornifin (SPRR) family. SPRR genes (formerly SPR) encode a novel class of polypeptides (small proline rich proteins) that are strongly induced during differentiation of human epidermal keratinocytes in vitro and in vivo.The most characteristic feature of the SPRR gene family resides in the structure of the central segments of the encoded polypeptides that are built up from tandemly repeated units of either eight (SPRR1 and SPRR3) or nine (SPRR2) amino acids with the general consensus XKXPEPXX where X is any amino acid.

SRGAP3

• rs.SRGAP3.F1 rs.SRGAP3.R1 96 168
• NCBIGene 36.3 9901
• Mutually exclusive exon skipping, size difference: 72
• Inclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_014850

• Changed! cd RhoGAP_srGAP 188aa 6e-99 in ref transcript
  • RhoGAP_srGAP: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in srGAPs. srGAPs are components of the intracellular part of Slit-Robo signalling pathway that is important for axon guidance and cell migration. srGAPs contain an N-terminal FCH domain, a central RhoGAP domain and a C-terminal SH3 domain; this SH3 domain interacts with the intracellular proline-rich-tail of the Roundabout receptor (Robo). This interaction with Robo then activates the rhoGAP domain which in turn inhibits Cdc42 activity. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
• cd SH3 50aa 2e-09 in ref transcript
  • Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
• smart RhoGAP 172aa 1e-51 in ref transcript
  • GTPase-activator protein for Rho-like GTPases. GTPase activator proteins towards Rho/Rac/Cdc42-like small GTPases. etter domain limits and outliers.
• pfam FCH 94aa 4e-10 in ref transcript
  • Fes/CIP4 homology domain. Alignment extended from. Highly alpha-helical.
• smart SH3 50aa 1e-09 in ref transcript
  • Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.
• Changed! cd RhoGAP_srGAP 177aa 1e-94 in modified transcript

SSBP3

• rs.SSBP3.F1 rs.SSBP3.R1 364 424
• NCBIGene 36.3 23648
• Single exon skipping, size difference: 60
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_145716

• Changed! pfam SSDP 144aa 2e-06 in ref transcript
  • Single-stranded DNA binding protein, SSDP. This is a family of eukaryotic single-stranded DNA binding proteins with specificity to a pyrimidine-rich element found in the promoter region of the alpha2(I) collagen gene.
• Changed! pfam SSDP 138aa 2e-07 in modified transcript

SSX5

• rs.SSX5.F1 rs.SSX5.R1 330 453
• NCBIGene 36.3 6758
• Single exon skipping, size difference: 123
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_021015

• Changed! smart KRAB 59aa 6e-11 in ref transcript
  • krueppel associated box.
• pfam SSXRD 34aa 5e-08 in ref transcript
  • SSXRD motif. SSX1 can repress transcription, and this has been attributed to a putative Kruppel associated box (KRAB) repression domain at the N-terminus. However, from the analysis of these deletion constructs further repression activity was found at the C-terminus of SSX1. Which has been called the SSXRD (SSX Repression Domain). The potent repression exerted by full-length SSX1 appears to localise to this region.
• Changed! smart KRAB 60aa 6e-11 in modified transcript

STAG2

• rs.STAG2.F1 rs.STAG2.R1 357 422
• NCBIGene 36.3 10735
• Single exon skipping, size difference: 65
• Exclusion in 5'UTR
• Reference transcript: NM_001042750

• pfam STAG 107aa 4e-44 in ref transcript
  • STAG domain. STAG domain proteins are subunits of cohesin complex - a protein complex required for sister chromatid cohesion in eukaryotes. The STAG domain is present in Schizosaccharomyces pombe mitotic cohesin Psc3, and the meiosis specific cohesin Rec11. Many organisms express a meiosis-specific STAG protein, for example, mice and humans have a meiosis specific variant called STAG3, although budding yeast does not have a meiosis specific version.
• COG IRR1 294aa 2e-18 in ref transcript
  • Cohesin [Cell division and chromosome partitioning].

STAG2

• rs.STAG2.F2 rs.STAG2.R2 208 319
• NCBIGene 36.3 10735
• Single exon skipping, size difference: 111
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001042749

• pfam STAG 107aa 4e-44 in ref transcript
  • STAG domain. STAG domain proteins are subunits of cohesin complex - a protein complex required for sister chromatid cohesion in eukaryotes. The STAG domain is present in Schizosaccharomyces pombe mitotic cohesin Psc3, and the meiosis specific cohesin Rec11. Many organisms express a meiosis-specific STAG protein, for example, mice and humans have a meiosis specific variant called STAG3, although budding yeast does not have a meiosis specific version.
• COG IRR1 294aa 2e-18 in ref transcript
  • Cohesin [Cell division and chromosome partitioning].

STAG3L1

• rs.STAG3L1.F1 rs.STAG3L1.R1 108 232
• NCBIGene 36.3 54441
• Single exon skipping, size difference: 124
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_018991

• Changed! COG IRR1 114aa 1e-08 in ref transcript
  • Cohesin [Cell division and chromosome partitioning].

STAT3

• rs.STAT3.F1 rs.STAT3.R1 105 127
• NCBIGene 36.3 6774
• Alternative 3-prime, size difference: 22
• Exclusion in 5'UTR
• Reference transcript: NM_139276

• cd SH2 92aa 4e-06 in ref transcript
  • Src homology 2 domains; Signal transduction, involved in recognition of phosphorylated tyrosine (pTyr). SH2 domains typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites.
• pfam STAT_bind 254aa 1e-123 in ref transcript
  • STAT protein, DNA binding domain. STAT proteins (Signal Transducers and Activators of Transcription) are a family of transcription factors that are specifically activated to regulate gene transcription when cells encounter cytokines and growth factors. This family represents the DNA binding domain of STAT, which has an ig-like fold. STAT proteins also include an SH2 domain pfam00017.
• pfam STAT_alpha 182aa 4e-63 in ref transcript
  • STAT protein, all-alpha domain. STAT proteins (Signal Transducers and Activators of Transcription) are a family of transcription factors that are specifically activated to regulate gene transcription when cells encounter cytokines and growth factors. STAT proteins also include an SH2 domain pfam00017.
• pfam STAT_int 115aa 4e-46 in ref transcript
  • STAT protein, protein interaction domain. STAT proteins (Signal Transducers and Activators of Transcription) are a family of transcription factors that are specifically activated to regulate gene transcription when cells encounter cytokines and growth factors. STAT proteins also include an SH2 domain pfam00017.
• pfam SH2 91aa 4e-09 in ref transcript
  • SH2 domain.

STAT3

• rs.STAT3.F2 rs.STAT3.R2 102 152
• NCBIGene 36.3 6774
• Alternative 3-prime, size difference: 50
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_139276

• cd SH2 92aa 4e-06 in ref transcript
  • Src homology 2 domains; Signal transduction, involved in recognition of phosphorylated tyrosine (pTyr). SH2 domains typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites.
• pfam STAT_bind 254aa 1e-123 in ref transcript
  • STAT protein, DNA binding domain. STAT proteins (Signal Transducers and Activators of Transcription) are a family of transcription factors that are specifically activated to regulate gene transcription when cells encounter cytokines and growth factors. This family represents the DNA binding domain of STAT, which has an ig-like fold. STAT proteins also include an SH2 domain pfam00017.
• pfam STAT_alpha 182aa 4e-63 in ref transcript
  • STAT protein, all-alpha domain. STAT proteins (Signal Transducers and Activators of Transcription) are a family of transcription factors that are specifically activated to regulate gene transcription when cells encounter cytokines and growth factors. STAT proteins also include an SH2 domain pfam00017.
• pfam STAT_int 115aa 4e-46 in ref transcript
  • STAT protein, protein interaction domain. STAT proteins (Signal Transducers and Activators of Transcription) are a family of transcription factors that are specifically activated to regulate gene transcription when cells encounter cytokines and growth factors. STAT proteins also include an SH2 domain pfam00017.
• pfam SH2 91aa 4e-09 in ref transcript
  • SH2 domain.

STAU1

• rs.STAU1.F1 rs.STAU1.R1 177 300
• NCBIGene 36.3 6780
• Single exon skipping, size difference: 123
• Inclusion in 5'UTR
• Reference transcript: NM_017453

• cd DSRM 67aa 1e-12 in ref transcript
  • Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, RNases H1, and dsRNA dependent adenosine deaminases.
• smart DSRM 67aa 3e-14 in ref transcript
  • Double-stranded RNA binding motif.
• smart DSRM 32aa 0.001 in ref transcript
• PRK rnc 72aa 1e-10 in ref transcript
  • ribonuclease III; Reviewed.

STEAP2

• rs.STEAP2.F1 rs.STEAP2.R1 303 353
• NCBIGene 36.3 261729
• Exon skipping and alternative 3-prime or 5-prime, size difference: 50
• Inclusion in 5'UTR, Exclusion in 5'UTR
• Reference transcript: NM_001040665

• pfam F420_oxidored 175aa 3e-37 in ref transcript
  • NADP oxidoreductase coenzyme F420-dependent.
• COG COG2085 186aa 4e-26 in ref transcript
  • Predicted dinucleotide-binding enzymes [General function prediction only].
• COG MgtA 151aa 0.001 in ref transcript
  • Cation transport ATPase [Inorganic ion transport and metabolism].

STK19

• rs.STK19.F1 rs.STK19.R1 100 112
• NCBIGene 36.3 8859
• Alternative 5-prime, size difference: 12
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_032454

• Changed! pfam Stk19 240aa 4e-83 in ref transcript
  • Serine-threonine protein kinase 19. This serine-threonine protein kinase number 19 is expressed from the MHC and predominantly in the nucleus. Protein kinases are involved in signal transduction pathways and play fundamental roles in the regulation of cell functions. This is a novel Ser/Thr protein kinase, that has Mn2+-dependent protein kinase activity that phosphorylates alpha -casein at Ser/Thr residues and histone at Ser residues. It can be covalently modified by the reactive ATP analogue 5'-p-fluorosulfonylbenzoyladenosine in the absence of ATP, and this modification is prevented in the presence of 1 mM ATP, indicating that the kinase domain of is capable of binding ATP.
• Changed! pfam Stk19 236aa 2e-83 in modified transcript

STRN3

• rs.STRN3.F1 rs.STRN3.R1 147 399
• NCBIGene 36.3 29966
• Multiple exon skipping, size difference: 252
• Exclusion in the protein (no frameshift), Exclusion in the protein (no frameshift)
• Reference transcript: NM_001083893

• cd WD40 322aa 9e-49 in ref transcript
  • WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.
• pfam Striatin 135aa 1e-41 in ref transcript
  • Striatin family. Striatin is an intracellular protein which has a caveolin-binding motif, a coiled-coil structure, a calmodulin-binding site, and a WD (pfam00400) repeat domain. It acts as a scaffold protein and is involved in signalling pathways.
• smart WD40 40aa 2e-06 in ref transcript
  • WD40 repeats. Note that these repeats are permuted with respect to the structural repeats (blades) of the beta propeller domain.
• smart WD40 40aa 5e-06 in ref transcript
• smart WD40 34aa 1e-05 in ref transcript
• smart WD40 38aa 2e-04 in ref transcript
• COG COG2319 318aa 1e-20 in ref transcript
  • FOG: WD40 repeat [General function prediction only].

SUMF2

• rs.SUMF2.F1 rs.SUMF2.R1 157 202
• NCBIGene 36.3 25870
• Single exon skipping, size difference: 45
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001042468

• Changed! pfam DUF323 269aa 9e-65 in ref transcript
  • Domain of unknown function (DUF323). This presumed domain is found in bacterial and eukaryotic proteins. In some cases these proteins also contain a protein kinase domain. The function of this domain is unknown. The domain has also been found in eukaryotic proteins required for post-translational sulphatase modification (SUMF1). These proteins are associated with the rare disorder multiple sulphatase deficiency (MSD).
• Changed! COG COG1262 275aa 1e-36 in ref transcript
  • Uncharacterized conserved protein [Function unknown].
• Changed! pfam DUF323 254aa 2e-63 in modified transcript
• Changed! COG COG1262 260aa 1e-37 in modified transcript

SUMO2

• rs.SUMO2.F1 rs.SUMO2.R1 250 322
• NCBIGene 36.3 6613
• Single exon skipping, size difference: 72
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_006937

• Changed! cd Sumo 87aa 6e-31 in ref transcript
  • Small ubiquitin-related modifier (SUMO) proteins are conjugated to numerous intracellular targets and serve to modulate protein interaction, localization, activity or stability. SUMO (also known as "Smt3" and "sentrin" in other organisms) is linked to several different pathways, including nucleocytoplasmic transport. Attachment of SUMO to targets proteins is stimulated by PIAS (Protein inhibitor of activated STATs) proteins which serve as E3-like ligases.
• Changed! smart UBQ 65aa 4e-08 in ref transcript
  • Ubiquitin homologues. Ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression.
• Changed! COG SMT3 91aa 8e-18 in ref transcript
  • Ubiquitin-like protein (sentrin) [Posttranslational modification, protein turnover, chaperones].
• Changed! cd Sumo 63aa 1e-16 in modified transcript
• Changed! COG SMT3 67aa 3e-08 in modified transcript

SYN1

• rs.SYN1.F1 rs.SYN1.R1 123 161
• NCBIGene 36.3 6853
• Alternative 3-prime, size difference: 38
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_006950

• pfam Synapsin_C 203aa 1e-121 in ref transcript
  • Synapsin, ATP binding domain. Ca dependent ATP binding in this ATP grasp fold. Function unknown.
• pfam Synapsin 98aa 7e-52 in ref transcript
  • Synapsin, N-terminal domain.
• pfam Synapsin_N 27aa 2e-10 in ref transcript
  • Synapsin N-terminal. This highly conserved domain of synapsin proteins has a serine at position 9 or 10 which is a phosphorylation site. The domain appears to be the part of the molecule that binds to calmodulin.
• COG RimK 298aa 4e-06 in ref transcript
  • Glutathione synthase/Ribosomal protein S6 modification enzyme (glutaminyl transferase) [Coenzyme metabolism / Translation, ribosomal structure and biogenesis].

SYNE2

• rs.SYNE2.F2 rs.SYNE2.R2 132 174
• NCBIGene 36.3 23224
• Alternative 3-prime, size difference: 42
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_182914

• cd SPEC 214aa 1e-12 in ref transcript
  • Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here.
• cd CH 103aa 5e-12 in ref transcript
  • Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav).
• cd SPEC 215aa 1e-10 in ref transcript
• cd CH 103aa 6e-10 in ref transcript
• cd SPEC 214aa 4e-09 in ref transcript
• cd SPEC 221aa 8e-08 in ref transcript
• Changed! cd SPEC 216aa 1e-07 in ref transcript
• cd SPEC 207aa 2e-05 in ref transcript
• pfam KASH 60aa 7e-14 in ref transcript
  • Nuclear envelope localisation domain. The KASH (for Klarsicht/ANC-1/Syne-1 homology) or KLS domain is a highly hydrophobic nuclear envelope localisation domain of approximately 60 amino acids comprising an 20-amino-acid transmembrane region and a 30-35-residue C-terminal region that lies between the inner and the outer nuclear membranes.
• pfam CH 99aa 2e-13 in ref transcript
  • Calponin homology (CH) domain. The CH domain is found in both cytoskeletal proteins and signal transduction proteins. The CH domain is involved in actin binding in some members of the family. However in calponins there is evidence that the CH domain is not involved in its actin binding activity. Most proteins have two copies of the CH domain, however some proteins such as calponin have only a single copy.
• smart CH 102aa 2e-13 in ref transcript
  • Calponin homology domain. Actin binding domains present in duplicate at the N-termini of spectrin-like proteins (including dystrophin, alpha-actinin). These domains cross-link actin filaments into bundles and networks. A calponin homology domain is predicted in yeasst Cdc24p.
• pfam SMC_N 302aa 1e-06 in ref transcript
  • RecF/RecN/SMC N terminal domain. This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.
• TIGR SMC_prok_B 305aa 4e-05 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• smart SPEC 102aa 9e-05 in ref transcript
  • Spectrin repeats.
• smart SPEC 104aa 3e-04 in ref transcript
• TIGR SMC_prok_A 303aa 3e-04 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent.
• TIGR SMC_prok_A 375aa 4e-04 in ref transcript
• pfam SMC_N 281aa 0.002 in ref transcript
• COG SAC6 255aa 3e-22 in ref transcript
  • Ca2+-binding actin-bundling protein fimbrin/plastin (EF-Hand superfamily) [Cytoskeleton].
• COG Smc 266aa 3e-04 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].
• Changed! cd SPEC 230aa 1e-05 in modified transcript

SYTL2

• rs.SYTL2.F1 rs.SYTL2.R1 110 158
• NCBIGene 36.3 54843
• Single exon skipping, size difference: 48
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_206927

• cd C2_1 127aa 9e-17 in ref transcript
  • Protein kinase C conserved region 2, subgroup 1; C2 Ca2+-binding motif present in phospholipases, protein kinases C, and synaptotagmins (amongst others); some PKCs lack calcium dependence. Particular C2s appear to bind phospholipids, inositol polyphosphates,and intracellular proteins. Two distinct C2 topologies generated by permutation of the sequence with respect to the N- and C-terminal beta strands are seen. In this subgroup, containing synaptotagmins, specific protein kinases C (PKC) subtypes and other proteins, the N-terminal beta strand occupies the position of what is the C-terminal strand in subgroup 2.
• cd C2_1 128aa 4e-15 in ref transcript
• pfam C2 90aa 2e-10 in ref transcript
  • C2 domain.
• pfam C2 88aa 7e-10 in ref transcript

TAC4

• rs.TAC4.F1 rs.TAC4.R1 102 120
• NCBIGene 36.3 255061
• Alternative 5-prime, size difference: 18
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_170685

TAC4

• rs.TAC4.F2 rs.TAC4.R2 139 172
• NCBIGene 36.3 255061
• Single exon skipping, size difference: 33
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_170685

TAC4

• rs.TAC4.F3 rs.TAC4.R3 164 224
• NCBIGene 36.3 255061
• Single exon skipping, size difference: 60
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_170685

TAX1BP1

• rs.TAX1BP1.F1 rs.TAX1BP1.R1 200 326
• NCBIGene 36.3 8887
• Alternative 5-prime, size difference: 126
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_006024

• pfam CALCOCO1 454aa 3e-51 in ref transcript
  • Calcium binding and coiled-coil domain (CALCOCO1) like. Proteins found in this family are similar to the coiled-coil transcriptional coactivator protein coexpressed by Mus musculus (CoCoA/CALCOCO1). This protein binds to a highly conserved N-terminal domain of p160 coactivators, such as GRIP1, and thus enhances transcriptional activation by a number of nuclear receptors. CALCOCO1 has a central coiled-coil region with three leucine zipper motifs, which is required for its interaction with GRIP1 and may regulate the autonomous transcriptional activation activity of the C-terminal region.
• TIGR SMC_prok_B 249aa 2e-05 in ref transcript
  • SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
• COG Smc 316aa 2e-10 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].

TBCE

• rs.TBCE.F1 rs.TBCE.R1 154 202
• NCBIGene 36.3 6905
• Alternative 5-prime, size difference: 48
• Exclusion in 5'UTR
• Reference transcript: NM_001079515

• cd LRR_RI 159aa 7e-05 in ref transcript
  • Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1).
• pfam CAP_GLY 67aa 9e-20 in ref transcript
  • CAP-Gly domain. Cytoskeleton-associated proteins (CAPs) are involved in the organisation of microtubules and transportation of vesicles and organelles along the cytoskeletal network. A conserved motif, CAP-Gly, has been identified in a number of CAPs, including CLIP-170 and dynactins. The crystal structure of Caenorhabditis elegans F53F4.3 protein CAP-Gly domain was recently solved. The domain contains three beta-strands. The most conserved sequence, GKNDG, is located in two consecutive sharp turns on the surface, forming the entrance to a groove.
• COG NIP100 67aa 1e-07 in ref transcript
  • Dynactin complex subunit involved in mitotic spindle partitioning in anaphase B [Cell division and chromosome partitioning].
• COG COG4886 217aa 4e-07 in ref transcript
  • Leucine-rich repeat (LRR) protein [Function unknown].

TBX3

• rs.TBX3.F1 rs.TBX3.R1 283 343
• NCBIGene 36.3 6926
• Single exon skipping, size difference: 60
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_016569

• Changed! cd TBOX 202aa 1e-85 in ref transcript
  • T-box DNA binding domain of the T-box family of transcriptional regulators. The T-box family is an ancient group that appears to play a critical role in development in all animal species. These genes were uncovered on the basis of similarity to the DNA binding domain of murine Brachyury (T) gene product, the defining feature of the family. Common features shared by T-box family members are DNA-binding and transcriptional regulatory activity, a role in development and conserved expression patterns, most of the known genes in all species being expressed in mesoderm or mesoderm precursors.
• Changed! pfam T-box 200aa 1e-97 in ref transcript
  • T-box. The T-box encodes a 180 amino acid domain that binds to DNA. Genes encoding T-box proteins are found in a wide range of animals, but not in other kingdoms such as plants. Family members are all thought to bind to the DNA consensus sequence TCACACCT. they are found exclusively in the nucleus, and perform DNA-binding and transcriptional activation/repression roles. They are generally required for development of the specific tissues they are expressed in, and mutations in T-box genes are implicated in human conditions such as DiGeorge syndrome and X-linked cleft palate, which feature malformations.
• Changed! cd TBOX 182aa 4e-89 in modified transcript
• Changed! pfam T-box 180aa 1e-101 in modified transcript

TCEAL1

• rs.TCEAL1.F1 rs.TCEAL1.R1 100 112
• NCBIGene 36.3 9338
• Alternative 5-prime, size difference: 12
• Exclusion in 5'UTR
• Reference transcript: NM_004780

• pfam TFA 86aa 3e-12 in ref transcript
  • Transcription elongation factor A, SII-related family. The function of this family is unclear, but two members from Homo sapiesn are described as transcription elongation factor A, SII-like proteins.

TCEAL3

• rs.TCEAL3.F1 rs.TCEAL3.R1 99 111
• NCBIGene 36.3 85012
• Alternative 5-prime, size difference: 12
• Exclusion in 5'UTR
• Reference transcript: NM_001006933

• pfam TFA 133aa 2e-11 in ref transcript
  • Transcription elongation factor A, SII-related family. The function of this family is unclear, but two members from Homo sapiesn are described as transcription elongation factor A, SII-like proteins.

TCEAL4

• rs.TCEAL4.F1 rs.TCEAL4.R1 178 237
• NCBIGene 36.3 79921
• Alternative 5-prime, size difference: 59
• Exclusion in 5'UTR
• Reference transcript: NM_024863

• pfam TFA 79aa 5e-08 in ref transcript
  • Transcription elongation factor A, SII-related family. The function of this family is unclear, but two members from Homo sapiesn are described as transcription elongation factor A, SII-like proteins.

TCF12

• rs.TCF12.F1 rs.TCF12.R1 90 100
• NCBIGene 36.3 6938
• Alternative 3-prime, size difference: 10
• Inclusion in 5'UTR
• Reference transcript: NM_207036

• cd HLH 61aa 1e-06 in ref transcript
  • Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins.
• smart HLH 54aa 7e-10 in ref transcript
  • helix loop helix domain.

TCF19

• rs.TCF19.F1 rs.TCF19.R1 124 370
• NCBIGene 36.3 6941
• Alternative 3-prime, size difference: 246
• Inclusion in 5'UTR
• Reference transcript: NM_001077511

• cd FHA 98aa 2e-08 in ref transcript
  • Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins localize to the nucleus, where they participate in establishing or maintaining cell cycle checkpoints, DNA repair, or transcriptional regulation. Members of the FHA family include: Dun1, Rad53, Cds1, Mek1, KAPP(kinase-associated protein phosphatase),and Ki-67 (a human nuclear protein related to cell proliferation).
• pfam FHA 72aa 4e-06 in ref transcript
  • FHA domain. The FHA (Forkhead-associated) domain is a phosphopeptide binding motif.
• pfam PHD 36aa 2e-05 in ref transcript
  • PHD-finger. PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.

TCF4

• rs.TCF4.F1 rs.TCF4.R1 101 113
• NCBIGene 36.3 6925
• Alternative 5-prime, size difference: 12
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001083962

• cd HLH 61aa 2e-07 in ref transcript
  • Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins.
• smart HLH 54aa 2e-10 in ref transcript
  • helix loop helix domain.

TCL6

• rs.TCL6.F1 rs.TCL6.R1 352 547
• NCBIGene 36.3 27004
• Mutually exclusive exon skipping, size difference: 195
• Inclusion in 5'UTR, Exclusion of the protein initiation site
• Reference transcript: NM_020554

TCOF1

• rs.TCOF1.F1 rs.TCOF1.R1 135 366
• NCBIGene 36.3 6949
• Single exon skipping, size difference: 231
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001008656

• pfam Treacle 321aa 9e-36 in ref transcript
  • Treacher Collins syndrome protein Treacle.

TCP11

• rs.TCP11.F1 rs.TCP11.R1 413 507
• NCBIGene 36.3 6954
• Mutually exclusive exon skipping, size difference: 94
• Inclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_001093728

• Changed! pfam Tcp11 433aa 1e-130 in ref transcript
  • T-complex protein 11. This family consists of several eukaryotic T-complex protein 11 (Tcp11) related sequences. Tcp11 is only expressed in fertile adult mammalian testes and is thought to be important in sperm function and fertility. The family also contains the yeast Sok1 protein which is known to suppress cyclic AMP-dependent protein kinase mutants.

TCTN1

• rs.TCTN1.F1 rs.TCTN1.R1 225 267
• NCBIGene 36.3 79600
• Mutually exclusive exon skipping, size difference: 42
• Inclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_001082538

• Changed! pfam DUF1619 310aa 1e-106 in ref transcript
  • Protein of unknown function (DUF1619). This is a family of sequences derived from hypothetical eukaryotic proteins. The region in question is approximately 330 residues long and has a cysteine rich amino-terminus.
• Changed! pfam DUF1619 296aa 8e-88 in modified transcript

TCTN1

• rs.TCTN1.F2 rs.TCTN1.R2 100 115
• NCBIGene 36.3 79600
• Alternative 3-prime, size difference: 15
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001082538

• pfam DUF1619 310aa 1e-106 in ref transcript
  • Protein of unknown function (DUF1619). This is a family of sequences derived from hypothetical eukaryotic proteins. The region in question is approximately 330 residues long and has a cysteine rich amino-terminus.

TDRKH

• rs.TDRKH.F1 rs.TDRKH.R1 143 278
• NCBIGene 36.3 11022
• Alternative 5-prime and 3-prime, size difference: 135
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_006862

• Changed! cd KH-I 63aa 6e-12 in ref transcript
  • K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
• cd TUDOR 48aa 2e-08 in ref transcript
  • Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal.
• pfam TUDOR 120aa 8e-30 in ref transcript
  • Tudor domain. Domain of unknown function present in several RNA-binding proteins. copies in the Drosophila Tudor protein.
• Changed! pfam KH_1 62aa 4e-13 in ref transcript
  • KH domain. KH motifs can bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.
• Changed! PRK PRK11824 65aa 0.001 in ref transcript
  • polynucleotide phosphorylase/polyadenylase; Provisional.
• Changed! cd KH-I 59aa 1e-09 in modified transcript
• Changed! pfam KH_1 59aa 6e-11 in modified transcript
• Changed! PRK PRK11824 33aa 0.004 in modified transcript

TDRKH

• rs.TDRKH.F2 rs.TDRKH.R2 141 166
• NCBIGene 36.3 11022
• Alternative 5-prime, size difference: 25
• Exclusion in 5'UTR
• Reference transcript: NM_006862

• cd KH-I 63aa 6e-12 in ref transcript
  • K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
• cd TUDOR 48aa 2e-08 in ref transcript
  • Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal.
• pfam TUDOR 120aa 8e-30 in ref transcript
  • Tudor domain. Domain of unknown function present in several RNA-binding proteins. copies in the Drosophila Tudor protein.
• pfam KH_1 62aa 4e-13 in ref transcript
  • KH domain. KH motifs can bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.
• PRK PRK11824 65aa 0.001 in ref transcript
  • polynucleotide phosphorylase/polyadenylase; Provisional.

TERF1

• rs.TERF1.F1 rs.TERF1.R1 104 164
• NCBIGene 36.3 7013
• Single exon skipping, size difference: 60
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_017489

• cd TRFH 188aa 5e-76 in ref transcript
  • Telomeric Repeat binding Factor or TTAGGG Repeat binding Factor, central (dimerization) domain Homology; TRFH. Telomeres are protein/DNA complexes that make up the physical ends of eukaryotic linear chromosomes and are essential for chromosome stability, protecting the chromosome ends from degradation and end-to-end fusion. Proteins TRF1, TRF2 and Taz1 bind telomeric DNA and are also involved in recruiting interacting proteins, TIN2, and Rap1, to the telomeres. It has also been demonstrated that PARP1 associates with TRF2 and is capable of poly(ADP-ribosyl)ation of TRF2, which affects binding of TRF2 to telomeric DNA. TRF1, TRF2 and Taz1 proteins contain three functional domains: an N-terminal acidic domain, a central TRF-specific/dimerization domain, and a C-terminal DNA binding domain with a single Myb-like repeat. Homodimerization, a prerequisite to DNA binding, results in the juxtaposition of two Myb DNA binding domains.
• cd SANT 47aa 2e-05 in ref transcript
  • 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
• pfam TRF 181aa 1e-78 in ref transcript
  • Telomere repeat binding factor (TRF). Telomere repeat binding factor (TRF) family proteins are important for the regulation of telomere stability. The two related human TRF proteins hTRF1 and hTRF2 form homodimers and bind directly to telomeric TTAGGG repeats via the myb DNA binding domain pfam00249 at the carboxy terminus. TRF1 is implicated in telomere length regulation and TRF2 in telomere protection. Other telomere complex associated proteins are recruited through their interaction with either TRF1 or TRF2. The fission yeast protein Taz1p (telomere-associated in Schizosaccharomyces pombe) has similarity to both hTRF1 and hTRF2 and may perform the dual functions of TRF1 and TRF2 at fission yeast telomeres. This domain is composed of multiple alpha helices arranged in a solenoid conformation similar to TPR repeats.
• pfam Myb_DNA-binding 49aa 1e-07 in ref transcript
  • Myb-like DNA-binding domain. This family contains the DNA binding domains from Myb proteins, as well as the SANT domain family.

TERT

• rs.TERT.F1 rs.TERT.R1 208 244
• NCBIGene 36.3 7015
• Alternative 3-prime, size difference: 36
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_198253

• cd TERT 112aa 8e-23 in ref transcript
  • TERT: Telomerase reverse transcriptase (TERT). Telomerase is a ribonucleoprotein (RNP) that synthesizes telomeric DNA repeats. The telomerase RNA subunit provides the template for synthesis of these repeats. The catalytic subunit of RNP is known as telomerase reverse transcriptase (TERT). The reverse transcriptase (RT) domain is located in the C-terminal region of the TERT polypeptide. Single amino acid substitutions in this region lead to telomere shortening and senescence. Telomerase is an enzyme that, in certain cells, maintains the physical ends of chromosomes (telomeres) during replication. In somatic cells, replication of the lagging strand requires the continual presence of an RNA primer approximately 200 nucleotides upstream, which is complementary to the template strand. Since there is a region of DNA less than 200 base pairs from the end of the chromosome where this is not possible, the chromosome is continually shortened. However, a surplus of repetitive DNA at the chromosome ends protects against the erosion of gene-encoding DNA. Telomerase is not normally expressed in somatic cells. It has been suggested that exogenous TERT may extend the lifespan of, or even immortalize, the cell. However, recent studies have shown that telomerase activity can be induced by a number of oncogenes. Conversely, the oncogene c-myc can be activated in human TERT immortalized cells. Sequence comparisons place the telomerase proteins in the RT family but reveal hallmarks that distinguish them from retroviral and retrotransposon relatives.

TH

• rs.TH.F1 rs.TH.R1 100 112
• NCBIGene 36.3 7054
• Alternative 5-prime, size difference: 12
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_199292

• cd eu_TyrOH 298aa 1e-166 in ref transcript
  • Eukaryotic tyrosine hydroxylase (TyrOH); a member of the biopterin-dependent aromatic amino acid hydroxylase family of non-heme, iron(II)-dependent enzymes that also includes prokaryotic and eukaryotic phenylalanine-4-hydroxylase (PheOH) and eukaryotic tryptophan hydroxylase (TrpOH). TyrOH catalyzes the conversion of tyrosine to L-dihydroxyphenylalanine (L-DOPA), the rate-limiting step in the biosynthesis of the catecholamines dopamine, noradrenaline, and adrenaline.
• cd ACT_TH 122aa 6e-30 in ref transcript
  • ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, tyrosine hydroxylases (TH). TH catalyses the hydroxylation of L-Tyr to 3,4-dihydroxyphenylalanine, the rate limiting step in the biosynthesis of catecholamines (dopamine, noradrenaline and adrenaline), functioning as hormones and neurotransmitters. The enzyme is not regulated by its amino acid substrate, but instead by phosphorylation at several serine residues located N-terminal of the ACT domain, and by feedback inhibition by catecholamines at the active site. Members of this CD belong to the superfamily of ACT regulatory domains.
• TIGR Tyr_3_monoox 457aa 0.0 in ref transcript
  • This model describes tyrosine 3-monooxygenase, a member of the family of tetrameric, biopterin-dependent aromatic amino acid hydroxylases found in metazoans. It is closely related to tetrameric phenylalanine-4-hydroxylase and tryptophan 5-monooxygenase, and more distantly related to the monomeric phenylalanine-4-hydroxylase found in some Gram-negative bacteria.
• PRK phhA 238aa 5e-61 in ref transcript
  • phenylalanine 4-monooxygenase; Reviewed.

THADA

• rs.THADA.F1 rs.THADA.R1 116 400
• NCBIGene 36.3 63892
• Alternative 5-prime, size difference: 284
• Exclusion in 5'UTR
• Reference transcript: NM_001083953

• pfam DUF2428 304aa 3e-68 in ref transcript
  • Putative death-receptor fusion protein (DUF2428). This is a family of proteins conserved from plants to humans. The function is not known. Several members have been annotated as being HEAT repeat-containing proteins while others are designated as death-receptor interacting proteins, but neither of these could be confirmed.
• COG COG5543 475aa 5e-37 in ref transcript
  • Uncharacterized conserved protein [Function unknown].

TIA1

• rs.TIA1.F1 rs.TIA1.R1 100 133
• NCBIGene 36.3 7072
• Single exon skipping, size difference: 33
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_022173

• cd RRM 74aa 3e-19 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• cd RRM 73aa 1e-15 in ref transcript
• cd RRM 69aa 6e-14 in ref transcript
• Changed! TIGR PABP-1234 269aa 2e-24 in ref transcript
  • There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, and of unknown tissue range.
• Changed! COG COG0724 177aa 1e-18 in ref transcript
  • RNA-binding proteins (RRM domain) [General function prediction only].
• Changed! COG COG0724 175aa 7e-12 in ref transcript
• Changed! TIGR PABP-1234 258aa 2e-27 in modified transcript
• Changed! COG COG0724 200aa 4e-19 in modified transcript

TIRAP

• rs.TIRAP.F1 rs.TIRAP.R1 100 116
• NCBIGene 36.3 114609
• Alternative 5-prime, size difference: 16
• Exclusion in 5'UTR
• Reference transcript: NM_148910

• smart TIR 83aa 3e-07 in ref transcript
  • Toll - interleukin 1 - resistance.

TJP2

• rs.TJP2.F1 rs.TJP2.R1 101 542
• NCBIGene 36.3 9414
• Multiple exon skipping, size difference: 441
• Exclusion in the protein (no frameshift), Exclusion in the protein (no frameshift)
• Reference transcript: NM_004817

• cd PDZ_signaling 86aa 9e-15 in ref transcript
  • PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of PDZ domains an N-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in proteases.
• cd PDZ_signaling 80aa 1e-09 in ref transcript
• cd PDZ_signaling 75aa 1e-07 in ref transcript
• smart GuKc 188aa 3e-33 in ref transcript
  • Guanylate kinase homologues. Active enzymes catalyze ATP-dependent phosphorylation of GMP to GDP. Structure resembles that of adenylate kinase. So-called membrane-associated guanylate kinase homologues (MAGUKs) do not possess guanylate kinase activities; instead at least some possess protein-binding functions.
• smart PDZ 90aa 6e-14 in ref transcript
  • Domain present in PSD-95, Dlg, and ZO-1/2. Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities.
• smart PDZ 72aa 1e-10 in ref transcript
• smart PDZ 78aa 3e-10 in ref transcript
• pfam SH3_2 59aa 0.001 in ref transcript
  • Variant SH3 domain. SH3 (Src homology 3) domains are often indicative of a protein involved in signal transduction related to cytoskeletal organisation. First described in the Src cytoplasmic tyrosine kinase. The structure is a partly opened beta barrel.
• COG Prc 88aa 1e-05 in ref transcript
  • Periplasmic protease [Cell envelope biogenesis, outer membrane].

TMC5

• rs.TMC5.F1 rs.TMC5.R1 100 274
• NCBIGene 36.3 79838
• Single exon skipping, size difference: 174
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001105248

• pfam TMC 107aa 3e-48 in ref transcript
  • TMC domain. These sequences are similar to a region conserved amongst various protein products of the transmembrane channel-like (TMC) gene family, such as Transmembrane channel-like protein 3 and EVIN2 - this region is termed the TMC domain. Mutations in these genes are implicated in a number of human conditions, such as deafness and epidermodysplasia verruciformis. TMC proteins are thought to have important cellular roles, and may be modifiers of ion channels or transporters.

TMEM134

• rs.TMEM134.F1 rs.TMEM134.R1 112 157
• NCBIGene 36.3 80194
• Single exon skipping, size difference: 45
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_025124

• Changed! pfam DUF872 81aa 7e-19 in ref transcript
  • Eukaryotic protein of unknown function (DUF872). This family consists of several uncharacterised eukaryotic proteins. The function of this family is unknown.
• Changed! pfam DUF872 38aa 8e-13 in modified transcript

TMEM134

• rs.TMEM134.F2 rs.TMEM134.R2 120 147
• NCBIGene 36.3 80194
• Alternative 3-prime, size difference: 27
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_025124

• pfam DUF872 81aa 7e-19 in ref transcript
  • Eukaryotic protein of unknown function (DUF872). This family consists of several uncharacterised eukaryotic proteins. The function of this family is unknown.

TMEM176B

• rs.TMEM176B.F1 rs.TMEM176B.R1 341 452
• NCBIGene 36.3 28959
• Single exon skipping, size difference: 111
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_014020

• Changed! pfam LR8 205aa 2e-75 in ref transcript
  • LR8 protein. This family consists of several LR8 like proteins from humans, mice and rats. The function of the human LR8 protein is unknown although it is known to be strongly expressed in the lung fibroblasts.
• Changed! pfam LR8 168aa 2e-61 in modified transcript

TMEM177

• rs.TMEM177.F1 rs.TMEM177.R1 105 446
• NCBIGene 36.3 80775
• Alternative 5-prime, size difference: 341
• Exclusion in 5'UTR
• Reference transcript: NM_001105198

TMEM22

• rs.TMEM22.F1 rs.TMEM22.R1 132 397
• NCBIGene 36.3 80723
• Alternative 5-prime, size difference: 265
• Exclusion in 5'UTR
• Reference transcript: NM_025246

• TIGR 2A78 258aa 1e-08 in ref transcript
• COG RhaT 288aa 2e-10 in ref transcript
  • Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only].

TMEM55B

• rs.TMEM55B.F1 rs.TMEM55B.R1 106 127
• NCBIGene 36.3 90809
• Alternative 5-prime, size difference: 21
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001100814

• Changed! pfam Tmemb_55A 277aa 3e-85 in ref transcript
  • Transmembrane protein 55A. Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
• Changed! pfam Tmemb_55A 270aa 3e-84 in modified transcript

TMEM70

• rs.TMEM70.F1 rs.TMEM70.R1 102 116
• NCBIGene 36.3 54968
• Alternative 5-prime, size difference: 14
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_017866

• Changed! pfam DUF1301 135aa 6e-56 in ref transcript
  • Protein of unknown function (DUF1301). This family contains a number of eukaryotic proteins of unknown function that are approximately 160 residues long.

TMEM80

• rs.TMEM80.F1 rs.TMEM80.R1 136 160
• NCBIGene 36.3 283232
• Alternative 5-prime, size difference: 24
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001042463

• pfam Transmemb_17 68aa 1e-05 in ref transcript
  • Predicted membrane protein. This is a 100 amino acid region of a family of proteins conserved from nematodes to humans. It is predicted to be a transmembrane region but its function is not known.

TMEM91

• rs.TMEM91.F1 rs.TMEM91.R1 222 376
• NCBIGene 36.3 641649
• Alternative 3-prime, size difference: 154
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_001098821

• Changed! pfam CD225 49aa 1e-08 in ref transcript
  • Interferon-induced transmembrane protein. This family includes the human leukocyte antigen CD225, which is an interferon inducible transmembrane protein, and is associated with interferon induced cell growth suppression.
• Changed! pfam CD225 29aa 0.003 in modified transcript

TMPO

• rs.TMPO.F1 rs.TMPO.R1 150 477
• NCBIGene 36.3 7112
• Multiple exon skipping, size difference: 327
• Exclusion in the protein (no frameshift), Exclusion in the protein (no frameshift), Exclusion in the protein (no frameshift)
• Reference transcript: NM_001032283

• pfam Thymopoietin 49aa 4e-19 in ref transcript
  • Thymopoietin protein. Short protein of 49 amino acid isolated from bovine spleen cells. Thymopoietins (TMPOs) are a group of ubiquitously expressed nuclear proteins. They are suggested to play an important role in nuclear envelope organisation and cell cycle control.
• pfam LEM 28aa 1e-04 in ref transcript
  • LEM domain. The LEM domain is 50 residues long and is composed of two parallel alpha helices. This domain is found in inner nuclear membrane proteins. It is called the LEM domain after LAP2, Emerin and Man1.

TMPRSS4

• rs.TMPRSS4.F1 rs.TMPRSS4.R1 104 119
• NCBIGene 36.3 56649
• Alternative 3-prime, size difference: 15
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_019894

• cd Tryp_SPc 228aa 2e-68 in ref transcript
  • Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
• cd LDLa 35aa 0.002 in ref transcript
  • Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure.
• smart Tryp_SPc 226aa 2e-77 in ref transcript
  • Trypsin-like serine protease. Many of these are synthesised as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. A few, however, are active as single chain molecules, and others are inactive due to substitutions of the catalytic triad residues.
• Changed! smart SR 91aa 9e-07 in ref transcript
  • Scavenger receptor Cys-rich. The sea ucrhin egg peptide speract contains 4 repeats of SR domains that contain 6 conserved cysteines. May bind bacterial antigens in the protein MARCO.
• pfam Ldl_recept_a 22aa 0.005 in ref transcript
  • Low-density lipoprotein receptor domain class A.
• COG COG5640 228aa 8e-26 in ref transcript
  • Secreted trypsin-like serine protease [Posttranslational modification, protein turnover, chaperones].
• Changed! smart SR 86aa 4e-07 in modified transcript

TMTC4

• rs.TMTC4.F1 rs.TMTC4.R1 143 353
• NCBIGene 36.3 84899
• Single exon skipping, size difference: 210
• Exclusion of the protein initiation site
• Reference transcript: NM_032813

• cd TPR 100aa 3e-12 in ref transcript
  • Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and Cdc27p components of the cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal targeting signals, the Tom70p co-receptor for mitochondrial targeting signals, Ser/Thr phosphatase 5C and the p110 subunit of O-GlcNAc transferase; three copies of the repeat are present here.
• cd TPR 99aa 4e-11 in ref transcript
• cd TPR 99aa 2e-07 in ref transcript
• cd TPR 85aa 1e-06 in ref transcript
• pfam DUF1736 80aa 5e-33 in ref transcript
  • Domain of unknown function (DUF1736). This domain of unknown function is found in various hypothetical metazoan proteins.
• TIGR PEP_TPR_lipo 231aa 1e-12 in ref transcript
  • This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of tetratricopeptide repeats (TPR) suggests protein-protein interaction, possibly for the regulation of PEP-CTERM protein expression, since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator.
• COG TadD 202aa 5e-08 in ref transcript
  • Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking and secretion].

TMUB2

• rs.TMUB2.F1 rs.TMUB2.R1 133 220
• NCBIGene 36.3 79089
• Alternative 3-prime, size difference: 87
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_001076674

• Changed! cd UBL 63aa 9e-06 in ref transcript
  • UBLs function by remodeling the surface of their target proteins, changing their target's half-life, enzymatic activity, protein-protein interactions, subcellular localization or other properties. At least 10 different ubiquitin-like modifications exist in mammals, and attachment of different ubls to a target leads to different biological consequences. Ubl-conjugation cascades are initiated by activating enzymes, which also coordinate the ubls with their downstream pathways.
• Changed! pfam ubiquitin 51aa 6e-08 in ref transcript
  • Ubiquitin family. This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue), Nedd8, Elongin B, Rub1, and Parkin. A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites.

TMUB2

• rs.TMUB2.F2 rs.TMUB2.R1 186 254
• NCBIGene 36.3 79089
• Single exon skipping, size difference: 68
• Exclusion of the protein initiation site
• Reference transcript: NM_001076674

• cd UBL 63aa 9e-06 in ref transcript
  • UBLs function by remodeling the surface of their target proteins, changing their target's half-life, enzymatic activity, protein-protein interactions, subcellular localization or other properties. At least 10 different ubiquitin-like modifications exist in mammals, and attachment of different ubls to a target leads to different biological consequences. Ubl-conjugation cascades are initiated by activating enzymes, which also coordinate the ubls with their downstream pathways.
• pfam ubiquitin 51aa 6e-08 in ref transcript
  • Ubiquitin family. This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue), Nedd8, Elongin B, Rub1, and Parkin. A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites.

TNRC15

• rs.TNRC15.F1 rs.TNRC15.R1 116 186
• NCBIGene 36.3 26058
• Single exon skipping, size difference: 70
• Inclusion in 5'UTR
• Reference transcript: NM_001103147

• cd GYF 56aa 5e-16 in ref transcript
  • GYF domain: contains conserved Gly-Tyr-Phe residues; Proline-binding domain in CD2-binding and other proteins. Involved in signaling lymphocyte activity. Also present in other unrelated proteins (mainly unknown) derived from diverse eukaryotic species.
• pfam GYF 56aa 4e-18 in ref transcript
  • GYF domain. The GYF domain is named because of the presence of Gly-Tyr-Phe residues. The GYF domain is a proline-binding domain in CD2-binding protein.

TNRC15

• rs.TNRC15.F2 rs.TNRC15.R2 100 118
• NCBIGene 36.3 26058
• Alternative 3-prime, size difference: 18
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001103147

• cd GYF 56aa 5e-16 in ref transcript
  • GYF domain: contains conserved Gly-Tyr-Phe residues; Proline-binding domain in CD2-binding and other proteins. Involved in signaling lymphocyte activity. Also present in other unrelated proteins (mainly unknown) derived from diverse eukaryotic species.
• pfam GYF 56aa 4e-18 in ref transcript
  • GYF domain. The GYF domain is named because of the presence of Gly-Tyr-Phe residues. The GYF domain is a proline-binding domain in CD2-binding protein.

TNRC15

• rs.TNRC15.F3 rs.TNRC15.R3 158 224
• NCBIGene 36.3 26058
• Single exon skipping, size difference: 66
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001103147

• cd GYF 56aa 5e-16 in ref transcript
  • GYF domain: contains conserved Gly-Tyr-Phe residues; Proline-binding domain in CD2-binding and other proteins. Involved in signaling lymphocyte activity. Also present in other unrelated proteins (mainly unknown) derived from diverse eukaryotic species.
• pfam GYF 56aa 4e-18 in ref transcript
  • GYF domain. The GYF domain is named because of the presence of Gly-Tyr-Phe residues. The GYF domain is a proline-binding domain in CD2-binding protein.

TNRC15

• rs.TNRC15.F4 rs.TNRC15.R4 106 176
• NCBIGene 36.3 26058
• Single exon skipping, size difference: 70
• Exclusion in 5'UTR
• Reference transcript: NM_001103147

• cd GYF 56aa 5e-16 in ref transcript
  • GYF domain: contains conserved Gly-Tyr-Phe residues; Proline-binding domain in CD2-binding and other proteins. Involved in signaling lymphocyte activity. Also present in other unrelated proteins (mainly unknown) derived from diverse eukaryotic species.
• pfam GYF 56aa 4e-18 in ref transcript
  • GYF domain. The GYF domain is named because of the presence of Gly-Tyr-Phe residues. The GYF domain is a proline-binding domain in CD2-binding protein.

TOM1L2

• rs.TOM1L2.F1 rs.TOM1L2.R1 159 309
• NCBIGene 36.3 146691
• Single exon skipping, size difference: 150
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001082968

• Changed! cd VHS_Tom1 141aa 2e-74 in ref transcript
  • VHS domain family, Tom1 subfamily; The VHS domain is an essential part of Tom1 (Target of myb1 - retroviral oncogene) protein. The VHS domain has a superhelical structure similar to the structure of the ARM repeats and is present at the very N-termini of proteins. It is a right-handed superhelix of eight alpha helices. The VHS domain has been found in a number of proteins, some of which have been implicated in intracellular trafficking and sorting. The VHS domain of the Tom1 protein is essential for the negative regulation of Interleukin-1 and Tumor Necrosis Factor-induced signaling pathways.
• Changed! smart VHS 136aa 2e-46 in ref transcript
  • Domain present in VPS-27, Hrs and STAM. Unpublished observations. Domain of unknown function.
• pfam GAT 93aa 5e-21 in ref transcript
  • GAT domain. The GAT domain is responsible for binding of GGA proteins to several members of the ARF family including ARF1 and ARF3. The GAT domain stabilises membrane bound ARF1 in its GTP bound state, by interfering with GAP proteins.
• Changed! cd VHS_Tom1 91aa 2e-39 in modified transcript
• Changed! smart VHS 86aa 1e-21 in modified transcript

TOX2

• rs.TOX2.F1 rs.TOX2.R1 272 353
• NCBIGene 36.3 84969
• Single exon skipping, size difference: 81
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001098797

• Changed! cd HMG-box 48aa 9e-10 in ref transcript
  • High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4; and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions.
• Changed! pfam HMG_box 49aa 4e-07 in ref transcript
  • HMG (high mobility group) box.
• Changed! COG NHP6B 48aa 3e-04 in ref transcript
  • Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics].
• Changed! cd HMG-box 43aa 1e-08 in modified transcript
• Changed! pfam HMG_box 44aa 3e-06 in modified transcript
• Changed! COG NHP6B 43aa 0.002 in modified transcript

TOX2

• rs.TOX2.F2 rs.TOX2.R2 103 228
• NCBIGene 36.3 84969
• Single exon skipping, size difference: 125
• Exclusion in 5'UTR
• Reference transcript: NM_032883

• cd HMG-box 48aa 1e-09 in ref transcript
  • High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4; and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions.
• pfam HMG_box 49aa 4e-07 in ref transcript
  • HMG (high mobility group) box.
• COG NHP6B 48aa 5e-04 in ref transcript
  • Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics].

TP53BP2

• rs.TP53BP2.F1 rs.TP53BP2.R1 304 436
• NCBIGene 36.3 7159
• Single exon skipping, size difference: 132
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_001031685

• Changed! cd ANK 118aa 4e-20 in ref transcript
  • ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats.
• Changed! cd SH3 51aa 2e-09 in ref transcript
  • Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
• Changed! smart SH3 49aa 2e-10 in ref transcript
  • Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.
• Changed! pfam Ank 32aa 2e-06 in ref transcript
  • Ankyrin repeat. There's no clear separation between noise and signal on the HMM search Ankyrin repeats generally consist of a beta, alpha, alpha, beta order of secondary structures. The repeats associate to form a higher order structure.
• Changed! pfam Ank 32aa 2e-05 in ref transcript
• Changed! pfam SMC_N 146aa 2e-05 in ref transcript
  • RecF/RecN/SMC N terminal domain. This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.
• Changed! COG Arp 95aa 6e-05 in ref transcript
  • FOG: Ankyrin repeat [General function prediction only].
• Changed! COG SbcC 144aa 1e-04 in ref transcript
  • ATPase involved in DNA repair [DNA replication, recombination, and repair].

TP53I11

• rs.TP53I11.F1 rs.TP53I11.R1 250 380
• NCBIGene 36.3 9537
• Single exon skipping, size difference: 130
• Exclusion in 5'UTR
• Reference transcript: NM_001076787

TPD52

• rs.TPD52.F1 rs.TPD52.R1 101 170
• NCBIGene 36.3 7163
• Multiple exon skipping, size difference: 69
• Inclusion in the protein (no stop codon or frameshift), Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_001025252

• Changed! pfam TPD52 159aa 1e-39 in ref transcript
  • Tumour protein D52 family. The hD52 gene was originally identified through its elevated expression level in human breast carcinoma. Cloning of D52 homologues from other species has indicated that D52 may play roles in calcium-mediated signal transduction and cell proliferation. Two human homologues of hD52, hD53 and hD54, have also been identified, demonstrating the existence of a novel gene/protein family. These proteins have an amino terminal coiled-coil that allows members to form homo- and heterodimers with each other.
• Changed! pfam TPD52 182aa 7e-37 in modified transcript

TPD52L2

• rs.TPD52L2.F1 rs.TPD52L2.R1 105 165
• NCBIGene 36.3 7165
• Single exon skipping, size difference: 60
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_199360

• Changed! pfam TPD52 163aa 4e-26 in ref transcript
  • Tumour protein D52 family. The hD52 gene was originally identified through its elevated expression level in human breast carcinoma. Cloning of D52 homologues from other species has indicated that D52 may play roles in calcium-mediated signal transduction and cell proliferation. Two human homologues of hD52, hD53 and hD54, have also been identified, demonstrating the existence of a novel gene/protein family. These proteins have an amino terminal coiled-coil that allows members to form homo- and heterodimers with each other.
• Changed! pfam TPD52 143aa 2e-29 in modified transcript

TPK1

• rs.TPK1.F1 rs.TPK1.R1 312 459
• NCBIGene 36.3 27010
• Single exon skipping, size difference: 147
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_022445

• Changed! TIGR thi_PPkinase 214aa 8e-40 in ref transcript
  • This model has been revised. Originally, it described strictly eukaryotic thiamine pyrophosphokinase. However, it is now expanded to include also homologous enzymes, apparently functionally equivalent, from species that rely on thiamine pyrophosphokinase rather than thiamine-monophosphate kinase (TIGR01379) to produce the active TPP cofactor. This includes the thiamine pyrophosphokinase from Bacillus subtilis, previously designated YloS.
• Changed! COG THI80 222aa 2e-27 in ref transcript
  • Thiamine pyrophosphokinase [Coenzyme metabolism].
• Changed! pfam TPK_catalytic 90aa 2e-27 in modified transcript
  • Thiamin pyrophosphokinase, catalytic domain. Family of thiamin pyrophosphokinase (EC:2.7.6.2). Thiamin pyrophosphokinase (TPK) catalyses the transfer of a pyrophosphate group from ATP to vitamin B1 (thiamin) to form the coenzyme thiamin pyrophosphate (TPP). Thus, TPK is important for the formation of a coenzyme required for central metabolic functions. The structure of thiamin pyrophosphokinase suggest that the enzyme may operate by a mechanism of pyrophosphoryl transfer similar to those described for pyrophosphokinases functioning in nucleotide biosynthesis.
• Changed! pfam TPK_B1_binding 70aa 6e-21 in modified transcript
  • Thiamin pyrophosphokinase, vitamin B1 binding domain. Family of thiamin pyrophosphokinase (EC:2.7.6.2). Thiamin pyrophosphokinase (TPK) catalyses the transfer of a pyrophosphate group from ATP to vitamin B1 (thiamin) to form the coenzyme thiamin pyrophosphate (TPP). Thus, TPK is important for the formation of a coenzyme required for central metabolic functions. The structure of thiamin pyrophosphokinase suggest that the enzyme may operate by a mechanism of pyrophosphoryl transfer similar to those described for pyrophosphokinases functioning in nucleotide biosynthesis.
• Changed! COG THI80 173aa 4e-16 in modified transcript

TPTE2

• rs.TPTE2.F1 rs.TPTE2.R1 171 291
• NCBIGene 36.3 93492
• Single exon skipping, size difference: 120
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_199254

• cd PTPc 89aa 8e-05 in ref transcript
  • Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active.
• pfam PTEN_C2 131aa 4e-30 in ref transcript
  • C2 domain of PTEN tumour-suppressor protein. This is the C2 domain-like domain, in greek key form, of the PTEN protein, phosphatidyl-inositol triphosphate phosphatase, and it is the C-terminus. This domain may well include a CBR3 loop which means it plays a central role in membrane binding. This domain associates across an extensive interface with the N-terminal phosphatase domain DSPc (pfam00782) suggesting that the C2 domain productively positions the catalytic part of the protein on the membrane 1].
• smart PTPc_motif 59aa 2e-04 in ref transcript
  • Protein tyrosine phosphatase, catalytic domain motif.
• pfam Y_phosphatase 108aa 4e-04 in ref transcript
  • Protein-tyrosine phosphatase.
• COG CDC14 126aa 8e-07 in ref transcript
  • Predicted protein-tyrosine phosphatase [Signal transduction mechanisms].

TPTE2

• rs.TPTE2.F2 rs.TPTE2.R2 374 485
• NCBIGene 36.3 93492
• Multiple exon skipping, size difference: 111
• Exclusion in the protein (no frameshift), Exclusion in the protein (no frameshift)
• Reference transcript: NM_199254

• cd PTPc 89aa 8e-05 in ref transcript
  • Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG. Characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active.
• pfam PTEN_C2 131aa 4e-30 in ref transcript
  • C2 domain of PTEN tumour-suppressor protein. This is the C2 domain-like domain, in greek key form, of the PTEN protein, phosphatidyl-inositol triphosphate phosphatase, and it is the C-terminus. This domain may well include a CBR3 loop which means it plays a central role in membrane binding. This domain associates across an extensive interface with the N-terminal phosphatase domain DSPc (pfam00782) suggesting that the C2 domain productively positions the catalytic part of the protein on the membrane 1].
• smart PTPc_motif 59aa 2e-04 in ref transcript
  • Protein tyrosine phosphatase, catalytic domain motif.
• pfam Y_phosphatase 108aa 4e-04 in ref transcript
  • Protein-tyrosine phosphatase.
• COG CDC14 126aa 8e-07 in ref transcript
  • Predicted protein-tyrosine phosphatase [Signal transduction mechanisms].

TRAF3

• rs.TRAF3.F1 rs.TRAF3.R1 201 340
• NCBIGene 36.3 7187
• Single exon skipping, size difference: 139
• Exclusion in 5'UTR
• Reference transcript: NM_145725

• cd MATH_TRAF3 186aa 1e-106 in ref transcript
  • Tumor Necrosis Factor Receptor (TNFR)-Associated Factor (TRAF) family, TRAF3 subfamily, TRAF domain; TRAF molecules serve as adapter proteins that link TNFRs and downstream kinase cascades resulting in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses. TRAF3 was first described as a molecule that binds the cytoplasmic tail of CD40. However, it is not required for CD40 signaling. More recently, TRAF3 has been identified as a key regulator of type I interferon (IFN) production and the mammalian innate antiviral immunity. It mediates IFN responses in Toll-like receptor (TLR)-dependent as well as TLR-independent viral recognition pathways. It is also a key element in immunological homeostasis through its regulation of the anti-inflammatory cytokine interleukin-10. TRAF3 contains a RING finger domain, five zinc finger domains, and a TRAF domain. The TRAF domain can be divided into a more divergent N-terminal alpha helical region (TRAF-N), and a highly conserved C-terminal MATH subdomain (TRAF-C) with an eight-stranded beta-sandwich structure. TRAF-N mediates trimerization while TRAF-C interacts with receptors.
• pfam MATH 126aa 4e-18 in ref transcript
  • MATH domain. This motif has been called the Meprin And TRAF-Homology (MATH) domain. This domain is hugely expanded in the nematode Caenorhabditis elegans.
• pfam zf-TRAF 57aa 1e-11 in ref transcript
  • TRAF-type zinc finger.
• pfam Cast 176aa 2e-05 in ref transcript
  • RIM-binding protein of the cytomatrix active zone. This is a family of proteins that form part of the CAZ (cytomatrix at the active zone) complex which is involved in determining the site of synaptic vesicle fusion. The C-terminus is a PDZ-binding motif that binds directly to RIM (a small G protein Rab-3A effector). The family also contains four coiled-coil domains.
• smart RING 36aa 0.002 in ref transcript
  • Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s).
• TIGR rad18 203aa 0.005 in ref transcript
  • This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
• COG Smc 161aa 5e-07 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].
• COG COG5222 59aa 0.005 in ref transcript
  • Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only].

TRAF3

• rs.TRAF3.F2 rs.TRAF3.R2 252 327
• NCBIGene 36.3 7187
• Single exon skipping, size difference: 75
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_145725

• cd MATH_TRAF3 186aa 1e-106 in ref transcript
  • Tumor Necrosis Factor Receptor (TNFR)-Associated Factor (TRAF) family, TRAF3 subfamily, TRAF domain; TRAF molecules serve as adapter proteins that link TNFRs and downstream kinase cascades resulting in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses. TRAF3 was first described as a molecule that binds the cytoplasmic tail of CD40. However, it is not required for CD40 signaling. More recently, TRAF3 has been identified as a key regulator of type I interferon (IFN) production and the mammalian innate antiviral immunity. It mediates IFN responses in Toll-like receptor (TLR)-dependent as well as TLR-independent viral recognition pathways. It is also a key element in immunological homeostasis through its regulation of the anti-inflammatory cytokine interleukin-10. TRAF3 contains a RING finger domain, five zinc finger domains, and a TRAF domain. The TRAF domain can be divided into a more divergent N-terminal alpha helical region (TRAF-N), and a highly conserved C-terminal MATH subdomain (TRAF-C) with an eight-stranded beta-sandwich structure. TRAF-N mediates trimerization while TRAF-C interacts with receptors.
• pfam MATH 126aa 4e-18 in ref transcript
  • MATH domain. This motif has been called the Meprin And TRAF-Homology (MATH) domain. This domain is hugely expanded in the nematode Caenorhabditis elegans.
• pfam zf-TRAF 57aa 1e-11 in ref transcript
  • TRAF-type zinc finger.
• Changed! pfam Cast 176aa 2e-05 in ref transcript
  • RIM-binding protein of the cytomatrix active zone. This is a family of proteins that form part of the CAZ (cytomatrix at the active zone) complex which is involved in determining the site of synaptic vesicle fusion. The C-terminus is a PDZ-binding motif that binds directly to RIM (a small G protein Rab-3A effector). The family also contains four coiled-coil domains.
• smart RING 36aa 0.002 in ref transcript
  • Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s).
• Changed! TIGR rad18 203aa 0.005 in ref transcript
  • This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
• COG Smc 161aa 5e-07 in ref transcript
  • Chromosome segregation ATPases [Cell division and chromosome partitioning].
• COG COG5222 59aa 0.005 in ref transcript
  • Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only].
• Changed! pfam Cast 155aa 6e-05 in modified transcript

TRAPPC5

• rs.TRAPPC5.F1 rs.TRAPPC5.R1 123 146
• NCBIGene 36.3 126003
• Alternative 5-prime, size difference: 23
• Exclusion in 5'UTR
• Reference transcript: NM_174894

• pfam TRAPP 139aa 5e-40 in ref transcript
  • Transport protein particle (TRAPP) component. TRAPP plays a key role in the targeting and/or fusion of ER-to-Golgi transport vesicles with their acceptor compartment. TRAPP is a large multimeric protein that contains at least 10 subunits. This family contains many TRAPP family proteins. The Bet3 subunit is one of the better characterised TRAPP proteins and has a dimeric structure with hydrophobic channels. The channel entrances are located on a putative membrane-interacting surface that is distinctively flat, wide and decorated with positively charged residues. Bet3 is proposed to localise TRAPP to the Golgi.
• COG COG5128 148aa 5e-29 in ref transcript
  • Transport protein particle (TRAPP) complex subunit [Intracellular trafficking and secretion].

TRAPPC6B

• rs.TRAPPC6B.F1 rs.TRAPPC6B.R1 142 226
• NCBIGene 36.3 122553
• Single exon skipping, size difference: 84
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001079537

• Changed! pfam TRAPP 153aa 4e-48 in ref transcript
  • Transport protein particle (TRAPP) component. TRAPP plays a key role in the targeting and/or fusion of ER-to-Golgi transport vesicles with their acceptor compartment. TRAPP is a large multimeric protein that contains at least 10 subunits. This family contains many TRAPP family proteins. The Bet3 subunit is one of the better characterised TRAPP proteins and has a dimeric structure with hydrophobic channels. The channel entrances are located on a putative membrane-interacting surface that is distinctively flat, wide and decorated with positively charged residues. Bet3 is proposed to localise TRAPP to the Golgi.
• Changed! COG COG5128 141aa 1e-05 in ref transcript
  • Transport protein particle (TRAPP) complex subunit [Intracellular trafficking and secretion].
• Changed! pfam TRAPP 125aa 1e-34 in modified transcript
• Changed! COG COG5128 113aa 0.001 in modified transcript

TRDMT1

• rs.TRDMT1.F1 rs.TRDMT1.R1 169 241
• NCBIGene 36.3 1787
• Single exon skipping, size difference: 72
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_004412

• Changed! cd Cyt_C5_DNA_methylase 176aa 4e-46 in ref transcript
  • Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the mammalian genome. These effects include transcriptional repression via inhibition of transcription factor binding or the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability.
• cd Cyt_C5_DNA_methylase 132aa 4e-14 in ref transcript
• Changed! TIGR dcm 382aa 1e-21 in ref transcript
  • All proteins in this family for which functions are known are DNA-cytosine methyltransferases. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
• Changed! COG Dcm 167aa 2e-33 in ref transcript
  • Site-specific DNA methylase [DNA replication, recombination, and repair].
• PRK PRK10458 47aa 0.002 in ref transcript
  • DNA cytosine methylase; Provisional.
• Changed! cd Cyt_C5_DNA_methylase 152aa 4e-36 in modified transcript
• Changed! TIGR dcm 358aa 5e-17 in modified transcript
• Changed! COG Dcm 143aa 2e-26 in modified transcript

TRO

• rs.TRO.F1 rs.TRO.R1 103 118
• NCBIGene 36.3 7216
• Alternative 3-prime, size difference: 15
• Exclusion in 5'UTR
• Reference transcript: NM_001039705

• pfam MAGE 170aa 9e-79 in ref transcript
  • MAGE family. The MAGE (melanoma antigen-encoding gene) family are expressed in a wide variety of tumours but not in normal cells, with the exception of the male germ cells, placenta, and, possibly, cells of the developing embryo. The cellular function of this family is unknown. This family also contains the yeast protein, Nse3. The Nse3 protein is part of the Smc5-6 complex. Nse3 has been demonstrated to be important for meiosis.

TRSPAP1

• rs.TRSPAP1.F1 rs.TRSPAP1.R1 298 446
• NCBIGene 36.3 54952
• Single exon skipping, size difference: 148
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_017846

• Changed! cd RRM 75aa 1e-09 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• cd RRM 69aa 3e-09 in ref transcript
• Changed! TIGR PABP-1234 182aa 1e-18 in ref transcript
  • There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, and of unknown tissue range.
• Changed! COG COG0724 97aa 2e-08 in ref transcript
  • RNA-binding proteins (RRM domain) [General function prediction only].
• Changed! COG COG0724 88aa 6e-07 in ref transcript
• Changed! smart RRM 66aa 1e-10 in modified transcript
  • RNA recognition motif.
• Changed! COG COG0724 70aa 3e-08 in modified transcript

TSC2

• rs.TSC2.F1 rs.TSC2.R1 210 279
• NCBIGene 36.3 7249
• Single exon skipping, size difference: 69
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000548

• pfam Rap_GAP 184aa 2e-82 in ref transcript
  • Rap/ran-GAP.
• pfam Tuberin 347aa 8e-53 in ref transcript
  • Tuberin. Tuberous sclerosis complex (TSC) is an autosomal dominant disorder and is characterised by the presence of hamartomas in many organs, such as brain, skin, heart, lung, and kidney. It is caused by mutation either TSC1 or TSC2 tumour suppressor gene. The TSC2 gene codes for tuberin and interacts with hamartin pfam04388, containing two coiled-coil regions, which have been shown to mediate binding to tuberin. These two proteins function within the same pathway(s) regulating cell cycle, cell growth, adhesion, and vesicular trafficking.

TSPAN4

• rs.TSPAN4.F1 rs.TSPAN4.R1 163 243
• NCBIGene 36.3 7106
• Single exon skipping, size difference: 80
• Exclusion of the protein initiation site
• Reference transcript: NM_003271

• cd NET-5_like_LEL 98aa 1e-40 in ref transcript
  • Tetraspanin, extracellular domain or large extracellular loop (LEL), NET-5_like family. Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. Tetraspanins are involved in diverse processes and their various functions may relate to their ability to act as molecular facilitators. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web". This sub-family contains proteins similar to human tetraspan NET-5.
• Changed! pfam Tetraspannin 222aa 3e-35 in ref transcript
  • Tetraspanin family.
• Changed! pfam Tetraspannin 166aa 3e-24 in modified transcript

TTC23

• rs.TTC23.F1 rs.TTC23.R1 229 351
• NCBIGene 36.3 64927
• Single exon skipping, size difference: 122
• Exclusion in 5'UTR
• Reference transcript: NM_001040655

TTLL3

• rs.TTLL3.F1 rs.TTLL3.R1 360 486
• NCBIGene 36.3 26140
• Single exon skipping, size difference: 129
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_001025930

• pfam TTL 292aa 7e-90 in ref transcript
  • Tubulin-tyrosine ligase family. Tubulins and microtubules are subjected to several post-translational modifications of which the reversible detyrosination/tyrosination of the carboxy-terminal end of most alpha-tubulins has been extensively analysed. This modification cycle involves a specific carboxypeptidase and the activity of the tubulin-tyrosine ligase (TTL). The true physiological function of TTL has so far not been established. Tubulin-tyrosine ligase (TTL) catalyses the ATP-dependent post-translational addition of a tyrosine to the carboxy terminal end of detyrosinated alpha-tubulin. In normally cycling cells, the tyrosinated form of tubulin predominates. However, in breast cancer cells, the detyrosinated form frequently predominates, with a correlation to tumour aggressiveness. On the other hand, 3-nitrotyrosine has been shown to be incorporated, by TTL, into the carboxy terminal end of detyrosinated alpha-tubulin. This reaction is not reversible by the carboxypeptidase enzyme. Cells cultured in 3-nitrotyrosine rich medium showed evidence of altered microtubule structure and function, including altered cell morphology, epithelial barrier dysfunction, and apoptosis.

TTLL3

• rs.TTLL3.F2 rs.TTLL3.R2 169 298
• NCBIGene 36.3 26140
• Single exon skipping, size difference: 129
• Inclusion in the protein (no stop codon or frameshift)
• Reference transcript: NM_001025930

• pfam TTL 292aa 7e-90 in ref transcript
  • Tubulin-tyrosine ligase family. Tubulins and microtubules are subjected to several post-translational modifications of which the reversible detyrosination/tyrosination of the carboxy-terminal end of most alpha-tubulins has been extensively analysed. This modification cycle involves a specific carboxypeptidase and the activity of the tubulin-tyrosine ligase (TTL). The true physiological function of TTL has so far not been established. Tubulin-tyrosine ligase (TTL) catalyses the ATP-dependent post-translational addition of a tyrosine to the carboxy terminal end of detyrosinated alpha-tubulin. In normally cycling cells, the tyrosinated form of tubulin predominates. However, in breast cancer cells, the detyrosinated form frequently predominates, with a correlation to tumour aggressiveness. On the other hand, 3-nitrotyrosine has been shown to be incorporated, by TTL, into the carboxy terminal end of detyrosinated alpha-tubulin. This reaction is not reversible by the carboxypeptidase enzyme. Cells cultured in 3-nitrotyrosine rich medium showed evidence of altered microtubule structure and function, including altered cell morphology, epithelial barrier dysfunction, and apoptosis.

TTN

• rs.TTN.F1 rs.TTN.R1 163 301
• NCBIGene 36.3 7273
• Single exon skipping, size difference: 138
• Exclusion in 5'UTR
• Reference transcript: NM_133378

• cd S_TKc 256aa 3e-62 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases of the serine or threonine-specific kinase subfamily. The enzymatic activity of these protein kinases is controlled by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conformational changes in the C-terminal autoregulatory tail.
• cd FN3 91aa 3e-16 in ref transcript
  • Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.
• cd FN3 93aa 1e-15 in ref transcript
• cd FN3 87aa 3e-15 in ref transcript
• cd FN3 93aa 4e-15 in ref transcript
• cd FN3 94aa 7e-15 in ref transcript
• cd FN3 89aa 1e-14 in ref transcript
• cd FN3 94aa 2e-14 in ref transcript
• cd FN3 93aa 3e-14 in ref transcript
• cd FN3 90aa 4e-14 in ref transcript
• cd FN3 90aa 5e-14 in ref transcript
• cd FN3 89aa 6e-14 in ref transcript
• cd FN3 90aa 6e-14 in ref transcript
• cd FN3 93aa 7e-14 in ref transcript
• cd FN3 94aa 1e-13 in ref transcript
• cd FN3 94aa 1e-13 in ref transcript
• cd FN3 94aa 1e-13 in ref transcript
• cd FN3 90aa 2e-13 in ref transcript
• cd FN3 86aa 2e-13 in ref transcript
• cd FN3 89aa 2e-13 in ref transcript
• cd FN3 92aa 2e-13 in ref transcript
• cd FN3 92aa 3e-13 in ref transcript
• cd FN3 93aa 3e-13 in ref transcript
• cd FN3 91aa 4e-13 in ref transcript
• cd FN3 94aa 4e-13 in ref transcript
• cd FN3 91aa 4e-13 in ref transcript
• cd FN3 91aa 4e-13 in ref transcript
• cd FN3 94aa 5e-13 in ref transcript
• cd FN3 92aa 6e-13 in ref transcript
• cd FN3 88aa 6e-13 in ref transcript
• cd FN3 94aa 1e-12 in ref transcript
• cd FN3 92aa 1e-12 in ref transcript
• cd FN3 93aa 1e-12 in ref transcript
• cd FN3 88aa 2e-12 in ref transcript
• cd FN3 86aa 2e-12 in ref transcript
• cd FN3 90aa 2e-12 in ref transcript
• cd FN3 84aa 2e-12 in ref transcript
• cd FN3 84aa 2e-12 in ref transcript
• cd FN3 84aa 2e-12 in ref transcript
• cd FN3 90aa 3e-12 in ref transcript
• cd FN3 90aa 4e-12 in ref transcript
• cd FN3 94aa 4e-12 in ref transcript
• cd FN3 84aa 4e-12 in ref transcript
• cd FN3 84aa 5e-12 in ref transcript
• cd FN3 94aa 5e-12 in ref transcript
• cd FN3 84aa 5e-12 in ref transcript
• cd FN3 92aa 6e-12 in ref transcript
• cd FN3 93aa 6e-12 in ref transcript
• cd FN3 90aa 6e-12 in ref transcript
• cd FN3 94aa 6e-12 in ref transcript
• cd FN3 90aa 7e-12 in ref transcript
• cd FN3 92aa 8e-12 in ref transcript
• cd FN3 79aa 8e-12 in ref transcript
• cd FN3 94aa 1e-11 in ref transcript
• cd FN3 92aa 1e-11 in ref transcript
• cd FN3 94aa 1e-11 in ref transcript
• cd FN3 94aa 2e-11 in ref transcript
• cd FN3 93aa 2e-11 in ref transcript
• cd FN3 91aa 2e-11 in ref transcript
• cd FN3 92aa 3e-11 in ref transcript
• cd FN3 93aa 3e-11 in ref transcript
• cd FN3 92aa 3e-11 in ref transcript
• cd IGcam 87aa 3e-11 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• cd FN3 82aa 4e-11 in ref transcript
• cd FN3 89aa 4e-11 in ref transcript
• cd FN3 99aa 5e-11 in ref transcript
• cd FN3 89aa 5e-11 in ref transcript
• cd FN3 88aa 5e-11 in ref transcript
• cd FN3 95aa 5e-11 in ref transcript
• cd FN3 82aa 6e-11 in ref transcript
• cd FN3 93aa 6e-11 in ref transcript
• cd FN3 92aa 7e-11 in ref transcript
• cd FN3 89aa 7e-11 in ref transcript
• cd FN3 88aa 8e-11 in ref transcript
• cd FN3 94aa 1e-10 in ref transcript
• cd FN3 94aa 1e-10 in ref transcript
• cd FN3 93aa 1e-10 in ref transcript
• cd FN3 92aa 2e-10 in ref transcript
• cd FN3 89aa 3e-10 in ref transcript
• cd FN3 85aa 3e-10 in ref transcript
• cd FN3 94aa 4e-10 in ref transcript
• cd FN3 80aa 4e-10 in ref transcript
• cd FN3 91aa 4e-10 in ref transcript
• cd FN3 94aa 4e-10 in ref transcript
• cd IGcam 89aa 4e-10 in ref transcript
• cd FN3 95aa 5e-10 in ref transcript
• cd FN3 94aa 5e-10 in ref transcript
• cd FN3 92aa 5e-10 in ref transcript
• cd FN3 82aa 6e-10 in ref transcript
• cd FN3 94aa 1e-09 in ref transcript
• cd FN3 89aa 1e-09 in ref transcript
• cd IGcam 86aa 1e-09 in ref transcript
• cd FN3 91aa 2e-09 in ref transcript
• cd FN3 94aa 2e-09 in ref transcript
• cd FN3 92aa 2e-09 in ref transcript
• cd FN3 97aa 2e-09 in ref transcript
• cd FN3 94aa 2e-09 in ref transcript
• cd IGcam 88aa 2e-09 in ref transcript
• cd FN3 90aa 3e-09 in ref transcript
• cd IGcam 77aa 5e-09 in ref transcript
• cd FN3 86aa 1e-08 in ref transcript
• cd FN3 94aa 1e-08 in ref transcript
• cd FN3 92aa 1e-08 in ref transcript
• cd IGcam 87aa 2e-08 in ref transcript
• cd IGcam 87aa 6e-08 in ref transcript
• cd FN3 92aa 8e-08 in ref transcript
• cd FN3 94aa 8e-08 in ref transcript
• cd FN3 84aa 8e-08 in ref transcript
• cd FN3 87aa 1e-07 in ref transcript
• cd IGcam 91aa 1e-07 in ref transcript
• cd IGcam 77aa 1e-07 in ref transcript
• cd FN3 84aa 3e-07 in ref transcript
• cd IGcam 92aa 3e-07 in ref transcript
• cd IGcam 82aa 3e-07 in ref transcript
• cd IGcam 79aa 3e-07 in ref transcript
• cd IGcam 88aa 4e-07 in ref transcript
• cd IGcam 80aa 1e-06 in ref transcript
• cd IGcam 88aa 1e-06 in ref transcript
• cd FN3 94aa 2e-06 in ref transcript
• cd IGcam 92aa 2e-06 in ref transcript
• cd IGcam 86aa 2e-06 in ref transcript
• cd IGcam 77aa 4e-06 in ref transcript
• cd IGcam 88aa 9e-06 in ref transcript
• cd IGcam 80aa 1e-05 in ref transcript
• cd IGcam 93aa 1e-05 in ref transcript
• cd IGcam 83aa 2e-05 in ref transcript
• cd FN3 94aa 3e-05 in ref transcript
• cd IGcam 92aa 4e-05 in ref transcript
• cd IGcam 92aa 4e-05 in ref transcript
• cd IGcam 79aa 4e-05 in ref transcript
• cd IGcam 82aa 4e-05 in ref transcript
• cd IGcam 78aa 5e-05 in ref transcript
• cd IGcam 91aa 6e-05 in ref transcript
• cd IGcam 83aa 6e-05 in ref transcript
• cd IGcam 85aa 8e-05 in ref transcript
• cd IGcam 86aa 9e-05 in ref transcript
• cd IGcam 91aa 1e-04 in ref transcript
• cd IG 72aa 1e-04 in ref transcript
  • Immunoglobulin domain family; members are components of immunoglobulins, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• cd FN3 90aa 2e-04 in ref transcript
• cd IGcam 79aa 2e-04 in ref transcript
• cd IGcam 81aa 2e-04 in ref transcript
• cd IGcam 75aa 3e-04 in ref transcript
• cd IGcam 78aa 4e-04 in ref transcript
• cd IGcam 74aa 4e-04 in ref transcript
• cd IGcam 82aa 6e-04 in ref transcript
• cd IGcam 92aa 0.001 in ref transcript
• cd IGcam 85aa 0.001 in ref transcript
• cd IGcam 72aa 0.001 in ref transcript
• cd IGcam 71aa 0.004 in ref transcript
• cd IGcam 92aa 0.007 in ref transcript
• cd IGcam 84aa 0.008 in ref transcript
• cd IGcam 77aa 0.009 in ref transcript
• smart S_TKc 244aa 2e-63 in ref transcript
  • Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
• pfam I-set 89aa 2e-23 in ref transcript
  • Immunoglobulin I-set domain.
• pfam I-set 88aa 4e-19 in ref transcript
• pfam I-set 90aa 5e-19 in ref transcript
• pfam I-set 90aa 1e-18 in ref transcript
• pfam I-set 93aa 2e-18 in ref transcript
• smart FN3 83aa 8e-17 in ref transcript
  • Fibronectin type 3 domain. One of three types of internal repeat within the plasma protein, fibronectin. The tenth fibronectin type III repeat contains a RGD cell recognition sequence in a flexible loop between 2 strands. Type III modules are present in both extracellular and intracellular proteins.
• pfam I-set 91aa 6e-16 in ref transcript
• pfam I-set 92aa 6e-16 in ref transcript
• smart FN3 84aa 1e-14 in ref transcript
• smart FN3 83aa 1e-14 in ref transcript
• pfam I-set 79aa 3e-14 in ref transcript
• pfam I-set 81aa 3e-14 in ref transcript
• smart FN3 86aa 3e-14 in ref transcript
• pfam I-set 92aa 5e-14 in ref transcript
• pfam I-set 81aa 8e-14 in ref transcript
• smart FN3 83aa 2e-13 in ref transcript
• smart FN3 84aa 4e-13 in ref transcript
• pfam I-set 90aa 8e-13 in ref transcript
• smart FN3 83aa 8e-13 in ref transcript
• pfam I-set 76aa 1e-12 in ref transcript
• smart FN3 80aa 1e-12 in ref transcript
• smart FN3 84aa 1e-12 in ref transcript
• smart FN3 81aa 1e-12 in ref transcript
• smart FN3 83aa 1e-12 in ref transcript
• smart FN3 85aa 1e-12 in ref transcript
• smart FN3 83aa 2e-12 in ref transcript
• pfam fn3 86aa 2e-12 in ref transcript
  • Fibronectin type III domain.
• smart FN3 84aa 3e-12 in ref transcript
• smart FN3 84aa 3e-12 in ref transcript
• smart FN3 82aa 3e-12 in ref transcript
• smart FN3 82aa 3e-12 in ref transcript
• smart FN3 84aa 4e-12 in ref transcript
• pfam I-set 87aa 5e-12 in ref transcript
• smart FN3 84aa 5e-12 in ref transcript
• smart FN3 82aa 6e-12 in ref transcript
• smart FN3 82aa 6e-12 in ref transcript
• pfam I-set 84aa 7e-12 in ref transcript
• pfam I-set 81aa 7e-12 in ref transcript
• smart FN3 83aa 7e-12 in ref transcript
• pfam I-set 81aa 8e-12 in ref transcript
• smart FN3 83aa 8e-12 in ref transcript
• smart FN3 85aa 9e-12 in ref transcript
• smart FN3 82aa 1e-11 in ref transcript
• smart FN3 82aa 1e-11 in ref transcript
• smart FN3 82aa 1e-11 in ref transcript
• pfam I-set 93aa 2e-11 in ref transcript
• smart FN3 83aa 2e-11 in ref transcript
• smart FN3 90aa 2e-11 in ref transcript
• smart FN3 81aa 2e-11 in ref transcript
• smart FN3 84aa 3e-11 in ref transcript
• smart FN3 83aa 3e-11 in ref transcript
• smart FN3 85aa 3e-11 in ref transcript
• smart FN3 84aa 3e-11 in ref transcript
• smart FN3 84aa 3e-11 in ref transcript
• smart FN3 84aa 3e-11 in ref transcript
• smart FN3 84aa 3e-11 in ref transcript
• pfam I-set 77aa 4e-11 in ref transcript
• smart FN3 84aa 4e-11 in ref transcript
• smart FN3 84aa 4e-11 in ref transcript
• smart FN3 84aa 4e-11 in ref transcript
• smart FN3 84aa 4e-11 in ref transcript
• smart FN3 84aa 4e-11 in ref transcript
• smart FN3 82aa 4e-11 in ref transcript
• smart FN3 84aa 4e-11 in ref transcript
• smart FN3 85aa 4e-11 in ref transcript
• smart FN3 83aa 4e-11 in ref transcript
• smart FN3 81aa 5e-11 in ref transcript
• smart FN3 81aa 5e-11 in ref transcript
• pfam I-set 81aa 6e-11 in ref transcript
• smart FN3 84aa 6e-11 in ref transcript
• smart FN3 82aa 6e-11 in ref transcript
• smart FN3 84aa 6e-11 in ref transcript
• pfam I-set 82aa 7e-11 in ref transcript
• smart FN3 81aa 7e-11 in ref transcript
• smart FN3 85aa 7e-11 in ref transcript
• smart FN3 83aa 7e-11 in ref transcript
• smart FN3 84aa 7e-11 in ref transcript
• smart FN3 83aa 7e-11 in ref transcript
• smart FN3 74aa 9e-11 in ref transcript
• smart FN3 84aa 9e-11 in ref transcript
• pfam I-set 84aa 1e-10 in ref transcript
• pfam I-set 72aa 1e-10 in ref transcript
• smart FN3 84aa 1e-10 in ref transcript
• smart FN3 81aa 1e-10 in ref transcript
• pfam I-set 90aa 2e-10 in ref transcript
• smart FN3 84aa 2e-10 in ref transcript
• smart FN3 83aa 2e-10 in ref transcript
• smart FN3 84aa 2e-10 in ref transcript
• smart FN3 84aa 2e-10 in ref transcript
• pfam I-set 81aa 4e-10 in ref transcript
• smart FN3 79aa 4e-10 in ref transcript
• pfam I-set 81aa 5e-10 in ref transcript
• smart FN3 84aa 5e-10 in ref transcript
• smart FN3 84aa 5e-10 in ref transcript
• smart FN3 84aa 6e-10 in ref transcript
• smart FN3 83aa 6e-10 in ref transcript
• smart FN3 83aa 6e-10 in ref transcript
• pfam fn3 80aa 6e-10 in ref transcript
• smart FN3 85aa 7e-10 in ref transcript
• pfam fn3 86aa 9e-10 in ref transcript
• smart FN3 82aa 1e-09 in ref transcript
• smart FN3 84aa 1e-09 in ref transcript
• smart FN3 85aa 1e-09 in ref transcript
• smart FN3 77aa 1e-09 in ref transcript
• pfam I-set 78aa 2e-09 in ref transcript
• smart FN3 84aa 2e-09 in ref transcript
• smart FN3 82aa 2e-09 in ref transcript
• smart FN3 81aa 2e-09 in ref transcript
• smart FN3 80aa 2e-09 in ref transcript
• smart FN3 83aa 2e-09 in ref transcript
• smart FN3 84aa 3e-09 in ref transcript
• pfam I-set 90aa 4e-09 in ref transcript
• smart FN3 85aa 4e-09 in ref transcript
• pfam I-set 72aa 5e-09 in ref transcript
• smart FN3 81aa 5e-09 in ref transcript
• smart FN3 84aa 5e-09 in ref transcript
• pfam fn3 87aa 5e-09 in ref transcript
• pfam I-set 88aa 6e-09 in ref transcript
• smart FN3 76aa 6e-09 in ref transcript
• pfam I-set 70aa 7e-09 in ref transcript
• smart FN3 84aa 7e-09 in ref transcript
• pfam I-set 90aa 8e-09 in ref transcript
• pfam I-set 82aa 9e-09 in ref transcript
• pfam I-set 93aa 1e-08 in ref transcript
• smart FN3 85aa 2e-08 in ref transcript
• pfam I-set 81aa 4e-08 in ref transcript
• smart FN3 84aa 5e-08 in ref transcript
• pfam I-set 77aa 6e-08 in ref transcript
• pfam I-set 81aa 7e-08 in ref transcript
• smart FN3 72aa 8e-08 in ref transcript
• pfam I-set 83aa 9e-08 in ref transcript
• pfam I-set 79aa 9e-08 in ref transcript
• smart FN3 84aa 9e-08 in ref transcript
• smart FN3 82aa 9e-08 in ref transcript
• pfam I-set 81aa 1e-07 in ref transcript
• pfam I-set 78aa 2e-07 in ref transcript
• smart FN3 84aa 2e-07 in ref transcript
• smart FN3 70aa 2e-07 in ref transcript
• smart FN3 84aa 2e-07 in ref transcript
• pfam I-set 60aa 3e-07 in ref transcript
• pfam I-set 83aa 3e-07 in ref transcript
• smart FN3 80aa 3e-07 in ref transcript
• pfam I-set 81aa 5e-07 in ref transcript
• smart FN3 85aa 5e-07 in ref transcript
• smart FN3 77aa 6e-07 in ref transcript
• pfam I-set 81aa 1e-06 in ref transcript
• pfam I-set 79aa 1e-06 in ref transcript
• smart FN3 84aa 3e-06 in ref transcript
• smart FN3 84aa 4e-06 in ref transcript
• pfam I-set 81aa 1e-05 in ref transcript
• pfam I-set 81aa 1e-05 in ref transcript
• smart FN3 77aa 2e-05 in ref transcript
• smart FN3 84aa 2e-05 in ref transcript
• pfam I-set 73aa 4e-05 in ref transcript
• pfam I-set 81aa 5e-05 in ref transcript
• pfam I-set 85aa 5e-05 in ref transcript
• pfam I-set 78aa 8e-05 in ref transcript
• COG SPS1 286aa 2e-28 in ref transcript
  • Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].
• COG COG4733 244aa 2e-04 in ref transcript
  • Phage-related protein, tail component [Function unknown].
• COG COG4733 213aa 2e-04 in ref transcript
• COG COG4733 184aa 0.004 in ref transcript

TXNDC2

• rs.TXNDC2.F1 rs.TXNDC2.R1 167 370
• NCBIGene 36.3 84203
• Alternative 5-prime, size difference: 203
• Exclusion of the protein initiation site
• Reference transcript: NM_001098529

• cd TRX_family 94aa 1e-19 in ref transcript
  • TRX family; composed of two groups: Group I, which includes proteins that exclusively encode a TRX domain; and Group II, which are composed of fusion proteins of TRX and additional domains. Group I TRX is a small ancient protein that alter the redox state of target proteins via the reversible oxidation of an active site dithiol, present in a CXXC motif, partially exposed at the protein's surface. TRX reduces protein disulfide bonds, resulting in a disulfide bond at its active site. Oxidized TRX is converted to the active form by TRX reductase, using reducing equivalents derived from either NADPH or ferredoxins. By altering their redox state, TRX regulates the functions of at least 30 target proteins, some of which are enzymes and transcription factors. It also plays an important role in the defense against oxidative stress by directly reducing hydrogen peroxide and certain radicals, and by serving as a reductant for peroxiredoxins. At least two major types of functional TRXs have been reported in most organisms; in eukaryotes, they are located in the cytoplasm and the mitochondria. Higher plants contain more types (at least 20 TRX genes have been detected in the genome of Arabidopsis thaliana), two of which (types f amd m) are located in the same compartment, the chloroplast. Also included in the alignment are TRX-like domains which show sequence homology to TRX but do not contain the redox active CXXC motif. Group II proteins, in addition to either a redox active TRX or a TRX-like domain, also contain additional domains, which may or may not possess homology to known proteins.
• pfam Thioredoxin 103aa 4e-18 in ref transcript
  • Thioredoxin. Thioredoxins are small enzymes that participate in redox reactions, via the reversible oxidation of an active centre disulfide bond. Some members with only the active site are not separated from the noise.
• pfam Glutenin_hmw 360aa 9e-13 in ref transcript
  • High molecular weight glutenin subunit. Members of this family include high molecular weight subunits of glutenin. This group of gluten proteins is thought to be largely responsible for the elastic properties of gluten, and hence, doughs. Indeed, glutenin high molecular weight subunits are classified as elastomeric proteins, because the glutenin network can withstand significant deformations without breaking, and return to the original conformation when the stress is removed. Elastomeric proteins differ considerably in amino acid sequence, but they are all polymers whose subunits consist of elastomeric domains, composed of repeated motifs, and non-elastic domains that mediate cross-linking between the subunits. The elastomeric domain motifs are all rich in glycine residues in addition to other hydrophobic residues. High molecular weight glutenin subunits have an extensive central elastomeric domain, flanked by two terminal non-elastic domains that form disulphide cross-links. The central elastomeric domain is characterised by the following three repeated motifs: PGQGQQ, GYYPTS[P/L]QQ, GQQ. It possesses overlapping beta-turns within and between the repeated motifs, and assumes a regular helical secondary structure with a diameter of approx. 1.9 nm and a pitch of approx. 1.5 nm.
• PTZ PTZ00051 99aa 2e-18 in ref transcript
  • thioredoxin; Provisional.
• PRK PRK07764 177aa 0.002 in ref transcript
  • DNA polymerase III subunits gamma and tau; Validated.

U2AF2

• rs.U2AF2.F1 rs.U2AF2.R1 104 116
• NCBIGene 36.3 11338
• Alternative 5-prime, size difference: 12
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_007279

• cd RRM 75aa 1e-12 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• cd RRM 79aa 4e-08 in ref transcript
• cd RRM 58aa 2e-05 in ref transcript
• Changed! TIGR U2AF_lg 412aa 1e-160 in ref transcript
  • Members of this subfamily are found in plants, metazoa and fungi.
• COG COG0724 82aa 2e-09 in ref transcript
  • RNA-binding proteins (RRM domain) [General function prediction only].
• COG COG0724 189aa 8e-06 in ref transcript
• Changed! TIGR U2AF_lg 408aa 1e-161 in modified transcript

UBE2C

• rs.UBE2C.F1 rs.UBE2C.R1 218 305
• NCBIGene 36.3 11065
• Single exon skipping, size difference: 87
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_007019

• Changed! cd UBCc 138aa 6e-45 in ref transcript
  • Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin protein ligase enzymes, E3. This pathway regulates many fundamental cellular processes. There are also other E2s which form thiol-ester linkages without the use of E3s as well as several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) which lack the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways which were omitted from the scope of this CD.
• Changed! pfam UQ_con 137aa 5e-53 in ref transcript
  • Ubiquitin-conjugating enzyme. Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. TSG101 is one of several UBC homologues that lacks this active site cysteine.
• Changed! COG COG5078 140aa 3e-43 in ref transcript
  • Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones].
• Changed! cd UBCc 98aa 1e-30 in modified transcript
• Changed! pfam UQ_con 98aa 3e-37 in modified transcript
• Changed! COG COG5078 100aa 3e-32 in modified transcript

UBE4B

• rs.UBE4B.F1 rs.UBE4B.R1 102 489
• NCBIGene 36.3 10277
• Single exon skipping, size difference: 387
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001105562

• pfam Ufd2P_core 623aa 0.0 in ref transcript
  • Ubiquitin elongating factor core. This is the most conserved part of the core region of Ufd2P ubiquitin elongating factor or E4, running from helix alpha-11 to alpha-38. It consists of 31 helices of variable length connected by loops of variable size forming a compact unit; the helical packing pattern of the compact unit consists of five structural repeats that resemble tandem Armadillo (ARM) repeats. This domain is involved in ubiquitination as it binds Cdc48p and escorts ubiquitinated proteins from Cdc48p to the proteasome for degradation. The core is structurally similar to the nuclear transporter protein importin-alpha. The core is associated with the U-box at the C-terminus, pfam04564, which has ligase activity.
• pfam U-box 74aa 2e-27 in ref transcript
  • U-box domain. This domain is related to the Ring finger pfam00097 but lacks the zinc binding residues.
• COG UFD2 804aa 1e-107 in ref transcript
  • Ubiquitin fusion degradation protein 2 [Posttranslational modification, protein turnover, chaperones].

UBL5

• rs.UBL5.F1 rs.UBL5.R1 109 189
• NCBIGene 36.3 59286
• Alternative 5-prime, size difference: 80
• Exclusion in 5'UTR
• Reference transcript: NM_024292

• cd Ubl5 73aa 3e-34 in ref transcript
  • UBL5 (also known as HUB1) is a ubiquitin-like modifier that is both widely expressed and highly phylogenetically conserved. At the C-terminal end of the ubiquitin-like fold of UBL5 is a di-tyrosine motif followed by a single variable residue instead of the characteristic di-glycine found in all other ubiquitin-like modifiers. ULB5 interacts with a cyclin-like kinase called CLK4 but not with other cyclin-like kinase family members.
• pfam ubiquitin 61aa 0.004 in ref transcript
  • Ubiquitin family. This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue), Nedd8, Elongin B, Rub1, and Parkin. A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites.

UBTF

• rs.UBTF.F1 rs.UBTF.R1 326 437
• NCBIGene 36.3 7343
• Single exon skipping, size difference: 111
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_014233

• Changed! cd HMGB-UBF_HMG-box 66aa 1e-06 in ref transcript
  • HMGB-UBF_HMG-box, class II and III members of the HMG-box superfamily of DNA-binding proteins. These proteins bind the minor groove of DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions.
• cd HMGB-UBF_HMG-box 60aa 4e-05 in ref transcript
• cd HMGB-UBF_HMG-box 63aa 2e-04 in ref transcript
• cd HMG-box 44aa 2e-04 in ref transcript
  • High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4; and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions.
• Changed! smart HMG 68aa 9e-08 in ref transcript
  • high mobility group.
• smart HMG 67aa 2e-06 in ref transcript
• smart HMG 62aa 4e-06 in ref transcript
• pfam HMG_box 44aa 4e-05 in ref transcript
  • HMG (high mobility group) box.
• pfam HMG_box 65aa 2e-04 in ref transcript
• smart HMG 65aa 3e-04 in ref transcript
• COG NHP6B 103aa 0.003 in ref transcript
  • Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics].

UBXD5

• rs.UBXD5.F1 rs.UBXD5.R1 133 493
• NCBIGene 36.3 91544
• Multiple exon skipping, size difference: 360
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_183008

• pfam SEP 72aa 6e-19 in ref transcript
  • SEP domain. The SEP domain is named after Saccharomyces cerevisiae Shp1, Drosophila melanogaster eyes closed gene (eyc), and vertebrate p47. In p47, the SEP domain has been shown to bind to and inhibit the cysteine protease cathepsin L. Most SEP domains are succeeded closely by a UBX domain.
• Changed! PRK bchH 138aa 0.007 in ref transcript
  • magnesium chelatase subunit H; Provisional.

UEVLD

• rs.UEVLD.F1 rs.UEVLD.R1 193 317
• NCBIGene 36.3 55293
• Single exon skipping, size difference: 124
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_001040697

• Changed! cd LDH_1 289aa 1e-117 in ref transcript
  • A subgroup of L-lactate dehydrogenases. L-lactate dehydrogenases (LDH) are tetrameric enzymes catalyzing the last step of glycolysis in which pyruvate is converted to L-lactate. This subgroup is composed of eukaryotic LDHs. Vertebrate LDHs are non-allosteric. This is in contrast to some bacterial LDHs that are activated by an allosteric effector such as fructose-1,6-bisphosphate. LDHs are part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)-binding domains of alcohol dehydrogenases, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate dehydrogenases, formate/glycerate dehydrogenases, siroheme synthases, 6-phosphogluconate dehydrogenases, aminoacid dehydrogenases, repressor rex, and NAD-binding potassium channel domains, among others.
• Changed! TIGR L-LDH-NAD 276aa 3e-52 in ref transcript
  • This model represents the NAD-dependent L-lactate dehydrogenases from bacteria and eukaryotes. This enzyme function as as the final step in anaerobic glycolysis. Although lactate dehydrogenases have in some cases been mistaken for malate dehydrogenases due to the similarity of these two substrates and the apparent ease with which evolution can toggle these activities, critical residues have been identified which can discriminate between the two activities. At the time of the creation of this model no hits above the trusted cutoff contained critical residues typical of malate dehydrogenases.
• pfam UEV 120aa 4e-52 in ref transcript
  • UEV domain. This family includes the eukaryotic tumour susceptibility gene 101 protein (TSG101). Altered transcripts of this gene have been detected in sporadic breast cancers and many other human malignancies. However, the involvement of this gene in neoplastic transformation and tumorigenesis is still elusive. TSG101 is required for normal cell function of embryonic and adult tissues but that this gene is not a tumour suppressor for sporadic forms of breast cancer. This family is related to the ubiquitin conjugating enzymes.
• Changed! COG Mdh 288aa 1e-44 in ref transcript
  • Malate/lactate dehydrogenases [Energy production and conversion].
• Changed! cd LDH_1 182aa 1e-75 in modified transcript
• Changed! TIGR L-LDH-NAD 173aa 2e-31 in modified transcript
• Changed! COG Mdh 176aa 5e-29 in modified transcript

UMOD

• rs.UMOD.F1 rs.UMOD.R1 107 170
• NCBIGene 36.3 7369
• Alternative 3-prime, size difference: 63
• Inclusion in 5'UTR
• Reference transcript: NM_001008389

• cd EGF_CA 42aa 2e-04 in ref transcript
  • Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements.
• cd EGF_CA 36aa 4e-04 in ref transcript
• smart ZP 250aa 1e-55 in ref transcript
  • Zona pellucida (ZP) domain. ZP proteins are responsible for sperm-adhesion fo the zona pellucida. ZP domains are also present in multidomain transmembrane proteins such as glycoprotein GP2, uromodulin and TGF-beta receptor type III (betaglycan).
• pfam EGF_CA 39aa 1e-06 in ref transcript
  • Calcium binding EGF domain.
• smart EGF_CA 42aa 1e-05 in ref transcript
  • Calcium-binding EGF-like domain.

UPF3B

• rs.UPF3B.F1 rs.UPF3B.R1 176 215
• NCBIGene 36.3 65109
• Single exon skipping, size difference: 39
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_080632

• pfam Smg4_UPF3 163aa 1e-34 in ref transcript
  • Smg-4/UPF3 family. This family contains proteins that are involved in nonsense mediated mRNA decay. A process that is triggered by premature stop codons in mRNA. The family includes Smg-4 and UPF3.

URG4

• rs.URG4.F1 rs.URG4.R1 100 127
• NCBIGene 36.3 55665
• Single exon skipping, size difference: 27
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001077663

• COG COG2433 120aa 4e-05 in ref transcript
  • Uncharacterized conserved protein [Function unknown].

USP5

• rs.USP5.F1 rs.USP5.R1 180 249
• NCBIGene 36.3 8078
• Alternative 5-prime, size difference: 69
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001098536

• cd Peptidase_C19B 272aa 6e-91 in ref transcript
  • A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
• cd Peptidase_C19B 58aa 8e-25 in ref transcript
• cd UBA 34aa 1e-07 in ref transcript
  • Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
• cd UBA 39aa 6e-06 in ref transcript
• pfam UCH 290aa 1e-44 in ref transcript
  • Ubiquitin carboxyl-terminal hydrolase.
• pfam zf-UBP 76aa 3e-20 in ref transcript
  • Zn-finger in ubiquitin-hydrolases and other protein.
• pfam UCH 70aa 2e-15 in ref transcript
• pfam UBA 35aa 5e-08 in ref transcript
  • UBA/TS-N domain. This small domain is composed of three alpha helices. This family includes the previously defined UBA and TS-N domains. The UBA-domain (ubiquitin associated domain) is a novel sequence motif found in several proteins having connections to ubiquitin and the ubiquitination pathway. The structure of the UBA domain consists of a compact three helix bundle. This domain is found at the N terminus of EF-TS hence the name TS-N. The structure of EF-TS is known and this domain is implicated in its interaction with EF-TU. The domain has been found in non EF-TS proteins such as alpha-NAC and MJ0280.
• pfam UBA 36aa 3e-05 in ref transcript
• Changed! COG UBP14 838aa 1e-101 in ref transcript
  • Isopeptidase T [Posttranslational modification, protein turnover, chaperones].
• Changed! COG UBP14 815aa 1e-105 in modified transcript

VCAM1

• rs.VCAM1.F1 rs.VCAM1.R1 110 386
• NCBIGene 36.3 7412
• Single exon skipping, size difference: 276
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001078

• cd IGcam 76aa 2e-08 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• cd IGcam 76aa 1e-07 in ref transcript
• cd IGcam 86aa 1e-05 in ref transcript
• Changed! cd IGcam 86aa 4e-05 in ref transcript
• cd IGcam 81aa 0.003 in ref transcript
• pfam C2-set 89aa 7e-15 in ref transcript
  • Immunoglobulin C2-set domain.
• pfam C2-set 89aa 6e-12 in ref transcript
• smart IGc2 61aa 6e-12 in ref transcript
  • Immunoglobulin C-2 Type.
• Changed! pfam I-set 87aa 2e-11 in ref transcript
  • Immunoglobulin I-set domain.
• pfam I-set 84aa 3e-11 in ref transcript
• smart IG_like 79aa 3e-09 in ref transcript
  • Immunoglobulin like. IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
• smart IG_like 78aa 9e-06 in ref transcript

VDR

• rs.VDR.F1 rs.VDR.R1 118 240
• NCBIGene 36.3 7421
• Single exon skipping, size difference: 122
• Exclusion in 5'UTR
• Reference transcript: NM_001017535

• cd NR_LBD_VDR 204aa 1e-117 in ref transcript
  • The ligand binding domain of vitamin D receptors, a member of the nuclear receptor superfamily. The ligand binding domain of vitamin D receptors (VDR): VDR is a member of the nuclear receptor (NR) superfamily that functions as classical endocrine receptors. VDR controls a wide range of biological activities including calcium metabolism, cell proliferation and differentiation, and immunomodulation. VDR is a high affinity receptor for the biologically most active Vitamin D metabolite, 1alpha,25-dihydroxyvitamin D3 (1alpha,25(OH)2D3). The binding of the ligand to the receptor induces a conformational change of the ligand binding domain (LBD) with consequent dissociation of corepressors. Upon ligand binding, VDR forms heterodimer with the retinoid X receptor (RXR) that binds to vitamin D response elements (VDREs), recruits coactivators. This leads to the expression of a large number of genes. Approximately 200 human genes are considered to be primary targets of VDR and even more genes are regulated indirectly. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, VDR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
• cd NR_LBD_VDR 36aa 8e-14 in ref transcript
• pfam Hormone_recep 187aa 5e-34 in ref transcript
  • Ligand-binding domain of nuclear hormone receptor. This all helical domain is involved in binding the hormone in these receptors.
• pfam zf-C4 76aa 1e-33 in ref transcript
  • Zinc finger, C4 type (two domains). In nearly all cases, this is the DNA binding domain of a nuclear hormone receptor. The alignment contains two Zinc finger domains that are too dissimilar to be aligned with each other.

VEGFA

• rs.VEGFA.F1 rs.VEGFA.R1 106 141
• NCBIGene 36.3 7422
• Alternative 5-prime, size difference: 35
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_001025366

• cd PDGF 84aa 2e-24 in ref transcript
  • Platelet-derived and vascular endothelial growth factors (PDGF, VEGF) family domain; PDGF is a potent activator for cells of mesenchymal origin; PDGF-A and PDGF-B form AA and BB homodimers and an AB heterodimer; VEGF is a potent mitogen in embryonic and somatic angiogenesis with a unique specificity for vascular endothelial cells; VEGF forms homodimers and exists in 4 different isoforms; overall, the VEGF monomer resembles that of PDGF, but its N-terminal segment is helical rather than extended; the cysteine knot motif is a common feature of this domain.
• smart PDGF 83aa 2e-33 in ref transcript
  • Platelet-derived and vascular endothelial growth factors (PDGF, VEGF) family. Platelet-derived growth factor is a potent activator for cells of mesenchymal origin. PDGF-A and PDGF-B form AA and BB homodimers and an AB heterodimer. Members of the VEGF family are homologues of PDGF.

VEGFA

• rs.VEGFA.F2 rs.VEGFA.R2 338 404
• NCBIGene 36.3 7422
• Alternative 3-prime, size difference: 66
• Exclusion of the stop codon
• Reference transcript: NM_001025366

• cd PDGF 84aa 2e-24 in ref transcript
  • Platelet-derived and vascular endothelial growth factors (PDGF, VEGF) family domain; PDGF is a potent activator for cells of mesenchymal origin; PDGF-A and PDGF-B form AA and BB homodimers and an AB heterodimer; VEGF is a potent mitogen in embryonic and somatic angiogenesis with a unique specificity for vascular endothelial cells; VEGF forms homodimers and exists in 4 different isoforms; overall, the VEGF monomer resembles that of PDGF, but its N-terminal segment is helical rather than extended; the cysteine knot motif is a common feature of this domain.
• smart PDGF 83aa 2e-33 in ref transcript
  • Platelet-derived and vascular endothelial growth factors (PDGF, VEGF) family. Platelet-derived growth factor is a potent activator for cells of mesenchymal origin. PDGF-A and PDGF-B form AA and BB homodimers and an AB heterodimer. Members of the VEGF family are homologues of PDGF.

VEGFA

• rs.VEGFA.F3 rs.VEGFA.R3 127 178
• NCBIGene 36.3 7422
• Alternative 5-prime, size difference: 51
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001025366

• cd PDGF 84aa 2e-24 in ref transcript
  • Platelet-derived and vascular endothelial growth factors (PDGF, VEGF) family domain; PDGF is a potent activator for cells of mesenchymal origin; PDGF-A and PDGF-B form AA and BB homodimers and an AB heterodimer; VEGF is a potent mitogen in embryonic and somatic angiogenesis with a unique specificity for vascular endothelial cells; VEGF forms homodimers and exists in 4 different isoforms; overall, the VEGF monomer resembles that of PDGF, but its N-terminal segment is helical rather than extended; the cysteine knot motif is a common feature of this domain.
• smart PDGF 83aa 2e-33 in ref transcript
  • Platelet-derived and vascular endothelial growth factors (PDGF, VEGF) family. Platelet-derived growth factor is a potent activator for cells of mesenchymal origin. PDGF-A and PDGF-B form AA and BB homodimers and an AB heterodimer. Members of the VEGF family are homologues of PDGF.

VHL

• rs.VHL.F1 rs.VHL.R1 304 427
• NCBIGene 36.3 7428
• Single exon skipping, size difference: 123
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_000551

• Changed! pfam VHL 156aa 2e-81 in ref transcript
  • von Hippel-Lindau disease tumour suppressor protein. VHL forms a ternary complex with the elonginB and elonginC proteins. This complex binds Cul2, which then is involved in regulation of vascular endothelial growth factor mRNA.
• Changed! pfam VHL 115aa 1e-49 in modified transcript

VPS13B

• rs.VPS13B.F1 rs.VPS13B.R1 314 389
• NCBIGene 36.3 157680
• Mutually exclusive exon skipping, size difference: 75
• Inclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_017890

• COG MRS6 199aa 7e-17 in ref transcript
  • Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion].
• COG MRS6 83aa 8e-11 in ref transcript

VPS16

• rs.VPS16.F1 rs.VPS16.R1 104 536
• NCBIGene 36.3 64601
• Multiple exon skipping, size difference: 432
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift, Exclusion in the protein (no frameshift), Exclusion in the protein causing a frameshift
• Reference transcript: NM_022575

• Changed! pfam Vps16_N 417aa 1e-167 in ref transcript
  • Vps16, N-terminal region. This protein forms part of the Class C vacuolar protein sorting (Vps) complex. Vps16 is essential for vacuolar protein sorting, which is essential for viability in plants, but not yeast. The Class C Vps complex is required for SNARE-mediated membrane fusion at the lysosome-like yeast vacuole. It is thought to play essential roles in membrane docking and fusion at the Golgi-to-endosome and endosome-to-vacuole stages of transport. The role of VPS16 in this complex is not known.
• pfam Vps16_C 319aa 1e-115 in ref transcript
  • Vps16, C-terminal region. This protein forms part of the Class C vacuolar protein sorting (Vps) complex. Vps16 is essential for vacuolar protein sorting, which is essential for viability in plants, but not yeast. The Class C Vps complex is required for SNARE-mediated membrane fusion at the lysosome-like yeast vacuole. It is thought to play essential roles in membrane docking and fusion at the Golgi-to-endosome and endosome-to-vacuole stages of transport. The role of VPS16 in this complex is not known.
• Changed! pfam Vps16_N 298aa 1e-108 in modified transcript

VPS26A

• rs.VPS26A.F1 rs.VPS26A.R1 133 276
• NCBIGene 36.3 9559
• Single exon skipping, size difference: 143
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_004896

• Changed! pfam Vps26 276aa 1e-135 in ref transcript
  • Vacuolar protein sorting-associated protein 26. Vacuolar protein sorting-associated protein (Vps) 26 is one of around 50 proteins involved in protein trafficking. In particular, Vps26 assembles into a retromer complex with at least four other proteins Vps5, Vps17, Vps29 and Vps35. This family also contains Down syndrome critical region 3/A.
• Changed! pfam Vps26 236aa 1e-110 in modified transcript

VPS29

• rs.VPS29.F1 rs.VPS29.R1 100 112
• NCBIGene 36.3 51699
• Single exon skipping, size difference: 12
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_057180

• Changed! TIGR yfcE 139aa 5e-23 in ref transcript
  • Members of this largely uncharacterized family share a motif approximating DXH(X25)GDXXD(X25)GNHD as found in several phosphoesterases, including the nucleases SbcD and Mre11, and a family of uncharacterized archaeal putative phosphoesterases described by TIGR00024. In this family, the His residue in GNHD portion of the motif is not conserved. The member MJ0936, one of two from Methanococcus jannaschii, was shown (PMID:15128743) to act on model phosphodiesterase substrates; a divalent cation was required.
• Changed! COG COG0622 173aa 3e-24 in ref transcript
  • Predicted phosphoesterase [General function prediction only].
• Changed! TIGR yfcE 140aa 5e-24 in modified transcript
• Changed! COG COG0622 174aa 4e-25 in modified transcript

VSIG4

• rs.VSIG4.F1 rs.VSIG4.R1 102 384
• NCBIGene 36.3 11326
• Single exon skipping, size difference: 282
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_007268

• Changed! cd IGcam 70aa 1e-06 in ref transcript
  • Immunoglobulin domain cell adhesion molecule (cam) subfamily; members are components of neural cell adhesion molecules (N-CAM L1), Fasciclin II and the insect immune protein Hemolin. The subfamily also includes receptor domains such as as the extracelluar ligand binding domain of Fibroblast Growth Factor Receptor 2. Members are phylogenetically diverse, occuring throughout metazoa, and are not components of the adaptive immune system molecules found in jawed vertebrates. A predominant feature of most Ig domains is a disulfide bridge connecting 2 beta-sheets with a Trp packing against the disulfide bond.
• Changed! pfam I-set 76aa 1e-06 in ref transcript
  • Immunoglobulin I-set domain.
• pfam V-set 115aa 6e-05 in ref transcript
  • Immunoglobulin V-set domain. This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.

WDR1

• rs.WDR1.F1 rs.WDR1.R1 100 520
• NCBIGene 36.3 9948
• Multiple exon skipping, size difference: 420
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_017491

• Changed! cd WD40 340aa 3e-43 in ref transcript
  • WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.
• Changed! cd WD40 291aa 5e-25 in ref transcript
• Changed! smart WD40 40aa 4e-06 in ref transcript
  • WD40 repeats. Note that these repeats are permuted with respect to the structural repeats (blades) of the beta propeller domain.
• pfam WD40 32aa 5e-05 in ref transcript
  • WD domain, G-beta repeat.
• Changed! smart WD40 34aa 1e-04 in ref transcript
• smart WD40 42aa 3e-04 in ref transcript
• Changed! pfam eIF2A 97aa 0.004 in ref transcript
  • Eukaryotic translation initiation factor eIF2A. This is a family of eukaryotic translation initiation factors.
• Changed! COG COG2319 427aa 1e-22 in ref transcript
  • FOG: WD40 repeat [General function prediction only].
• Changed! COG COG2319 223aa 1e-10 in ref transcript
• Changed! cd WD40 378aa 2e-31 in modified transcript
• Changed! cd WD40 78aa 1e-05 in modified transcript
• Changed! pfam WD40 39aa 1e-05 in modified transcript
• Changed! pfam WD40 33aa 2e-04 in modified transcript
• Changed! pfam eIF2A 89aa 0.006 in modified transcript
• Changed! COG COG2319 420aa 1e-21 in modified transcript

WDR16

• rs.WDR16.F1 rs.WDR16.R1 198 402
• NCBIGene 36.3 146845
• Exon skipping and alternative 3-prime or 5-prime, size difference: 204
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_145054

• cd WD40 285aa 9e-34 in ref transcript
  • WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.
• Changed! cd WD40 343aa 3e-16 in ref transcript
• smart WD40 40aa 0.005 in ref transcript
  • WD40 repeats. Note that these repeats are permuted with respect to the structural repeats (blades) of the beta propeller domain.
• smart WD40 42aa 0.008 in ref transcript
• COG COG2319 286aa 9e-21 in ref transcript
  • FOG: WD40 repeat [General function prediction only].
• Changed! COG COG2319 353aa 3e-14 in ref transcript
• Changed! cd WD40 343aa 5e-14 in modified transcript
• Changed! COG COG2319 315aa 8e-11 in modified transcript

WDR62

• rs.WDR62.F1 rs.WDR62.R1 99 114
• NCBIGene 36.3 284403
• Alternative 3-prime, size difference: 15
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001083961

• cd WD40 253aa 2e-25 in ref transcript
  • WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.
• cd WD40 138aa 8e-12 in ref transcript
• cd WD40 200aa 2e-10 in ref transcript
• cd WD40 294aa 1e-09 in ref transcript
• smart WD40 40aa 0.001 in ref transcript
  • WD40 repeats. Note that these repeats are permuted with respect to the structural repeats (blades) of the beta propeller domain.
• COG COG2319 307aa 3e-18 in ref transcript
  • FOG: WD40 repeat [General function prediction only].
• COG COG2319 350aa 5e-11 in ref transcript

WHSC1

• rs.WHSC1.F1 rs.WHSC1.R1 172 352
• NCBIGene 36.3 7468
• Single exon skipping, size difference: 180
• Exclusion in 5'UTR
• Reference transcript: NM_133330

• cd MSH6_like 120aa 2e-43 in ref transcript
  • The PWWP domain is present in MSH6, a mismatch repair protein homologous to bacterial MutS. The PWWP domain of histone-lysine N-methyltransferase, also known as Nuclear SET domain-containing protein 3, is also included. Mutations in MSH6 have been linked to increased cancer susceptibility, particularly in hereditary nonpolyposis colorectal cancer in humans. The role of the PWWP domain in MSH6 is not clear; MSH6 orthologs found in S. cerevisiae, Caenorhabditis elegans and Arabidopsis thaliana lack the PWWP domain. Histone methyltransferases (HMTases) induce the posttranslational methylation of lysine residues in histones and play a role in apoptosis. In the HMTase Whistle, the PWWP domain is necessary for HMTase activity. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
• cd WHSC1_related 95aa 2e-40 in ref transcript
  • The PWWP domain was first identified in the WHSC1 (Wolf-Hirschhorn syndrome candidate 1) protein, a protein implicated in Wolf-Hirschhorn syndrome (WHS). When translocated, WHSC1 plays a role in lymphoid multiple myeloma (MM) disease, also known as plasmacytoma. WHCS1 proteins typically contain two copies of the PWWP domain. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
• cd HMG-box 50aa 2e-06 in ref transcript
  • High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4; and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions.
• pfam SET 126aa 1e-36 in ref transcript
  • SET domain. SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure.
• smart PWWP 63aa 3e-18 in ref transcript
  • domain with conserved PWWP motif. conservation of Pro-Trp-Trp-Pro residues.
• smart AWS 51aa 2e-10 in ref transcript
  • associated with SET domains. subdomain of PRESET.
• smart PWWP 63aa 2e-09 in ref transcript
• smart HMG 63aa 1e-06 in ref transcript
  • high mobility group.
• pfam PHD 43aa 2e-06 in ref transcript
  • PHD-finger. PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.
• pfam PHD 45aa 0.004 in ref transcript
• COG COG2940 245aa 5e-19 in ref transcript
  • Proteins containing SET domain [General function prediction only].
• COG NHP6B 66aa 0.003 in ref transcript
  • Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics].

WISP1

• rs.WISP1.F1 rs.WISP1.R1 125 386
• NCBIGene 36.3 8840
• Single exon skipping, size difference: 261
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_003882

• Changed! pfam VWC 58aa 5e-04 in ref transcript
  • von Willebrand factor type C domain. The high cutoff was used to prevent overlap with pfam00094.
• pfam TSP_1 40aa 5e-04 in ref transcript
  • Thrombospondin type 1 domain.

WSB1

• rs.WSB1.F1 rs.WSB1.R1 106 544
• NCBIGene 36.3 26118
• Multiple exon skipping, size difference: 438
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_015626

• Changed! cd WD40 244aa 9e-44 in ref transcript
  • WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.
• cd SOCS_WSB1_SWIP1 40aa 7e-17 in ref transcript
  • SOCS (suppressors of cytokine signaling) box of WSB1/SWiP1-like proteins. This subfamily contains WSB-1 (SOCS-box-containing WD-40 protein), part of an E3 ubiquitin ligase for the thyroid-hormone-activating type 2 iodothyronine deiodinase (D2) and SWiP-1 (SOCS box and WD-repeats in Protein), a WD40-containing protein that is expressed in embryonic structures of chickens and regulated by Sonic Hedgehog (Shh). The general function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions.
• smart SOCS 43aa 2e-12 in ref transcript
  • suppressors of cytokine signalling. suppressors of cytokine signalling.
• pfam WD40 36aa 7e-06 in ref transcript
  • WD domain, G-beta repeat.
• Changed! smart WD40 41aa 6e-05 in ref transcript
  • WD40 repeats. Note that these repeats are permuted with respect to the structural repeats (blades) of the beta propeller domain.
• smart WD40 40aa 7e-05 in ref transcript
• pfam eIF2A 77aa 0.003 in ref transcript
  • Eukaryotic translation initiation factor eIF2A. This is a family of eukaryotic translation initiation factors.
• Changed! COG COG2319 345aa 2e-30 in ref transcript
  • FOG: WD40 repeat [General function prediction only].
• Changed! cd WD40 227aa 4e-38 in modified transcript
• Changed! pfam WD40 40aa 8e-05 in modified transcript
• Changed! COG COG2319 230aa 8e-26 in modified transcript

WT1

• rs.WT1.F1 rs.WT1.R1 344 395
• NCBIGene 36.3 7490
• Single exon skipping, size difference: 51
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_024426

• Changed! pfam WT1 321aa 1e-143 in ref transcript
  • Wilm's tumour protein.
• COG COG5048 129aa 2e-05 in ref transcript
  • FOG: Zn-finger [General function prediction only].
• Changed! pfam WT1 304aa 1e-132 in modified transcript

XAGE1D

• rs.XAGE1D.F1 rs.XAGE1D.R1 111 431
• NCBIGene 36.3 9503
• Alternative 5-prime, size difference: 320
• Exclusion of the protein initiation site
• Reference transcript: NM_133431

• Changed! pfam GAGE 27aa 0.003 in modified transcript
  • GAGE protein. This family consists of several GAGE and XAGE proteins which are found exclusively in humans. The function of this family is unknown although they have been implicated in human cancers.

XCR1

• rs.XCR1.F1 rs.XCR1.R1 181 303
• NCBIGene 36.3 2829
• Single exon skipping, size difference: 122
• Exclusion in 5'UTR
• Reference transcript: NM_005283

• pfam 7tm_1 234aa 2e-26 in ref transcript
  • 7 transmembrane receptor (rhodopsin family). This family contains, amongst other G-protein-coupled receptors (GCPRs), members of the opsin family, which have been considered to be typical members of the rhodopsin superfamily. They share several motifs, mainly the seven transmembrane helices, GCPRs of the rhodopsin superfamily. All opsins bind a chromophore, such as 11-cis-retinal. The function of most opsins other than the photoisomerases is split into two steps: light absorption and G-protein activation. Photoisomerases, on the other hand, are not coupled to G-proteins - they are thought to generate and supply the chromophore that is used by visual opsins.

XPO7

• rs.XPO7.F1 rs.XPO7.R1 191 218
• NCBIGene 36.3 23039
• Alternative 5-prime, size difference: 27
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001100161

• pfam IBN_N 67aa 6e-08 in ref transcript
  • Importin-beta N-terminal domain.
• Changed! COG CRM1 286aa 2e-05 in ref transcript
  • Importin beta-related nuclear transport receptor [Nuclear structure / Intracellular trafficking and secretion].
• Changed! COG CRM1 277aa 1e-05 in modified transcript

XRCC3

• rs.XRCC3.F1 rs.XRCC3.R1 103 140
• NCBIGene 36.3 7517
• Alternative 3-prime, size difference: 37
• Inclusion in 5'UTR
• Reference transcript: NM_005432

• cd Rad51_DMC1_radA 257aa 2e-64 in ref transcript
  • Rad51_DMC1_radA,B. This group of recombinases includes the eukaryotic proteins RAD51, RAD55/57 and the meiosis-specific protein DMC1, and the archaeal proteins radA and radB. They are closely related to the bacterial RecA group. Rad51 proteins catalyze a similiar recombination reaction as RecA, using ATP-dependent DNA binding activity and a DNA-dependent ATPase. However, this reaction is less efficient and requires accessory proteins such as RAD55/57.
• TIGR recomb_radA 258aa 2e-26 in ref transcript
  • This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.
• PRK radA 275aa 3e-27 in ref transcript
  • DNA repair and recombination protein RadA; Validated.

XRN1

• rs.XRN1.F1 rs.XRN1.R1 187 226
• NCBIGene 36.3 54464
• Single exon skipping, size difference: 39
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_019001

• pfam XRN_N 228aa 1e-113 in ref transcript
  • XRN 5'-3' exonuclease N-terminus. This family aligns residues towards the N-terminus of several proteins with multiple functions. The members of this family all appear to possess 5'-3' exonuclease activity EC:3.1.11.-. Thus, the aligned region may be necessary for 5'->3' exonuclease function. The family also contains several Xrn1 and Xrn2 proteins. The 5'-3' exoribonucleases Xrn1p and Xrn2p/Rat1p function in the degradation and processing of several classes of RNA in Saccharomyces cerevisiae. Xrn1p is the main enzyme catalysing cytoplasmic mRNA degradation in multiple decay pathways, whereas Xrn2p/Rat1p functions in the processing of rRNAs and small nucleolar RNAs (snoRNAs) in the nucleus.
• COG XRN1 396aa 1e-119 in ref transcript
  • 5'-3' exonuclease [DNA replication, recombination, and repair / Cell division and chromosome partitioning / Translation].
• COG XRN1 304aa 6e-66 in ref transcript

YIPF5

• rs.YIPF5.F1 rs.YIPF5.R1 133 384
• NCBIGene 36.3 81555
• Alternative 5-prime, size difference: 251
• Exclusion in 5'UTR
• Reference transcript: NM_001024947

• pfam Yip1 145aa 1e-32 in ref transcript
  • Yip1 domain. The Yip1 integral membrane domain contains four transmembrane alpha helices. The domain is characterised by the motifs DLYGP and GY. The Yip1 protein is a golgi protein involved in vesicular transport that interacts with GTPases.
• COG YIP1 172aa 2e-36 in ref transcript
  • Rab GTPase interacting factor, Golgi membrane protein [Intracellular trafficking and secretion].

ZBTB40

• rs.ZBTB40.F1 rs.ZBTB40.R1 110 398
• NCBIGene 36.3 9923
• Single exon skipping, size difference: 288
• Exclusion in 5'UTR
• Reference transcript: NM_001083621

• pfam BTB 95aa 5e-17 in ref transcript
  • BTB/POZ domain. The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN.
• COG SFP1 80aa 0.002 in ref transcript
  • Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning].
• COG COG5048 182aa 0.002 in ref transcript
  • FOG: Zn-finger [General function prediction only].

ZFAND5

• rs.ZFAND5.F1 rs.ZFAND5.R1 263 400
• NCBIGene 36.3 7763
• Single exon skipping, size difference: 137
• Exclusion in 5'UTR
• Reference transcript: NM_001102420

• pfam zf-AN1 40aa 7e-13 in ref transcript
  • AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis. The following pattern describes the zinc finger. C-X2-C-X(9-12)-C-X(1-2)-C-X4-C-X2-H-X5-H-X-C Where X can be any amino acid, and numbers in brackets indicate the number of residues.
• smart ZnF_A20 25aa 0.001 in ref transcript
  • A20-like zinc fingers. A20- (an inhibitor of cell death)-like zinc fingers. The zinc finger mediates self-association in A20. These fingers also mediate IL-1-induced NF-kappaB activation.

ZFYVE16

• rs.ZFYVE16.F1 rs.ZFYVE16.R1 238 366
• NCBIGene 36.3 9765
• Single exon skipping, size difference: 128
• Exclusion in 5'UTR
• Reference transcript: NM_001105251

• cd FYVE 54aa 4e-17 in ref transcript
  • FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;.
• pfam FYVE 65aa 2e-24 in ref transcript
  • FYVE zinc finger. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn++ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. We have included members which do not conserve these histidine residues but are clearly related.
• PTZ PTZ00303 93aa 0.003 in ref transcript
  • phosphatidylinositol kinase; Provisional.

ZFYVE27

• rs.ZFYVE27.F1 rs.ZFYVE27.R1 117 138
• NCBIGene 36.3 118813
• Single exon skipping, size difference: 21
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001002261

• cd FYVE 59aa 3e-07 in ref transcript
  • FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;.
• smart FYVE 63aa 5e-09 in ref transcript
  • Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the PH D finger and the RI NG finger. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. The FYVE finger functions in the membrane recruitment of cytosolic proteins by binding to phosphatidylinositol 3-phosphate (PI3P), which is prominent on endosomes. The R+HHC+XCG motif is critical for PI3P binding.

ZFYVE27

• rs.ZFYVE27.F2 rs.ZFYVE27.R2 107 122
• NCBIGene 36.3 118813
• Alternative 3-prime, size difference: 15
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001002261

• cd FYVE 59aa 3e-07 in ref transcript
  • FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;.
• smart FYVE 63aa 5e-09 in ref transcript
  • Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the PH D finger and the RI NG finger. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. The FYVE finger functions in the membrane recruitment of cytosolic proteins by binding to phosphatidylinositol 3-phosphate (PI3P), which is prominent on endosomes. The R+HHC+XCG motif is critical for PI3P binding.

ZGPAT

• rs.ZGPAT.F1 rs.ZGPAT.R1 172 232
• NCBIGene 36.3 84619
• Alternative 3-prime, size difference: 60
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_032527

• cd TUDOR 31aa 0.005 in ref transcript
  • Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal.
• pfam G-patch 42aa 2e-08 in ref transcript
  • G-patch domain. This domain is found in a number of RNA binding proteins, and is also found in proteins that contain RNA binding domains. This suggests that this domain may have an RNA binding function. This domain has seven highly conserved glycines.
• smart ZnF_C3H1 22aa 6e-04 in ref transcript
  • zinc finger.
• smart TUDOR 36aa 0.006 in ref transcript
  • Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).

ZMYM5

• rs.ZMYM5.F1 rs.ZMYM5.R1 150 436
• NCBIGene 36.3 9205
• Single exon skipping, size difference: 286
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_001039650

• Changed! pfam zf-FCS 36aa 2e-06 in ref transcript
  • MYM-type Zinc finger with FCS sequence motif. MYM-type zinc fingers were identified in MYM family proteins. Human zinc finger protein 261 is involved in a chromosomal translocation and may be responsible for X-linked retardation in XQ13.1. Human zinc finger protein 198 is also involved in disease. In myeloproliferative disorders it is fused to FGF receptor 1; in atypical myeloproliferative disorders it is rearranged. Members of the family generally are involved in development. This Zn-finger domain functions as a transcriptional trans-activator of late vaccinia viral genes, and orthologues are also found in all nucleocytoplasmic large DNA viruses, NCLDV. This domain is also found fused to the C termini of recombinases from certain prokaryotic transposons.

ZNF133

• rs.ZNF133.F1 rs.ZNF133.R1 138 550
• NCBIGene 36.3 7692
• Exon skipping and alternative 3-prime or 5-prime, size difference: 412
• Inclusion in 5'UTR, Exclusion in 5'UTR, Exclusion in 5'UTR, Exclusion in 5'UTR
• Reference transcript: NM_003434

• smart KRAB 60aa 6e-28 in ref transcript
  • krueppel associated box.
• COG COG5048 410aa 2e-11 in ref transcript
  • FOG: Zn-finger [General function prediction only].

ZNF142

• rs.ZNF142.F1 rs.ZNF142.R1 284 406
• NCBIGene 36.3 7701
• Single exon skipping, size difference: 122
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_001105537

ZNF142

• rs.ZNF142.F2 rs.ZNF142.R2 252 347
• NCBIGene 36.3 7701
• Alternative 3-prime, size difference: 95
• Inclusion in 5'UTR
• Reference transcript: NM_001105537

ZNF146

• rs.ZNF146.F1 rs.ZNF146.R1 111 185
• NCBIGene 36.3 7705
• Single exon skipping, size difference: 74
• Exclusion in 5'UTR
• Reference transcript: NM_007145

• COG COG5048 254aa 5e-04 in ref transcript
  • FOG: Zn-finger [General function prediction only].

ZNF155

• rs.ZNF155.F1 rs.ZNF155.R1 193 270
• NCBIGene 36.3 7711
• Alternative 5-prime, size difference: 77
• Exclusion in 5'UTR
• Reference transcript: NM_003445

• pfam KRAB 41aa 4e-19 in ref transcript
  • KRAB box. The KRAB domain (or Kruppel-associated box) is present in about a third of zinc finger proteins containing C2H2 fingers. The KRAB domain is found to be involved in protein-protein interactions. The KRAB domain is generally encoded by two exons. The regions coded by the two exons are known as KRAB-A and KRAB-B. The A box plays an important role in repression by binding to corepressors, while the B box is thought to enhance this repression brought about by the A box. KRAB-containing proteins are thought to have critical functions in cell proliferation and differentiation, apoptosis and neoplastic transformation.
• COG COG5048 285aa 5e-06 in ref transcript
  • FOG: Zn-finger [General function prediction only].

ZNF187

• rs.ZNF187.F1 rs.ZNF187.R1 102 506
• NCBIGene 36.3 7741
• Alternative 5-prime, size difference: 404
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_152736

• Changed! COG COG5048 154aa 9e-04 in ref transcript
  • FOG: Zn-finger [General function prediction only].
• Changed! smart SCAN 27aa 1e-07 in modified transcript
  • leucine rich region.

ZNF205

• rs.ZNF205.F1 rs.ZNF205.R1 181 249
• NCBIGene 36.3 7755
• Alternative 3-prime, size difference: 68
• Inclusion in 5'UTR
• Reference transcript: NM_001042428

• pfam KRAB 39aa 4e-13 in ref transcript
  • KRAB box. The KRAB domain (or Kruppel-associated box) is present in about a third of zinc finger proteins containing C2H2 fingers. The KRAB domain is found to be involved in protein-protein interactions. The KRAB domain is generally encoded by two exons. The regions coded by the two exons are known as KRAB-A and KRAB-B. The A box plays an important role in repression by binding to corepressors, while the B box is thought to enhance this repression brought about by the A box. KRAB-containing proteins are thought to have critical functions in cell proliferation and differentiation, apoptosis and neoplastic transformation.
• pfam zf-C2H2 23aa 0.004 in ref transcript
  • Zinc finger, C2H2 type. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter.
• pfam zf-C2H2 23aa 0.006 in ref transcript
• COG COG5048 162aa 6e-08 in ref transcript
  • FOG: Zn-finger [General function prediction only].
• COG COG5048 67aa 4e-04 in ref transcript

ZNF226

• rs.ZNF226.F1 rs.ZNF226.R1 98 267
• NCBIGene 36.3 7769
• Alternative 3-prime, size difference: 169
• Inclusion in 5'UTR
• Reference transcript: NM_001032373

• smart KRAB 60aa 7e-19 in ref transcript
  • krueppel associated box.
• COG COG5048 407aa 4e-13 in ref transcript
  • FOG: Zn-finger [General function prediction only].

ZNF228

• rs.ZNF228.F1 rs.ZNF228.R1 170 219
• NCBIGene 36.3 7771
• Single exon skipping, size difference: 49
• Exclusion of the protein initiation site
• Reference transcript: NM_001083335

• smart KRAB 61aa 3e-20 in ref transcript
  • krueppel associated box.
• COG COG5048 393aa 3e-05 in ref transcript
  • FOG: Zn-finger [General function prediction only].
• COG COG5048 388aa 3e-04 in ref transcript

ZNF239

• rs.ZNF239.F1 rs.ZNF239.R1 199 240
• NCBIGene 36.3 8187
• Single exon skipping, size difference: 41
• Exclusion in 5'UTR
• Reference transcript: NM_001099282

• COG COG5048 201aa 0.003 in ref transcript
  • FOG: Zn-finger [General function prediction only].

ZNF273

• rs.ZNF273.F1 rs.ZNF273.R1 185 274
• NCBIGene 36.3 10793
• Single exon skipping, size difference: 89
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_021148

• Changed! smart KRAB 61aa 1e-26 in ref transcript
  • krueppel associated box.
• Changed! COG COG5048 369aa 9e-06 in ref transcript
  • FOG: Zn-finger [General function prediction only].

ZNF280D

• rs.ZNF280D.F1 rs.ZNF280D.R1 406 475
• NCBIGene 36.3 54816
• Single exon skipping, size difference: 69
• Exclusion of the protein initiation site
• Reference transcript: NM_017661

ZNF295

• rs.ZNF295.F1 rs.ZNF295.R1 108 173
• NCBIGene 36.3 49854
• Single exon skipping, size difference: 65
• Exclusion in 5'UTR
• Reference transcript: NM_001098402

• pfam BTB 101aa 1e-21 in ref transcript
  • BTB/POZ domain. The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN.

ZNF30

• rs.ZNF30.F1 rs.ZNF30.R1 238 304
• NCBIGene 36.3 90075
• Alternative 5-prime, size difference: 66
• Exclusion in 5'UTR
• Reference transcript: NM_001099438

• smart KRAB 62aa 3e-23 in ref transcript
  • krueppel associated box.
• COG COG5048 366aa 2e-10 in ref transcript
  • FOG: Zn-finger [General function prediction only].
• COG COG5048 217aa 5e-05 in ref transcript

ZNF331

• rs.ZNF331.F1 rs.ZNF331.R1 113 143
• NCBIGene 36.3 55422
• Single exon skipping, size difference: 30
• Exclusion in 5'UTR
• Reference transcript: NM_001079907

• pfam KRAB 41aa 7e-21 in ref transcript
  • KRAB box. The KRAB domain (or Kruppel-associated box) is present in about a third of zinc finger proteins containing C2H2 fingers. The KRAB domain is found to be involved in protein-protein interactions. The KRAB domain is generally encoded by two exons. The regions coded by the two exons are known as KRAB-A and KRAB-B. The A box plays an important role in repression by binding to corepressors, while the B box is thought to enhance this repression brought about by the A box. KRAB-containing proteins are thought to have critical functions in cell proliferation and differentiation, apoptosis and neoplastic transformation.
• COG COG5048 315aa 1e-05 in ref transcript
  • FOG: Zn-finger [General function prediction only].

ZNF334

• rs.ZNF334.F1 rs.ZNF334.R1 163 315
• NCBIGene 36.3 55713
• Single exon skipping, size difference: 152
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_018102

• Changed! smart KRAB 61aa 2e-29 in ref transcript
  • krueppel associated box.
• Changed! COG COG5048 441aa 2e-04 in ref transcript
  • FOG: Zn-finger [General function prediction only].

ZNF419

• rs.ZNF419.F2 rs.ZNF419.R2 256 355
• NCBIGene 36.3 79744
• Exon skipping and alternative 3-prime or 5-prime, size difference: 99
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_001098491

• Changed! smart KRAB 61aa 8e-22 in ref transcript
  • krueppel associated box.
• COG COG5048 156aa 1e-06 in ref transcript
  • FOG: Zn-finger [General function prediction only].
• COG COG5048 331aa 2e-04 in ref transcript
• Changed! pfam KRAB 41aa 1e-18 in modified transcript
  • KRAB box. The KRAB domain (or Kruppel-associated box) is present in about a third of zinc finger proteins containing C2H2 fingers. The KRAB domain is found to be involved in protein-protein interactions. The KRAB domain is generally encoded by two exons. The regions coded by the two exons are known as KRAB-A and KRAB-B. The A box plays an important role in repression by binding to corepressors, while the B box is thought to enhance this repression brought about by the A box. KRAB-containing proteins are thought to have critical functions in cell proliferation and differentiation, apoptosis and neoplastic transformation.

ZNF468

• rs.ZNF468.F1 rs.ZNF468.R1 126 244
• NCBIGene 36.3 90333
• Single exon skipping, size difference: 118
• Inclusion in the protein causing a frameshift
• Reference transcript: NM_001008801

• Changed! pfam KRAB 41aa 2e-21 in ref transcript
  • KRAB box. The KRAB domain (or Kruppel-associated box) is present in about a third of zinc finger proteins containing C2H2 fingers. The KRAB domain is found to be involved in protein-protein interactions. The KRAB domain is generally encoded by two exons. The regions coded by the two exons are known as KRAB-A and KRAB-B. The A box plays an important role in repression by binding to corepressors, while the B box is thought to enhance this repression brought about by the A box. KRAB-containing proteins are thought to have critical functions in cell proliferation and differentiation, apoptosis and neoplastic transformation.
• Changed! COG COG5048 196aa 4e-05 in ref transcript
  • FOG: Zn-finger [General function prediction only].
• Changed! smart KRAB 42aa 9e-20 in modified transcript
  • krueppel associated box.

ZNF493

• rs.ZNF493.F1 rs.ZNF493.R1 117 340
• NCBIGene 36.3 284443
• Multiple exon skipping, size difference: 223
• Exclusion in the protein causing a frameshift, Exclusion in the protein (no frameshift)
• Reference transcript: NM_001076678

• Changed! smart KRAB 61aa 2e-26 in ref transcript
  • krueppel associated box.
• Changed! COG COG5048 415aa 8e-12 in ref transcript
  • FOG: Zn-finger [General function prediction only].
• Changed! COG SFP1 80aa 0.004 in ref transcript
  • Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning].

ZNF557

• rs.ZNF557.F1 rs.ZNF557.R1 107 119
• NCBIGene 36.3 79230
• Alternative 5-prime, size difference: 12
• Exclusion in 5'UTR
• Reference transcript: NM_024341

• smart KRAB 58aa 4e-28 in ref transcript
  • krueppel associated box.
• pfam zf-C2H2 23aa 0.006 in ref transcript
  • Zinc finger, C2H2 type. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter.
• COG COG5048 286aa 3e-05 in ref transcript
  • FOG: Zn-finger [General function prediction only].

ZNF557

• rs.ZNF557.F2 rs.ZNF557.R2 119 140
• NCBIGene 36.3 79230
• Alternative 3-prime, size difference: 21
• Exclusion in the protein (no frameshift)
• Reference transcript: NM_001044387

• smart KRAB 58aa 4e-28 in ref transcript
  • krueppel associated box.
• pfam zf-C2H2 23aa 0.006 in ref transcript
  • Zinc finger, C2H2 type. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter.
• COG COG5048 286aa 3e-05 in ref transcript
  • FOG: Zn-finger [General function prediction only].

ZNF586

• rs.ZNF586.F1 rs.ZNF586.R1 181 308
• NCBIGene 36.3 54807
• Single exon skipping, size difference: 127
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_017652

• Changed! pfam KRAB 41aa 3e-16 in ref transcript
  • KRAB box. The KRAB domain (or Kruppel-associated box) is present in about a third of zinc finger proteins containing C2H2 fingers. The KRAB domain is found to be involved in protein-protein interactions. The KRAB domain is generally encoded by two exons. The regions coded by the two exons are known as KRAB-A and KRAB-B. The A box plays an important role in repression by binding to corepressors, while the B box is thought to enhance this repression brought about by the A box. KRAB-containing proteins are thought to have critical functions in cell proliferation and differentiation, apoptosis and neoplastic transformation.
• Changed! COG COG5048 154aa 2e-04 in ref transcript
  • FOG: Zn-finger [General function prediction only].

ZNF596

• rs.ZNF596.F1 rs.ZNF596.R1 217 287
• NCBIGene 36.3 169270
• Alternative 5-prime, size difference: 70
• Exclusion in 5'UTR
• Reference transcript: NM_001042416

• smart KRAB 59aa 2e-20 in ref transcript
  • krueppel associated box.
• COG COG5048 142aa 2e-05 in ref transcript
  • FOG: Zn-finger [General function prediction only].
• COG COG5048 398aa 8e-05 in ref transcript

ZNF613

• rs.ZNF613.F1 rs.ZNF613.R1 330 438
• NCBIGene 36.3 79898
• Single exon skipping, size difference: 208
• Exclusion of the protein initiation site
• Reference transcript: NM_001031721

• Changed! smart KRAB 60aa 3e-27 in ref transcript
  • krueppel associated box.
• COG COG5048 339aa 6e-04 in ref transcript
  • FOG: Zn-finger [General function prediction only].
• Changed! smart KRAB 31aa 5e-09 in modified transcript

ZNF621

• rs.ZNF621.F1 rs.ZNF621.R1 108 344
• NCBIGene 36.3 285268
• Alternative 5-prime, size difference: 236
• Exclusion in 5'UTR
• Reference transcript: NM_198484

• smart KRAB 61aa 2e-22 in ref transcript
  • krueppel associated box.
• COG SFP1 84aa 0.004 in ref transcript
  • Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning].
• COG COG4049 54aa 0.005 in ref transcript
  • Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only].

ZNF638

• rs.ZNF638.F1 rs.ZNF638.R1 90 100
• NCBIGene 36.3 27332
• Alternative 5-prime, size difference: 10
• Exclusion in 5'UTR
• Reference transcript: NM_014497

• cd RRM 70aa 3e-04 in ref transcript
  • RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
• smart ZnF_U1 33aa 5e-05 in ref transcript
  • U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
• TIGR hnRNP-L_PTB 68aa 7e-04 in ref transcript
  • Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).
• TIGR hnRNP-L_PTB 67aa 0.003 in ref transcript

ZNF655

• rs.ZNF655.F1 rs.ZNF655.R1 182 395
• NCBIGene 36.3 79027
• Multiple exon skipping, size difference: 213
• Exclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
• Reference transcript: NM_024061

• Changed! pfam KRAB 41aa 4e-19 in ref transcript
  • KRAB box. The KRAB domain (or Kruppel-associated box) is present in about a third of zinc finger proteins containing C2H2 fingers. The KRAB domain is found to be involved in protein-protein interactions. The KRAB domain is generally encoded by two exons. The regions coded by the two exons are known as KRAB-A and KRAB-B. The A box plays an important role in repression by binding to corepressors, while the B box is thought to enhance this repression brought about by the A box. KRAB-containing proteins are thought to have critical functions in cell proliferation and differentiation, apoptosis and neoplastic transformation.

ZNF706

• rs.ZNF706.F1 rs.ZNF706.R1 246 361
• NCBIGene 36.3 51123
• Single exon skipping, size difference: 115
• Exclusion in 5'UTR
• Reference transcript: NM_001042510

• pfam DUF1909 33aa 9e-06 in ref transcript
  • Domain of unknown function (DUF1909). This domain is found in a set of hypothetical eukaryotic proteins.

ZNF707

• rs.ZNF707.F1 rs.ZNF707.R1 169 243
• NCBIGene 36.3 286075
• Single exon skipping, size difference: 74
• Exclusion in 5'UTR
• Reference transcript: NM_173831

• smart KRAB 61aa 6e-26 in ref transcript
  • krueppel associated box.
• COG COG5048 162aa 1e-07 in ref transcript
  • FOG: Zn-finger [General function prediction only].

ZNF74

• rs.ZNF74.F1 rs.ZNF74.R1 263 349
• NCBIGene 36.3 7625
• Single exon skipping, size difference: 86
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_003426

• Changed! smart KRAB 61aa 1e-27 in ref transcript
  • krueppel associated box.
• Changed! COG COG5048 157aa 2e-05 in ref transcript
  • FOG: Zn-finger [General function prediction only].

ZNF807

• rs.ZNF807.F1 rs.ZNF807.R1 235 289
• NCBIGene 36.3 643719
• Alternative 3-prime, size difference: 54
• Inclusion in the protein causing a new stop codon
• Reference transcript: XM_001718828

ZNF83

• rs.ZNF83.F1 rs.ZNF83.R1 316 406
• NCBIGene 36.3 55769
• Single exon skipping, size difference: 90
• Exclusion in 5'UTR
• Reference transcript: NM_001105549

• COG COG5048 391aa 8e-07 in ref transcript
  • FOG: Zn-finger [General function prediction only].

ZNF92

• rs.ZNF92.F1 rs.ZNF92.R1 183 310
• NCBIGene 36.3 168374
• Single exon skipping, size difference: 127
• Exclusion in the protein causing a frameshift
• Reference transcript: NM_152626

• Changed! smart KRAB 61aa 2e-27 in ref transcript
  • krueppel associated box.
• Changed! COG COG5048 381aa 3e-08 in ref transcript
  • FOG: Zn-finger [General function prediction only].

ZWILCH

• rs.ZWILCH.F1 rs.ZWILCH.R1 306 401
• NCBIGene 36.3 55055
• Alternative 3-prime, size difference: 95
• Inclusion in the protein causing a new stop codon
• Reference transcript: NM_017975

• Changed! pfam DUF2352 556aa 0.0 in ref transcript
  • Uncharacterized conserved protein (DUF2352). Members of this family of uncharacterised proteins have no known function.