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Home Public data LGFUS Public Data Cancer-associated regulation of alternative splicing 09. Protein Maps

09. Protein Maps ⚙

Documentation : Protein Maps

This page contains all the Fox responsive and cancer responsive 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.

Protein Maps : Documentation

Download summary file (XLS)

APP

APP.F9 APP.R1 286 343
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.

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

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

GPR137

C11ORF4.F3 C11ORF4.R3 124 274
AceView 36.Apr07 GPR137
Single exon skipping, size difference: 150
Exclusion in the protein (no frameshift)
Reference transcript: GPR137.bApr07

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 259 374
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.

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.

DDR1

DDR1.F8 DDR1.R9 172 282
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].

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.

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].

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

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

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].

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.

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].

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].

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].

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.

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

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].

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].

TLK1

TLK1.u.f.12 TLK1.u.r.10 142 205
AceView 36.Apr07 TLK1
Single exon skipping, size difference: 63
Exclusion in the protein (no frameshift)
Reference transcript: TLK1.aApr07

cd S_TKc 280aa 2e-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 268aa 2e-61 in ref transcript
- Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
pfam SMC_N 235aa 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 SPS1 268aa 1e-27 in ref transcript
- Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair].

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

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.

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

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.

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.

C11orf17

C11orf17.F2 C11orf17.R7 392 473
AceView 36.Apr07 C11orf17
Single exon skipping, size difference: 81
Exclusion in the protein (no frameshift)
Reference transcript: C11orf17.bApr07

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

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.

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].

FGFR1

FGFR1.F11 FGFR1.R11 165 432
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

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.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.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.56 FN1.u.r.67 231 324
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

GATA3

GATA3.F2 GATA3.R5 274 417
AceView 36.Apr07 GATA3
Single exon skipping, size difference: 143
Exclusion in the protein causing a frameshift
Reference transcript: GATA3.bApr07

Changed! cd ZnF_GATA 51aa 2e-11 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.
Changed! cd ZnF_GATA 51aa 4e-09 in ref transcript
Changed! smart ZnF_GATA 47aa 1e-10 in ref transcript
- zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Changed! smart ZnF_GATA 50aa 2e-09 in ref transcript
Changed! COG GAT1 86aa 2e-05 in ref transcript
- GATA Zn-finger-containing transcription factor [Transcription].

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].

GPR137

C11ORF4.F1 C11ORF4.R14 231 607
AceView 36.Apr07 GPR137
Multiple exon skipping, size difference: 376
Exclusion in the protein causing a frameshift, Exclusion in the protein (no frameshift)
Reference transcript: GPR137.bApr07

HMGA1

HMGA1.au.0.f HMGA1.u.r.18 268 301
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

HSCB

HSC20.u.f.10 HSC20.au.2.r 316 461
AceView 36.Apr07 HSCB
Single exon skipping, size difference: 145
Exclusion in the protein causing a frameshift
Reference transcript: HSCB.aApr07

cd DnaJ 60aa 4e-06 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! TIGR hscB 141aa 1e-17 in ref transcript
- This model describes the small subunit, Hsc20 (20K heat shock cognate protein) of a pair of proteins Hsc66-Hsc20, related to the DnaK-DnaJ heat shock proteins, which also serve as molecular chaperones. Hsc20, unlike DnaJ, appears not to have chaperone activity on its own, but to act solely as a regulatory subunit for Hsc66 (i.e., to be a co-chaperone). The gene for Hsc20 in E. coli, hscB, is not induced by heat shock.
Changed! PRK hscB 149aa 6e-22 in ref transcript
- co-chaperone HscB; Provisional.
Changed! TIGR hscB 60aa 2e-10 in modified transcript
Changed! PRK hscB 71aa 2e-14 in modified transcript

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).

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.

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].

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

RAD52

RAD52.u.f.18 RAD52.u.r.18 236 387
AceView 36.Apr07 RAD52
Single exon skipping, size difference: 151
Inclusion in the protein causing a frameshift
Reference transcript: RAD52.aApr07

Changed! TIGR rad52 162aa 2e-83 in ref transcript
- This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Changed! COG RAD52 148aa 2e-44 in ref transcript
- Recombination DNA repair protein (RAD52 pathway) [DNA replication, recombination, and repair].
Changed! TIGR rad52 119aa 5e-64 in modified transcript
Changed! COG RAD52 126aa 9e-40 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

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).

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].

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.

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

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].

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

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.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

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.

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

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.

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.

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.

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

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

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

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

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

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.

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].

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.

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

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.

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

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.

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

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

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.

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

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

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

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.

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

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.

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

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.

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

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

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].

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.

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

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].

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.

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

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].

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.

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

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].

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

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

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].

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.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.

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.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

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.

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.

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.

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

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

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.

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.

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

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.

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.

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.

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].

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

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.

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].

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

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

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

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.

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.

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].

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.

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.

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].

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.

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

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

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.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.

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].

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.

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.

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.

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.

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].

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.

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

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].

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

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.

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

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].

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

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

HHLA3

refseq_HHLA3.F4 refseq_HHLA3.R4 292 389
NCBIGene 36.3 11147
Alternative 5-prime, size difference: 97
Inclusion in the protein causing a frameshift
Reference transcript: NM_001031693

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

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].

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

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

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

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.

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

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

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.

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

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

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

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

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.

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.

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

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].

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

LOC219854

refseq_LOC219854.F3 refseq_LOC219854.R3 185 278
NCBIGene 36.2 219854
Alternative 5-prime, size difference: 93
Exclusion of the protein initiation site
Reference transcript: XM_933894

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

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].

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].

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].

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

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].

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

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.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.

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.

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

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

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.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.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

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].

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].

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

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.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

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.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.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.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.

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

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].

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].

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.

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.

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

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

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.

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.

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

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.

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.

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.

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.

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.

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.

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].

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

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

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

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

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

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].

NCOA1

refseq_NCOA1.F1 refseq_NCOA1.R1 117 174
NCBIGene 36.3 8648
Single exon skipping, size difference: 57
Inclusion in the protein causing a new stop codon
Reference transcript: NM_003743

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.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].

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].

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.

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].

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.

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

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].

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.

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.

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].

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.

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

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.

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.

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.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

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

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

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

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.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

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.

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.

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.

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].

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.

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

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.

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.

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.

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.

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].

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].

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

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

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

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.

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

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

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].

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].

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].

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].

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].

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].

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].

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

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

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].

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].

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.

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].

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].

RCHY1

refseq_RCHY1.F1 refseq_RCHY1.R1 143 170
NCBIGene 36.3 25898
Single exon skipping, size difference: 27
Exclusion in the protein (no frameshift)
Reference transcript: NM_015436

pfam zf-CHY 75aa 3e-16 in ref transcript
- CHY zinc finger. This family of domains are likely to bind to zinc ions. They contain many conserved cysteine and histidine residues. We have named this domain after the N-terminal motif CXHY. This domain can be found in isolation in some proteins, but is also often associated with pfam00097. One of the proteins in this family is a mitochondrial intermembrane space protein called Hot13. This protein is involved in the assembly of small TIM complexes.
Changed! COG COG5540 42aa 6e-04 in ref transcript
- RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones].

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

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

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].

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].

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.

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].

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.

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.

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

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.

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.

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

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.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.

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].

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

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.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].

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

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

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

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

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].

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].

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

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.

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.

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

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].

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

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.

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.

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

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

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

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.

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

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].

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].

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

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

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

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.

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

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

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.

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.

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.

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

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.

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.

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.

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.

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.

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

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

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].

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

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.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

TSC2

refseq_TSC2.F2 refseq_TSC2.R2 171 300
NCBIGene 36.3 7249
Exon skipping and alternative 3-prime or 5-prime, size difference: 132
Exclusion in the protein (no frameshift), 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.

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].

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.

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].

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].

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.

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

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

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.

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.

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.

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.

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

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.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

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

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.

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

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].

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

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

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

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.

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.

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.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

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.

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

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.

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

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

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].

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.

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].

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

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

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.

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].

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

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.

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.

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.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.

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.

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

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

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

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

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

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].

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

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].

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.

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.

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.

CACNB2

refseq_CACNB2.F1 refseq_CACNB2.R1 136 208
NCBIGene 36.3 783
Mutually exclusive exon skipping, size difference: 72
Inclusion in the protein causing a frameshift, Exclusion in the protein causing a frameshift
Reference transcript: NM_201596

cd SH3 57aa 9e-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.
pfam Ca_channel_B 189aa 1e-110 in ref transcript
- Dihydropyridine sensitive L-type calcium channel (Beta subunit).
smart SH3 61aa 6e-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.

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].

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.

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].

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

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

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.

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.

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

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].

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

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.

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

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

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

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

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.

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

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.

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

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.

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

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

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.

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

AKAP11

FOX.AKAP11.F1 FOX.AKAP11.R1 189 273
AceView 36.Apr07 AKAP11
Single exon skipping, size difference: 84
Exclusion in the protein (no frameshift)
Reference transcript: AKAP11.aApr07

smart AKAP_110 97aa 4e-05 in ref transcript
- A-kinase anchor protein 110 kDa. This family consists of several mammalian protein kinase A anchoring protein 3 (PRKA3) or A-kinase anchor protein 110 kDa (AKAP 110) sequences. Agents that increase intracellular cAMP are potent stimulators of sperm motility. Anchoring inhibitor peptides, designed to disrupt the interaction of the cAMP-dependent protein kinase A (PKA) with A kinase-anchoring proteins (AKAPs), are potent inhibitors of sperm motility. PKA anchoring is a key biochemical mechanism controlling motility. AKAP110 shares compartments with both RI and RII isoforms of PKA and may function as a regulator of both motility- and head-associated functions such as capacitation and the acrosome reaction PUBMED:10319321.

An_peroxidase.0

FOX.An_peroxidase.0.F1 FOX.An_peroxidase.0.R1 108 180
AceView 36.Apr07 An_peroxidase.0
Single exon skipping, size difference: 72
Exclusion in the protein (no frameshift)
Reference transcript: An_peroxidase.0.aApr07

cd IGcam 84aa 3e-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 87aa 2e-14 in ref transcript
cd IGcam 85aa 2e-13 in ref transcript
cd IGcam 86aa 2e-13 in ref transcript
pfam An_peroxidase 549aa 0.0 in ref transcript
- Animal haem peroxidase.
pfam I-set 87aa 3e-25 in ref transcript
- Immunoglobulin I-set domain.
pfam I-set 88aa 2e-20 in ref transcript
pfam I-set 87aa 2e-19 in ref transcript
pfam I-set 88aa 1e-16 in ref transcript
smart VWC 56aa 7e-11 in ref transcript
- von Willebrand factor (vWF) type C domain.
TIGR PCC 310aa 1e-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.
Changed! COG COG4886 254aa 7e-04 in ref transcript
- Leucine-rich repeat (LRR) protein [Function unknown].
Changed! COG COG4886 231aa 8e-06 in modified transcript

APBB2

FOX.APBB2.F1 FOX.APBB2.R1 106 169
AceView 36.Apr07 APBB2
Single exon skipping, size difference: 63
Exclusion in the protein (no frameshift)
Reference transcript: APBB2.aApr07

cd FE65_N 138aa 2e-66 in ref transcript
- Fe65 Phosphotyrosine-binding (PTB) domain. Fe65 is an amyloid beta A4 precursor protein-binding. It contains an N-terminal WW domain followed by two PTB domains. 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 Fe65_C 124aa 4e-61 in ref transcript
- Fe65 C-terminal Phosphotyrosine-binding (PTB) domain. Fe65 is an amyloid beta A4 precursor (APP) protein-binding. It contains an N-terminal WW domain followed by two PTB domains. The C-terminal PTB domain is responsible for APP binding. 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 WW 29aa 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.
pfam PID 137aa 2e-39 in ref transcript
- Phosphotyrosine interaction domain (PTB/PID).
pfam PID 123aa 1e-31 in ref transcript
pfam WW 29aa 3e-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.

ATXN7L4

FOX.ATXN7L4.F1 FOX.ATXN7L4.R1 321 390
AceView 36.Apr07 ATXN7L4
Single exon skipping, size difference: 69
Exclusion in the protein (no frameshift)
Reference transcript: ATXN7L4.aApr07

pfam SCA7 67aa 4e-22 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).

beerarbo

FOX.beerarbo.F1 FOX.beerarbo.R1 216 362
AceView 36.Apr07 beerarbo
Single exon skipping, size difference: 146
Inclusion in the protein causing a frameshift
Reference transcript: beerarbo.aApr07

C18orf58

FOX.C18orf58.F1 FOX.C18orf58.R1 159 198
AceView 36.Apr07 C18orf58
Single exon skipping, size difference: 39
Exclusion in the protein (no frameshift)
Reference transcript: C18orf58.bApr07

DCAMKL2

FOX.DCAMKL2.F1 FOX.DCAMKL2.R1 185 268
AceView 36.Apr07 DCAMKL2
Single exon skipping, size difference: 83
Inclusion in the protein causing a new stop codon
Reference transcript: DCAMKL2.cApr07

cd S_TKc 259aa 9e-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.
cd DCX 83aa 7e-24 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 7e-20 in ref transcript
smart S_TKc 247aa 2e-80 in ref transcript
- Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
smart DCX 91aa 1e-26 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 1e-23 in ref transcript
PTZ PTZ00263 253aa 4e-40 in ref transcript
- protein kinase A catalytic subunit; Provisional.

DIAPH2andRPA4

FOX.DIAPH2andRPA4.F1 FOX.DIAPH2andRPA4.R1 140 173
AceView 36.Apr07 DIAPH2andRPA4
Single exon skipping, size difference: 33
Exclusion in the protein (no frameshift)
Reference transcript: DIAPH2andRPA4.aApr07

pfam FH2 374aa 1e-105 in ref transcript
- Formin Homology 2 Domain.
pfam Drf_FH3 194aa 2e-53 in ref transcript
- Diaphanous FH3 Domain. This region is found in the Formin-like and and diaphanous proteins.
pfam Drf_GBD 194aa 5e-46 in ref transcript
- Diaphanous GTPase-binding Domain. This domain is bound to by GTP-attached Rho proteins, leading to activation of the Drf protein.

DNAH1

FOX.DNAH1.F1 FOX.DNAH1.R1 178 309
AceView 36.Apr07 DNAH1
Single exon skipping, size difference: 131
Exclusion in 3'UTR
Reference transcript: DNAH1.aApr07

cd AAA 116aa 4e-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.
pfam DHC_N2 411aa 1e-138 in ref transcript
- Dynein heavy chain, N-terminal region 2. Dyneins are described as motor proteins of eukaryotic cells, as they can convert energy derived from the hydrolysis of ATP to force and movement along cytoskeletal polymers, such as microtubules. This region is found C-terminal to the dynein heavy chain N-terminal region 1 (pfam08385) in many members of this family. No functions seem to have been attributed specifically to this region.
pfam AAA_5 154aa 9e-09 in ref transcript
- ATPase family associated with various cellular activities (AAA). This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model.
pfam AAA_5 147aa 7e-06 in ref transcript
COG DYN1 898aa 2e-50 in ref transcript
- Dynein, heavy chain [Cytoskeleton].
COG DYN1 762aa 2e-24 in ref transcript

EHMT2

FOX.EHMT2.F1 FOX.EHMT2.R1 141 243
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

EPB41L2

FOX.EPB41L2.F1 FOX.EPB41L2.R1 166 229
AceView 36.Apr07 EPB41L2
Single exon skipping, size difference: 63
Inclusion in the protein (no stop codon or frameshift)
Reference transcript: EPB41L2.fApr07

pfam 4_1_CTD 114aa 5e-21 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 SAB 39aa 1e-12 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 44aa 3e-14 in modified transcript

EXOC1

FOX.EXOC1.F1 FOX.EXOC1.R1 138 183
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

FMNL3

FOX.FMNL3.F1 FOX.FMNL3.R1 252 367
AceView 36.Apr07 FMNL3
Single exon skipping, size difference: 115
Inclusion in the protein causing a new stop codon
Reference transcript: FMNL3.aApr07

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.
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.
pfam Drf_GBD 49aa 1e-12 in ref transcript

GABRE

FOX.GABRE.F1 FOX.GABRE.R1 188 366
NCBIGene 36.3 2564
Single exon skipping, size difference: 178
Inclusion in the protein causing a new stop codon
Reference transcript: NM_004961

Changed! TIGR LIC 292aa 2e-64 in ref transcript
- selective while glycine receptors are anion selective).

GMIP

FOX.GMIP.F1 FOX.GMIP.R1 122 319
AceView 36.Apr07 GMIP
Single exon skipping, size difference: 197
Exclusion in the protein causing a frameshift
Reference transcript: GMIP.aApr07

Changed! cd RhoGAP_GMIP 204aa 6e-91 in ref transcript
- RhoGAP_GMIP: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of GMIP (Gem interacting protein). GMIP plays important roles in neurite growth and axonal guidance, and interacts with Gem, a member of the RGK subfamily of the Ras small GTPase superfamily, through the N-terminal half of the protein. GMIP contains a C-terminal RhoGAP domain. GMIP inhibits RhoA function, but is inactive towards Rac1 and Cdc41. 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 C1 43aa 0.002 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 RhoGAP 162aa 1e-47 in ref transcript
- RhoGAP domain. GTPase activator proteins towards Rho/Rac/Cdc42-like small GTPases.
smart C1 44aa 5e-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.
smart FCH 72aa 0.002 in ref transcript
- Fes/CIP4 homology domain. Alignment extended from original report. Highly alpha-helical. Also known as the RAEYL motif or the S. pombe Cdc15 N-terminal domain.
Changed! cd RhoGAP_GMIP 81aa 4e-40 in modified transcript
Changed! pfam RhoGAP 65aa 5e-18 in modified transcript

GOLGA2

FOX.GOLGA2.F1 FOX.GOLGA2.R1 142 223
AceView 36.Apr07 GOLGA2
Single exon skipping, size difference: 81
Inclusion in the protein (no stop codon or frameshift)
Reference transcript: GOLGA2.aApr07

TIGR SMC_prok_B 327aa 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 308aa 0.002 in ref transcript
- Chromosome segregation ATPases [Cell division and chromosome partitioning].

HISPPD1

FOX.HISPPD1.F1 FOX.HISPPD1.R1 128 302
AceView 36.Apr07 HISPPD1
Single exon skipping, size difference: 174
Exclusion in the protein (no frameshift)
Reference transcript: HISPPD1.aApr07

cd HP_HAP_like 80aa 2e-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 141aa 4e-11 in ref transcript
pfam Acid_phosphat_A 390aa 3e-36 in ref transcript
- Histidine acid phosphatase.
pfam Acid_phosphat_A 68aa 3e-07 in ref transcript
pfam RimK 195aa 0.007 in ref transcript
- RimK-like ATP-grasp domain. This ATP-grasp domain is found in the ribosomal S6 modification enzyme RimK.
COG RimK 276aa 8e-07 in ref transcript
- Glutathione synthase/Ribosomal protein S6 modification enzyme (glutaminyl transferase) [Coenzyme metabolism / Translation, ribosomal structure and biogenesis].

KIAA0672

FOX.KIAA0672.F1 FOX.KIAA0672.R1 204 256
AceView 36.Apr07 KIAA0672
Single exon skipping, size difference: 52
Inclusion in the protein causing a new stop codon
Reference transcript: KIAA0672.aApr07

cd RhoGAP_nadrin 201aa 4e-71 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.
smart BAR 242aa 8e-50 in ref transcript
- BAR domain.
smart RhoGAP 176aa 8e-44 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.

MALT1

FOX.MALT1.F1 FOX.MALT1.R1 151 184
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].

MYO5A

FOX.MYO5A.F1 FOX.MYO5A.R1 138 219
AceView 36.Apr07 MYO5A
Single exon skipping, size difference: 81
Exclusion in the protein (no frameshift)
Reference transcript: MYO5A.aApr07

cd MYSc_type_V 693aa 0.0 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 699aa 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 DIL 106aa 4e-37 in ref transcript
- DIL domain. The DIL domain has no known function.
TIGR SMC_prok_B 308aa 5e-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! TIGR SMC_prok_B 267aa 3e-04 in ref transcript
smart IQ 23aa 3e-04 in ref transcript
- Short calmodulin-binding motif containing conserved Ile and Gln residues. Calmodulin-binding motif.
COG COG5022 1179aa 0.0 in ref transcript
- Myosin heavy chain [Cytoskeleton].
Changed! COG COG5022 571aa 1e-13 in ref transcript
Changed! TIGR SMC_prok_B 339aa 0.006 in modified transcript
Changed! COG COG5022 541aa 1e-13 in modified transcript

NEK1

FOX.NEK1.F1 FOX.NEK1.R1 132 216
AceView 36.Apr07 NEK1
Single exon skipping, size difference: 84
Exclusion in the protein (no frameshift)
Reference transcript: NEK1.aApr07

cd S_TKc 256aa 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.
smart S_TKc 245aa 5e-71 in ref transcript
- Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily.
PTZ PTZ00283 252aa 9e-42 in ref transcript
- serine/threonine protein kinase; Provisional.

NLGN2

FOX.NLGN2.F1 FOX.NLGN2.R1 200 251
AceView 36.Apr07 NLGN2
Single exon skipping, size difference: 51
Exclusion in the protein (no frameshift)
Reference transcript: NLGN2.aApr07

Changed! cd Esterase_lipase 545aa 1e-102 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 564aa 1e-153 in ref transcript
- Carboxylesterase.
Changed! COG PnbA 562aa 4e-74 in ref transcript
- Carboxylesterase type B [Lipid metabolism].
Changed! cd Esterase_lipase 528aa 1e-104 in modified transcript
Changed! pfam COesterase 547aa 1e-154 in modified transcript
Changed! COG PnbA 545aa 6e-76 in modified transcript

NPHP3andACAD11

FOX.NPHP3andACAD11.F1 FOX.NPHP3andACAD11.R1 226 309
AceView 36.Apr07 NPHP3andACAD11
Single exon skipping, size difference: 83
Exclusion in the protein causing a frameshift
Reference transcript: NPHP3andACAD11.aApr07

Changed! cd TPR 116aa 2e-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.
Changed! cd TPR 82aa 5e-05 in ref transcript
Changed! cd TPR 75aa 6e-05 in ref transcript
Changed! cd TPR 116aa 0.004 in ref transcript
Changed! TIGR PEP_TPR_lipo 384aa 6e-13 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 223aa 5e-08 in ref transcript
- Tfp pilus assembly protein PilF [Cell motility and secretion / Intracellular trafficking and secretion].
Changed! COG PilF 144aa 2e-04 in ref transcript
Changed! pfam OmpH 87aa 0.003 in modified 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.

JAG2

FOX.NUDT14andJAG2.F1 FOX.NUDT14andJAG2.R1 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

PLAT

FOX.PLAT.F1 FOX.PLAT.R1 152 290
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].

PLEKHM2

FOX.PLEKHM2.F1 FOX.PLEKHM2.R1 184 244
AceView 36.Apr07 PLEKHM2
Single exon skipping, size difference: 60
Exclusion in the protein (no frameshift)
Reference transcript: PLEKHM2.aApr07

cd PH 98aa 3e-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.
pfam RUN 109aa 8e-27 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.
pfam PH 102aa 1e-06 in ref transcript
- PH domain. PH stands for pleckstrin homology.

PPFIBP1

FOX.PPFIBP1.F1 FOX.PPFIBP1.R1 142 175
AceView 36.Apr07 PPFIBP1
Single exon skipping, size difference: 33
Inclusion in the protein (no stop codon or frameshift)
Reference transcript: PPFIBP1.aApr07

cd SAM 63aa 5e-09 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 61aa 7e-05 in ref transcript
pfam SAM_1 62aa 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.
pfam SAM_2 69aa 3e-08 in ref transcript
- SAM domain (Sterile alpha motif).
pfam SAM_1 61aa 3e-07 in ref transcript
pfam SMC_N 248aa 5e-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 247aa 2e-06 in ref transcript
- Chromosome segregation ATPases [Cell division and chromosome partitioning].

SCRIB

FOX.SCRIB.F1 FOX.SCRIB.R1 110 173
AceView 36.Apr07 SCRIB
Single exon skipping, size difference: 63
Exclusion in the protein (no frameshift)
Reference transcript: SCRIB.aApr07

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

SLMAP

FOX.SLMAP.F1 FOX.SLMAP.R1 177 267
AceView 36.Apr07 SLMAP
Single exon skipping, size difference: 90
Inclusion in the protein causing a new stop codon
Reference transcript: SLMAP.aApr07

cd FHA 98aa 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).
TIGR SMC_prok_B 640aa 4e-15 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 FHA 79aa 3e-12 in ref transcript
- FHA domain. The FHA (Forkhead-associated) domain is a phosphopeptide binding motif.
Changed! COG Smc 634aa 3e-12 in ref transcript
- Chromosome segregation ATPases [Cell division and chromosome partitioning].
COG COG1716 98aa 0.004 in ref transcript
- FOG: FHA domain [Signal transduction mechanisms].
Changed! COG Smc 641aa 5e-13 in modified transcript

SMC5

FOX.SMC5.F1 FOX.SMC5.R1 167 212
AceView 36.Apr07 SMC5
Single exon skipping, size difference: 45
Exclusion in the protein (no frameshift)
Reference transcript: SMC5.aApr07

cd ABC_SMC5_euk 103aa 2e-51 in ref transcript
- Eukaryotic SMC5 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_SMC5_euk 146aa 4e-44 in ref transcript
pfam SMC_N 410aa 8e-14 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 405aa 3e-11 in ref transcript
TIGR SMC_prok_B 630aa 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! COG Smc 1022aa 5e-46 in ref transcript
- Chromosome segregation ATPases [Cell division and chromosome partitioning].
Changed! pfam SMC_N 390aa 9e-13 in modified transcript
Changed! COG Smc 875aa 5e-26 in modified transcript

TMEM178

FOX.TMEM178.F1 FOX.TMEM178.R1 240 378
AceView 36.Apr07 TMEM178
Single exon skipping, size difference: 138
Exclusion in the protein (no frameshift)
Reference transcript: TMEM178.aApr07

USP37

FOX.USP37.F1 FOX.USP37.R1 258 324
AceView 36.Apr07 USP37
Single exon skipping, size difference: 66
Exclusion in the protein (no frameshift)
Reference transcript: USP37.bApr07

cd peptidase_C19C 260aa 3e-24 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 264aa 1e-48 in ref transcript
- Ubiquitin carboxyl-terminal hydrolase.
pfam UCH 68aa 4e-04 in ref transcript
COG UBP14 228aa 4e-17 in ref transcript
- Isopeptidase T [Posttranslational modification, protein turnover, chaperones].

WDFY3

FOX.WDFY3.F2 FOX.WDFY3.R2 200 251
AceView 36.Apr07 WDFY3
Single exon skipping, size difference: 51
Exclusion in the protein (no frameshift)
Reference transcript: WDFY3.aApr07

cd Beach 282aa 1e-134 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 202aa 9e-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 FYVE 53aa 5e-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 Beach 282aa 1e-135 in ref transcript
- Beige/BEACH domain.
pfam FYVE 67aa 2e-22 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.
pfam WD40 38aa 0.006 in ref transcript
- WD domain, G-beta repeat.
COG COG2319 193aa 5e-07 in ref transcript
- FOG: WD40 repeat [General function prediction only].
PTZ PTZ00303 60aa 0.005 in ref transcript
- phosphatidylinositol kinase; Provisional.

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.