×
1 warning:
  • Access restricted to public data.
    Please sign in at Rnomics Platform to access your data.
Navigation
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