Back to Rnomics Platform
 Open Session
×
1 warning:
  • Access restricted to public data.
    Please sign in at Rnomics Platform to access your data.
Navigation
Home Public data LGFUS Public Data SYK Alternative Splicing Regulates Mitosis and Cell Survival Protein Maps for Ovary 40 Hits permalink
Protein Maps for Ovary 40 Hits ⚙
Protein Maps : .
This page contains ASEs represented as a graph of the mRNA exonic structure mapped to the protein primary sequence. Exons are shown in white with black outline. The reference form is represented above the alternative form. Coding regions are shown with blue horizontal bars. These can be interrupted by red blocks for absent regions. Below are the domains in the protein obtained from NCBI's Conserved Domain Database. Domains that are affected by the ASE are outlined in red.

Further information can be obtained in the help page

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.

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).

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.

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.

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

AGR3

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

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

BMP4

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

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

BTC

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

C11orf17

  • C11orf17.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

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.

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.

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

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.

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].

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.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

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].

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

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

CADM1

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

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

INSR

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

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

KITLG

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

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

LGALS9

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

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

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].

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.

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

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].

PTPN13

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

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

PTPRB

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

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

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

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

SYK

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

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

SYNE2

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

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

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

Copyright ©2008,2017, all rights reserved.