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    COL6A3 collagen, type VI, alpha 3 [ Homo sapiens ]

    Gene ID: 1293, updated on 19-May-2012

    Summary

    Official Symbol
    COL6A3provided by HGNC
    Official Full Name
    collagen, type VI, alpha 3provided by HGNC
    Primary source
    HGNC:2213
    See related
    Ensembl:ENSG00000163359; HPRD:00371; MIM:120250; Vega:OTTHUMG00000150020
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    FLJ34702; FLJ98399; DKFZp686N0262; DKFZp686D23123; DKFZp686K04147
    Summary
    This gene encodes the alpha-3 chain, one of the three alpha chains of type VI collagen, a beaded filament collagen found in most connective tissues. The alpha-3 chain of type VI collagen is much larger than the alpha-1 and -2 chains. This difference in size is largely due to an increase in the number of subdomains, similar to von Willebrand Factor type A domains, that are found in the amino terminal globular domain of all the alpha chains. These domains have been shown to bind extracellular matrix proteins, an interaction that explains the importance of this collagen in organizing matrix components. Mutations in the type VI collagen genes are associated with Bethlem myopathy, a rare autosomal dominant proximal myopathy with early childhood onset. Mutations in this gene are also a cause of Ullrich congenital muscular dystrophy, also referred to as Ullrich scleroatonic muscular dystrophy, an autosomal recessive congenital myopathy that is more severe than Bethlem myopathy. Multiple transcript variants have been identified, but the full-length nature of only some of these variants has been described. [provided by RefSeq, Jun 2009]

    Genomic context

    Location :
    2q37
    Sequence :
    Chromosome: 2; NC_000002.11 (238232655..238322850, complement)
    See COL6A3 in Epigenomics, MapViewer

    Chromosome 2 - NC_000002.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC93463 Neighboring gene COP9 constitutive photomorphogenic homolog subunit 8 (Arabidopsis) Neighboring gene melanophilin Neighboring gene prolactin releasing hormone

    Genomic regions, transcripts, and products

    Bibliography

    GeneRIFs: Gene References Into Functions What's a GeneRIF?

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description
    P12111 P08253 MMP2    HPRD  PubMed  

    General gene information

    Markers

    Homology

    Pathways from BioSystems

    • Axon guidance, organism-specific biosystem (from REACTOME)
      Axon guidance, organism-specific biosystemAxon guidance / axon pathfinding is the process by which neurons send out axons to reach the correct targets. Growing axons have a highly motile structure at the growing tip called the growth cone, w...
    • Developmental Biology, organism-specific biosystem (from REACTOME)
      Developmental Biology, organism-specific biosystemAs a first step towards capturing the array of processes by which a fertilized egg gives rise to the diverse tissues of the body, examples of three kinds of processes have been annotated. These are a...
    • ECM-receptor interaction, organism-specific biosystem (from KEGG)
      ECM-receptor interaction, organism-specific biosystemThe extracellular matrix (ECM) consists of a complex mixture of structural and functional macromolecules and serves an important role in tissue and organ morphogenesis and in the maintenance of cell ...
    • ECM-receptor interaction, conserved biosystem (from KEGG)
      ECM-receptor interaction, conserved biosystemThe extracellular matrix (ECM) consists of a complex mixture of structural and functional macromolecules and serves an important role in tissue and organ morphogenesis and in the maintenance of cell ...
    • Focal adhesion, organism-specific biosystem (from KEGG)
      Focal adhesion, organism-specific biosystemCell-matrix adhesions play essential roles in important biological processes including cell motility, cell proliferation, cell differentiation, regulation of gene expression and cell survival. At the...
    • Focal adhesion, conserved biosystem (from KEGG)
      Focal adhesion, conserved biosystemCell-matrix adhesions play essential roles in important biological processes including cell motility, cell proliferation, cell differentiation, regulation of gene expression and cell survival. At the...
    • NCAM signaling for neurite out-growth, organism-specific biosystem (from REACTOME)
      NCAM signaling for neurite out-growth, organism-specific biosystemThe neural cell adhesion molecule, NCAM, is a member of the immunoglobulin (Ig) superfamily and is involved in a variety of cellular processes of importance for the formation and maintenance of the n...
    • NCAM1 interactions, organism-specific biosystem (from REACTOME)
      NCAM1 interactions, organism-specific biosystemThe neural cell adhesion molecule, NCAM1 is generally considered as a cell adhesion mediator, but it is also considered to be a signal transducing receptor molecule. NCAM1 is involved in multiple cis...
    • Protein digestion and absorption, organism-specific biosystem (from KEGG)
      Protein digestion and absorption, organism-specific biosystemProtein is a dietary component essential for nutritional homeostasis in humans. Normally, ingested protein undergoes a complex series of degradative processes following the action of gastric, pancrea...
    • Protein digestion and absorption, conserved biosystem (from KEGG)
      Protein digestion and absorption, conserved biosystemProtein is a dietary component essential for nutritional homeostasis in humans. Normally, ingested protein undergoes a complex series of degradative processes following the action of gastric, pancrea...
    • Signal Transduction, organism-specific biosystem (from REACTOME)
      Signal Transduction, organism-specific biosystemSignal transduction is a process in which extracellular signals elicit changes in cell state and activity. Transmembrane receptors sense changes in the cellular environment by binding ligands, such a...
    • Signaling by PDGF, organism-specific biosystem (from REACTOME)
      Signaling by PDGF, organism-specific biosystemPlatelet-derived Growth Factor (PDGF) is a potent stimulator of growth and motility of connective tissue cells such as fibroblasts and smooth muscle cells as well as other cells such as capillary end...

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    peptidase inhibitor activity IEA
    Inferred from Electronic Annotation
    more info
     
    serine-type endopeptidase inhibitor activity IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    axon guidance TAS
    Traceable Author Statement
    more info
     
    cell adhesion IEA
    Inferred from Electronic Annotation
    more info
     
    muscle organ development TAS
    Traceable Author Statement
    more info
    PubMed 
    response to glucose stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    collagen IEA
    Inferred from Electronic Annotation
    more info
     
    collagen type VI TAS
    Traceable Author Statement
    more info
    PubMed 
    extracellular matrix IDA
    Inferred from Direct Assay
    more info
    PubMed 
    colocalizes_with extracellular matrix IDA
    Inferred from Direct Assay
    more info
     
    colocalizes_with extracellular matrix ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    extracellular region TAS
    Traceable Author Statement
    more info
     
    extracellular space IDA
    Inferred from Direct Assay
    more info
     
    sarcolemma IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    collagen alpha-3(VI) chain
    Names
    collagen alpha-3(VI) chain
    collagen VI, alpha-3 polypeptide

    NCBI Reference Sequences (RefSeq)

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_008676.1 RefSeqGene

      Range
      5001..95196
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_004369.3NP_004360.2  collagen alpha-3(VI) chain isoform 1 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the full-length isoform (1).
      Source sequence(s)
      AK092021, AK308451, BC033174, BU687672, BX647500, DC411101, X52022
      Consensus CDS
      CCDS33412.1
      UniProtKB/TrEMBL
      D9ZGF2
      UniProtKB/Swiss-Prot
      P12111
      UniProtKB/TrEMBL
      Q63HQ4
      UniProtKB/TrEMBL
      Q8N4Z1
      Related
      ENSP00000295550, OTTHUMP00000195994, ENST00000295550, OTTHUMT00000315790
      Conserved Domains (6) summary
      cd00109
      Location:31103162
      Blast Score: 247
      KU; 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.
      cd01450
      Location:24012543
      Blast Score: 212
      vWFA_subfamily_ECM; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
      cd01481
      Location:14351599
      Blast Score: 661
      vWA_collagen_alpha3-VI-like; VWA_collagen alpha 3(VI) like: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than ...
      pfam01391
      Location:23162371
      Blast Score: 187
      Collagen; Collagen triple helix repeat (20 copies)
      cl00057
      Location:10281191
      Blast Score: 546
      vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
      cl00065
      Location:29933061
      Blast Score: 98
      FN3; 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 ...
    2. NM_057164.4NP_476505.3  collagen alpha-3(VI) chain isoform 2 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks two alternate in-frame exons in the 5' coding region, lacks several exons in the 3' coding region, but contains an alternate 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (2) is significantly shorter and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AK092021, BX647500, DC411101
      Consensus CDS
      CCDS54439.1
      UniProtKB/TrEMBL
      Q63HQ4
      Related
      ENSP00000375860, OTTHUMP00000195996, ENST00000392003, OTTHUMT00000315792
      Conserved Domains (2) summary
      cd01481
      Location:37201
      Blast Score: 626
      vWA_collagen_alpha3-VI-like; VWA_collagen alpha 3(VI) like: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than ...
      cl00057
      Location:231395
      Blast Score: 536
      vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
    3. NM_057165.4NP_476506.3  collagen alpha-3(VI) chain isoform 3 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an alternate in-frame exon in the 5' coding region, lacks several exons in the 3' coding region, but contains an alternate 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (3) is significantly shorter and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AK304870, BX647500, DC411101
      Consensus CDS
      CCDS33411.2
      UniProtKB/TrEMBL
      B4E3U5
      UniProtKB/TrEMBL
      E9PGQ9
      UniProtKB/TrEMBL
      Q63HQ4
      Related
      ENSP00000375861, OTTHUMP00000195995, ENST00000392004, OTTHUMT00000315791
      Conserved Domains (2) summary
      cd01481
      Location:238402
      Blast Score: 624
      vWA_collagen_alpha3-VI-like; VWA_collagen alpha 3(VI) like: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than ...
      cl00057
      Location:432596
      Blast Score: 534
      vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
    4. NM_057166.4NP_476507.3  collagen alpha-3(VI) chain isoform 4 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks three alternate in-frame exons in the 5' coding region, compared to variant 1, resulting in an isoform (4) that is shorter than isoform 1.
      Source sequence(s)
      BC144595, BC171790, BU687672, DC411101
      Consensus CDS
      CCDS33410.2
      UniProtKB/TrEMBL
      B7ZMJ7
      UniProtKB/TrEMBL
      B7ZW00
      UniProtKB/TrEMBL
      E9PFQ6
      Related
      ENSP00000418285, OTTHUMP00000213923, ENST00000472056, OTTHUMT00000353032
      Conserved Domains (6) summary
      cd00109
      Location:25032555
      Blast Score: 245
      KU; 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.
      cd01450
      Location:17941936
      Blast Score: 214
      vWFA_subfamily_ECM; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
      cd01481
      Location:828992
      Blast Score: 662
      vWA_collagen_alpha3-VI-like; VWA_collagen alpha 3(VI) like: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than ...
      pfam01391
      Location:17091764
      Blast Score: 183
      Collagen; Collagen triple helix repeat (20 copies)
      cl00057
      Location:229392
      Blast Score: 480
      vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
      cl00065
      Location:23862454
      Blast Score: 98
      FN3; 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 ...
    5. NM_057167.3NP_476508.2  collagen alpha-3(VI) chain isoform 5 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1, resulting in an isoform (5) that is shorter than isoform 1.
      Source sequence(s)
      AK092021, AK308451, BC033174, BU687672, BX647500, DC411101, X52022
      Consensus CDS
      CCDS33409.1
      UniProtKB/Swiss-Prot
      P12111
      UniProtKB/TrEMBL
      Q63HQ4
      UniProtKB/TrEMBL
      Q8N4Z1
      Related
      ENSP00000315873, ENST00000353578
      Conserved Domains (6) summary
      cd00109
      Location:29042956
      Blast Score: 247
      KU; 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.
      cd01450
      Location:21952337
      Blast Score: 212
      vWFA_subfamily_ECM; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
      cd01481
      Location:12291393
      Blast Score: 660
      vWA_collagen_alpha3-VI-like; VWA_collagen alpha 3(VI) like: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than ...
      pfam01391
      Location:21102165
      Blast Score: 186
      Collagen; Collagen triple helix repeat (20 copies)
      cl00057
      Location:432596
      Blast Score: 546
      vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
      cl00065
      Location:27872855
      Blast Score: 98
      FN3; 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 ...

    RefSeqs of Annotated Genomes: Build 37.3

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh37.p5 Primary Assembly

    Genomic

    1. NC_000002.11 Reference GRCh37.p5 Primary Assembly

      Range
      238232655..238322850, complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate HuRef

    Genomic

    1. AC_000134.1 Alternate HuRef

      Range
      230024688..230114910, complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

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