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    COL6A2 collagen type VI alpha 2 chain [ Homo sapiens (human) ]

    Gene ID: 1292, updated on 3-Jun-2018
    Official Symbol
    COL6A2provided by HGNC
    Official Full Name
    collagen type VI alpha 2 chainprovided by HGNC
    Primary source
    HGNC:HGNC:2212
    See related
    Ensembl:ENSG00000142173 MIM:120240; Vega:OTTHUMG00000090489
    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
    UCMD1; BTHLM1; PP3610
    Summary
    This gene encodes one of the three alpha chains of type VI collagen, a beaded filament collagen found in most connective tissues. The product of this gene contains several domains similar to von Willebrand Factor type A domains. 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 this gene are associated with Bethlem myopathy and Ullrich scleroatonic muscular dystrophy. Three transcript variants have been identified for this gene. [provided by RefSeq, Jul 2008]
    Expression
    Broad expression in placenta (RPKM 164.0), endometrium (RPKM 155.3) and 22 other tissues See more
    Orthologs
    See COL6A2 in Genome Data Viewer
    Location:
    21q22.3
    Exon count:
    30
    Annotation release Status Assembly Chr Location
    109 current GRCh38.p12 (GCF_000001405.38) 21 NC_000021.9 (46098071..46132849)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (47518033..47552763)

    Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene proline-rich protein 36-like Neighboring gene proteasome subunit alpha 6 pseudogene 3 Neighboring gene formimidoyltransferase cyclodeaminase Neighboring gene FTCD antisense RNA 1 Neighboring gene spermatogenesis and centriole associated 1 like

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Jun 15 11:32:44 2016

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    • Assembly of collagen fibrils and other multimeric structures, organism-specific biosystem (from REACTOME)
      Assembly of collagen fibrils and other multimeric structures, organism-specific biosystemCollagen trimers in triple-helical form, referred to as procollagen or collagen molecules, are exported from the ER and trafficked through the Golgi network before secretion into the extracellular sp...
    • 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...
    • Collagen biosynthesis and modifying enzymes, organism-specific biosystem (from REACTOME)
      Collagen biosynthesis and modifying enzymes, organism-specific biosystemThe biosynthesis of collagen is a multistep process. Collagen propeptides are cotranslationally translocated into the ER lumen. Propeptides undergo a number of post-translational modifications. Proli...
    • Collagen chain trimerization, organism-specific biosystem (from REACTOME)
      Collagen chain trimerization, organism-specific biosystemThe C-propeptides of collagen propeptide chains are essential for the association of three peptide chains into a trimeric but non-helical procollagen. This initial binding event determines the compo...
    • Collagen formation, organism-specific biosystem (from REACTOME)
      Collagen formation, organism-specific biosystemCollagen is a family of at least 29 structural proteins derived from over 40 human genes (Myllyharju & Kivirikko 2004). It is the main component of connective tissue, and the most abundant protein in...
    • 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 ...
    • Extracellular matrix organization, organism-specific biosystem (from REACTOME)
      Extracellular matrix organization, organism-specific biosystemThe extracellular matrix is a component of all mammalian tissues, a network consisting largely of the fibrous proteins collagen, elastin and associated-microfibrils, fibronectin and laminins embedded...
    • Focal Adhesion, organism-specific biosystem (from WikiPathways)
      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, 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...
    • PI3K-Akt signaling pathway, organism-specific biosystem (from KEGG)
      PI3K-Akt signaling pathway, organism-specific biosystemThe phosphatidylinositol 3' -kinase(PI3K)-Akt signaling pathway is activated by many types of cellular stimuli or toxic insults and regulates fundamental cellular functions such as transcription, tra...
    • PI3K-Akt signaling pathway, conserved biosystem (from KEGG)
      PI3K-Akt signaling pathway, conserved biosystemThe phosphatidylinositol 3' -kinase(PI3K)-Akt signaling pathway is activated by many types of cellular stimuli or toxic insults and regulates fundamental cellular functions such as transcription, tra...
    • 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...
    • miRNA targets in ECM and membrane receptors, organism-specific biosystem (from WikiPathways)
      miRNA targets in ECM and membrane receptors, organism-specific biosystemBased on the KEGG ECM-receptor interactions pathway (hsa04512), a depiction a plausible mechanism, where miRNAs regulate components of both extracellular matrix (top panel) and transmembrane receptor...
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Clone Names

    • FLJ46862, DKFZp586E1322

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    cell adhesion IEA
    Inferred from Electronic Annotation
    more info
     
    extracellular matrix organization TAS
    Traceable Author Statement
    more info
     
    growth plate cartilage chondrocyte morphogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    protein heterotrimerization IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    response to glucose IEA
    Inferred from Electronic Annotation
    more info
     
    Preferred Names
    collagen alpha-2(VI) chain
    Names
    collagen VI, alpha-2 polypeptide
    collagen, type VI, alpha 2
    human mRNA for collagen VI alpha-2 C-terminal globular domain

    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_008675.1 RefSeqGene

      Range
      5001..39731
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_476

    mRNA and Protein(s)

    1. NM_001849.3NP_001840.3  collagen alpha-2(VI) chain isoform 2C2 precursor

      See identical proteins and their annotated locations for NP_001840.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2C2), that differs from the other variants in the last exon, encodes the full-length protein.
      Source sequence(s)
      AL044156, AY029208, BC065509, CN352095, CN352155
      Consensus CDS
      CCDS13728.1
      UniProtKB/Swiss-Prot
      P12110
      Related
      ENSP00000300527.4, OTTHUMP00000115568, ENST00000300527.8, OTTHUMT00000206971
      Conserved Domains (3) summary
      pfam01391
      Location:439498
      Collagen; Collagen triple helix repeat (20 copies)
      cd01480
      Location:612803
      vWA_collagen_alpha_1-VI-type; VWA_collagen alpha(VI) type: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than ...
      pfam00092
      Location:8331007
      VWA; von Willebrand factor type A domain
    2. NM_058174.2NP_478054.2  collagen alpha-2(VI) chain isoform 2C2a precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2C2a) has a different last exon than the other variants. Isoform 2C2a is 101 amino acids shorter than isoform 2C2 and 91 amino acids longer than isoform 2C2a'.
      Source sequence(s)
      AI275476, BC065509, BM989656, CN352095, CN352155, X15977
      Consensus CDS
      CCDS13729.1
      UniProtKB/Swiss-Prot
      P12110
      Related
      ENSP00000380870.1, OTTHUMP00000115569, ENST00000397763.5, OTTHUMT00000206972
      Conserved Domains (2) summary
      pfam01391
      Location:439498
      Collagen; Collagen triple helix repeat (20 copies)
      cd01480
      Location:612803
      vWA_collagen_alpha_1-VI-type; VWA_collagen alpha(VI) type: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than ...
    3. NM_058175.2NP_478055.2  collagen alpha-2(VI) chain isoform 2C2a' precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2C2a') encodes the shortest polypeptide. The last exon in this variant results in the use of a stop codon that shortens the protein by 192 amino acids compared to the full-length protein, although the transcripts are nearly the same length.
      Source sequence(s)
      AI275476, BC065509, BM989656, CN352095, CN352155, M34570
      Consensus CDS
      CCDS13730.1
      UniProtKB/Swiss-Prot
      P12110
      Related
      ENSP00000312529.5, ENST00000310645.9
      Conserved Domains (2) summary
      pfam01391
      Location:439498
      Collagen; Collagen triple helix repeat (20 copies)
      cd01480
      Location:612803
      vWA_collagen_alpha_1-VI-type; VWA_collagen alpha(VI) type: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than ...

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

    Reference GRCh38.p12 Primary Assembly

    Genomic

    1. NC_000021.9 Reference GRCh38.p12 Primary Assembly

      Range
      46098071..46132849
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011529451.1XP_011527753.1  collagen alpha-2(VI) chain isoform X1

      See identical proteins and their annotated locations for XP_011527753.1

      UniProtKB/Swiss-Prot
      P12110
      Conserved Domains (3) summary
      pfam01391
      Location:439498
      Collagen; Collagen triple helix repeat (20 copies)
      cd01480
      Location:612803
      vWA_collagen_alpha_1-VI-type; VWA_collagen alpha(VI) type: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than ...
      pfam00092
      Location:8331007
      VWA; von Willebrand factor type A domain

    RNA

    1. XR_937438.2 RNA Sequence

    2. XR_937439.2 RNA Sequence

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