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    COL4A1 collagen type IV alpha 1 chain [ Homo sapiens (human) ]

    Gene ID: 1282, updated on 14-Apr-2018
    Official Symbol
    COL4A1provided by HGNC
    Official Full Name
    collagen type IV alpha 1 chainprovided by HGNC
    Primary source
    HGNC:HGNC:2202
    See related
    Ensembl:ENSG00000187498 MIM:120130; Vega:OTTHUMG00000017342
    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
    BSVD; RATOR
    Summary
    This gene encodes a type IV collagen alpha protein. Type IV collagen proteins are integral components of basement membranes. This gene shares a bidirectional promoter with a paralogous gene on the opposite strand. The protein consists of an amino-terminal 7S domain, a triple-helix forming collagenous domain, and a carboxy-terminal non-collagenous domain. It functions as part of a heterotrimer and interacts with other extracellular matrix components such as perlecans, proteoglycans, and laminins. In addition, proteolytic cleavage of the non-collagenous carboxy-terminal domain results in a biologically active fragment known as arresten, which has anti-angiogenic and tumor suppressor properties. Mutations in this gene cause porencephaly, cerebrovascular disease, and renal and muscular defects. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2014]
    Expression
    Biased expression in placenta (RPKM 204.1), fat (RPKM 72.2) and 9 other tissues See more
    Orthologs
    Location:
    13q34
    Exon count:
    54
    Annotation release Status Assembly Chr Location
    109 current GRCh38.p12 (GCF_000001405.38) 13 NC_000013.11 (110148958..110307157, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (110801310..110959496, complement)

    Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105370361 Neighboring gene uncharacterized LOC101927712 Neighboring gene collagen type IV alpha 2 chain Neighboring gene microRNA 8073 Neighboring gene COL4A2 antisense 2

    • 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?

    NHGRI GWAS Catalog

    Description
    COL4A1 is associated with arterial stiffness by genome-wide association scan.
    NHGRI GWA Catalog
    Genome-wide association study for coronary artery calcification with follow-up in myocardial infarction.
    NHGRI GWA Catalog
    Large-scale association analysis identifies 13 new susceptibility loci for coronary artery disease.
    NHGRI GWA Catalog
    Meta-analysis of genome-wide association studies in multiethnic Asians identifies two loci for age-related nuclear cataract.
    NHGRI GWA Catalog
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    NHGRI GWA Catalog
    Shared genetic susceptibility to ischemic stroke and coronary artery disease: a genome-wide analysis of common variants.
    NHGRI GWA Catalog

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp160, precursor env HIV-1 gp160 and serum-free macrophage supernatant (MSP) enhance synthesis of type IV collagen by mesangial cells; anti-TGF-beta antibodies attenuate this gp160/MSP-induced collagen synthesis PubMed
    Tat tat Treatment with cannabinoids inhibits HIV-1 Tat-enhanced attachment of U937 cells to collagen IV, laminin, or ECM1 proteins, which is linked to the cannabinoid receptor type 2 and the modulation of beta1-integrin and actin distribution PubMed
    tat HIV-1 Tat enhances adhesion of human U937 monocyte-like cells to proteins of the extracellular matrix, such as collagen IV, laminin, and ECM1 PubMed

    Go to the HIV-1, Human Interaction Database

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    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Clone Names

    • FLJ10041, FLJ25428

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    extracellular matrix constituent conferring elasticity IC
    Inferred by Curator
    more info
    PubMed 
    extracellular matrix structural constituent IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    platelet-derived growth factor binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    basement membrane organization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    blood vessel morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    brain development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    branching involved in blood vessel morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    cellular response to amino acid stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    collagen catabolic process TAS
    Traceable Author Statement
    more info
     
    collagen-activated tyrosine kinase receptor signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    epithelial cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    extracellular matrix organization TAS
    Traceable Author Statement
    more info
     
    neuromuscular junction development IEA
    Inferred from Electronic Annotation
    more info
     
    renal tubule morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    retinal blood vessel morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    basement membrane IC
    Inferred by Curator
    more info
    PubMed 
    collagen type IV trimer IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    endoplasmic reticulum lumen TAS
    Traceable Author Statement
    more info
     
    extracellular matrix HDA PubMed 
    extracellular matrix IDA
    Inferred from Direct Assay
    more info
    PubMed 
    colocalizes_with extracellular matrix ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    extracellular region NAS
    Non-traceable Author Statement
    more info
    PubMed 
    extracellular region TAS
    Traceable Author Statement
    more info
     
    Preferred Names
    collagen alpha-1(IV) chain
    Names
    COL4A1 NC1 domain
    arresten
    collagen IV, alpha-1 polypeptide
    collagen of basement membrane, alpha-1 chain

    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_011544.2 RefSeqGene

      Range
      4993..163192
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001303110.1NP_001290039.1  collagen alpha-1(IV) chain isoform 2 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks alternate exons in the 3' region and contains an alternate 3' terminal exon, resulting in a distinct 3' coding region and 3' UTR compared to variant 1. The encoded isoform (2) has a distinct and shorter C-terminus compared to isoform 1.
      Source sequence(s)
      AL161773, AL390755, BC142626, X05561
      Consensus CDS
      CCDS76649.1
      UniProtKB/Swiss-Prot
      P02462
      UniProtKB/TrEMBL
      A5PKV2, F5H5K0
      Related
      ENSP00000443348.1, OTTHUMP00000276058, ENST00000543140.5, OTTHUMT00000476753
      Conserved Domains (2) summary
      pfam01391
      Location:275325
      Collagen; Collagen triple helix repeat (20 copies)
      cl25751
      Location:231310
      DUF4045; Domain of unknown function (DUF4045)
    2. NM_001845.5NP_001836.3  collagen alpha-1(IV) chain isoform 1 preproprotein

      See identical proteins and their annotated locations for NP_001836.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AA678474, AL161773, AL390755, BC047305, BC151220, H40591, X05561, Y00706
      Consensus CDS
      CCDS9511.1
      UniProtKB/Swiss-Prot
      P02462
      Related
      ENSP00000364979.4, OTTHUMP00000018698, ENST00000375820.8, OTTHUMT00000045759
      Conserved Domains (2) summary
      pfam01391
      Location:9751033
      Collagen; Collagen triple helix repeat (20 copies)
      pfam01413
      Location:15561666
      C4; C-terminal tandem repeated domain in type 4 procollagen

    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_000013.11 Reference GRCh38.p12 Primary Assembly

      Range
      110148958..110307157 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011521048.2XP_011519350.1  collagen alpha-1(IV) chain isoform X1

      Conserved Domains (2) summary
      pfam01391
      Location:911969
      Collagen; Collagen triple helix repeat (20 copies)
      pfam01413
      Location:14921602
      C4; C-terminal tandem repeated domain in type 4 procollagen
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