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

    Gene ID: 1282, updated on 23-Nov-2023

    Summary

    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; AllianceGenome:HGNC:2202
    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; BSVD1; RATOR; PADMAL; COL4A1s
    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See COL4A1 in Genome Data Viewer
    Location:
    13q34
    Exon count:
    53
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (110148963..110307157, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (109377773..109536621, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (110801310..110959504, complement)

    Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 3082 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7991 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr13:110774733-110775932 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:110778445-110779253 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:110779254-110780061 Neighboring gene uncharacterized LOC101927712 Neighboring gene uncharacterized LOC124903272 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:110789313-110789927 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:110788698-110789312 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5500 Neighboring gene long intergenic non-protein coding RNA 3032 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr13:110806879-110807510 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr13:110807511-110808142 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr13:110846747-110847946 Neighboring gene uncharacterized LOC124903212 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:110935768-110936268 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:110959260-110960093 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:110960094-110960926 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr13:110971991-110973190 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:110979365-110980133 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:110990505-110991006 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5501 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr13:110994550-110995499 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:110995500-110996448 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:110999397-111000255 Neighboring gene collagen type IV alpha 2 chain Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:111005255-111005767 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:111012706-111013206 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:111013207-111013707 Neighboring gene microRNA 8073 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:111031805-111032755 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:111039396-111040260 Neighboring gene Sharpr-MPRA regulatory region 13414 Neighboring gene small nucleolar RNA U13

    Genomic regions, transcripts, and products

    Expression

    • 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 Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

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

    HIV-1 interactions

    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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ10041, FLJ25428

    Gene Ontology Provided by GOA

    Component Evidence Code Pubs
    is_active_in basement membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in basement membrane IC
    Inferred by Curator
    more info
    PubMed 
    part_of collagen type IV trimer IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    located_in collagen-containing extracellular matrix HDA PubMed 
    colocalizes_with collagen-containing extracellular matrix ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    located_in endoplasmic reticulum lumen TAS
    Traceable Author Statement
    more info
     
    located_in extracellular region NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in extracellular region TAS
    Traceable Author Statement
    more info
     
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
     

    General protein information

    Preferred Names
    collagen alpha-1(IV) chain
    Names
    COL4A1 NC1 domain
    arresten
    collagen IV, alpha-1 polypeptide
    collagen of basement membrane, alpha-1 chain

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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..163187
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_1116

    mRNA and Protein(s)

    1. NM_001303110.2NP_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/TrEMBL
      A5PKV2
      Related
      ENSP00000443348.1, ENST00000543140.6
      Conserved Domains (2) summary
      PTZ00449
      Location:231310
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
      pfam01391
      Location:275325
      Collagen; Collagen triple helix repeat (20 copies)
    2. NM_001845.6NP_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, X05561, Y00706
      Consensus CDS
      CCDS9511.1
      UniProtKB/Swiss-Prot
      A7E2W4, B1AM70, F5H5K0, P02462, Q1P9S9, Q5VWF6, Q86X41, Q8NF88, Q9NYC5
      Related
      ENSP00000364979.4, ENST00000375820.10
      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: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000013.11 Reference GRCh38.p14 Primary Assembly

      Range
      110148963..110307157 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060937.1 Alternate T2T-CHM13v2.0

      Range
      109377773..109536621 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)