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    COL4A3 collagen type IV alpha 3 chain [ Homo sapiens (human) ]

    Gene ID: 1285, updated on 9-Dec-2024

    Summary

    Official Symbol
    COL4A3provided by HGNC
    Official Full Name
    collagen type IV alpha 3 chainprovided by HGNC
    Primary source
    HGNC:HGNC:2204
    See related
    Ensembl:ENSG00000169031 MIM:120070; AllianceGenome:HGNC:2204
    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
    ATS2; ATS3; BFH2; ATS3A; ATS3B
    Summary
    Type IV collagen, the major structural component of basement membranes, is a multimeric protein composed of 3 alpha subunits. These subunits are encoded by 6 different genes, alpha 1 through alpha 6, each of which can form a triple helix structure with 2 other subunits to form type IV collagen. This gene encodes alpha 3. In the Goodpasture syndrome, autoantibodies bind to the collagen molecules in the basement membranes of alveoli and glomeruli. The epitopes that elicit these autoantibodies are localized largely to the non-collagenous C-terminal domain of the protein. A specific kinase phosphorylates amino acids in this same C-terminal region and the expression of this kinase is upregulated during pathogenesis. This gene is also linked to an autosomal recessive form of Alport syndrome. The mutations contributing to this syndrome are also located within the exons that encode this C-terminal region. Like the other members of the type IV collagen gene family, this gene is organized in a head-to-head conformation with another type IV collagen gene so that each gene pair shares a common promoter. [provided by RefSeq, Jun 2010]
    Expression
    Biased expression in kidney (RPKM 8.1), lung (RPKM 7.4) and 12 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See COL4A3 in Genome Data Viewer
    Location:
    2q36.3
    Exon count:
    54
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (227164624..227314792)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (227647382..227797471)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (228029340..228179508)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 11623 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12389 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:227661675-227662624 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12390 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12391 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12392 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12393 Neighboring gene insulin receptor substrate 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:227677874-227678445 Neighboring gene Sharpr-MPRA regulatory region 3963 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12394 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17195 Neighboring gene rhomboid domain containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12395 Neighboring gene MPRA-validated peak4067 silencer Neighboring gene small nucleolar RNA SNORA48 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17196 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:227859794-227860993 Neighboring gene collagen type IV alpha 4 chain Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:227929821-227930408 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:228028248-228029149 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12397 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:228050272-228050810 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr2:228055439-228056638 Neighboring gene MFF divergent transcript Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:228185522-228186050 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17198 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12398 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:228235290-228236489 Neighboring gene MPRA-validated peak4069 silencer Neighboring gene stress induced phosphoprotein 1 pseudogene 2 Neighboring gene mitochondrial fission factor Neighboring gene transmembrane 4 L six family member 20

    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

    Associated conditions

    Description Tests
    Alport syndrome
    MedGen: C1567741 GeneReviews: Not available
    not available
    Alport syndrome 3b, autosomal recessive
    MedGen: C5882699 OMIM: 620536 GeneReviews: Alport Syndrome
    not available
    Autosomal dominant Alport syndrome
    MedGen: C5882663 OMIM: 104200 GeneReviews: Alport Syndrome
    not available
    Hematuria, benign familial, 2
    MedGen: C5830421 OMIM: 620320 GeneReviews: Not available
    not available

    EBI GWAS Catalog

    Description
    Genome-wide association analyses identify multiple loci associated with central corneal thickness and keratoconus.
    EBI GWAS Catalog
    Genome-wide association study of monoamine metabolite levels in human cerebrospinal fluid.
    EBI GWAS Catalog

    HIV-1 interactions

    Replication interactions

    Interaction Pubs
    Knockdown of collagen, type IV, alpha 3 (COL4A3) by siRNA enhances the early stages of HIV-1 replication in HeLa-CD4 cells infected with viral pseudotypes HIV89.6R and HIV8.2N PubMed

    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

    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 IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of collagen type IV trimer IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in collagen-containing extracellular matrix HDA PubMed 
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
     
    located_in endoplasmic reticulum lumen TAS
    Traceable Author Statement
    more info
     
    located_in extracellular region TAS
    Traceable Author Statement
    more info
     
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
     

    General protein information

    Preferred Names
    collagen alpha-3(IV) chain
    Names
    collagen IV, alpha-3 polypeptide
    collagen, type IV, alpha 3 (Goodpasture antigen)
    tumstatin

    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_011591.1 RefSeqGene

      Range
      5001..155228
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_230

    mRNA and Protein(s)

    1. NM_000091.5NP_000082.2  collagen alpha-3(IV) chain precursor

      See identical proteins and their annotated locations for NP_000082.2

      Status: REVIEWED

      Source sequence(s)
      AC097662, AC107069, AU099354, BM670570, BM712932, CD675393, X80031
      Consensus CDS
      CCDS42829.1
      UniProtKB/Swiss-Prot
      Q01955, Q53QQ1, Q53R14, Q53RW8, Q9BQT2, Q9NYC4, Q9UDJ9, Q9UDK9, Q9UDL0, Q9UDL1
      Related
      ENSP00000379823.3, ENST00000396578.8
      Conserved Domains (2) summary
      pfam01391
      Location:67124
      Collagen; Collagen triple helix repeat (20 copies)
      pfam01413
      Location:14461552
      C4; C-terminal tandem repeated domain in type 4 procollagen

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      227164624..227314792
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005246277.4XP_005246334.1  collagen alpha-3(IV) chain isoform X1

      Conserved Domains (2) summary
      pfam01391
      Location:67124
      Collagen; Collagen triple helix repeat (20 copies)
      pfam01413
      Location:14111517
      C4; C-terminal tandem repeated domain in type 4 procollagen
    2. XM_011510555.2XP_011508857.1  collagen alpha-3(IV) chain isoform X2

      Conserved Domains (3) summary
      pfam01391
      Location:67124
      Collagen; Collagen triple helix repeat (20 copies)
      pfam01413
      Location:14461552
      C4; C-terminal tandem repeated domain in type 4 procollagen
      cl02467
      Location:15561586
      C4; C-terminal tandem repeated domain in type 4 procollagen
    3. XM_047443224.1XP_047299180.1  collagen alpha-3(IV) chain isoform X3

    4. XM_006712245.4XP_006712308.1  collagen alpha-3(IV) chain isoform X4

      Conserved Domains (1) summary
      pfam01391
      Location:67124
      Collagen; Collagen triple helix repeat (20 copies)
    5. XM_017003295.2XP_016858784.1  collagen alpha-3(IV) chain isoform X5

    6. XM_005246280.4XP_005246337.1  collagen alpha-3(IV) chain isoform X6

      Conserved Domains (1) summary
      pfam01391
      Location:67124
      Collagen; Collagen triple helix repeat (20 copies)

    RNA

    1. XR_001738601.2 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      227647382..227797471
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054340431.1XP_054196406.1  collagen alpha-3(IV) chain isoform X1

    2. XM_054340432.1XP_054196407.1  collagen alpha-3(IV) chain isoform X2

    3. XM_054340433.1XP_054196408.1  collagen alpha-3(IV) chain isoform X3

    4. XM_054340434.1XP_054196409.1  collagen alpha-3(IV) chain isoform X4

    5. XM_054340435.1XP_054196410.1  collagen alpha-3(IV) chain isoform X5

    6. XM_054340436.1XP_054196411.1  collagen alpha-3(IV) chain isoform X6

    RNA

    1. XR_008486262.1 RNA Sequence

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_031362.2: Suppressed sequence

      Description
      NM_031362.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
    2. NM_031363.1: Suppressed sequence

      Description
      NM_031363.1: This RefSeq was permanently suppressed because it is a nonsense-mediated decay (NMD) candidate.
    3. NM_031364.1: Suppressed sequence

      Description
      NM_031364.1: This RefSeq was permanently suppressed because it is a nonsense-mediated decay (NMD) candidate.
    4. NM_031365.2: Suppressed sequence

      Description
      NM_031365.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
    5. NM_031366.2: Suppressed sequence

      Description
      NM_031366.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.