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

Gene ID: 1285, updated on 10-Apr-2021

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
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
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
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Genomic context

See COL4A3 in Genome Data Viewer
Location:
2q36.3
Exon count:
54
Annotation release Status Assembly Chr Location
109.20210226 current GRCh38.p13 (GCF_000001405.39) 2 NC_000002.12 (227164589..227314792)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (228029340..228179508)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene insulin receptor substrate 1 Neighboring gene rhomboid domain containing 1 Neighboring gene collagen type IV alpha 4 chain Neighboring gene MFF divergent transcript 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
Compare labs
Alport syndrome 3, autosomal dominant
MedGen: C4746547 OMIM: 104200 GeneReviews: Alport Syndrome
Compare labs
Alport syndrome, autosomal recessive
MedGen: C4746745 OMIM: 203780 GeneReviews: Alport Syndrome
Compare labs
Benign familial hematuria
MedGen: C0241908 OMIM: 141200 GeneReviews: Not available
Compare labs
Genome-wide association analyses identify multiple loci associated with central corneal thickness and keratoconus.
GeneReviews: Not available
Genome-wide association study of monoamine metabolite levels in human cerebrospinal fluid.
GeneReviews: Not available

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

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
extracellular matrix structural constituent IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
extracellular matrix structural constituent conferring tensile strength HDA PubMed 
extracellular matrix structural constituent conferring tensile strength RCA
inferred from Reviewed Computational Analysis
more info
PubMed 
integrin binding IDA
Inferred from Direct Assay
more info
PubMed 
integrin binding TAS
Traceable Author Statement
more info
PubMed 
metalloendopeptidase inhibitor activity NAS
Non-traceable Author Statement
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
structural molecule activity NAS
Non-traceable Author Statement
more info
PubMed 
Process Evidence Code Pubs
activation of cysteine-type endopeptidase activity involved in apoptotic process IDA
Inferred from Direct Assay
more info
PubMed 
blood circulation TAS
Traceable Author Statement
more info
PubMed 
cell adhesion IEA
Inferred from Electronic Annotation
more info
 
cell surface receptor signaling pathway NAS
Non-traceable Author Statement
more info
PubMed 
collagen-activated tyrosine kinase receptor signaling pathway IEA
Inferred from Electronic Annotation
more info
 
endothelial cell apoptotic process IDA
Inferred from Direct Assay
more info
PubMed 
extracellular matrix organization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
extracellular matrix organization TAS
Traceable Author Statement
more info
 
glomerular basement membrane development ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of angiogenesis IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of cell population proliferation TAS
Traceable Author Statement
more info
PubMed 
negative regulation of endopeptidase activity IEA
Inferred from Electronic Annotation
more info
 
negative regulation of vascular endothelial cell proliferation IDA
Inferred from Direct Assay
more info
PubMed 
response to glucose IEA
Inferred from Electronic Annotation
more info
 
sensory perception of sound TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
basement membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
basement membrane IDA
Inferred from Direct Assay
more info
PubMed 
collagen type IV trimer IDA
Inferred from Direct Assay
more info
PubMed 
collagen-containing extracellular matrix HDA PubMed 
endoplasmic reticulum IDA
Inferred from Direct Assay
more info
 
endoplasmic reticulum lumen TAS
Traceable Author Statement
more info
 
extracellular matrix IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
extracellular region TAS
Traceable Author Statement
more info
 
extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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)

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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
    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: Homo sapiens Updated Annotation Release 109.20210226

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p13 Primary Assembly

    Range
    227164589..227314792
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005246277.3XP_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_011510555.1XP_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_006712245.3XP_006712308.1  collagen alpha-3(IV) chain isoform X4

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

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

    Conserved Domains (1) summary
    pfam01391
    Location:67124
    Collagen; Collagen triple helix repeat (20 copies)
  6. XM_011510556.2XP_011508858.1  collagen alpha-3(IV) chain isoform X3

    Conserved Domains (2) summary
    pfam01391
    Location:417472
    Collagen; Collagen triple helix repeat (20 copies)
    pfam01413
    Location:10331139
    C4; C-terminal tandem repeated domain in type 4 procollagen

RNA

  1. XR_241280.3 RNA Sequence

  2. XR_001738601.1 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.
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