Format

Send to:

Choose Destination

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

Gene ID: 1285, updated on 3-Oct-2018

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; Vega:OTTHUMG00000149891
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
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

Genomic context

See COL4A3 in Genome Data Viewer
Location:
2q36.3
Exon count:
54
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 2 NC_000002.12 (227164565..227314792)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (228029281..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 uncharacterized LOC654841 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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

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

  • AGE-RAGE signaling pathway in diabetic complications, organism-specific biosystem (from KEGG)
    AGE-RAGE signaling pathway in diabetic complications, organism-specific biosystemAdvanced glycation end products (AGEs) are a complex group of compounds produced through the non-enzymatic glycation and oxidation of proteins, lipids and nucleic acids, primarily due to aging and un...
  • AGE-RAGE signaling pathway in diabetic complications, conserved biosystem (from KEGG)
    AGE-RAGE signaling pathway in diabetic complications, conserved biosystemAdvanced glycation end products (AGEs) are a complex group of compounds produced through the non-enzymatic glycation and oxidation of proteins, lipids and nucleic acids, primarily due to aging and un...
  • Amoebiasis, organism-specific biosystem (from KEGG)
    Amoebiasis, organism-specific biosystemEntamoeba histolytica, an extracellular protozoan parasite is a human pathogen that invades the intestinal epithelium. Infection occurs on ingestion of contaminated water and food. The pathogenesis o...
  • Amoebiasis, conserved biosystem (from KEGG)
    Amoebiasis, conserved biosystemEntamoeba histolytica, an extracellular protozoan parasite is a human pathogen that invades the intestinal epithelium. Infection occurs on ingestion of contaminated water and food. The pathogenesis o...
  • 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 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...
  • Integrin cell surface interactions, organism-specific biosystem (from REACTOME)
    Integrin cell surface interactions, organism-specific biosystemThe extracellular matrix (ECM) is a network of macro-molecules that underlies all epithelia and endothelia and that surrounds all connective tissue cells. This matrix provides the mechanical strength...
  • Integrins in angiogenesis, organism-specific biosystem (from Pathway Interaction Database)
    Integrins in angiogenesis, organism-specific biosystem
    Integrins in angiogenesis
  • 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...
  • Pathways in cancer, organism-specific biosystem (from KEGG)
    Pathways in cancer, organism-specific biosystem
    Pathways in cancer
  • Primary Focal Segmental Glomerulosclerosis FSGS, organism-specific biosystem (from WikiPathways)
    Primary Focal Segmental Glomerulosclerosis FSGS, organism-specific biosystemPrimary or idiopathic focal segmental glomerulosclerosis (FSGS) a cause of nephrotic syndrome in children and adolescents, as well as an important cause of end stage renal disease in adults. FSGS is ...
  • 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...
  • Small cell lung cancer, organism-specific biosystem (from KEGG)
    Small cell lung cancer, organism-specific biosystemLung cancer is a leading cause of cancer death among men and women in industrialized countries. Small cell lung carcinoma (SCLC) is a highly aggressive neoplasm, which accounts for approximately 25% ...
  • Small cell lung cancer, conserved biosystem (from KEGG)
    Small cell lung cancer, conserved biosystemLung cancer is a leading cause of cancer death among men and women in industrialized countries. Small cell lung carcinoma (SCLC) is a highly aggressive neoplasm, which accounts for approximately 25% ...

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 
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 proliferation IDA
Inferred from Direct Assay
more info
PubMed 
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 proliferation TAS
Traceable Author Statement
more info
PubMed 
negative regulation of endopeptidase activity IEA
Inferred from Electronic Annotation
more info
 
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 IDA
Inferred from Direct Assay
more info
PubMed 
collagen type IV trimer IBA
Inferred from Biological aspect of Ancestor
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)

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_000091.4NP_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, OTTHUMP00000203997, ENST00000396578.7, OTTHUMT00000331409
    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 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_000002.12 Reference GRCh38.p12 Primary Assembly

    Range
    227164565..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.
Support Center