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

Gene ID: 1282, updated on 18-Nov-2018

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; 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

Genomic context

See COL4A1 in Genome Data Viewer
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

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
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

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 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...
  • Binding and Uptake of Ligands by Scavenger Receptors, organism-specific biosystem (from REACTOME)
    Binding and Uptake of Ligands by Scavenger Receptors, organism-specific biosystemScavenger receptors bind free extracellular ligands as the initial step in clearance of the ligands from the body (reviewed in Ascenzi et al. 2005, Areschoug and Gordon 2009, Nielsen et al. 2010). So...
  • 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 WikiPathways)
    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, 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...
  • 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...
  • Overview of nanoparticle effects, organism-specific biosystem (from WikiPathways)
    Overview of nanoparticle effects, organism-specific biosystemThis pathway is giving a summary of currently known nanoparticle effects on cells and organisms. Although there is currently no nanoparticle specific effect known, there is a cascade of effects trigg...
  • 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
  • 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...
  • Scavenging by Class A Receptors, organism-specific biosystem (from REACTOME)
    Scavenging by Class A Receptors, organism-specific biosystemClass A scavenger receptors contain an intracellular domain, a transmembrane region, a coiled-coil domain, a collagenous domain, and the SR cysteine-rich domain (reviewed in Areschoug and Gordon 2009...
  • 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% ...
  • Spinal Cord Injury, organism-specific biosystem (from WikiPathways)
    Spinal Cord Injury, organism-specific biosystemThis pathway provides an overview of cell types, therapeutic targets, drugs, new proposed targets and pathways implicated in spinal cord injury. Spinal cord injury is a complex multistep process that...
  • Vesicle-mediated transport, organism-specific biosystem (from REACTOME)
    Vesicle-mediated transport, organism-specific biosystemThe transit of proteins and other cargo through the cell requires a cellular transport process in which transported substances are moved in membrane-bounded vesicles. Transported substances are enclo...
  • miRNA targets in ECM and membrane receptors, organism-specific biosystem (from WikiPathways)
    miRNA targets in ECM and membrane receptors, organism-specific biosystemBased on the KEGG ECM-receptor interactions pathway (hsa04512), a depiction a plausible mechanism, where miRNAs regulate components of both extracellular matrix (top panel) and transmembrane receptor...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ10041, FLJ25428

Gene Ontology Provided by GOA

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-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 IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
collagen type IV trimer IMP
Inferred from Mutant Phenotype
more info
PubMed 
collagen-containing extracellular matrix HDA PubMed 
colocalizes_with collagen-containing extracellular matrix ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
endoplasmic reticulum lumen TAS
Traceable Author Statement
more info
 
extracellular matrix IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
extracellular region NAS
Non-traceable Author Statement
more info
PubMed 
extracellular region TAS
Traceable Author Statement
more info
 
extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

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)

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, ENST00000543140.6, 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, ENST00000375820.9, 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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