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Aliases for COL4A1 Gene

Aliases for COL4A1 Gene

  • Collagen, Type IV, Alpha 1 2 3
  • Collagen Of Basement Membrane, Alpha-1 Chain 3
  • Collagen IV, Alpha-1 Polypeptide 3
  • Collagen Alpha-1(IV) Chain 3
  • COL4A1 NC1 Domain 3
  • EC 6.3.1.2 64
  • EC 3.4.23 64
  • Arresten 3
  • POREN1 6
  • HANAC 6
  • BSVD 3
  • ICH 6

External Ids for COL4A1 Gene

Summaries for COL4A1 Gene

Entrez Gene Summary for COL4A1 Gene

  • 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]

GeneCards Summary for COL4A1 Gene

COL4A1 (Collagen, Type IV, Alpha 1) is a Protein Coding gene. Diseases associated with COL4A1 include col4a1-related disorders and porencephaly 1. Among its related pathways are PI3K-Akt signaling pathway and Signaling by FGFR. GO annotations related to this gene include extracellular matrix structural constituent and platelet-derived growth factor binding. An important paralog of this gene is COL3A1.

UniProtKB/Swiss-Prot for COL4A1 Gene

  • Type IV collagen is the major structural component of glomerular basement membranes (GBM), forming a chicken-wire meshwork together with laminins, proteoglycans and entactin/nidogen

  • Arresten, comprising the C-terminal NC1 domain, inhibits angiogenesis and tumor formation. The C-terminal half is found to possess the anti-angiogenic activity. Specifically inhibits endothelial cell proliferation, migration and tube formation. Inhibits expression of hypoxia-inducible factor 1alpha and ERK1/2 and p38 MAPK activation. Ligand for alpha1/beta1 integrin

Gene Wiki entry for COL4A1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for COL4A1 Gene

Genomics for COL4A1 Gene

Genomic Location for COL4A1 Gene

Start:
110,148,963 bp from pter
End:
110,307,149 bp from pter
Size:
158,187 bases
Orientation:
Minus strand

Genomic View for COL4A1 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for COL4A1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for COL4A1 Gene

Regulatory Elements for COL4A1 Gene

Proteins for COL4A1 Gene

  • Protein details for COL4A1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P02462-CO4A1_HUMAN
    Recommended name:
    Collagen alpha-1(IV) chain
    Protein Accession:
    P02462
    Secondary Accessions:
    • A7E2W4
    • B1AM70
    • Q1P9S9
    • Q5VWF6
    • Q86X41
    • Q8NF88
    • Q9NYC5

    Protein attributes for COL4A1 Gene

    Size:
    1669 amino acids
    Molecular mass:
    160615 Da
    Quaternary structure:
    • There are six type IV collagen isoforms, alpha 1(IV)-alpha 6(IV), each of which can form a triple helix structure with 2 other chains to generate type IV collagen network

    Three dimensional structures from OCA and Proteopedia for COL4A1 Gene

    Alternative splice isoforms for COL4A1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for COL4A1 Gene

Proteomics data for COL4A1 Gene at MOPED

Selected DME Specific Peptides for COL4A1 Gene

Post-translational modifications for COL4A1 Gene

  • Lysines at the third position of the tripeptide repeating unit (G-X-Y) are hydroxylated in all cases and bind carbohydrates
  • Prolines at the third position of the tripeptide repeating unit (G-X-Y) are hydroxylated in some or all of the chains
  • Proteolytic processing produces the C-terminal NC1 peptide, arresten
  • The trimeric structure of the NC1 domains is stabilized by covalent bonds between Lys and Met residues
  • Type IV collagens contain numerous cysteine residues which are involved in inter- and intramolecular disulfide bonding. 12 of these, located in the NC1 domain, are conserved in all known type IV collagens
  • Modification sites at PhosphoSitePlus
  • Glycosylation at Asn126

Other Protein References for COL4A1 Gene

ENSEMBL proteins:
Reactome Protein details:
REFSEQ proteins:

Domains for COL4A1 Gene

Gene Families for COL4A1 Gene

HGNC:

UniProtKB/Swiss-Prot:

CO4A1_HUMAN
Domain:
  • Alpha chains of type IV collagen have a non-collagenous domain (NC1) at their C-terminus, frequent interruptions of the G-X-Y repeats in the long central triple-helical domain (which may cause flexibility in the triple helix), and a short N-terminal triple-helical 7S domain:
    • P02462
  • Contains 1 collagen IV NC1 (C-terminal non-collagenous) domain.:
    • P02462
Family:
  • Belongs to the type IV collagen family.:
    • P02462
genes like me logo Genes that share domains with COL4A1: view

Function for COL4A1 Gene

Molecular function for COL4A1 Gene

GENATLAS Biochemistry: collagen type IV,alpha 1,basement membrane,all tissues,expressed in the dermoepidermal junction during fetal skin development
UniProtKB/Swiss-Prot Function: Type IV collagen is the major structural component of glomerular basement membranes (GBM), forming a chicken-wire meshwork together with laminins, proteoglycans and entactin/nidogen
UniProtKB/Swiss-Prot Function: Arresten, comprising the C-terminal NC1 domain, inhibits angiogenesis and tumor formation. The C-terminal half is found to possess the anti-angiogenic activity. Specifically inhibits endothelial cell proliferation, migration and tube formation. Inhibits expression of hypoxia-inducible factor 1alpha and ERK1/2 and p38 MAPK activation. Ligand for alpha1/beta1 integrin

Enzyme Numbers (IUBMB) for COL4A1 Gene

Gene Ontology (GO) - Molecular Function for COL4A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005201 extracellular matrix structural constituent IMP 16107487
GO:0005515 protein binding IPI 12011424
GO:0030023 extracellular matrix constituent conferring elasticity IC 16107487
GO:0048407 platelet-derived growth factor binding IDA 8900172
genes like me logo Genes that share ontologies with COL4A1: view
genes like me logo Genes that share phenotypes with COL4A1: view

Animal Models for COL4A1 Gene

MGI Knock Outs for COL4A1:

No data available for Transcription Factor Targeting and HOMER Transcription for COL4A1 Gene

Localization for COL4A1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for COL4A1 Gene

Secreted, extracellular space, extracellular matrix, basement membrane.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for COL4A1 Gene COMPARTMENTS Subcellular localization image for COL4A1 gene
Compartment Confidence
extracellular 5
endoplasmic reticulum 4
mitochondrion 1
peroxisome 1
plasma membrane 1

Gene Ontology (GO) - Cellular Components for COL4A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0005581 collagen trimer --
GO:0005587 collagen type IV trimer IMP 16107487
GO:0005604 basement membrane IC 23065703
GO:0005788 endoplasmic reticulum lumen TAS --
genes like me logo Genes that share ontologies with COL4A1: view

Pathways for COL4A1 Gene

genes like me logo Genes that share pathways with COL4A1: view

Gene Ontology (GO) - Biological Process for COL4A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001569 patterning of blood vessels IMP 20818663
GO:0006898 receptor-mediated endocytosis TAS --
GO:0007411 axon guidance TAS --
GO:0007420 brain development IMP 16107487
GO:0007528 neuromuscular junction development IEA --
genes like me logo Genes that share ontologies with COL4A1: view

Compounds for COL4A1 Gene

(2) Novoseek inferred chemical compound relationships for COL4A1 Gene

Compound -log(P) Hits PubMed IDs
arresten 93.3 6
tyrosine 0 2
genes like me logo Genes that share compounds with COL4A1: view

Transcripts for COL4A1 Gene

Unigene Clusters for COL4A1 Gene

Collagen, type IV, alpha 1:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for COL4A1 Gene

No ASD Table

Relevant External Links for COL4A1 Gene

GeneLoc Exon Structure for
COL4A1
ECgene alternative splicing isoforms for
COL4A1

Expression for COL4A1 Gene

mRNA expression in normal human tissues for COL4A1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for COL4A1 Gene

This gene is overexpressed in Artery - Coronary (4.8) and Artery - Tibial (4.2).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for COL4A1 Gene

SOURCE GeneReport for Unigene cluster for COL4A1 Gene Hs.17441

mRNA Expression by UniProt/SwissProt for COL4A1 Gene

P02462-CO4A1_HUMAN
Tissue specificity: Highly expressed in placenta.
genes like me logo Genes that share expressions with COL4A1: view

Orthologs for COL4A1 Gene

This gene was present in the common ancestor of animals.

Orthologs for COL4A1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia COL4A1 36
  • 99.15 (n)
  • 99.36 (a)
COL4A1 37
  • 99 (a)
OneToOne
cow
(Bos Taurus)
Mammalia COL4A1 36
  • 83.4 (n)
  • 89.75 (a)
COL4A1 37
  • 90 (a)
OneToOne
dog
(Canis familiaris)
Mammalia COL4A1 36
  • 84.45 (n)
  • 90.31 (a)
COL4A1 37
  • 90 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Col4a1 36
  • 83.48 (n)
  • 90.71 (a)
Col4a1 16
Col4a1 37
  • 91 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia COL4A1 37
  • 81 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia COL4A1 37
  • 73 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Col4a1 36
  • 84.1 (n)
  • 90.83 (a)
chicken
(Gallus gallus)
Aves COL4A1 36
  • 69.83 (n)
  • 74.64 (a)
COL4A1 37
  • 74 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia COL4A1 37
  • 71 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia col4a1 36
  • 64.36 (n)
  • 66.06 (a)
zebrafish
(Danio rerio)
Actinopterygii col4a1 36
  • 61.26 (n)
  • 63.33 (a)
col4a1 37
  • 63 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta vkg 37
  • 37 (a)
OneToMany
Cg25C 38
  • 41 (a)
worm
(Caenorhabditis elegans)
Secernentea emb-9 37
  • 46 (a)
ManyToMany
let-2 37
  • 49 (a)
ManyToMany
let-2 38
  • 66 (a)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.3677 36
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10972 37
  • 46 (a)
ManyToMany
CSA.6298 37
  • 43 (a)
ManyToMany
Species with no ortholog for COL4A1:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for COL4A1 Gene

ENSEMBL:
Gene Tree for COL4A1 (if available)
TreeFam:
Gene Tree for COL4A1 (if available)

Paralogs for COL4A1 Gene

Selected SIMAP similar genes for COL4A1 Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with COL4A1: view

Variants for COL4A1 Gene

Sequence variations from dbSNP and Humsavar for COL4A1 Gene

SNP ID Clin Chr 13 pos Sequence Context AA Info Type MAF
rs7273 -- 110,149,231(-) CCTCA(A/G)CAGGG utr-variant-3-prime
rs8229 -- 110,198,583(-) TGAAA(A/G)AGGAG missense, reference
rs13260 -- 110,149,776(+) AAATT(G/T)TGATT utr-variant-3-prime
rs72509 -- 110,250,840(+) ACGGA(G/T)CCCCT intron-variant
rs472457 -- 110,180,119(-) GACAA(A/G)TAGGG intron-variant

Structural Variations from Database of Genomic Variants (DGV) for COL4A1 Gene

Variant ID Type Subtype PubMed ID
nsv901006 CNV Gain 21882294
nsv456115 CNV Loss 19166990
nsv901007 CNV Loss 21882294
esv3081 CNV Deletion 18987735
esv2748000 CNV Deletion 23290073
nsv520696 CNV Loss 19592680
nsv1182 CNV Loss 18451855
dgv241n27 CNV Loss 19166990
nsv64357 CNV Loss 16902084
nsv521901 CNV Loss 19592680
esv2748001 CNV Deletion 23290073
esv1710742 CNV Deletion 17803354
esv2748002 CNV Deletion 23290073
esv2741067 CNV Deletion 23290073
esv2748003 CNV Deletion 23290073
nsv523051 CNV Loss 19592680
esv27869 CNV Loss 19812545

Relevant External Links for COL4A1 Gene

HapMap Linkage Disequilibrium report
COL4A1
Human Gene Mutation Database (HGMD)
COL4A1

Disorders for COL4A1 Gene

(4) OMIM Diseases for COL4A1 Gene (120130)

UniProtKB/Swiss-Prot

CO4A1_HUMAN
  • Brain small vessel disease with or without ocular anomalies (BSVD) [MIM:607595]: An autosomal dominant disease characterized by weakening of the blood vessels in the brain and retinal arteriolar tortuosity. In affected individuals, stroke is often the first symptom and is usually caused by bleeding in the brain (hemorrhagic stroke) rather than a lack of blood flow in the brain (ischemic stroke). Patients also have leukoencephalopathy and may experience seizures and migraine headaches accompanied by visual sensations known as auras. {ECO:0000269 PubMed:16598045, ECO:0000269 PubMed:17379824, ECO:0000269 PubMed:17696175, ECO:0000269 PubMed:19477666, ECO:0000269 PubMed:20385946}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Hereditary angiopathy with nephropathy aneurysms and muscle cramps (HANAC) [MIM:611773]: The clinical renal manifestations include hematuria and bilateral large cysts. Histologic analysis revealed complex basement membrane defects in kidney and skin. The systemic angiopathy appears to affect both small vessels and large arteries. {ECO:0000269 PubMed:18160688, ECO:0000269 PubMed:20818663}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Porencephaly 1 (POREN1) [MIM:175780]: A neurologic disorder characterized by a fluid-filled cysts or cavities within the cerebral hemispheres, neurologic manifestations, facial paresis, and visual defects. Affected individuals typically have hemiplegia, seizures, and intellectual disability. Porencephaly type 1 is usually unilateral and results from focal destructive lesions such as fetal vascular occlusion or birth trauma. {ECO:0000269 PubMed:15905400, ECO:0000269 PubMed:16107487, ECO:0000269 PubMed:19194877}. Note=The disease is caused by mutations affecting the gene represented in this entry.

(2) University of Copenhagen DISEASES for COL4A1 Gene

(5) Novoseek inferred disease relationships for COL4A1 Gene

Disease -log(P) Hits PubMed IDs
porencephaly 82.4 3
intracerebral hemorrhage 47.9 2
neovascularization 35.1 1
renal disease 31.9 3
diabetic nephropathies 23.7 2

Relevant External Links for COL4A1

GeneTests
COL4A1
GeneReviews
COL4A1
Genetic Association Database (GAD)
COL4A1
Human Genome Epidemiology (HuGE) Navigator
COL4A1
genes like me logo Genes that share disorders with COL4A1: view

Publications for COL4A1 Gene

  1. Anti-angiogenic cues from vascular basement membrane collagen. (PMID: 10811134) Colorado P.C. … Kalluri R. (Cancer Res. 2000) 3 4 23
  2. Human alpha1 type IV collagen NC1 domain exhibits distinct antiangiogenic activity mediated by alpha1beta1 integrin. (PMID: 16151532) Sudhakar A. … Kalluri R. (J. Clin. Invest. 2005) 3 4 23
  3. COL4A1 mutation in two preterm siblings with antenatal onset of parenchymal hemorrhage. (PMID: 19194877) de Vries L.S. … Mancini G. (Ann. Neurol. 2009) 3 4 23
  4. Genetic risk for myocardial infarction determined by polymorphisms of candidate genes in a Japanese population. (PMID: 18077766) Yamada Y. … Nozawa Y. (J. Med. Genet. 2008) 3 23 49
  5. COL4A1 mutations and hereditary angiopathy, nephropathy, aneurysms, and muscle cramps. (PMID: 18160688) Plaisier E. … Ronco P. (N. Engl. J. Med. 2007) 3 4 23

Products for COL4A1 Gene

Sources for COL4A1 Gene

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