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Aliases for COL4A1 Gene

Aliases for COL4A1 Gene

  • Collagen Type IV Alpha 1 2 3
  • Collagen, Type IV, Alpha 1 2 3 5
  • Collagen Of Basement Membrane, Alpha-1 Chain 3
  • Collagen IV, Alpha-1 Polypeptide 3
  • COL4A1 NC1 Domain 3
  • EC 6.3.1.2 63
  • EC 3.4.23 63
  • Arresten 3
  • RATOR 3
  • BSVD 3

External Ids for COL4A1 Gene

Previous GeneCards Identifiers for COL4A1 Gene

  • GC13M109161
  • GC13M105188
  • GC13M109638
  • GC13M108499
  • GC13M109599
  • GC13M110801
  • GC13M091400

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 angiopathy, hereditary, with nephropathy, aneurysms, and muscle cramps and brain small vessel disease with or without ocular anomalies. Among its related pathways are Degradation of the extracellular matrix and Signaling by GPCR. GO annotations related to this gene include extracellular matrix structural constituent and extracellular matrix constituent conferring elasticity. 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

Regulatory Elements for COL4A1 Gene

Promoters for COL4A1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around COL4A1 on UCSC Golden Path with GeneCards custom track

Genomic Location for COL4A1 Gene

Chromosome:
13
Start:
110,148,958 bp from pter
End:
110,307,157 bp from pter
Size:
158,200 bases
Orientation:
Minus strand

Genomic View for COL4A1 Gene

Genes around COL4A1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
COL4A1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for COL4A1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence 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.
  • Glycosylation at Asn 126
  • Modification sites at PhosphoSitePlus

Other Protein References for COL4A1 Gene

Antibody Products

  • R&D Systems Antibodies for COL4A1 (Collagen IV alpha 1)

Domains & Families for COL4A1 Gene

Gene Families for COL4A1 Gene

Suggested Antigen Peptide Sequences for COL4A1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P02462

UniProtKB/Swiss-Prot:

CO4A1_HUMAN :
  • 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.
  • Belongs to the type IV collagen family.
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.
  • Contains 1 collagen IV NC1 (C-terminal non-collagenous) domain.
Family:
  • Belongs to the type IV collagen family.
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:0030023 extracellular matrix constituent conferring elasticity IC 16107487
genes like me logo Genes that share ontologies with COL4A1: view
genes like me logo Genes that share phenotypes with COL4A1: view

Human Phenotype Ontology for COL4A1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

Inhibitory RNA Products

Cell Line Products

In Situ Assay Products

Flow Cytometry Products

No data available for Animal Models , Transcription Factor Targets 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
endoplasmic reticulum 5
extracellular 5
cytosol 2
nucleus 2
plasma membrane 2
mitochondrion 1
peroxisome 1

No data available for Gene Ontology (GO) - Cellular Components for COL4A1 Gene

Pathways & Interactions 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:0022617 extracellular matrix disassembly TAS --
GO:0048514 blood vessel morphogenesis IMP 20818663
GO:0061333 renal tubule morphogenesis IMP 18160688
GO:0071230 cellular response to amino acid stimulus IEA --
genes like me logo Genes that share ontologies with COL4A1: view

No data available for SIGNOR curated interactions for COL4A1 Gene

Drugs & Compounds for COL4A1 Gene

(1) Drugs for COL4A1 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(1) Additional Compounds for COL4A1 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
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 (x4.8) and Artery - Tibial (x4.2).

Protein differential expression in normal tissues from HIPED for COL4A1 Gene

This gene is overexpressed in Amniocyte (24.5), Gallbladder (7.0), Colon muscle (6.3), and Adipocyte (6.1).

Integrated Proteomics: protein expression in normal tissues and cell lines 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 expression patterns with COL4A1: view

Protein tissue co-expression partners for COL4A1 Gene

- Elite partner

Primer Products

In Situ Assay Products

Orthologs for COL4A1 Gene

This gene was present in the common ancestor of animals.

Orthologs for COL4A1 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia COL4A1 35
  • 83.4 (n)
  • 89.75 (a)
COL4A1 36
  • 90 (a)
OneToOne
dog
(Canis familiaris)
Mammalia COL4A1 35
  • 84.45 (n)
  • 90.31 (a)
COL4A1 36
  • 90 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Col4a1 35
  • 83.48 (n)
  • 90.71 (a)
Col4a1 16
Col4a1 36
  • 91 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia COL4A1 35
  • 99.15 (n)
  • 99.36 (a)
COL4A1 36
  • 99 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Col4a1 35
  • 84.1 (n)
  • 90.83 (a)
oppossum
(Monodelphis domestica)
Mammalia COL4A1 36
  • 81 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia COL4A1 36
  • 73 (a)
OneToOne
chicken
(Gallus gallus)
Aves COL4A1 35
  • 69.83 (n)
  • 74.64 (a)
COL4A1 36
  • 74 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia COL4A1 36
  • 71 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia col4a1 35
  • 64.36 (n)
  • 66.06 (a)
zebrafish
(Danio rerio)
Actinopterygii col4a1 35
  • 61.26 (n)
  • 63.33 (a)
col4a1 36
  • 63 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta Cg25C 37
  • 41 (a)
vkg 36
  • 37 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea let-2 37
  • 66 (a)
emb-9 36
  • 46 (a)
ManyToMany
let-2 36
  • 49 (a)
ManyToMany
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.3677 35
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10972 36
  • 46 (a)
ManyToMany
CSA.6298 36
  • 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

(8) 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
rs3742207 - 110,166,251(-) GATCA(A/C/T)GGCGT reference, missense
VAR_030027 -
VAR_030028 Brain small vessel disease with or without ocular anomalies (BSVD)
VAR_030029 Porencephaly 1 (POREN1)
VAR_030030 Porencephaly 1 (POREN1)

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

Variation tolerance for COL4A1 Gene

Residual Variation Intolerance Score: 1.48% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 13.09; 95.09% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for COL4A1 Gene

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

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for COL4A1 Gene

Disorders for COL4A1 Gene

MalaCards: The human disease database

(22) MalaCards diseases for COL4A1 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
angiopathy, hereditary, with nephropathy, aneurysms, and muscle cramps
  • hereditary angiopathy with nephropathy, aneurysms, and muscle cramps syndrome
brain small vessel disease with or without ocular anomalies
  • brain small vessel disease with axenfeld-rieger anomaly
porencephaly 1
  • autosomal dominant type 1 porencephaly
retinal arteries, tortuosity of
  • retinal hemorrhage with vascular tortuosity
hemorrhage, intracerebral
  • stroke, hemorrhagic
- elite association - COSMIC cancer census association via MalaCards

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, ECO:0000269 PubMed:22574627, ECO:0000269 PubMed:23394911, ECO:0000269 PubMed:24628545}. 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.
  • Intracerebral hemorrhage (ICH) [MIM:614519]: A pathological condition characterized by bleeding into one or both cerebral hemispheres including the basal ganglia and the cerebral cortex. It is often associated with hypertension and craniocerebral trauma. Intracerebral bleeding is a common cause of stroke. {ECO:0000269 PubMed:22522439}. Note=Disease susceptibility is associated with variations 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.
  • Schizencephaly (SCHZC) [MIM:269160]: Extremely rare human congenital disorder characterized by a full-thickness cleft within the cerebral hemispheres. These clefts are lined with gray matter and most commonly involve the parasylvian regions. Large portions of the cerebral hemispheres may be absent and replaced by cerebro-spinal fluid. {ECO:0000269 PubMed:23225343}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Tortuosity of retinal arteries (RATOR) [MIM:180000]: A disease characterized by marked tortuosity of second- and third-order retinal arteries with normal first-order arteries and venous system. Most patients manifest variable degrees of symptomatic transient vision loss due to retinal hemorrhage following minor stress or trauma. {ECO:0000269 PubMed:25228067}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for COL4A1

Genetic Association Database (GAD)
COL4A1
Human Genome Epidemiology (HuGE) Navigator
COL4A1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
COL4A1
genes like me logo Genes that share disorders with COL4A1: view

No data available for Genatlas for COL4A1 Gene

Publications for COL4A1 Gene

  1. Complete primary structure of the alpha 1-chain of human basement membrane (type IV) collagen. (PMID: 3691802) Soininen R. … Tryggvason K. (FEBS Lett. 1987) 2 3 4 67
  2. COL4A1 mutation in two preterm siblings with antenatal onset of parenchymal hemorrhage. (PMID: 19194877) de Vries L.S. … Mancini G. (Ann. Neurol. 2009) 3 23
  3. 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
  4. Gene expression profiling identifies genes predictive of oral squamous cell carcinoma. (PMID: 18669583) Chen C. … Zhao L.P. (Cancer Epidemiol. Biomarkers Prev. 2008) 3 23
  5. Characterization of the anti-angiogenic properties of arresten, an alpha1beta1 integrin-dependent collagen-derived tumor suppressor. (PMID: 18775695) Nyberg P. … Kalluri R. (Exp. Cell Res. 2008) 3 23

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Sources for COL4A1 Gene

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