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Col4a1 collagen, type IV, alpha 1 [ Mus musculus (house mouse) ]

Gene ID: 12826, updated on 5-Mar-2024

Summary

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Official Symbol
Col4a1provided by MGI
Official Full Name
collagen, type IV, alpha 1provided by MGI
Primary source
MGI:MGI:88454
See related
Ensembl:ENSMUSG00000031502 AllianceGenome:MGI:88454
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
Bru; Raw; Svc; Col4a-1
Summary
This gene encodes the alpha-1 subunit of the type IV collagens, an essential component of basement membranes. The encoded protein forms a triple helical heterotrimer comprised of two alpha-1 and one alpha-2 subunits that assembles into a type IV collagen network. This gene is located adjacent to the gene encoding alpha-2 subunit. Mice lacking both the alpha-1 and alpha-2 subunits of collagen IV die in utero due to structural deficiencies in the basement membranes and certain mutations in this gene cause perinatal cerebral hemorrhage and porencephaly. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Nov 2015]
Expression
Broad expression in subcutaneous fat pad adult (RPKM 160.4), lung adult (RPKM 107.4) and 21 other tissues See more
Orthologs
human all
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Genomic context

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Location:
8 A1.1; 8 5.53 cM
Exon count:
52
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 8 NC_000074.7 (11248423..11362889, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 8 NC_000074.6 (11198423..11312889, complement)

Chromosome 8 - NC_000074.7Genomic Context describing neighboring genes Neighboring gene RIKEN cDNA 9530052E02 gene Neighboring gene STARR-positive B cell enhancer ABC_E3768 Neighboring gene insulin receptor substrate 2 Neighboring gene predicted gene 44717 Neighboring gene predicted gene 15418 Neighboring gene predicted gene, 32709 Neighboring gene collagen, type IV, alpha 2 Neighboring gene predicted gene, 46030 Neighboring gene STARR-seq mESC enhancer starr_20711 Neighboring gene predicted gene 15419

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

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Related articles in PubMed

  1. Use of sodium 4-phenylbutyrate to define therapeutic parameters for reducing intracerebral hemorrhage and myopathy in Col4a1 mutant mice. Hayashi G, et al. Dis Model Mech, 2018 Jul 4. PMID 29895609, Free PMC Article
  2. Severity of arterial defects in the retina correlates with the burden of intracerebral haemorrhage in COL4A1-related stroke. Ratelade J, et al. J Pathol, 2018 Apr. PMID 29266233
  3. Col4a1 mutation generates vascular abnormalities correlated with neuronal damage in a mouse model of HANAC syndrome. Trouillet A, et al. Neurobiol Dis, 2017 Apr. PMID 28057519
  4. HANAC Col4a1 Mutation in Mice Leads to Skeletal Muscle Alterations due to a Primary Vascular Defect. Guiraud S, et al. Am J Pathol, 2017 Mar. PMID 28056338, Free PMC Article
  5. ER stress and basement membrane defects combine to cause glomerular and tubular renal disease resulting from Col4a1 mutations in mice. Jones FE, et al. Dis Model Mech, 2016 Feb. PMID 26839400, Free PMC Article

See all (226) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Impaired intracellular Ca[2+] signaling contributes to age-related cerebral small vessel disease in Col4a1 mutant mice.
    Title: Impaired intracellular Ca(2+) signaling contributes to age-related cerebral small vessel disease in Col4a1 mutant mice.
  2. Elevated TGFbeta signaling contributes to cerebral small vessel disease in mouse models of Gould syndrome.
    Title: Elevated TGFβ signaling contributes to cerebral small vessel disease in mouse models of Gould syndrome.
  3. Elevated TGFbeta signaling contributes to ocular anterior segment dysgenesis in Col4a1 mutant mice.
    Title: Elevated TGFβ signaling contributes to ocular anterior segment dysgenesis in Col4a1 mutant mice.
  4. Identification of fibronectin 1 as a candidate genetic modifier in a Col4a1 mutant mouse model of Gould syndrome.
    Title: Identification of fibronectin 1 as a candidate genetic modifier in a Col4a1 mutant mouse model of Gould syndrome.
  5. COL4A1 Mutations are associated with Neuromuscular Disease.
    Title: COL4A1 Mutations Cause Neuromuscular Disease with Tissue-Specific Mechanistic Heterogeneity.
  6. Smooth muscle cell degeneration is a critical factor underlying the partial penetrance of COL4A1-stroke related macrohaemorrhages.
    Title: Severity of arterial defects in the retina correlates with the burden of intracerebral haemorrhage in COL4A1-related stroke.
  7. This work presents binding data consistent with a major role of 3-hydroxyproline in interactions of collagen IV with glycoprotein VI and nidogens 1 and 2.
    Title: Post-translational modification of type IV collagen with 3-hydroxyproline affects its interactions with glycoprotein VI and nidogens 1 and 2.
  8. Col4a1 mutation generates vascular abnormalities correlated with neuronal damage in a mouse model of HANAC syndrome
    Title: Col4a1 mutation generates vascular abnormalities correlated with neuronal damage in a mouse model of HANAC syndrome.
  9. Embryo implantation triggers dynamic spatiotemporal expression of the basement membrane toolkit (Col4a1, GPBP, Lamc1, peroxidasin) during uterine reprogramming.
    Title: Embryo implantation triggers dynamic spatiotemporal expression of the basement membrane toolkit during uterine reprogramming.
  10. DDR1 kinase activity is required for regulating collagen IV synthesis.
    Title: Discoidin domain receptor 1 kinase activity is required for regulating collagen IV synthesis.
Submit: New GeneRIF Correction See all GeneRIFs (32)

Phenotypes

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Associated conditions

Description Tests
bruised
GeneReviews: Not available
retinal anteriolar wiring
GeneReviews: Not available
small with vacuolar cataract
GeneReviews: Not available

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables extracellular matrix structural constituent ISO
Inferred from Sequence Orthology
more info
  
enables extracellular matrix structural constituent conferring tensile strength IBA
Inferred from Biological aspect of Ancestor
more info
  
enables extracellular matrix structural constituent conferring tensile strength ISO
Inferred from Sequence Orthology
more info
  
enables extracellular matrix structural constituent conferring tensile strength RCA
inferred from Reviewed Computational Analysis
more info
 PubMed 
enables platelet-derived growth factor binding ISO
Inferred from Sequence Orthology
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within angiogenesis IEA
Inferred from Electronic Annotation
more info
  
involved_in basement membrane organization ISO
Inferred from Sequence Orthology
more info
  
involved_in blood vessel morphogenesis ISO
Inferred from Sequence Orthology
more info
  
involved_in brain development ISO
Inferred from Sequence Orthology
more info
  
involved_in branching involved in blood vessel morphogenesis ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within cellular response to amino acid stimulus IDA
Inferred from Direct Assay
more info
 PubMed 
acts_upstream_of_or_within collagen-activated tyrosine kinase receptor signaling pathway IGI
Inferred from Genetic Interaction
more info
 PubMed 
involved_in extracellular matrix organization IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within neuromuscular junction development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in renal tubule morphogenesis ISO
Inferred from Sequence Orthology
more info
  
involved_in retinal blood vessel morphogenesis ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
is_active_in basement membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in basement membrane IDA
Inferred from Direct Assay
more info
 PubMed 
part_of collagen trimer IEA
Inferred from Electronic Annotation
more info
  
part_of collagen type IV trimer IDA
Inferred from Direct Assay
more info
 PubMed 
part_of collagen type IV trimer ISO
Inferred from Sequence Orthology
more info
  
located_in collagen-containing extracellular matrix HDA PubMed 
located_in extracellular region IEA
Inferred from Electronic Annotation
more info
  
located_in extracellular region TAS
Traceable Author Statement
more info
  
located_in extracellular space HDA PubMed 
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
collagen alpha-1(IV) chain
Names
alpha-1 type IV collagen
alpha1(IV) collagen
procollagen, type IV, alpha 1

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.

mRNA and Protein(s)

  1. NM_009931.2 → NP_034061.2  collagen alpha-1(IV) chain precursor

    See identical proteins and their annotated locations for NP_034061.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the shorter transcript and encodes the functional protein.
    Source sequence(s)
    AC114598, AC115800, AK147661, CJ108618, CJ248638
    Consensus CDS
    CCDS40219.1
    UniProtKB/Swiss-Prot
    P02463, Q3UHJ4, Q3UJE7, Q3UQV2, Q53X35, Q6GQS7, Q6PHB5, Q99LQ8
    UniProtKB/TrEMBL
    A0A1B0GSI7
    Related
    ENSMUSP00000033898.10, ENSMUST00000033898.10
    Conserved Domains (2) summary
    pfam01391
    Location:1088 → 1147
    Collagen; Collagen triple helix repeat (20 copies)
    pfam01413
    Location:1556 → 1666
    C4; C-terminal tandem repeated domain in type 4 procollagen

RNA

  1. NR_133670.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains an alternate exon in the 3' region, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC114598, BC072650, CJ108618, CJ248638
    Related
    ENSMUST00000209735.2

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000074.7 Reference GRCm39 C57BL/6J

    Range
    11248423..11362889 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RNA

  1. XR_004934755.1 RNA Sequence

Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P02463.4 GenPept UniProtKB/Swiss-Prot:P02463

Gene LinkOut

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