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

    Gene ID: 12826, updated on 28-Oct-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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    See Col4a1 in Genome Data Viewer
    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 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. 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
    2. Tendon is covered by a basement membrane epithelium that is required for cell retention and the prevention of adhesion formation. Taylor SH, et al. PLoS One, 2011 Jan 26. PMID 21298098, Free PMC Article
    3. Isolation of cDNA clones for basal lamina components: type IV procollagen. Kurkinen M, et al. Nucleic Acids Res, 1983 Sep 24. PMID 6312413, Free PMC Article
    4. Dominant mutations of Col4a1 result in basement membrane defects which lead to anterior segment dysgenesis and glomerulopathy. Van Agtmael T, et al. Hum Mol Genet, 2005 Nov 1. PMID 16159887
    5. Isolation of an alpha 1 type-IV collagen cDNA clone using a synthetic oligodeoxynucleotide. Nath P, et al. Gene, 1986. PMID 3755692

    See all (244) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. TGFbeta Signaling Dysregulation May Contribute to COL4A1-Related Glaucomatous Optic Nerve Damage.
      Title: TGFβ Signaling Dysregulation May Contribute to COL4A1-Related Glaucomatous Optic Nerve Damage.
    2. A temporally-restricted pattern of endothelial cell collagen 4 alpha 1 expression during embryonic development determined with a novel knockin Col4a1-P2A-eGFP mouse line.
      Title: A temporally-restricted pattern of endothelial cell collagen 4 alpha 1 expression during embryonic development determined with a novel knockin Col4a1-P2A-eGFP mouse line.
    3. 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.
    4. 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.
    5. 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.
    6. 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.
    7. COL4A1 Mutations are associated with Neuromuscular Disease.
      Title: COL4A1 Mutations Cause Neuromuscular Disease with Tissue-Specific Mechanistic Heterogeneity.
    8. 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.
    9. 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.
    10. 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.
    Submit: New GeneRIF Correction See all GeneRIFs (34)

    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
    involved_in basement membrane organization 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 IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in brain development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in branching involved in blood vessel morphogenesis IEA
    Inferred from Electronic Annotation
    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 epithelial cell differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    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 IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in renal tubule morphogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in retinal blood vessel morphogenesis IEA
    Inferred from Electronic Annotation
    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 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 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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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