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

    Gene ID: 12826, updated on 18-Apr-2019

    Summary

    Official Symbol
    Col4a1provided by MGI
    Official Full Name
    collagen, type IV, alpha 1provided by MGI
    Primary source
    MGI:MGI:88454
    See related
    Ensembl:ENSMUSG00000031502
    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

    Genomic context

    See Col4a1 in Genome Data Viewer
    Location:
    8 A1.1; 8 5.53 cM
    Exon count:
    53
    Annotation release Status Assembly Chr Location
    106 current GRCm38.p4 (GCF_000001635.24) 8 NC_000074.6 (11198423..11312826, complement)
    Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 8 NC_000074.5 (11198423..11312826, complement)

    Chromosome 8 - NC_000074.6Genomic Context describing neighboring genes Neighboring gene RIKEN cDNA 3930402G23 gene Neighboring gene RIKEN cDNA 9530052E02 gene Neighboring gene insulin receptor substrate 2 Neighboring gene predicted gene, 32709 Neighboring gene collagen, type IV, alpha 2 Neighboring gene predicted gene, 46030 Neighboring gene RIKEN cDNA E230013L22 gene Neighboring gene RAB20, member RAS oncogene family

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Phenotypes

    Associated conditions

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

    Variation

    Alleles

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

    Pathways from BioSystems

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by MGI

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

    General protein information

    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)

    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_009931.2NP_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
      Related
      ENSMUSP00000033898.9, ENSMUST00000033898.9
      Conserved Domains (2) summary
      pfam01391
      Location:10881147
      Collagen; Collagen triple helix repeat (20 copies)
      pfam01413
      Location:15561666
      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
      ENSMUST00000209735.1

    RefSeqs of Annotated Genomes: Mus musculus Annotation Release 106

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

    Reference GRCm38.p4 C57BL/6J

    Genomic

    1. NC_000074.6 Reference GRCm38.p4 C57BL/6J

      Range
      11198423..11312826 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017312555.1XP_017168044.1  collagen alpha-1(IV) chain isoform X1

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