U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    Col4a4 collagen, type IV, alpha 4 [ Mus musculus (house mouse) ]

    Gene ID: 12829, updated on 9-Dec-2024

    Summary

    Official Symbol
    Col4a4provided by MGI
    Official Full Name
    collagen, type IV, alpha 4provided by MGI
    Primary source
    MGI:MGI:104687
    See related
    Ensembl:ENSMUSG00000067158 AllianceGenome:MGI:104687
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    [a]4(IV); E130010M05Rik
    Summary
    An extracellular matrix structural constituent. Acts upstream of or within glomerular basement membrane development. Located in basement membrane. Part of collagen type IV trimer. Is expressed in embryo; glomerular tuft; and testis. Used to study autosomal recessive Alport syndrome. Human ortholog(s) of this gene implicated in autosomal recessive Alport syndrome; benign familial hematuria; and end stage renal disease. Orthologous to human COL4A4 (collagen type IV alpha 4 chain). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in kidney adult (RPKM 12.0), lung adult (RPKM 10.4) and 6 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See Col4a4 in Genome Data Viewer
    Location:
    1 C5; 1 42.2 cM
    Exon count:
    50
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 1 NC_000067.7 (82426140..82564570, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 1 NC_000067.6 (82448419..82587034, complement)

    Chromosome 1 - NC_000067.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_01474 Neighboring gene STARR-seq mESC enhancer starr_01475 Neighboring gene insulin receptor substrate 1 Neighboring gene STARR-seq mESC enhancer starr_01476 Neighboring gene rhomboid domain containing 1 Neighboring gene predicted gene, 46095 Neighboring gene STARR-seq mESC enhancer starr_01477 Neighboring gene collagen, type IV, alpha 3 Neighboring gene RIKEN cDNA C430014B12 gene Neighboring gene STARR-seq mESC enhancer starr_01479 Neighboring gene mitochondrial fission factor

    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

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Chemically induced (ENU) (2)  1 citation
    • Endonuclease-mediated (3) 
    • Gene trapped (1) 
    • Spontaneous (1)  1 citation

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by MGI

    Process Evidence Code Pubs
    involved_in glomerular basement membrane development IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of_or_within glomerular basement membrane development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in glomerular basement membrane development ISO
    Inferred from Sequence Orthology
    more info
     
    Component Evidence Code Pubs
    located_in basement membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in basement membrane ISO
    Inferred from Sequence Orthology
    more info
     
    located_in basement membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    part_of collagen type IV trimer IBA
    Inferred from Biological aspect of Ancestor
    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 
    is_active_in collagen-containing extracellular matrix IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
     

    General protein information

    Preferred Names
    collagen alpha-4(IV) chain
    Names
    procollagen, type IV, alpha 4

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_007735.2NP_031761.1  collagen alpha-4(IV) chain precursor

      See identical proteins and their annotated locations for NP_031761.1

      Status: VALIDATED

      Source sequence(s)
      AC160543, AF169388, AK164732
      Consensus CDS
      CCDS35630.1
      UniProtKB/Swiss-Prot
      Q149M2, Q64457, Q9QZR9
      Related
      ENSMUSP00000084282.6, ENSMUST00000087050.7
      Conserved Domains (2) summary
      pfam01391
      Location:54111
      Collagen; Collagen triple helix repeat (20 copies)
      pfam01413
      Location:14581562
      C4; C-terminal tandem repeated domain in type 4 procollagen

    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_000067.7 Reference GRCm39 C57BL/6J

      Range
      82426140..82564570 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011238652.1XP_011236954.1  collagen alpha-4(IV) chain isoform X1

      Conserved Domains (2) summary
      pfam01391
      Location:792851
      Collagen; Collagen triple helix repeat (20 copies)
      pfam01413
      Location:13611465
      C4; C-terminal tandem repeated domain in type 4 procollagen
    2. XM_011238653.4XP_011236955.1  collagen alpha-4(IV) chain isoform X2

      Conserved Domains (1) summary
      pfam01391
      Location:54111
      Collagen; Collagen triple helix repeat (20 copies)