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    Col4a5 collagen, type IV, alpha 5 [ Mus musculus (house mouse) ]

    Gene ID: 12830, updated on 9-Dec-2024

    Summary

    Official Symbol
    Col4a5provided by MGI
    Official Full Name
    collagen, type IV, alpha 5provided by MGI
    Primary source
    MGI:MGI:88456
    See related
    Ensembl:ENSMUSG00000031274 AllianceGenome:MGI:88456
    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
    Summary
    Predicted to be an extracellular matrix structural constituent conferring tensile strength. Acts upstream of or within collagen-activated tyrosine kinase receptor signaling pathway and neuromuscular junction development. Located in basement membrane and neuromuscular junction. Part of collagen type IV trimer. Is expressed in several structures, including alimentary system; brain; extraembryonic component; genitourinary system; and salivary gland primordium. Used to study X-linked Alport syndrome. Human ortholog(s) of this gene implicated in Alport syndrome and X-linked Alport syndrome. Orthologous to human COL4A5 (collagen type IV alpha 5 chain). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Broad expression in bladder adult (RPKM 17.4), lung adult (RPKM 8.1) and 15 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See Col4a5 in Genome Data Viewer
    Location:
    X F2; X 62.16 cM
    Exon count:
    53
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) X NC_000086.8 (140258367..140472232)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) X NC_000086.7 (141475370..141689236)

    Chromosome X - NC_000086.8Genomic Context describing neighboring genes Neighboring gene collagen, type IV, alpha 6 Neighboring gene predicted gene, 39539 Neighboring gene STARR-seq mESC enhancer starr_48012 Neighboring gene prohibitin pseudogene Neighboring gene STARR-seq mESC enhancer starr_48013 Neighboring gene predicted gene 15295 Neighboring gene STARR-seq mESC enhancer starr_48014 Neighboring gene insulin receptor substrate 4 Neighboring gene STARR-seq mESC enhancer starr_48015 Neighboring gene high-mobility group nucleosomal binding domain 2-like 6

    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 Functions

    What's a GeneRIF?

    Variation

    Alleles

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

    Pathways from PubChem

    General protein information

    Preferred Names
    collagen alpha-5(IV) chain
    Names
    collagen type IV alpha5 chain
    procollagen type IV alpha 5

    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_001163155.1NP_001156627.1  collagen alpha-5(IV) chain isoform 1 precursor

      See identical proteins and their annotated locations for NP_001156627.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript. Both variants encode the same protein.
      Source sequence(s)
      AK133179, AL713983, BX571779, CN668672
      Consensus CDS
      CCDS41154.1
      UniProtKB/TrEMBL
      Q63ZW6
      Related
      ENSMUSP00000108553.2, ENSMUST00000112931.8
      Conserved Domains (2) summary
      pfam01391
      Location:10741132
      Collagen; Collagen triple helix repeat (20 copies)
      pfam01413
      Location:15791688
      C4; C-terminal tandem repeated domain in type 4 procollagen
    2. NM_001411947.1NP_001398876.1  collagen alpha-5(IV) chain isoform 2 precursor

      Status: VALIDATED

      Source sequence(s)
      AL671856, AL713983, BX571779
    3. NM_007736.4NP_031762.2  collagen alpha-5(IV) chain isoform 1 precursor

      See identical proteins and their annotated locations for NP_031762.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Both variants encode the same protein.
      Source sequence(s)
      AK133179, BX571779
      Consensus CDS
      CCDS41154.1
      UniProtKB/TrEMBL
      Q63ZW6
      Related
      ENSMUSP00000108552.2, ENSMUST00000112930.8
      Conserved Domains (2) summary
      pfam01391
      Location:10741132
      Collagen; Collagen triple helix repeat (20 copies)
      pfam01413
      Location:15791688
      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_000086.8 Reference GRCm39 C57BL/6J

      Range
      140258367..140472232
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006528696.4XP_006528759.1  collagen alpha-5(IV) chain isoform X1

      Conserved Domains (2) summary
      pfam01391
      Location:10741132
      Collagen; Collagen triple helix repeat (20 copies)
      pfam01413
      Location:14651571
      C4; C-terminal tandem repeated domain in type 4 procollagen
    2. XM_017318372.3XP_017173861.1  collagen alpha-5(IV) chain isoform X3

      Conserved Domains (2) summary
      pfam01391
      Location:10591117
      Collagen; Collagen triple helix repeat (20 copies)
      pfam01413
      Location:14531559
      C4; C-terminal tandem repeated domain in type 4 procollagen