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    Col5a1 collagen, type V, alpha 1 [ Mus musculus (house mouse) ]

    Gene ID: 12831, updated on 7-Sep-2021

    Summary

    Official Symbol
    Col5a1provided by MGI
    Official Full Name
    collagen, type V, alpha 1provided by MGI
    Primary source
    MGI:MGI:88457
    See related
    Ensembl:ENSMUSG00000026837
    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
    AI413331
    Expression
    Broad expression in limb E14.5 (RPKM 82.9), bladder adult (RPKM 28.4) and 15 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See Col5a1 in Genome Data Viewer
    Location:
    2 A3; 2 19.38 cM
    Exon count:
    67
    Annotation release Status Assembly Chr Location
    109 current GRCm39 (GCF_000001635.27) 2 NC_000068.8 (27776393..27929522)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 2 NC_000068.7 (27886381..28039510)
    Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 2 NC_000068.6 (27741945..27895030)

    Chromosome 2 - NC_000068.8Genomic Context describing neighboring genes Neighboring gene retinoid X receptor alpha Neighboring gene predicted gene, 39777 Neighboring gene predicted gene 13372 Neighboring gene RIKEN cDNA F730016J06 gene Neighboring gene ficolin B

    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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables extracellular matrix structural constituent IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables extracellular matrix structural constituent IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables extracellular matrix structural constituent conferring tensile strength RCA
    inferred from Reviewed Computational Analysis
    more info
    PubMed 
    enables heparin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables heparin binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables platelet-derived growth factor binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables proteoglycan binding ISO
    Inferred from Sequence Orthology
    more info
     
    Process Evidence Code Pubs
    acts_upstream_of_or_within blood vessel development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in cell adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in cell adhesion ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in cell migration ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in collagen biosynthetic process ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in collagen fibril organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    acts_upstream_of_or_within collagen fibril organization IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within collagen fibril organization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in collagen fibril organization ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in extracellular matrix organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in eye morphogenesis ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within heart morphogenesis IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in integrin biosynthetic process ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of endodermal cell differentiation ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within regulation of cellular component organization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within skin development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in skin development ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in supramolecular fiber organization ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within tendon development IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within tendon development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in wound healing, spreading of epidermal cells ISO
    Inferred from Sequence Orthology
    more info
     
    Component Evidence Code Pubs
    located_in basement membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of collagen trimer IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of collagen trimer IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    part_of collagen type V trimer IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    part_of collagen type V trimer ISO
    Inferred from Sequence Orthology
    more info
     
    located_in collagen-containing extracellular matrix HDA PubMed 
    located_in collagen-containing extracellular matrix ISO
    Inferred from Sequence Orthology
    more info
     
    is_active_in extracellular matrix IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in extracellular matrix IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
     
    located_in extracellular space HDA PubMed 
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 

    General protein information

    Preferred Names
    collagen alpha-1(V) chain
    Names
    alpha1(V) collagen
    pro-alpha1(V) collagen
    procollagen type V alpha 1

    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_015734.2NP_056549.2  collagen alpha-1(V) chain precursor

      See identical proteins and their annotated locations for NP_056549.2

      Status: VALIDATED

      Source sequence(s)
      AB009993, AK148055, AL731778, BP759660, BQ768928, BQ885116, BY713878
      Consensus CDS
      CCDS15831.1
      UniProtKB/Swiss-Prot
      O88207
      UniProtKB/TrEMBL
      B1AWB9
      Related
      ENSMUSP00000028280.8, ENSMUST00000028280.14
      Conserved Domains (3) summary
      pfam01391
      Location:871930
      Collagen; Collagen triple helix repeat (20 copies)
      smart00210
      Location:39230
      TSPN; Thrombospondin N-terminal -like domains
      pfam01410
      Location:16101836
      COLFI; Fibrillar collagen C-terminal domain

    RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...Open this link in a new tab

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000068.8 Reference GRCm39 C57BL/6J

      Range
      27776393..27929522
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006497644.5XP_006497707.1  collagen alpha-1(V) chain isoform X1

      Conserved Domains (3) summary
      pfam01391
      Location:871930
      Collagen; Collagen triple helix repeat (20 copies)
      smart00210
      Location:39230
      TSPN; Thrombospondin N-terminal -like domains
      pfam01410
      Location:16071836
      COLFI; Fibrillar collagen C-terminal domain
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