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    Col2a1 collagen, type II, alpha 1 [ Mus musculus (house mouse) ]

    Gene ID: 12824, updated on 12-Jun-2018
    Official Symbol
    Col2a1provided by MGI
    Official Full Name
    collagen, type II, alpha 1provided by MGI
    Primary source
    MGI:MGI:88452
    See related
    Ensembl:ENSMUSG00000022483 Vega:OTTMUSG00000021708
    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
    Dmm; Lpk; Col2; Del1; Col2a; Col2a-1; M100413; Rgsc413; Rgsc856
    Summary
    This gene encodes the alpha-1 subunit of the fibril-forming type II collagen, the major component of cartilage and the vitreous humor of the eye. The encoded preproprotein forms homotrimeric, triple helical procollagen that undergoes proteolytic processing during fibirl formation. Mice harboring certain mutations in this gene exhibit severe chondrodysplasia characterized by short limbs and trunch, craniofacial deformities and cleft palate. A complete lack of the encoded protein in mice results in postnatal lethality. Alternative splicing results in multiple transcript variants encoding different isoforms that may undergo similar proteolytic processing. [provided by RefSeq, Dec 2015]
    Expression
    Biased expression in limb E14.5 (RPKM 504.7), CNS E14 (RPKM 67.6) and 1 other tissue See more
    Orthologs
    See Col2a1 in Genome Data Viewer
    Location:
    15 F1; 15 53.97 cM
    Exon count:
    55
    Annotation release Status Assembly Chr Location
    106 current GRCm38.p4 (GCF_000001635.24) 15 NC_000081.6 (97975602..98004724, complement)
    Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 15 NC_000081.5 (97806033..97835155, complement)

    Chromosome 15 - NC_000081.6Genomic Context describing neighboring genes Neighboring gene predicted gene, 33690 Neighboring gene vitamin D (1,25-dihydroxyvitamin D3) receptor Neighboring gene transmembrane protein 106C Neighboring gene predicted gene, 46536 Neighboring gene predicted gene, 41395 Neighboring gene SUMO1/sentrin specific peptidase 1 Neighboring gene predicted gene, 26513 Neighboring gene phosphofructokinase, muscle

    • 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

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Clone Names

    • MGC90638

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    MHC class II protein binding ISO
    Inferred from Sequence Orthology
    more info
     
    extracellular matrix structural constituent IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    extracellular matrix structural constituent IEA
    Inferred from Electronic Annotation
    more info
     
    identical protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    platelet-derived growth factor binding ISO
    Inferred from Sequence Orthology
    more info
     
    Process Evidence Code Pubs
    anterior head development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    bone development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    cartilage condensation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    cartilage development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    cartilage development involved in endochondral bone morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    cellular response to BMP stimulus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    central nervous system development IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    chondrocyte differentiation IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    chondrocyte differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    collagen fibril organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    collagen fibril organization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    collagen fibril organization ISO
    Inferred from Sequence Orthology
    more info
     
    embryonic skeletal joint morphogenesis ISO
    Inferred from Sequence Orthology
    more info
     
    endochondral ossification IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    extracellular matrix organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    heart morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    inner ear development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    inner ear morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    limb bud formation IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    limb morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    negative regulation of extrinsic apoptotic signaling pathway in absence of ligand IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    notochord development IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    notochord development IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    ossification IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    otic vesicle development IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    proteoglycan metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    roof of mouth development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    sensory perception of sound ISO
    Inferred from Sequence Orthology
    more info
     
    skeletal system development IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    skeletal system development ISO
    Inferred from Sequence Orthology
    more info
     
    skeletal system morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    tissue homeostasis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    visual perception ISO
    Inferred from Sequence Orthology
    more info
     
    Component Evidence Code Pubs
    basement membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    collagen trimer IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    collagen trimer IDA
    Inferred from Direct Assay
    more info
    PubMed 
    collagen type II trimer IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    collagen type II trimer IDA
    Inferred from Direct Assay
    more info
    PubMed 
    collagen type II trimer IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    collagen type II trimer ISO
    Inferred from Sequence Orthology
    more info
     
    collagen-containing extracellular matrix ISO
    Inferred from Sequence Orthology
    more info
     
    cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cytoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    extracellular matrix IDA
    Inferred from Direct Assay
    more info
    PubMed 
    extracellular region IEA
    Inferred from Electronic Annotation
    more info
     
    extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    extracellular space IDA
    Inferred from Direct Assay
    more info
    PubMed 
    extracellular space ISO
    Inferred from Sequence Orthology
    more info
     
    Preferred Names
    collagen alpha-1(II) chain
    Names
    alpha-1 type II collagen
    chondrocalcin
    procollagen, type II, alpha 1

    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_001113515.2NP_001106987.2  collagen alpha-1(II) chain isoform 2 precursor

      See identical proteins and their annotated locations for NP_001106987.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon, compared to variant 1, resulting in a shorter protein (isoform 2), compared to isoform 1. This isoform (2) may undergo proteolytic processing similar to isoform 1.
      Source sequence(s)
      AC113444, BC082331
      Consensus CDS
      CCDS49716.1
      UniProtKB/Swiss-Prot
      P28481
      Related
      ENSMUSP00000085693.5, OTTMUSP00000024256, ENSMUST00000088355.11, OTTMUST00000051505
      Conserved Domains (2) summary
      pfam01391
      Location:733792
      Collagen; Collagen triple helix repeat (20 copies)
      pfam01410
      Location:11861418
      COLFI; Fibrillar collagen C-terminal domain
    2. NM_031163.3NP_112440.2  collagen alpha-1(II) chain isoform 1 preproprotein

      See identical proteins and their annotated locations for NP_112440.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC113444, BC082331
      Consensus CDS
      CCDS37189.2
      UniProtKB/Swiss-Prot
      P28481
      Related
      ENSMUSP00000023123.8, OTTMUSP00000024255, ENSMUST00000023123.14, OTTMUST00000051504
      Conserved Domains (3) summary
      pfam01391
      Location:801860
      Collagen; Collagen triple helix repeat (20 copies)
      pfam00093
      Location:3488
      VWC; von Willebrand factor type C domain
      pfam01410
      Location:12541486
      COLFI; Fibrillar collagen C-terminal domain

    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_000081.6 Reference GRCm38.p4 C57BL/6J

      Range
      97975602..98004724 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006520386.3XP_006520449.1  collagen alpha-1(II) chain isoform X1

      Conserved Domains (2) summary
      pfam01391
      Location:619678
      Collagen; Collagen triple helix repeat (20 copies)
      pfam01410
      Location:10721304
      COLFI; Fibrillar collagen C-terminal domain
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