U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

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

    Gene ID: 12824, updated on 9-Dec-2024

    Summary

    Official Symbol
    Col2a1provided by MGI
    Official Full Name
    collagen, type II, alpha 1provided by MGI
    Primary source
    MGI:MGI:88452
    See related
    Ensembl:ENSMUSG00000022483 AllianceGenome:MGI:88452
    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
    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See Col2a1 in Genome Data Viewer
    Location:
    15 F1; 15 53.97 cM
    Exon count:
    54
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 15 NC_000081.7 (97873483..97902525, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 15 NC_000081.6 (97975602..98004724, complement)

    Chromosome 15 - NC_000081.7Genomic Context describing neighboring genes Neighboring gene vitamin D (1,25-dihydroxyvitamin D3) receptor Neighboring gene predicted gene, 52171 Neighboring gene STARR-positive B cell enhancer mm9_chr15:97738623-97738923 Neighboring gene transmembrane protein 106C Neighboring gene predicted gene, 46536 Neighboring gene predicted gene, 41395 Neighboring gene SUMO1/sentrin specific peptidase 1 Neighboring gene CapStarr-seq enhancer MGSCv37_chr15:97898039-97898148 Neighboring gene predicted gene, 25668

    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

    Clone Names

    • MGC90638

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables MHC class II protein binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables MHC class II protein binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables extracellular matrix structural constituent IEA
    Inferred from Electronic Annotation
    more info
     
    enables extracellular matrix structural constituent conferring tensile strength IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables extracellular matrix structural constituent conferring tensile strength RCA
    inferred from Reviewed Computational Analysis
    more info
    PubMed 
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables platelet-derived growth factor binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables protein homodimerization activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein homodimerization activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables proteoglycan binding ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within anterior head development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within bone development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within cartilage condensation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within cartilage development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within cartilage development involved in endochondral bone morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within cellular response to BMP stimulus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in central nervous system development IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in chondrocyte differentiation IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    acts_upstream_of_or_within chondrocyte differentiation IMP
    Inferred from Mutant Phenotype
    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 embryonic skeletal joint morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in embryonic skeletal joint morphogenesis ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within endochondral ossification IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in extracellular matrix organization IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of extrinsic apoptotic signaling pathway in absence of ligand IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within heart morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within inner ear development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within inner ear morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in limb bud formation IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    acts_upstream_of_or_within limb morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within negative regulation of extrinsic apoptotic signaling pathway in absence of ligand IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in notochord development IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in ossification IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in otic vesicle development IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    acts_upstream_of_or_within proteoglycan metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within roof of mouth development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in sensory perception of sound IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in sensory perception of sound ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in skeletal system development ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within skeletal system morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within tissue homeostasis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in visual perception IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in visual perception 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 type II trimer IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of collagen type II trimer IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of collagen type II trimer IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    part_of collagen type II trimer ISO
    Inferred from Sequence Orthology
    more info
     
    part_of collagen type XI trimer NAS
    Non-traceable Author Statement
    more info
    PubMed 
    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 collagen-containing extracellular matrix ISO
    Inferred from Sequence Orthology
    more info
     
    located_in collagen-containing extracellular matrix NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in extracellular matrix IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in extracellular space IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in extracellular space ISO
    Inferred from Sequence Orthology
    more info
     

    General protein information

    Preferred Names
    collagen alpha-1(II) chain
    Names
    alpha-1 type II collagen
    chondrocalcin
    procollagen, type II, 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_001113515.3NP_001106987.2  collagen alpha-1(II) chain isoform 2 precursor

      See identical proteins and their annotated locations for NP_001106987.2

      Status: VALIDATED

      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, AC134554
      Consensus CDS
      CCDS49716.1
      UniProtKB/Swiss-Prot
      P28481
      Related
      ENSMUSP00000085693.6, ENSMUST00000088355.12
      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_031163.4NP_112440.2  collagen alpha-1(II) chain isoform 1 preproprotein

      See identical proteins and their annotated locations for NP_112440.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC113444, AC134554
      Consensus CDS
      CCDS37189.2
      UniProtKB/Swiss-Prot
      P28481, Q61428, Q62031, Q62032, Q62033, Q641K3, Q6LDB1, Q6LDI8, Q6LDI9, Q80VY3, Q80X38, Q8CEF7, Q8K0N6
      Related
      ENSMUSP00000023123.9, ENSMUST00000023123.15
      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

    RNA

    1. NR_177066.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC113444, AC134554

    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_000081.7 Reference GRCm39 C57BL/6J

      Range
      97873483..97902525 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)