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    Col2a1 collagen type II alpha 1 chain [ Rattus norvegicus (Norway rat) ]

    Gene ID: 25412, updated on 9-Dec-2024

    Summary

    Official Symbol
    Col2a1provided by RGD
    Official Full Name
    collagen type II alpha 1 chainprovided by RGD
    Primary source
    RGD:2375
    See related
    EnsemblRapid:ENSRNOG00000058560 AllianceGenome:RGD:2375
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    CG2A1A; COLLII
    Summary
    Predicted to enable several functions, including MHC class II protein binding activity; platelet-derived growth factor binding activity; and protein homodimerization activity. Predicted to be an extracellular matrix structural constituent conferring tensile strength. Involved in several processes, including cartilage development; cellular response to insulin-like growth factor stimulus; and cellular response to mechanical stimulus. Located in collagen-containing extracellular matrix. Used to study degenerative disc disease; hypothyroidism; and osteoarthritis. Biomarker of degenerative disc disease and osteonecrosis. Human ortholog(s) of this gene implicated in Stickler syndrome (multiple); bone disease (multiple); cleft palate; eye disease (multiple); and multiple epiphyseal dysplasia with myopia and deafness. Orthologous to human COL2A1 (collagen type II alpha 1 chain). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Muscle (RPKM 27.9), Lung (RPKM 21.2) and 4 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See Col2a1 in Genome Data Viewer
    Location:
    7q36
    Exon count:
    54
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 7 NC_086025.1 (130977561..131006627, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 7 NC_051342.1 (129098489..129127560, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 7 NC_005106.4 (139454945..139484403, complement)

    Chromosome 7 - NC_086025.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC108351548 Neighboring gene vitamin D receptor Neighboring gene transmembrane protein 106C Neighboring gene SUMO specific peptidase 1 Neighboring gene small nucleolar RNA SNORA17 Neighboring gene uncharacterized LOC134479569 Neighboring gene phosphofructokinase, muscle

    Genomic regions, transcripts, and products

    Expression

    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by RGD

    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 identical protein binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables platelet-derived growth factor 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 IEA
    Inferred from Electronic Annotation
    more info
     
    enables proteoglycan binding ISO
    Inferred from Sequence Orthology
    more info
     
    Process Evidence Code Pubs
    involved_in animal organ morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in anterior head development IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within anterior head development ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within bone development ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in cartilage condensation IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within cartilage condensation ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in cartilage development IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    acts_upstream_of_or_within cartilage development ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in cartilage development involved in endochondral bone morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cartilage development involved in endochondral bone morphogenesis IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    acts_upstream_of_or_within cartilage development involved in endochondral bone morphogenesis ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in cellular response to BMP stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within cellular response to BMP stimulus ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in cellular response to insulin-like growth factor stimulus IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in cellular response to mechanical stimulus IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in cellular response to nicotine IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in cellular response to parathyroid hormone stimulus IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in cellular response to peptide hormone stimulus IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in cellular response to retinoic acid IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in cellular response to tumor necrosis factor IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in cellular response to vitamin E IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in central nervous system development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in central nervous system development ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in chondrocyte differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in chondrocyte differentiation IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    acts_upstream_of_or_within chondrocyte differentiation ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in chondrocyte differentiation ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in collagen fibril organization IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within collagen fibril organization ISO
    Inferred from Sequence Orthology
    more info
     
    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
     
    involved_in endochondral ossification IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within endochondral ossification ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in extracellular matrix organization IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in extrinsic apoptotic signaling pathway in absence of ligand IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of extrinsic apoptotic signaling pathway in absence of ligand ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in growth plate cartilage development IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in heart morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within heart morphogenesis ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within inner ear development ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in inner ear morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within inner ear morphogenesis ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in limb bud formation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in limb bud formation ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within limb morphogenesis ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of extrinsic apoptotic signaling pathway in absence of ligand IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within negative regulation of extrinsic apoptotic signaling pathway in absence of ligand ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in notochord development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in notochord development ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in ossification ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in otic vesicle development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in otic vesicle development ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in proteoglycan metabolic process IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within proteoglycan metabolic process ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in regulation of gene expression IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within regulation of gene expression ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in response to X-ray IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in response to fibroblast growth factor IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in response to mechanical stimulus IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in roof of mouth development IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within roof of mouth development ISO
    Inferred from Sequence Orthology
    more info
     
    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 ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in tissue homeostasis IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within tissue homeostasis ISO
    Inferred from Sequence Orthology
    more info
     
    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 IEA
    Inferred from Electronic Annotation
    more info
     
    located_in basement membrane ISO
    Inferred from Sequence Orthology
    more info
     
    part_of collagen trimer IEA
    Inferred from Electronic Annotation
    more info
     
    part_of collagen trimer ISO
    Inferred from Sequence Orthology
    more info
     
    part_of collagen type II trimer IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of collagen type II trimer IEA
    Inferred from Electronic Annotation
    more info
     
    part_of collagen type II trimer ISO
    Inferred from Sequence Orthology
    more info
     
    is_active_in collagen-containing extracellular matrix IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in collagen-containing extracellular matrix IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in collagen-containing extracellular matrix IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    located_in extracellular matrix ISO
    Inferred from Sequence Orthology
    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
     
    located_in extracellular space IEA
    Inferred from Electronic Annotation
    more info
     
    located_in extracellular space ISO
    Inferred from Sequence Orthology
    more info
     

    General protein information

    Preferred Names
    collagen alpha-1(II) chain
    Names
    Procollagen II alpha 1
    alpha-1 type II collagen
    collagen type II (Col2A1) gene, enhancer region
    collagen, type II, alpha 1
    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_001414896.1NP_001401825.1  collagen alpha-1(II) chain isoform 1 precursor

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000007
      UniProtKB/TrEMBL
      A0A8I6AM44
      Related
      ENSRNOP00000094699.1, ENSRNOT00000107179.2
    2. NM_012929.2NP_037061.2  collagen alpha-1(II) chain isoform 2 precursor

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000007
      UniProtKB/TrEMBL
      F1LRM7
      Related
      ENSRNOP00000071077.1, ENSRNOT00000086062.3

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086025.1 Reference GRCr8

      Range
      130977561..131006627 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)