U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    Col9a2 collagen type IX alpha 2 chain [ Rattus norvegicus (Norway rat) ]

    Gene ID: 362584, updated on 9-Dec-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    Col9a2provided by RGD
    Official Full Name
    collagen type IX alpha 2 chainprovided by RGD
    Primary source
    RGD:1307029
    See related
    EnsemblRapid:ENSRNOG00000011502 AllianceGenome:RGD:1307029
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable protein homodimerization activity. Predicted to be an extracellular matrix structural constituent conferring tensile strength. Predicted to be involved in extracellular matrix organization. Predicted to be part of collagen type IX trimer. Predicted to be active in collagen-containing extracellular matrix and extracellular space. Human ortholog(s) of this gene implicated in Stickler syndrome; multiple epiphyseal dysplasia 2; and osteochondrodysplasia. Orthologous to human COL9A2 (collagen type IX alpha 2 chain). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Brain (RPKM 33.2), Lung (RPKM 12.0) and 7 other tissues See more
    Orthologs
    human mouse all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See Col9a2 in Genome Data Viewer
    Location:
    5q36
    Exon count:
    32
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 5 NC_086023.1 (139892798..139910131)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 5 NC_051340.1 (134607616..134624678)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 5 NC_005104.4 (139962684..139979865)

    Chromosome 5 - NC_086023.1Genomic Context describing neighboring genes Neighboring gene small ArfGAP2 Neighboring gene ribosomal protein L10A like 3 Neighboring gene uncharacterized LOC108351024 Neighboring gene zinc metallopeptidase STE24 Neighboring gene transmembrane and coiled-coil domains 2

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • 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

    Go to the top of the pageHelp

    Related articles in PubMed

    1. A mutation in the gene encoding the alpha 2 chain of the fibril-associated collagen IX, COL9A2, causes multiple epiphyseal dysplasia (EDM2). Muragaki Y, et al. Nat Genet, 1996 Jan. PMID 8528240
    2. Collagen type IX from human cartilage: a structural profile of intermolecular cross-linking sites. Diab M, et al. Biochem J, 1996 Feb 15. PMID 8660302, Free PMC Article
    3. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

    Go to the top of the page Help

    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables extracellular matrix structural constituent conferring tensile strength IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein homodimerization activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    involved_in extracellular matrix organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    part_of collagen type IX trimer ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in collagen-containing extracellular matrix IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    collagen alpha-2(IX) chain
    Names
    alpha 1 type IX collagen
    collagen, type IX, alpha 2
    procollagen, type IX, alpha 2

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    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_001108675.1 → NP_001102145.1  collagen alpha-2(IX) chain precursor

      See identical proteins and their annotated locations for NP_001102145.1

      Status: PROVISIONAL

      Source sequence(s)
      CH473968
      UniProtKB/TrEMBL
      A6IS03, D3ZNT5
      Related
      ENSRNOP00000049994.3, ENSRNOT00000048506.5
      Conserved Domains (1) summary
      pfam01391
      Location:360 → 418
      Collagen; Collagen triple helix repeat (20 copies)

    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_086023.1 Reference GRCr8

      Range
      139892798..139910131
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039110306.2 → XP_038966234.1  collagen alpha-2(IX) chain isoform X1

      Conserved Domains (1) summary
      pfam01391
      Location:144 → 199
      Collagen; Collagen triple helix repeat (20 copies)
    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools
    Miscellaneous