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    Col9a1 collagen type IX alpha 1 chain [ Rattus norvegicus (Norway rat) ]

    Gene ID: 305104, updated on 2-May-2024

    Summary

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    Official Symbol
    Col9a1provided by RGD
    Official Full Name
    collagen type IX alpha 1 chainprovided by RGD
    Primary source
    RGD:1309425
    See related
    Ensembl:ENSRNOG00000012920 AllianceGenome:RGD:1309425
    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
    Summary
    Predicted to be an extracellular matrix structural constituent. Involved in chondrocyte differentiation. Predicted to be part of collagen type IX trimer. Predicted to be active in basement membrane and extracellular space. Human ortholog(s) of this gene implicated in Stickler syndrome; multiple epiphyseal dysplasia 6; and osteochondrodysplasia. Orthologous to human COL9A1 (collagen type IX alpha 1 chain). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Lung (RPKM 6.6), Kidney (RPKM 4.9) and 4 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Col9a1 in Genome Data Viewer
    Location:
    9q21
    Exon count:
    39
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 9 NC_086027.1 (34081364..34164552)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 9 NC_051344.1 (26585034..26668222)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 9 NC_005108.4 (30419001..30502307)

    Chromosome 9 - NC_086027.1Genomic Context describing neighboring genes Neighboring gene family with sequence similarity 135, member A Neighboring gene uncharacterized LOC102553447 Neighboring gene uncharacterized LOC134480563 Neighboring gene collagen type XIX alpha 1 chain Neighboring gene ADP-ribosylation factor-like protein 3 pseudogene

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. Establishment of bone morphogenetic protein 2 responsive chondrogenic cell line. Aikawa T, et al. J Bone Miner Res, 1996 Apr. PMID 8992886
    2. Altered cartilage phenotype expressed during intramembranous bone formation. Ting K, et al. J Bone Miner Res, 1993 Nov. PMID 8266829
    3. Molecular cloning of rat and human type IX collagen cDNA and localization of the alpha 1(IX) gene on the human chromosome 6. Kimura T, et al. Eur J Biochem, 1989 Jan 15. PMID 2465149
    4. Mice lacking alpha 1 (IX) collagen develop noninflammatory degenerative joint disease. Fässler R, et al. Proc Natl Acad Sci U S A, 1994 May 24. PMID 8197187, Free PMC Article
    5. Ablation of collagen IX and COMP disrupts epiphyseal cartilage architecture. Blumbach K, et al. Matrix Biol, 2008 May. PMID 18191556

    See all (12) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Collagen type IX alpha1 was found within the tectorial membrane as well as fibrocytes in the spiral ligament.
      Title: The localization of proteins encoded by CRYM, KIAA1199, UBA52, COL9A3, and COL9A1, genes highly expressed in the cochlea.
    Submit: New GeneRIF Correction

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables carbohydrate binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables carbohydrate binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein homodimerization activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein homodimerization activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within bone morphogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within cartilage development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in chondrocyte differentiation IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    acts_upstream_of_or_within chondrocyte proliferation ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within growth plate cartilage development ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within skeletal system development ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within tissue homeostasis ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    part_of collagen trimer IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of collagen type IX trimer IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of collagen type IX trimer ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    collagen alpha-1(IX) chain
    Names
    collagen, type IX, alpha 1
    procollagen, type IX, alpha 1

    NCBI Reference Sequences (RefSeq)

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    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_001100842.1 → NP_001094312.1  collagen alpha-1(IX) chain precursor

      Status: VALIDATED

      Source sequence(s)
      BQ191679, DY313373, DY316977, JAXUCZ010000009
      UniProtKB/TrEMBL
      F1LQ93
      Related
      ENSRNOP00000018116.6, ENSRNOT00000018116.7
      Conserved Domains (2) summary
      pfam01391
      Location:506 → 565
      Collagen; Collagen triple helix repeat (20 copies)
      smart00210
      Location:63 → 257
      TSPN; Thrombospondin N-terminal -like domains

    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_086027.1 Reference GRCr8

      Range
      34081364..34164552
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039083449.1 → XP_038939377.1  collagen alpha-1(IX) chain isoform X1

      UniProtKB/TrEMBL
      A0A8I5ZSW9
      Related
      ENSRNOP00000081771.1, ENSRNOT00000115769.1
      Conserved Domains (1) summary
      pfam01391
      Location:342 → 396
      Collagen; Collagen triple helix repeat (20 copies)
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P20850.1 GenPept UniProtKB/Swiss-Prot:P20850

    Gene LinkOut

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

    Chemical Information
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