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    Col9a3 collagen, type IX, alpha 3 [ Mus musculus (house mouse) ]

    Gene ID: 12841, updated on 30-Apr-2024

    Summary

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    Official Symbol
    Col9a3provided by MGI
    Official Full Name
    collagen, type IX, alpha 3provided by MGI
    Primary source
    MGI:MGI:894686
    See related
    Ensembl:ENSMUSG00000027570 AllianceGenome:MGI:894686
    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
    Summary
    Predicted to be an extracellular matrix structural constituent. Acts upstream of or within female gonad development and male gonad development. Located in collagen-containing extracellular matrix. Is expressed in several structures, including brain; cranium; eye; hindlimb digit mesenchyme; and reproductive system. Human ortholog(s) of this gene implicated in multiple epiphyseal dysplasia 3 and osteochondrodysplasia. Orthologous to human COL9A3 (collagen type IX alpha 3 chain). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in limb E14.5 (RPKM 147.4), CNS E14 (RPKM 29.8) and 2 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Col9a3 in Genome Data Viewer
    Location:
    2 H4; 2 103.14 cM
    Exon count:
    32
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 2 NC_000068.8 (180239895..180263985)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 2 NC_000068.7 (180598102..180622192)

    Chromosome 2 - NC_000068.8Genomic Context describing neighboring genes Neighboring gene predicted gene, 30144 Neighboring gene STARR-positive B cell enhancer ABC_E4530 Neighboring gene MRG/MORF4L binding protein Neighboring gene opioid growth factor receptor Neighboring gene transcription factor-like 5 (basic helix-loop-helix) Neighboring gene predicted gene, 54097 Neighboring gene death inducer-obliterator 1 Neighboring gene predicted gene, 22502

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. Early changes in morphology, bone mineral density and matrix composition of vertebrae lead to disc degeneration in aged collagen IX -/- mice. Kamper M, et al. Matrix Biol, 2016 Jan. PMID 26429145
    2. Comparative proteomic analysis of normal and collagen IX null mouse cartilage reveals altered extracellular matrix composition and novel components of the collagen IX interactome. Brachvogel B, et al. J Biol Chem, 2013 May 10. PMID 23530037, Free PMC Article
    3. Expression patterns of cartilage collagens and Sox9 during mouse heart development. Rahkonen O, et al. Histochem Cell Biol, 2003 Aug. PMID 12883905
    4. Type II and type IX collagen transcript isoforms are expressed during mouse testis development. McClive PJ, et al. Biol Reprod, 2003 May. PMID 12606408
    5. The complete primary structure of the long form of mouse alpha 1(IX) collagen chain and its expression during limb development. Abe N, et al. Biochim Biophys Acta, 1994 Jan 11. PMID 8305476

    See all (47) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SOX9-COL9A3-dependent regulation of choroid plexus epithelial polarity governs blood-cerebrospinal fluid barrier integrity.
      Title: SOX9-COL9A3-dependent regulation of choroid plexus epithelial polarity governs blood-cerebrospinal fluid barrier integrity.
    2. Results show that absence of Col IX induces early developmental, structural and biomechanical alterations in both vertebral body and intervertebral disc which eventually cause severe degenerative changes in the aging spine.
      Title: Early changes in morphology, bone mineral density and matrix composition of vertebrae lead to disc degeneration in aged collagen IX -/- mice.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (4) 

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    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 protein homodimerization activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in extracellular matrix organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in female gonad development IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in male gonad development IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of collagen type IX trimer IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of collagen type IX trimer ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in collagen-containing extracellular matrix HDA PubMed 
    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

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    Preferred Names
    collagen alpha-3(IX) chain
    Names
    procollagen, type IX, alpha 3

    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_001378777.1 → NP_001365706.1  collagen alpha-3(IX) chain isoform 1 precursor

      Status: VALIDATED

      Source sequence(s)
      AL669926
      Conserved Domains (1) summary
      pfam01391
      Location:324 → 378
      Collagen; Collagen triple helix repeat (20 copies)

    2. NM_009936.2 → NP_034066.2  collagen alpha-3(IX) chain isoform 2 precursor

      See identical proteins and their annotated locations for NP_034066.2

      Status: VALIDATED

      Source sequence(s)
      AK030350, AK038481, CK623954
      Consensus CDS
      CCDS17180.1
      UniProtKB/TrEMBL
      A2ACT7
      Related
      ENSMUSP00000099348.2, ENSMUST00000103059.2
      Conserved Domains (1) summary
      pfam01391
      Location:315 → 374
      Collagen; Collagen triple helix repeat (20 copies)

    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_000068.8 Reference GRCm39 C57BL/6J

      Range
      180239895..180263985
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006500553.3 → XP_006500616.1  collagen alpha-3(IX) chain isoform X1

      Conserved Domains (1) summary
      pfam01391
      Location:279 → 338
      Collagen; Collagen triple helix repeat (20 copies)
    Nucleotide Protein Strain
    Heading Accession and Version

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