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    col9a3 collagen, type IX, alpha 3 [ Danio rerio (zebrafish) ]

    Gene ID: 567110, updated on 2-Nov-2024

    Summary

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    Official Symbol
    col9a3provided by ZNC
    Official Full Name
    collagen, type IX, alpha 3provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-030131-9799
    See related
    Ensembl:ENSDARG00000037845 AllianceGenome:ZFIN:ZDB-GENE-030131-9799
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    cb367; sb:cb367; wu:fa04f01; si:ch73-162j3.1
    Summary
    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 trimer. Predicted to be active in collagen-containing extracellular matrix and extracellular space. Is expressed in several structures, including head mesenchyme; hypochord; mesoderm; notochord; and pectoral fin. Human ortholog(s) of this gene implicated in Stickler syndrome; multiple epiphyseal dysplasia 3; and osteochondrodysplasia. Orthologous to human COL9A3 (collagen type IX alpha 3 chain). [provided by Alliance of Genome Resources, Nov 2024]
    Orthologs
    human mouse all
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    Genomic context

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    See col9a3 in Genome Data Viewer
    Location:
    chromosome: 23
    Exon count:
    32
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 23 NC_007134.7 (495514..524780, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 23 NC_007134.6 (482721..511987, complement)

    Chromosome 23 - NC_007134.7Genomic Context describing neighboring genes Neighboring gene si:ch73-181d5.4 Neighboring gene histocompatibility (minor) 13 Neighboring gene SAM domain and HD domain 1 Neighboring gene mitochondrial ribosome-associated GTPase 2

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • BioProject: PRJEB1986
    • Analysis date: Fri Dec 8 19:48:10 2017

    Bibliography

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    Related articles in PubMed

    1. Prednisolone suppresses collagen-encoding gene expression causing cartilage defects in zebrafish larvae. Jiang Y, et al. Environ Toxicol Pharmacol, 2021 Oct. PMID 34332081
    2. Foxc1 establishes enhancer accessibility for craniofacial cartilage differentiation. Xu P, et al. Elife, 2021 Jan 27. PMID 33501917, Free PMC Article
    3. Elucidation of possible molecular mechanisms underlying the estrogen-induced disruption of cartilage development in zebrafish larvae. He H, et al. Toxicol Lett, 2018 Jun 1. PMID 29499231
    4. Ccn2a-FGFR1-SHH signaling is necessary for intervertebral disc homeostasis and regeneration in adult zebrafish. Rayrikar AY, et al. Development, 2023 Jan 1. PMID 36458546, Free PMC Article
    5. Fishing for collagen function: About development, regeneration and disease. Bretaud S, et al. Semin Cell Dev Biol, 2019 May. PMID 30312775

    See all (10) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables extracellular matrix structural constituent conferring tensile strength IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in extracellular matrix organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    part_of collagen trimer IEA
    Inferred from Electronic Annotation
    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

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

    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_001305573.1 → NP_001292502.1  collagen alpha-3(IX) chain precursor

      Status: VALIDATED

      Source sequence(s)
      BX323461
      UniProtKB/TrEMBL
      A0A8M1P1U1, F1R1F1
      Related
      ENSDARP00000055138.5, ENSDART00000055139.6
      Conserved Domains (1) summary
      pfam01391
      Location:448 → 505
      Collagen; Collagen triple helix repeat (20 copies)

    RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007134.7 Reference GRCz11 Primary Assembly

      Range
      495514..524780 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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