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    COL9A3 collagen type IX alpha 3 chain [ Homo sapiens (human) ]

    Gene ID: 1299, updated on 9-Dec-2024

    Summary

    Official Symbol
    COL9A3provided by HGNC
    Official Full Name
    collagen type IX alpha 3 chainprovided by HGNC
    Primary source
    HGNC:HGNC:2219
    See related
    Ensembl:ENSG00000092758 MIM:120270; AllianceGenome:HGNC:2219
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    IDD; MED; EDM3; STL6; DJ885L7.4.1
    Summary
    This gene encodes one of the three alpha chains of type IX collagen, the major collagen component of hyaline cartilage. Type IX collagen, a heterotrimeric molecule, is usually found in tissues containing type II collagen, a fibrillar collagen. Mutations in this gene are associated with multiple epiphyseal dysplasia type 3. [provided by RefSeq, Jan 2010]
    Expression
    Broad expression in thyroid (RPKM 8.5), salivary gland (RPKM 6.2) and 17 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See COL9A3 in Genome Data Viewer
    Location:
    20q13.33
    Exon count:
    33
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (62816213..62841159)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (64616007..64640720)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (61448402..61472511)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13120 Neighboring gene MRG domain binding protein Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:61435960-61436865 Neighboring gene OGFR antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13124 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13125 Neighboring gene opioid growth factor receptor Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:61446582-61447268 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:61447957-61448642 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:61449331-61450016 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:61450017-61450704 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:61454586-61455274 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:61455275-61455962 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13126 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:61461792-61462748 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:61462749-61463704 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:61463705-61464661 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:61464662-61465617 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr20:61467141-61468340 Neighboring gene Sharpr-MPRA regulatory region 13411 Neighboring gene transcription factor like 5 Neighboring gene diphthamide biosynthesis 3 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13127 Neighboring gene uncharacterized LOC105372717 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:61492967-61493621 Neighboring gene ARF GTPase 4 pseudogene 2

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    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

    Clone Names

    • FLJ90759

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in extracellular matrix organization IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Component Evidence Code Pubs
    is_active_in basement membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of collagen type IX trimer IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of collagen type IX trimer IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of collagen type IX trimer IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    located_in collagen-containing extracellular matrix HDA PubMed 
    located_in endoplasmic reticulum lumen TAS
    Traceable Author Statement
    more info
     
    located_in extracellular region TAS
    Traceable Author Statement
    more info
     
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
     

    General protein information

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

    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.

    Genomic

    1. NG_016353.1 RefSeqGene

      Range
      4989..29098
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_1253

    mRNA and Protein(s)

    1. NM_001853.4NP_001844.3  collagen alpha-3(IX) chain precursor

      See identical proteins and their annotated locations for NP_001844.3

      Status: REVIEWED

      Source sequence(s)
      AK075240, AL035669, BC004412, BC011705
      Consensus CDS
      CCDS13505.1
      UniProtKB/Swiss-Prot
      Q13681, Q14050, Q9H4G9, Q9UPE2
      Related
      ENSP00000496793.1, ENST00000649368.1
      Conserved Domains (1) summary
      pfam01391
      Location:289347
      Collagen; Collagen triple helix repeat (20 copies)

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000020.11 Reference GRCh38.p14 Primary Assembly

      Range
      62816213..62841159
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047439894.1XP_047295850.1  collagen alpha-3(IX) chain isoform X2

    2. XM_047439893.1XP_047295849.1  collagen alpha-3(IX) chain isoform X1

    3. XM_047439895.1XP_047295851.1  collagen alpha-3(IX) chain isoform X4

    4. XM_017027666.2XP_016883155.1  collagen alpha-3(IX) chain isoform X3

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060944.1 Alternate T2T-CHM13v2.0

      Range
      64616007..64640720
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054322984.1XP_054178959.1  collagen alpha-3(IX) chain isoform X1

    2. XM_054322986.1XP_054178961.1  collagen alpha-3(IX) chain isoform X4

    3. XM_054322985.1XP_054178960.1  collagen alpha-3(IX) chain isoform X3