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    COL9A2 collagen type IX alpha 2 chain [ Homo sapiens (human) ]

    Gene ID: 1298, updated on 3-May-2024

    Summary

    Official Symbol
    COL9A2provided by HGNC
    Official Full Name
    collagen type IX alpha 2 chainprovided by HGNC
    Primary source
    HGNC:HGNC:2218
    See related
    Ensembl:ENSG00000049089 MIM:120260; AllianceGenome:HGNC:2218
    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
    MED; EDM2; STL5; DJ39G22.4
    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. This chain is unusual in that, unlike the other two type IX alpha chains, it contains a covalently attached glycosaminoglycan side chain. Mutations in this gene are associated with multiple epiphyseal dysplasia. [provided by RefSeq, Jul 2008]
    Expression
    Broad expression in prostate (RPKM 5.8), brain (RPKM 5.5) and 20 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Location:
    1p34.2
    Exon count:
    35
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (40300489..40317286, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (40169995..40187371, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (40766161..40782958, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 834 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 835 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 836 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 837 Neighboring gene transmembrane and coiled-coil domains 2 Neighboring gene zinc metallopeptidase STE24 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 838 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 839 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 840 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 841 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 842 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 723 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 724 Neighboring gene H3K4me1 hESC enhancers GRCh37_chr1:40781816-40782452 and GRCh37_chr1:40782453-40783089 Neighboring gene ribosomal protein L21 pseudogene 20 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 843 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 844 Neighboring gene small ArfGAP2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 726 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 727 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:40839657-40840156 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 845

    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?

    Phenotypes

    Copy number response

    Description
    Copy number response
    Haploinsufficency

    No evidence available (Last evaluated 2013-10-09)

    ClinGen Genome Curation Page
    Triplosensitivity

    No evidence available (Last evaluated 2013-10-09)

    ClinGen Genome Curation Page

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in extracellular matrix organization IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in skeletal system development TAS
    Traceable Author Statement
    more info
    PubMed 
    Component Evidence Code Pubs
    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 
    is_active_in collagen-containing extracellular matrix IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    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-2(IX) chain
    Names
    alpha 2 type IX collagen
    collagen IX, alpha-2 polypeptide
    collagen, type IX, alpha 2

    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_008031.1 RefSeqGene

      Range
      4982..21779
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001852.4NP_001843.1  collagen alpha-2(IX) chain precursor

      See identical proteins and their annotated locations for NP_001843.1

      Status: REVIEWED

      Source sequence(s)
      BC136326, CB305733, CD722372
      Consensus CDS
      CCDS450.1
      UniProtKB/Swiss-Prot
      B2RMP9, Q14055
      Related
      ENSP00000361834.3, ENST00000372748.8
      Conserved Domains (1) summary
      pfam01391
      Location:259316
      Collagen; Collagen triple helix repeat (20 copies)

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      40300489..40317286 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017000332.2XP_016855821.1  collagen alpha-2(IX) chain isoform X1

      Conserved Domains (1) summary
      pfam01391
      Location:263320
      Collagen; Collagen triple helix repeat (20 copies)
    2. XM_011540715.3XP_011539017.1  collagen alpha-2(IX) chain isoform X2

      See identical proteins and their annotated locations for XP_011539017.1

      Conserved Domains (1) summary
      pfam01391
      Location:169226
      Collagen; Collagen triple helix repeat (20 copies)
    3. XM_017000333.2XP_016855822.1  collagen alpha-2(IX) chain isoform X3

      Conserved Domains (1) summary
      pfam01391
      Location:165222
      Collagen; Collagen triple helix repeat (20 copies)
    4. XM_011540716.3XP_011539018.1  collagen alpha-2(IX) chain isoform X2

      See identical proteins and their annotated locations for XP_011539018.1

      Conserved Domains (1) summary
      pfam01391
      Location:169226
      Collagen; Collagen triple helix repeat (20 copies)
    5. XM_047446392.1XP_047302348.1  collagen alpha-2(IX) chain isoform X4

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      40169995..40187371 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054334467.1XP_054190442.1  collagen alpha-2(IX) chain isoform X5

    2. XM_054334466.1XP_054190441.1  collagen alpha-2(IX) chain isoform X1

    3. XM_054334469.1XP_054190444.1  collagen alpha-2(IX) chain isoform X2

    4. XM_054334468.1XP_054190443.1  collagen alpha-2(IX) chain isoform X2

    5. XM_054334470.1XP_054190445.1  collagen alpha-2(IX) chain isoform X3