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    COL9A1 collagen type IX alpha 1 chain [ Homo sapiens (human) ]

    Gene ID: 1297, updated on 3-May-2024

    Summary

    Official Symbol
    COL9A1provided by HGNC
    Official Full Name
    collagen type IX alpha 1 chainprovided by HGNC
    Primary source
    HGNC:HGNC:2217
    See related
    Ensembl:ENSG00000112280 MIM:120210; AllianceGenome:HGNC:2217
    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; EDM6; STL4; DJ149L1.1.2
    Summary
    This gene encodes one of the three alpha chains of type IX collagen, which is a minor (5-20%) collagen component of hyaline cartilage. Type IX collagen is usually found in tissues containing type II collagen, a fibrillar collagen. Studies in knockout mice have shown that synthesis of the alpha 1 chain is essential for assembly of type IX collagen molecules, a heterotrimeric molecule, and that lack of type IX collagen is associated with early onset osteoarthritis. Mutations in this gene are associated with osteoarthritis in humans, with multiple epiphyseal dysplasia, 6, a form of chondrodysplasia, and with Stickler syndrome, a disease characterized by ophthalmic, orofacial, articular, and auditory defects. Two transcript variants that encode different isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]
    Expression
    Biased expression in prostate (RPKM 6.1), testis (RPKM 1.3) and 6 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See COL9A1 in Genome Data Viewer
    Location:
    6q13
    Exon count:
    43
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (70215061..70303084, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (71395620..71483638, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (70924764..71012787, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene LMBR1 domain containing 1 Neighboring gene uncharacterized LOC124901337 Neighboring gene glyceraldehyde 3 phosphate dehydrogenase pseudogene 42 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:70505853-70506409 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:70506410-70506965 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24728 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24729 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17314 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17315 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17316 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:70597939-70598122 Neighboring gene NANOG hESC enhancer GRCh37_chr6:70623798-70624319 Neighboring gene collagen type XIX alpha 1 chain Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:70627263-70628462 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:70845103-70845604 Neighboring gene ribosomal protein L37 pseudogene 15 Neighboring gene MPRA-validated peak5887 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24730 Neighboring gene uncharacterized LOC105377848 Neighboring gene Sharpr-MPRA regulatory region 4194 Neighboring gene uncharacterized LOC105377847 Neighboring gene long intergenic non-protein coding RNA 1610

    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 2013-11-06)

    ClinGen Genome Curation Page
    Triplosensitivity

    No evidence available (Last evaluated 2013-11-06)

    ClinGen Genome Curation Page

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ40263

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in animal organ morphogenesis TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in extracellular matrix organization IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    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 IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of collagen type IX trimer IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    part_of collagen type IX trimer TAS
    Traceable Author Statement
    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-1(IX) chain
    Names
    alpha-1(IX) collagen chain
    cartilage-specific short collagen
    collagen IX, alpha-1 polypeptide
    collagen, type IX, alpha 1

    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_011654.1 RefSeqGene

      Range
      5000..91958
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001377289.1NP_001364218.1  collagen alpha-1(IX) chain isoform 3 precursor

      Status: REVIEWED

      Source sequence(s)
      AL080275, AL160262
      Consensus CDS
      CCDS93940.1
      UniProtKB/TrEMBL
      A0A804HIB6
      Related
      ENSP00000506990.1, ENST00000683980.2
      Conserved Domains (1) summary
      pfam01391
      Location:253309
      Collagen; Collagen triple helix repeat (20 copies)
    2. NM_001377290.1NP_001364219.1  collagen alpha-1(IX) chain isoform 4 precursor

      Status: REVIEWED

      Source sequence(s)
      AL080275, AL160262
      Related
      ENSP00000508147.1, ENST00000683758.1
      Conserved Domains (1) summary
      pfam01391
      Location:244298
      Collagen; Collagen triple helix repeat (20 copies)
    3. NM_001377291.1NP_001364220.1  collagen alpha-1(IX) chain isoform 5 precursor

      Status: REVIEWED

      Source sequence(s)
      AL080275
      Consensus CDS
      CCDS93941.1
      Related
      ENSP00000359527.3, ENST00000370496.3
      Conserved Domains (1) summary
      smart00210
      Location:50244
      TSPN; Thrombospondin N-terminal -like domains
    4. NM_001851.6NP_001842.3  collagen alpha-1(IX) chain isoform 1 precursor

      See identical proteins and their annotated locations for NP_001842.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1, also known as the long form).
      Source sequence(s)
      AL080275, AL160262
      Consensus CDS
      CCDS4971.1
      UniProtKB/Swiss-Prot
      P20849, Q13699, Q13700, Q5TF52, Q6P467, Q96BM8, Q99225, Q9H151, Q9H152, Q9Y6P2, Q9Y6P3
      Related
      ENSP00000349790.6, ENST00000357250.11
      Conserved Domains (2) summary
      pfam01391
      Location:493552
      Collagen; Collagen triple helix repeat (20 copies)
      smart00210
      Location:50244
      TSPN; Thrombospondin N-terminal -like domains
    5. NM_078485.4NP_511040.2  collagen alpha-1(IX) chain isoform 2 precursor

      See identical proteins and their annotated locations for NP_511040.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and lacks several exons in the 5' coding region, compared to variant 1. These differences cause translation initiation at a unique AUG and an isoform (2, also known as the short form) with a shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AL160262, AW021120, BC063646, BF196880, CA392556, X54412
      Consensus CDS
      CCDS47447.1
      UniProtKB/Swiss-Prot
      P20849
      Related
      ENSP00000315252.7, ENST00000320755.12
      Conserved Domains (1) summary
      pfam01391
      Location:250309
      Collagen; Collagen triple helix repeat (20 copies)

    RNA

    1. NR_165185.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL080275, AL160262

    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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      70215061..70303084 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011535429.4XP_011533731.1  collagen alpha-1(IX) chain isoform X1

      Conserved Domains (2) summary
      pfam01391
      Location:493552
      Collagen; Collagen triple helix repeat (20 copies)
      smart00210
      Location:50244
      TSPN; Thrombospondin N-terminal -like domains
    2. XM_017010246.3XP_016865735.1  collagen alpha-1(IX) chain isoform X2

    3. XM_047418180.1XP_047274136.1  collagen alpha-1(IX) chain isoform X4

    4. XM_047418179.1XP_047274135.1  collagen alpha-1(IX) chain isoform X3

    5. XM_017010247.3XP_016865736.1  collagen alpha-1(IX) chain isoform X5

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      71395620..71483638 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054354214.1XP_054210189.1  collagen alpha-1(IX) chain isoform X1

    2. XM_054354215.1XP_054210190.1  collagen alpha-1(IX) chain isoform X2

    3. XM_054354217.1XP_054210192.1  collagen alpha-1(IX) chain isoform X4

    4. XM_054354216.1XP_054210191.1  collagen alpha-1(IX) chain isoform X3

    5. XM_054354218.1XP_054210193.1  collagen alpha-1(IX) chain isoform X5