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

    Gene ID: 1297, updated on 12-Aug-2018

    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; Vega:OTTHUMG00000014988
    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

    Genomic context

    See COL9A1 in Genome Data Viewer
    Location:
    6q13
    Exon count:
    41
    Annotation release Status Assembly Chr Location
    109 current GRCh38.p12 (GCF_000001405.38) 6 NC_000006.12 (70216040..70303083, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (70925743..71012786, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene LMBR1 domain containing 1 Neighboring gene glyceraldehyde 3 phosphate dehydrogenase pseudogene 42 Neighboring gene collagen type XIX alpha 1 chain Neighboring gene ribosomal protein L37 pseudogene 15 Neighboring gene uncharacterized LOC105377848 Neighboring gene uncharacterized LOC105377847 Neighboring gene uncharacterized LOC101928353

    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 Jun 15 11:32:44 2016

    Bibliography

    GeneRIFs: Gene References Into FunctionsWhat'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 BioSystems

    • Assembly of collagen fibrils and other multimeric structures, organism-specific biosystem (from REACTOME)
      Assembly of collagen fibrils and other multimeric structures, organism-specific biosystemCollagen trimers in triple-helical form, referred to as procollagen or collagen molecules, are exported from the ER and trafficked through the Golgi network before secretion into the extracellular sp...
    • Axon guidance, organism-specific biosystem (from REACTOME)
      Axon guidance, organism-specific biosystemAxon guidance / axon pathfinding is the process by which neurons send out axons to reach the correct targets. Growing axons have a highly motile structure at the growing tip called the growth cone, w...
    • Collagen biosynthesis and modifying enzymes, organism-specific biosystem (from REACTOME)
      Collagen biosynthesis and modifying enzymes, organism-specific biosystemThe biosynthesis of collagen is a multistep process. Collagen propeptides are cotranslationally translocated into the ER lumen. Propeptides undergo a number of post-translational modifications. Proli...
    • Collagen chain trimerization, organism-specific biosystem (from REACTOME)
      Collagen chain trimerization, organism-specific biosystemThe C-propeptides of collagen propeptide chains are essential for the association of three peptide chains into a trimeric but non-helical procollagen. This initial binding event determines the compo...
    • Collagen degradation, organism-specific biosystem (from REACTOME)
      Collagen degradation, organism-specific biosystemCollagen fibril diameter and spatial organisation are dependent on the species, tissue type and stage of development (Parry 1988). The lengths of collagen fibrils in mature tissues are largely unknow...
    • Collagen formation, organism-specific biosystem (from REACTOME)
      Collagen formation, organism-specific biosystemCollagen is a family of at least 29 structural proteins derived from over 40 human genes (Myllyharju & Kivirikko 2004). It is the main component of connective tissue, and the most abundant protein in...
    • Degradation of the extracellular matrix, organism-specific biosystem (from REACTOME)
      Degradation of the extracellular matrix, organism-specific biosystemMatrix metalloproteinases (MMPs), previously referred to as matrixins because of their role in degradation of the extracellular matrix (ECM), are zinc and calcium dependent proteases belonging to the...
    • Developmental Biology, organism-specific biosystem (from REACTOME)
      Developmental Biology, organism-specific biosystemAs a first step towards capturing the array of processes by which a fertilized egg gives rise to the diverse tissues of the body, examples of three kinds of processes have been annotated. These are a...
    • ECM proteoglycans, organism-specific biosystem (from REACTOME)
      ECM proteoglycans, organism-specific biosystemProteoglycans are major components of the extracellular matrix. In cartilage the matrix constitutes more than 90% of tissue dry weight. Proteoglycans are proteins substituted with glycosaminoglycans ...
    • ECM-receptor interaction, organism-specific biosystem (from KEGG)
      ECM-receptor interaction, organism-specific biosystemThe extracellular matrix (ECM) consists of a complex mixture of structural and functional macromolecules and serves an important role in tissue and organ morphogenesis and in the maintenance of cell ...
    • ECM-receptor interaction, conserved biosystem (from KEGG)
      ECM-receptor interaction, conserved biosystemThe extracellular matrix (ECM) consists of a complex mixture of structural and functional macromolecules and serves an important role in tissue and organ morphogenesis and in the maintenance of cell ...
    • Extracellular matrix organization, organism-specific biosystem (from REACTOME)
      Extracellular matrix organization, organism-specific biosystemThe extracellular matrix is a component of all mammalian tissues, a network consisting largely of the fibrous proteins collagen, elastin and associated-microfibrils, fibronectin and laminins embedded...
    • Focal adhesion, organism-specific biosystem (from KEGG)
      Focal adhesion, organism-specific biosystemCell-matrix adhesions play essential roles in important biological processes including cell motility, cell proliferation, cell differentiation, regulation of gene expression and cell survival. At the...
    • Focal adhesion, conserved biosystem (from KEGG)
      Focal adhesion, conserved biosystemCell-matrix adhesions play essential roles in important biological processes including cell motility, cell proliferation, cell differentiation, regulation of gene expression and cell survival. At the...
    • Gastric Cancer Network 2, organism-specific biosystem (from WikiPathways)
      Gastric Cancer Network 2, organism-specific biosystemNetwork generated by mapping candidate oncogenes and tumor suppressor genes identified by integrated analysis of expression array and aCGH data. Network generated by Ingenuity Pathway Analysis.
    • Integrin cell surface interactions, organism-specific biosystem (from REACTOME)
      Integrin cell surface interactions, organism-specific biosystemThe extracellular matrix (ECM) is a network of macro-molecules that underlies all epithelia and endothelia and that surrounds all connective tissue cells. This matrix provides the mechanical strength...
    • NCAM signaling for neurite out-growth, organism-specific biosystem (from REACTOME)
      NCAM signaling for neurite out-growth, organism-specific biosystemThe neural cell adhesion molecule, NCAM, is a member of the immunoglobulin (Ig) superfamily and is involved in a variety of cellular processes of importance for the formation and maintenance of the n...
    • NCAM1 interactions, organism-specific biosystem (from REACTOME)
      NCAM1 interactions, organism-specific biosystemThe neural cell adhesion molecule, NCAM1 is generally considered as a cell adhesion mediator, but it is also considered to be a signal transducing receptor molecule. NCAM1 is involved in multiple cis...
    • PI3K-Akt signaling pathway, organism-specific biosystem (from KEGG)
      PI3K-Akt signaling pathway, organism-specific biosystemThe phosphatidylinositol 3' -kinase(PI3K)-Akt signaling pathway is activated by many types of cellular stimuli or toxic insults and regulates fundamental cellular functions such as transcription, tra...
    • PI3K-Akt signaling pathway, conserved biosystem (from KEGG)
      PI3K-Akt signaling pathway, conserved biosystemThe phosphatidylinositol 3' -kinase(PI3K)-Akt signaling pathway is activated by many types of cellular stimuli or toxic insults and regulates fundamental cellular functions such as transcription, tra...
    • Protein digestion and absorption, organism-specific biosystem (from KEGG)
      Protein digestion and absorption, organism-specific biosystemProtein is a dietary component essential for nutritional homeostasis in humans. Normally, ingested protein undergoes a complex series of degradative processes following the action of gastric, pancrea...
    • Protein digestion and absorption, conserved biosystem (from KEGG)
      Protein digestion and absorption, conserved biosystemProtein is a dietary component essential for nutritional homeostasis in humans. Normally, ingested protein undergoes a complex series of degradative processes following the action of gastric, pancrea...
    • Signal Transduction, organism-specific biosystem (from REACTOME)
      Signal Transduction, organism-specific biosystemSignal transduction is a process in which extracellular signals elicit changes in cell state and activity. Transmembrane receptors sense changes in the cellular environment by binding ligands, such a...
    • Signaling by PDGF, organism-specific biosystem (from REACTOME)
      Signaling by PDGF, organism-specific biosystemPlatelet-derived Growth Factor (PDGF) is a potent stimulator of growth and motility of connective tissue cells such as fibroblasts and smooth muscle cells as well as other cells such as capillary end...

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • FLJ40263

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    extracellular matrix structural constituent IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    extracellular matrix structural constituent conferring tensile strength IC
    Inferred by Curator
    more info
    PubMed 
    metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    animal organ morphogenesis TAS
    Traceable Author Statement
    more info
    PubMed 
    extracellular matrix organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    extracellular matrix organization TAS
    Traceable Author Statement
    more info
     
    Component Evidence Code Pubs
    collagen type IX trimer IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    collagen type IX trimer IDA
    Inferred from Direct Assay
    more info
    PubMed 
    collagen type IX trimer TAS
    Traceable Author Statement
    more info
    PubMed 
    endoplasmic reticulum lumen TAS
    Traceable Author Statement
    more info
     
    extracellular matrix IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    extracellular region TAS
    Traceable Author Statement
    more info
     
    extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 

    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)

    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
      5001..92044
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001851.4NP_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)
      AU118474, AW021120, BC015409, BC063646, BF196880, X54412
      Consensus CDS
      CCDS4971.1
      UniProtKB/Swiss-Prot
      P20849
      Related
      ENSP00000349790.6, OTTHUMP00000016698, ENST00000357250.10, OTTHUMT00000041131
      Conserved Domains (2) summary
      pfam01391
      Location:493552
      Collagen; Collagen triple helix repeat (20 copies)
      smart00210
      Location:50244
      TSPN; Thrombospondin N-terminal -like domains
    2. NM_078485.3NP_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)
      AW021120, BC063646, BF196880, CA392556, X54412
      Consensus CDS
      CCDS47447.1
      UniProtKB/Swiss-Prot
      P20849
      Related
      ENSP00000315252.7, OTTHUMP00000016699, ENST00000320755.12, OTTHUMT00000041132
      Conserved Domains (1) summary
      pfam01391
      Location:250309
      Collagen; Collagen triple helix repeat (20 copies)

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

    Reference GRCh38.p12 Primary Assembly

    Genomic

    1. NC_000006.12 Reference GRCh38.p12 Primary Assembly

      Range
      70216040..70303083 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011535429.3XP_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_017010246.2XP_016865735.1  collagen alpha-1(IX) chain isoform X2

    3. XM_011535430.3XP_011533732.1  collagen alpha-1(IX) chain isoform X3

      Conserved Domains (1) summary
      pfam01391
      Location:250309
      Collagen; Collagen triple helix repeat (20 copies)
    4. XM_017010247.2XP_016865736.1  collagen alpha-1(IX) chain isoform X4

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