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FLASH GENE
Symbol COL9A1 contributors: shn - updated : 23-02-2012
HGNC name collagen, type IX, alpha 1
HGNC id 2217
Corresponding disease
EDM6 multiple epiphyseal dysplasia 6
STL4 Stickler syndrome 4
Location 6q13      Physical location : 70.925.743 - 71.012.786
Synonym name
  • cartilage-specific short collagen
  • collagen alpha-1
  • alpha-1(IX) collagen chain
  • collagen IX
  • alpha-1 polypeptide
  • Synonym symbol(s) DJ149L1.1.2, MED, FLJ40263, RP1-138F4.2,EDM6, STL4
    DNA
    TYPE functioning gene
    STRUCTURE 87.04 kb     38 Exon(s)
    10 Kb 5' upstream gene genomic sequence study
    MAPPING cloned Y linked Y status confirmed
    Map pter - D6S1718 - MFD183 - COL9A1 - D6S1557 - D6S455 - qter
    Authors Warman (93)
    RNA
    TRANSCRIPTS type messenger
    identificationnb exonstypebpproduct
    ProteinkDaAAspecific expressionYearPubmed
    32 splicing initiation site 3073 - 678 - -
    38 splicing 3805 - 921 - -
    EXPRESSION
    Type restricted
       expressed in (based on citations)
    organ(s)
    SystemOrgan level 1Organ level 2Organ level 3Organ level 4LevelPubmedSpeciesStageRna symbol
    Hearing/Equilibriumear   highly Homo sapiens
    Nervousbrain   moderately Homo sapiens
    Reproductivemale systemtestis  lowly Homo sapiens
    Respiratoryrespiratory tract   moderately Homo sapiens
    Visualeye   moderately Homo sapiens
    tissue
    SystemTissueTissue level 1Tissue level 2LevelPubmedSpeciesStageRna symbol
    Connectivecartilagehyaline  
    Muscularstriatumskeletal lowly Homo sapiens
    Nervouscentral   
    cell lineage
    cell lines
    fluid/secretion
    at STAGE
    physiological period fetal
    Text cartilage, cochlea
    PROTEIN
    PHYSICAL PROPERTIES
    STRUCTURE
    motifs/domains
  • N-terminal, globular noncollagenous domain (NC4) protrudes away from the surface of the fibrils into the surrounding matrix and is available for molecular interactions
  • fibril associated collagen with interrupted triple helices (FACIT) family
  • thrombospondin N terminal-like domain
  • twenty GXY repeats
  • a glycosaminoglycan attachment site (
  • conjugated GlycoP
    mono polymer heteromer , trimer
    HOMOLOGY
    interspecies homolog to Col9A1, Mus musculus
    ortholog to col9a1, Danio rerio
    ortholog to Col9a1, Rattus norvegicus
    ortholog to COL9A1, Pan troglodytes
    Homologene
    FAMILY collagen superfamily
    CATEGORY structural protein
    SUBCELLULAR LOCALIZATION extracellular
    text extracellular matrix (cuticles and basement membrane), ocular vitreous body
    basic FUNCTION
  • essential for the assembly of type IX collagen molecules and of extracellular matrix
  • CELLULAR PROCESS cell organization/biogenesis
    PHYSIOLOGICAL PROCESS development
    text skeletal, histogenesis
    PATHWAY
    metabolism
    signaling
    a component heterotrimerizing with COL9A2 and COL9A3
    INTERACTION
    DNA
    RNA
    small molecule
    protein
  • soluble myelin-associated glycoprotein, MAG (
  • collagen II (
  • heparin, cartilage oligomeric matrix protein (
  • interaction between the NC4 domain of COL9A1 and FN1 may represent an interaction in cartilage that could contribute to the matrix integrity of the tissue
  • cell & other
    REGULATION
    ASSOCIATED DISORDERS
    corresponding disease(s) EDM6 , STL4
    Susceptibility
    Variant & Polymorphism
    Candidate gene
    Marker
    Therapy target
    ANIMAL & CELL MODELS
  • mice homozygous for the COL9A1 transgene developed mild chondrodysplasia i.e., mild dwarfism, anterior tonguing in the vertebral bodies, and ophthalmopathy (
  • homozygous mutant mice, lacking both isoforms of the alpha 1(IX) chain, are viable and show no detectable abnormalities at birth but develop a severe degenerative joint disease (
  • deficiency in mouse alpha1(IX) chains leads to a functional knock-out of all polypeptides of collagen IX, whereas the Col9a2 and Col9a3 genes were normally transcribed (