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COL9A1 Gene

protein-coding   GIFtS: 63
GCID: GC06M070924

Collagen, Type IX, Alpha 1

  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Collagen, Type IX, Alpha 11 2     Alpha-1(IX) Collagen Chain2
EDM62 5     Cartilage-Specific Short Collagen2
STL42 5     Collagen Alpha-1(IX) Chain2
DJ149L1.1.22     Collagen IX, Alpha-1 Polypeptide2
MED2     

External Ids:    HGNC: 22171   Entrez Gene: 12972   Ensembl: ENSG000001122807   OMIM: 1202105   UniProtKB: P208493   

Export aliases for COL9A1 gene to outside databases

Previous GC identifers: GC06M070884 GC06M070921 GC06M070982 GC06M068124


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for COL9A1 Gene:
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)

GeneCards Summary for COL9A1 Gene:
COL9A1 (collagen, type IX, alpha 1) is a protein-coding gene. Diseases associated with COL9A1 include stickler syndrome, type iv, and col9a1-related multiple epiphyseal dysplasia. GO annotations related to this gene include extracellular matrix structural constituent conferring tensile strength. An important paralog of this gene is COL25A1.

UniProtKB/Swiss-Prot: CO9A1_HUMAN, P20849
Function: Structural component of hyaline cartilage and vitreous of the eye

Gene Wiki entry for COL9A1 (Collagen, type IX, alpha 1) Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000006.12  NT_025741.16  NC_018917.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the COL9A1 gene promoter:
         IRF-2   Nkx2-2   FOXD3   AP-4   IRF-1   Pax-4a   C/EBPalpha   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): COL9A1 promoter sequence
   Search Chromatin IP Primers for COL9A1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat COL9A1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 6q13   Ensembl cytogenetic band:  6q13   HGNC cytogenetic band: 6q13

COL9A1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
COL9A1 gene location

GeneLoc information about chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06M070924:  view genomic region     (about GC identifiers)

Start:
70,924,764 bp from pter      End:
71,012,786 bp from pter
Size:
88,023 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: CO9A1_HUMAN, P20849 (See protein sequence)
Recommended Name: Collagen alpha-1(IX) chain precursor  
Size: 921 amino acids; 91869 Da
Subunit: Heterotrimer of an alpha 1(IX), an alpha 2(IX) and an alpha 3(IX) chain
1 PDB 3D structure from and Proteopedia for COL9A1:
2UUR (3D)    
Secondary accessions: Q13699 Q13700 Q5TF52 Q6P467 Q96BM8 Q99225 Q9H151 Q9H152 Q9Y6P2 Q9Y6P3
Alternative splicing: 3 isoforms:  P20849-1   P20849-2   P20849-3   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for COL9A1: NX_P20849

Explore proteomics data for COL9A1 at MOPED

Post-translational modifications: 

  • Covalently linked to the telopeptides of type II collagen by lysine-derived cross-links1
  • Prolines at the third position of the tripeptide repeating unit (G-X-Y) are hydroxylated in some or all of the
    chains1
  • Glycosylation2 at Asn171

  • See COL9A1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_001842.3  NP_511040.2  

    ENSEMBL proteins: 
     ENSP00000349790   ENSP00000315252   ENSP00000359527   ENSP00000359530  
    Reactome Protein details: P20849

    COL9A1 Human Recombinant Protein Products:

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    COLPG: Proteoglycans / Extracellular Matrix : Collagen proteoglycans
    COLLAGEN: Collagens

    4 InterPro protein domains:
     IPR013320 ConA-like_subgrp
     IPR001791 Laminin_G
     IPR008160 Collagen
     IPR008985 ConA-like_lec_gl_sf

    Graphical View of Domain Structure for InterPro Entry P20849

    ProtoNet protein and cluster: P20849

    3 Blocks protein domains:
    IPB003129 Thrombospondin
    IPB008160 Collagen triple helix repeat
    IPB008161 Collagen helix repeat


    UniProtKB/Swiss-Prot: CO9A1_HUMAN, P20849
    Domain: Each subunit is composed of three triple-helical domains interspersed with non-collagenous domains. The
    globular domain at the N-terminus of type IX collagen molecules represents the NC4 domain which may participate
    in electrostatic interactions with polyanionic glycosaminoglycans in cartilage
    Similarity: Belongs to the fibril-associated collagens with interrupted helices (FACIT) family
    Similarity: Contains 10 collagen-like domains
    Similarity: Contains 1 laminin G-like domain


    COL9A1 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: CO9A1_HUMAN, P20849
    Function: Structural component of hyaline cartilage and vitreous of the eye

         Genatlas biochemistry entry for COL9A1:
    collagen,type IX,alpha 1,fibril associated collagen with interrupted triple helices (FACIT),expressed in cartilage

         Gene Ontology (GO): 2 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0030020extracellular matrix structural constituent conferring tensile strength IC8660302
    GO:0046872metal ion binding IEA--
         
    COL9A1 for ontologies           About GeneDecksing


    Phenotypes:
         3 GenomeRNAi human phenotypes for COL9A1:
     Decreased nuclei size in G2M  Elongated cells  Increased gamma-H2AX phosphory 

         6 MGI mutant phenotypes (inferred from 1 allele(MGI details for Col9a1):
     hearing/vestibular/ear  homeostasis/metabolism  immune system  limbs/digits/tail  skeleton 
     vision/eye 

    COL9A1 for phenotypes           About GeneDecksing

    Animal Models:
         MGI mouse knock-out Col9a1tm1Jae for COL9A1

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for COL9A1
       inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for COL9A1

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for COL9A1
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for COL9A1

    miRNA
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    1 qRT-PCR Assays for microRNA that regulate COL9A1:
    hsa-miR-9
    SwitchGear 3'UTR luciferase reporter plasmidCOL9A1 3' UTR sequence
    Inhib. RNA
    Products:
        
    OriGene RNAi products in human, mouse, rat for COL9A1
    Predesigned siRNA for gene silencing in human, mouse, rat COL9A1

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    GenScript: all cDNA clones in your preferred vector (see all 2): COL9A1 (NM_078485)
    Sino Biological Human cDNA Clone for COL9A1
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for COL9A1
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat COL9A1

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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for COL9A1


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    CO9A1_HUMAN, P20849: Secreted, extracellular space, extracellular matrix (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    extracellular5
    endoplasmic reticulum4
    plasma membrane2
    golgi apparatus1
    lysosome1
    mitochondrion1
    peroxisome1

    Gene Ontology (GO): 3 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005576extracellular region TAS--
    GO:0005594collagen type IX TAS9707347
    GO:0005788endoplasmic reticulum lumen TAS--

    COL9A1 for ontologies           About GeneDecksing


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    SuperPaths for COL9A1 About   (see all 13)  
    See pathways by source

    SuperPathContained pathways About
    1Collagen biosynthesis and modifying enzymes
    Collagen biosynthesis and modifying enzymes0.75
    Intrinsic Prothrombin Activation Pathway0.39
    Collagen formation0.75
    Blood Coagulation Cascade0.38
    2Integrin Pathway
    FAK1 Signaling0.67
    UPA-UPAR Pathway0.56
    Integrin Pathway0.67
    Inhibition of Angiogenesis by TSP10.50
    GnRH Signaling0.56
    Transendothelial Migration of Leukocytes0.38
    3ERK Signaling
    Rho Family GTPases0.61
    Molecular Mechanisms of Cancer0.51
    ERK Signaling0.61
    ILK Signaling0.49
    MAPK Signaling0.58
    4Degradation of the extracellular matrix
    Degradation of the extracellular matrix0.43
    Extracellular matrix organization0.34
    Collagen degradation0.43
    5L1CAM interactions
    Axon guidance0.63
    Developmental Biology0.63

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    Selected Downloadable PowerPoint Slides of GeneGlobe Pathway Central Maps for COL9A1 (see all 15)
        MAPK Signaling
    Molecular Mechanisms of Cancer
    PTEN Pathway
    Transendothelial Migration of Leukocytes
    UPA-UPAR Pathway

    1 BioSystems Pathway for COL9A1
        Gastric cancer network 2


    Selected Reactome Pathways for COL9A1 (see all 6)
        ECM proteoglycans
    Integrin cell surface interactions
    NCAM1 interactions
    Collagen biosynthesis and modifying enzymes
    Signaling by PDGF


    1 Kegg Pathway  (Kegg details for COL9A1):
        Protein digestion and absorption


    COL9A1 for pathways           About GeneDecksing

        Pathway & Disease-focused RT2 Profiler PCR Array including COL9A1: 
              Stem Cells in human mouse rat

    Interactions:

        Search GeneGlobe Interaction Network for COL9A1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for COL9A1 (P208493 ENSP000003497904) via UniProtKB, MINT, STRING, and/or I2D (see all 43)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    COL9A2Q140553, ENSP000003618344I2D: score=1 STRING: ENSP00000361834
    COMPP497473, ENSP000002222714I2D: score=1 STRING: ENSP00000222271
    COL9A3Q140503, ENSP000003416404I2D: score=1 STRING: ENSP00000341640
    COL2A1P024583, ENSP000003698894I2D: score=1 STRING: ENSP00000369889
    MAGP209163I2D: score=3 
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 8):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001894tissue homeostasis IEA--
    GO:0003417growth plate cartilage development IEA--
    GO:0007411axon guidance TAS--
    GO:0009887organ morphogenesis TAS3473493
    GO:0022617extracellular matrix disassembly TAS--

    COL9A1 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for COL9A1 (CO9A1)



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for COL9A1 gene (2 alternative transcripts): 
    NM_001851.4  NM_078485.3  

    Unigene Cluster for COL9A1:

    Collagen, type IX, alpha 1
    Hs.590892  [show with all ESTs]
    Unigene Representative Sequence: NM_001851
    11 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000357250(uc003pfg.4) ENST00000320755(uc003pfe.4 uc003pff.4)
    ENST00000486080 ENST00000489611 ENST00000447041 ENST00000493682 ENST00000360859
    ENST00000489861 ENST00000470652 ENST00000370496 ENST00000370499
    miRNA
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    1 qRT-PCR Assays for microRNA that regulate COL9A1:
    hsa-miR-9
    SwitchGear 3'UTR luciferase reporter plasmidCOL9A1 3' UTR sequence
    Inhib. RNA
    Products:
         
    OriGene RNAi products in human, mouse, rat for COL9A1
    Predesigned siRNA for gene silencing in human, mouse, rat COL9A1
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    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat COL9A1
      QuantiTect SYBR Green Assays in human, mouse, rat COL9A1
      QuantiFast Probe-based Assays in human, mouse, rat COL9A1

    Additional mRNA sequence: 

    AK097582.1 AK125738.1 BC008620.1 BC015409.1 BC063646.1 X54412.1 X54413.1 

    9 DOTS entries:

    DT.91850102  DT.209488  DT.100024648  DT.95185541  DT.99931581  DT.100024649  DT.121344198  DT.99935914 
    DT.121344211 

    Selected AceView cDNA sequences (see all 93):

    BQ573750 AI270780 CA415443 BE221644 AI273829 N67231 BQ007752 BI492066 
    BC015409 BG030514 BQ573748 BI492246 H89286 CB215908 AW950082 N63235 
    AI986458 BQ772356 CA412796 AI277812 N66382 AL044696 AU119275 AK125738 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    COL9A1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TTCAATGAAA
    COL9A1 Expression
    About this image


    COL9A1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 10) fully expand
     
     Bone (Muscoskeletal System)    fully expand to see all 20 entries
             Prechondrocytes Autopod Epiphyseal End
             Endochondral Facial Bones
             Micromass-induced chondrocytes
     
     Cartilage (Muscoskeletal System)    fully expand to see all 15 entries
             Prechondrocytes Autopod Epiphyseal End
             Laryngeal Cartilage
             Juvenile neocartilage (RevaFlex)
             Micromass-induced chondrocytes
     
     Kidney (Urinary System)    fully expand to see all 3 entries
             Metanephric Mesenchyme Cells Metanephric Mesenchyme
             Metanephros
     
     Heart (Cardiovascular System)    fully expand to see all 2 entries
             Atrioventricular Canal Cells Atrioventricular Canal
     
     Limb (Muscoskeletal System)    fully expand to see all 3 entries
             Central Intermediate Lamina Cells Zeugopod Synovial Joint
             Pelvic Girdle
    COL9A1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    COL9A1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.590892
        Pathway & Disease-focused RT2 Profiler PCR Array including COL9A1: 
              Stem Cells in human mouse rat

    Primer
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    OriGene qPCR primer pairs and template standards for COL9A1
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    QuantiFast Probe-based Assays in human, mouse, rat COL9A1
    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for COL9A1

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of animals.

    Orthologs for COL9A1 gene from Selected species (see all 15)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Col9a11 , 5 collagen, type IX, alpha 11, 5 86.78(n)1
    90.11(a)1
      1 (9.95 cM)5
    128391  NM_007740.31  NP_031766.31 
     241776105 
    chicken
    (Gallus gallus)
    Aves COL9A11 collagen, type IX, alpha 1 73.41(n)
    74.43(a)
      771873  NM_001100911.1  NP_001094381.1 
    lizard
    (Anolis carolinensis)
    Reptilia --
    --
    --
    73(a)
    71(a)
    1 ↔ many
    1 ↔ many
    1(167420281-167433580)
    1(167454638-167518315)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.160422 Xenopus laevis, Similar to collagen, type IX, alpha more 71.66(n)    BC045244.1 
    zebrafish
    (Danio rerio)
    Actinopterygii CD778000.12   -- 73.63(n)   335031  CD778000.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG423426
    --
    28(a)
    1 → many
    3R(12328523-12397082)
    worm
    (Caenorhabditis elegans)
    Secernentea col-996
    Protein COL-99, isoform a (col-99) mRNA, complete ...
    31(a)
    1 → many
    IV(138461-147919) WBGene00000674


    ENSEMBL Gene Tree for COL9A1 (if available)
    TreeFam Gene Tree for COL9A1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for COL9A1 gene
    COL25A12  COL19A12  COL22A12  COL13A12  COL9A32  COL9A22  COL16A12  COL23A12  
    COL21A12  
    6 SIMAP similar genes for COL9A1 using alignment to 2 protein entries:     CO9A1_HUMAN (see all proteins):
    FCN2    COL9A2    COL9A3    C1QTNF9    MARCO    C1QTNF9B

    COL9A1 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for COL9A1 (see all 2237)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 6 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs717496911,2
    C--70930093(+) GCAGG-/GTGT  
            
    GTGTG
    2 -- int10--------
    rs721550961,2
    C--70930093(+) GCAGG-/GTGTGT
            
    GTGTG
    2 -- int10--------
    rs593969981,2
    C--70930116(+) GTGTG-/TGTGTG
            
    GTCAT
    2 -- int11Minor allele frequency- TGTGTG:0.00NA 2
    rs582072131,2
    C--70930802(+) TTTTT-/TAAACA 2 -- int10--------
    rs38404081,2
    C--70932442(+) TTTTTT/-ATTCA 2 -- int11Minor allele frequency- -:0.00NA 2
    rs38426091,2
    C--70934598(+) TCATG-/TTTTTT 2 -- int10--------
    rs38426101,2
    C--70941266(+) AAAAA-/ATGTAA 2 -- int10--------
    rs360548521,2
    C--70941418(+) AAAAAA/-CAACC 2 -- int12Minor allele frequency- -:0.25NA 4
    rs358948051,2
    C--70941767(+) AAAAAA/-TCCAT 2 -- int11Minor allele frequency- -:0.00NA 2
    rs1487883351,2
    C--70942870(+) TATGT-/GGAAGC 2 -- int10--------

    HapMap Linkage Disequilibrium report for COL9A1 (70924764 - 71012786 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 5 variations for COL9A1:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv271252CNV Insertion20981092
    nsv830683CNV Gain17160897
    nsv886143CNV Gain21882294
    nsv524328CNV Gain19592680
    nsv886142CNV Gain21882294

    Human Gene Mutation Database (HGMD): COL9A1
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing COL9A1
    DNA2.0 Custom Variant and Variant Library Synthesis for COL9A1

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 120210   
    OMIM disorders: 614135  614134  
    UniProtKB/Swiss-Prot: CO9A1_HUMAN, P20849
  • Multiple epiphyseal dysplasia 6 (EDM6) [MIM:614135]: A generalized skeletal dysplasia associated with
    significant morbidity. Joint pain, joint deformity, waddling gait, and short stature are the main clinical signs
    and symptoms. Radiological examination of the skeleton shows delayed, irregular mineralization of the epiphyseal
    ossification centers and of the centers of the carpal and tarsal bones. Multiple epiphyseal dysplasia is broadly
    categorized into the more severe Fairbank and the milder Ribbing types. The Fairbank type is characterized by
    shortness of stature, short and stubby fingers, small epiphyses in several joints, including the knee, ankle,
    hand, and hip. The Ribbing type is confined predominantly to the hip joints and is characterized by hands that
    are normal and stature that is normal or near-normal. Note=The disease is caused by mutations affecting the gene
    represented in this entry
  • Stickler syndrome 4 (STL4) [MIM:614134]: An autosomal recessive form of Stickler syndrome, an inherited
    disorder that associates ocular signs with more or less complete forms of Pierre Robin sequence, bone disorders
    and sensorineural deafness. Ocular disorders may include juvenile cataract, myopia, strabismus, vitreoretinal or
    chorioretinal degeneration, retinal detachment, and chronic uveitis. Robin sequence includes an opening in the
    roof of the mouth (a cleft palate), a large tongue (macroglossia), and a small lower jaw (micrognathia). Bones
    are affected by slight platyspondylisis and large, often defective epiphyses. Juvenile joint laxity is followed
    by early signs of arthrosis. The degree of hearing loss varies among affected individuals and may become more
    severe over time. Syndrome expressivity is variable. Note=The disease is caused by mutations affecting the gene
    represented in this entry

  • Selected diseases for COL9A1 (see all 37):    
    About MalaCards
    stickler syndrome, type iv    col9a1-related multiple epiphyseal dysplasia    epiphyseal dysplasia, multiple, 6    interstitial keratitis
    col9a1-related stickler syndrome    lipoid proteinosis    osteoarthritis    talipes equinovarus
    multiple epiphyseal dysplasia, dominant    stickler syndrome    pierre robin sequence    multiple epiphyseal dysplasia
    macroglossia    osteochondritis dissecans    pseudoachondroplasia    spinal stenosis
    chondrodysplasia    chorioretinitis    keratitis    retinal detachment

    6 diseases from the University of Copenhagen DISEASES database for COL9A1:
    Multiple epiphyseal dysplasia     Clubfoot     Stickler syndrome     Pseudoachondroplasia
    Osteoarthritis     Osteochondritis dissecans

    COL9A1 for disorders           About GeneDecksing

    4 Novoseek inferred disease relationships for COL9A1 gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    multiple epiphyseal dysplasia 93 1 11565064 (1)
    psach 73 1 11968079 (1)
    osteoarthritis 55.9 3 8244386 (1), 15733274 (1)
    collagen fibril 53.6 2 15869539 (1), 2007255 (1)

    GeneTests: COL9A1
    GeneReviews: COL9A1
    Genetic Association Database (GAD): COL9A1
    Human Genome Epidemiology (HuGE) Navigator: COL9A1 (10 documents)

    Export disorders for COL9A1 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for COL9A1 gene, integrated from 10 sources (see all 80):
    (articles sorted by number of sources associating them with COL9A1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. A mutation in COL9A1 causes multiple epiphyseal dysplasia: further evidence for locus heterogeneity. (PubMed id 11565064)1, 2, 9 Czarny-Ratajczak M.... Ala-Kokko L. (Am. J. Hum. Genet. 2001)
    2. [Analysis of association between COL9A1 gene and idiopathic congenital talipes equinovarus]. (PubMed id 17548304)1, 4, 9 Liu L.Y....Sun K.L. (Yi Chuan 2007)
    3. A new autosomal recessive form of Stickler syndrome is caused by a mutation in the COL9A1 gene. (PubMed id 16909383)1, 2, 9 Van Camp G.... Usami S. (Am. J. Hum. Genet. 2006)
    4. Human COL9A1 and COL9A2 genes. Two genes of 90 and 15 kb code for similar polypeptides of the same collagen molecule. (PubMed id 9707347)1, 2, 9 Pihlajamaa T....Ala-Kokko L. (Matrix Biol. 1998)
    5. Evidence for a role of the genomic region of the gene encoding for the alpha1 chain of type IX collagen (COL9A1) in hip osteoarthritis: A population-based study. (PubMed id 15880806)1, 4, 9 Alizadeh B.Z....Duijn C.M. (Arthritis Rheum. 2005)
    6. Mutations in the known genes are not the major cause of MED; distinctive phenotypic entities among patients with no identified mutations. (PubMed id 15523498)1, 4, 9 Jakkula E....Ala-Kokko L. (Eur. J. Hum. Genet. 2005)
    7. The role of sequence variations within the genes encoding collagen II, IX and XI in non-syndromic, early-onset osteoarthritis. (PubMed id 15922184)1, 4, 9 Jakkula E....Ala-Kokko L. (Osteoarthr. Cartil. 2005)
    8. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1, 4 Rose J.E....Uhl G.R. (Mol. Med. 2010)
    9. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PubMed id 20628086)1, 4 Bailey S.D....Anand S. (Diabetes Care 2010)
    10. Associations of 25 structural, degradative, and inflammatory candidate genes with lumbar disc desiccation, bulging, and height narrowing. (PubMed id 19180518)1, 4 Videman T....BattiAc M.C. (Arthritis Rheum. 2009)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 1297 HGNC: 2217 AceView: COL9A1 Ensembl:ENSG00000112280 euGenes: HUgn1297
    ECgene: COL9A1 Kegg: 1297 H-InvDB: COL9A1

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for COL9A1 Pharmacogenomics, SNPs, Pathways
    GeneReviewshttp://www.ncbi.nlm.nih.gov/books/NBK1116/?term=COL9A1[genesymbol]

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for COL9A1 gene:
    Search GeneIP for patents involving COL9A1

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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