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COL9A2 Gene

protein-coding   GIFtS: 63
GCID: GC01M040766

Collagen, Type IX, Alpha 2


(Previous symbol: EDM2)
  See COL9A2-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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This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
Collagen, Type IX, Alpha 21 2     MED2
EDM21 2 5     Alpha 2 Type IX Collagen2
STL52 5     Collagen Alpha-2(IX) Chain2
DJ39G22.42     Collagen IX, Alpha-2 Polypeptide2

External Ids:    HGNC: 22181   Entrez Gene: 12982   Ensembl: ENSG000000490897   OMIM: 1202605   UniProtKB: Q140553   
ORGUL members:         

Export aliases for COL9A2 gene to outside databases

Previous GC identifers: GC01M040801 GC01M039769 GC01M040228 GC01M040179 GC01M040435 GC01M040538 GC01M038884


(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 COL9A2 Gene:
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)

GeneCards Summary for COL9A2 Gene:
COL9A2 (collagen, type IX, alpha 2) is a protein-coding gene. Diseases associated with COL9A2 include stickler syndrome, and col9a2-related stickler syndrome. 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: CO9A2_HUMAN, Q14055
Function: Structural component of hyaline cartilage and vitreous of the eye

Gene Wiki entry for COL9A2 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 at NCBI GenBank:
NC_000001.10  NT_032977.10  NC_018912.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the COL9A2 gene promoter:
         Elk-1   Sp1   AML1a   Olf-1   LUN-1   GATA-1   AREB6   HEN1   NRF-2   Ik-2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidCOL9A2 promoter sequence
   Search Chromatin IP Primers for COL9A2

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat COL9A2


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

Entrez Gene cytogenetic band: 1p33-p32   Ensembl cytogenetic band:  1p34.2   HGNC cytogenetic band: 1p33-p32

COL9A2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
COL9A2 gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01M040766:  view genomic region     (about GC identifiers)

Start:
40,766,159 bp from pter      End:
40,783,488 bp from pter
Size:
17,330 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, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, 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: CO9A2_HUMAN, Q14055 (See protein sequence)
Recommended Name: Collagen alpha-2(IX) chain precursor  
Size: 689 amino acids; 65131 Da
Subunit: Heterotrimer of an alpha 1(IX), an alpha 2(IX) and an alpha 3(IX) chain
Secondary accessions: B2RMP9

Explore the universe of human proteins at neXtProt for COL9A2: NX_Q14055

Explore proteomics data for COL9A2 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 Ser169

  • See COL9A2 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_001843.1  
    ENSEMBL proteins: 
     ENSP00000361834   ENSP00000407377   ENSP00000388493   ENSP00000361821  
    Reactome Protein details: Q14055

    COL9A2 Human Recombinant Protein Products:

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    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates
    Browse ProSpec Recombinant Proteins
    Browse Proteins at Cloud-Clone Corp.

     
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    COL9A2 Antibody Products:

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    COL9A2 Assay Products:

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    Browse ELISAs at Cloud-Clone Corp.
    Browse CLIAs at Cloud-Clone Corp.
    Search eBioscience for ELISAs for COL9A2 


    (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

    1 InterPro protein domain:
     IPR008160 Collagen

    Graphical View of Domain Structure for InterPro Entry Q14055

    ProtoNet protein and cluster: Q14055

    2 Blocks protein domains:
    IPB008160 Collagen triple helix repeat
    IPB008161 Collagen helix repeat


    UniProtKB/Swiss-Prot: CO9A2_HUMAN, Q14055
    Similarity: Belongs to the fibril-associated collagens with interrupted helices (FACIT) family


    Find genes that share domains with COL9A2           About GenesLikeMe


    (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, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: CO9A2_HUMAN, Q14055
    Function: Structural component of hyaline cartilage and vitreous of the eye

         Genatlas biochemistry entry for COL9A2:
    collagen,type IX,alpha 2,fibril associated collagen with interrupted triple helices (FACIT),expressed in cartilage

         Gene Ontology (GO): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0030020extracellular matrix structural constituent conferring tensile strength IC8660302
         
    Find genes that share ontologies with COL9A2           About GenesLikeMe


    Phenotypes:
         2 GenomeRNAi human phenotypes for COL9A2:
     Decreased DCP1a protein expres  Increased gamma-H2AX phosphory 

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for COL9A2
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       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for COL9A2
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for COL9A2

    miRNA
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    miRTarBase miRNAs that target COL9A2:
    hsa-mir-335-5p (MIRT019087)

    Block miRNA regulation of human, mouse, rat COL9A2 using miScript Target Protectors
    5 qRT-PCR Assays for microRNAs that regulate COL9A2:
    hsa-miR-4264 hsa-miR-3679-3p hsa-miR-873 hsa-miR-525-5p hsa-miR-520a-5p
    SwitchGear 3'UTR luciferase reporter plasmidCOL9A2 3' UTR sequence
    Inhib. RNA
    Products:
        
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    Predesigned siRNA for gene silencing in human, mouse, rat COL9A2

    Gene Editing
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    GenScript: all cDNA clones in your preferred vector: COL9A2 (NM_001852)
    Sino Biological Human cDNA Clone for COL9A2
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for COL9A2
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat COL9A2

    Cell Line
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    ESI BIO PureStem Progenitors for COL9A2: 
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    In Situ Assay
    Products:
       

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for COL9A2


    (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
    CO9A2_HUMAN, Q14055: Secreted, extracellular space, extracellular matrix (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    endoplasmic reticulum4
    extracellular4
    golgi apparatus1
    plasma membrane1

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005576extracellular region TAS--
    GO:0005594collagen type IX IDA8660302
    GO:0005788endoplasmic reticulum lumen TAS--

    Find genes that share ontologies with COL9A2           About GenesLikeMe


    (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 COL9A2 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


    Find genes that share SuperPaths with COL9A2           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    Selected Downloadable PowerPoint Slides of GeneGlobe Pathway Central Maps for COL9A2 (see all 15)
        MAPK Signaling
    Molecular Mechanisms of Cancer
    PTEN Pathway
    Transendothelial Migration of Leukocytes
    UPA-UPAR Pathway


    Selected Reactome Pathways for COL9A2 (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 COL9A2):
        Protein digestion and absorption

        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for COL9A2
    Interactions:

        Search GeneGlobe Interaction Network for COL9A2

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

    Selected Interacting proteins for COL9A2 (Q140553 ENSP000003618344) via UniProtKB, MINT, STRING, and/or I2D (see all 45)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    COL9A1P208493, ENSP000003497904I2D: score=1 STRING: ENSP00000349790
    COL2A1P024583, ENSP000003698894I2D: score=2 STRING: ENSP00000369889
    NOA1Q8NC603, ENSP000002642304I2D: score=4 STRING: ENSP00000264230
    FEZ1Q996893I2D: score=4 
    HAP1P542573I2D: score=3 
    About this table

    Gene Ontology (GO): 5 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001501skeletal system development TAS10364514
    GO:0007411axon guidance TAS--
    GO:0022617extracellular matrix disassembly TAS--
    GO:0030198extracellular matrix organization TAS--
    GO:0030574collagen catabolic process TAS--

    Find genes that share ontologies with COL9A2           About GenesLikeMe



    (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 COL9A2 (CO9A2)

    2 Novoseek inferred chemical compound relationships for COL9A2 gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    col 3 86.5 1 10090888 (1)
    glutamine 7.77 1 11805640 (1)



    Find genes that share compounds with COL9A2           About GenesLikeMe



    (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, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for COL9A2 gene: 
    NM_001852.3  

    Unigene Cluster for COL9A2:

    Collagen, type IX, alpha 2
    Hs.418012  [show with all ESTs]
    Unigene Representative Sequence: BC041479
    11 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000372748(uc001cfh.1) ENST00000482722(uc001cfi.1) ENST00000466267
    ENST00000427563 ENST00000488463 ENST00000417105 ENST00000496215 ENST00000372736
    ENST00000461118 ENST00000490132 ENST00000495948
    miRNA
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    5 qRT-PCR Assays for microRNAs that regulate COL9A2:
    hsa-miR-4264 hsa-miR-3679-3p hsa-miR-873 hsa-miR-525-5p hsa-miR-520a-5p
    SwitchGear 3'UTR luciferase reporter plasmidCOL9A2 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat COL9A2
    Clone
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    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector: COL9A2 (NM_001852)
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    Primer
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      QuantiTect SYBR Green Assays in human, mouse, rat COL9A2
      QuantiFast Probe-based Assays in human, mouse, rat COL9A2

    Additional mRNA sequence: 

    AK021682.1 BC041479.1 BC065715.1 BC136326.1 BC136327.1 M95610.1 

    8 DOTS entries:

    DT.453284  DT.100781754  DT.91988516  DT.102828128  DT.92423205  DT.100650897  DT.99988192  DT.121348861 

    Selected AceView cDNA sequences (see all 122):

    AI733465 CD722241 BC041479 BM676391 CD675253 CD672813 AA605000 AI003467 
    AW163711 AI802108 BM670695 BQ181321 AA488854 AI815378 CD672313 BX119530 
    NM_001852 BQ774324 AI292185 CD722372 AI291668 AI277434 BE561386 M95610 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for COL9A2 (see all 10)    About this scheme

    ExUns: 1 ^ 2a · 2b ^ 3 ^ 4 ^ 5a · 5b · 5c · 5d ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12a · 12b ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^
    SP1:                                                                                                                                                            
    SP2:                                                                                                                                                            
    SP3:                    -           -     -     -     -                                                                                                         
    SP4:                    -                                                                                                                                       
    SP5:                                                                                                                                                            

    ExUns: 22 ^ 23 ^ 24 ^ 25 ^ 26 ^ 27a · 27b ^ 28 ^ 29 ^ 30 ^ 31
    SP1:                                                                  
    SP2:                                                                  
    SP3:                                                                  
    SP4:                                                                  
    SP5:                                                                  


    ECgene alternative splicing isoforms for COL9A2

    (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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    COL9A2 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GGCACCTCGG
    COL9A2 Expression
    About this image


    COL9A2 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 13) fully expand
     
     Bone (Muscoskeletal System)    fully expand to see all 28 entries
             Chondrocytes Vertebrae
             Rib
             HyStem+TGFbeta3+GDF5-induced MEL2 cells
     
     Cartilage (Muscoskeletal System)    fully expand to see all 28 entries
             Chondrocytes Stylopod Epiphyseal End
             HyStem+TGFbeta3+GDF5-induced MEL2 cells
     
     Adipose (Muscoskeletal System)    fully expand to see all 3 entries
             HyStem+BMP4-induced E15 cells
     
     Neural Crest (Gastrulation Derivatives)    fully expand to see all 2 entries
             PureStem 7PEND24, NCr-fac & Meso-prx Progenitor
     
     NULL (Uncategorized)    fully expand to see all 2 entries
             Endoderm progenitor-like cells
    COL9A2 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    COL9A2 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.418012
        Custom PCR Arrays for COL9A2
    Primer
    Products:
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    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat COL9A2
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    QuantiFast Probe-based Assays in human, mouse, rat COL9A2
    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for COL9A2

    (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 COL9A2 gene from Selected species (see all 13)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Col9a21 , 5 collagen, type IX, alpha 21, 5 87.27(n)1
    91.93(a)1
      4 (56.78 cM)5
    128401  NM_007741.21  NP_031767.21 
     1210393855 
    chicken
    (Gallus gallus)
    Aves COL9A21 collagen, type IX, alpha 2 71.95(n)
    79.04(a)
      396524  NM_001271988.1  NP_001258917.1 
    lizard
    (Anolis carolinensis)
    Reptilia COL9A26
    collagen, type IX, alpha 2
    79(a)
    1 ↔ 1
    GL343498.1(319704-332310)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia col9a21 collagen, type IX, alpha 2 66.46(n)
    74.14(a)
      100036633  NM_001097192.1  NP_001090661.1 
    zebrafish
    (Danio rerio)
    Actinopterygii AY113700.12   -- 72.16(n)    AY113700.1 
    worm
    (Caenorhabditis elegans)
    Secernentea col-1356
    Protein COL-135, isoform a (col-135) mRNA, complet...
    37(a)
    1 → many
    IV(15129662-15131786) WBGene00000708


    ENSEMBL Gene Tree for COL9A2 (if available)
    TreeFam Gene Tree for COL9A2 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for COL9A2 gene
    COL25A12  COL19A12  COL9A12  COL22A12  COL13A12  COL9A32  COL16A12  COL21A12  
    COL23A12  
    9 SIMAP similar genes for COL9A2 using alignment to 5 protein entries:     CO9A2_HUMAN (see all proteins):
    COL9A1    COL9A3    FCN2    C1QTNF9    C1QTNF9B    MARCO
    COL7A1    COL28A1    COL6A3

    Find genes that share paralogs with COL9A2           About GenesLikeMe



    (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 COL9A2 (see all 610)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 1 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0126584
    Intervertebral disc disease (IDD)4--see VAR_0126582 Q W mis40--------
    rs1503805531,2
    --38884158(+) TGGTAC/GAGATC 1 -- ds50010--------
    rs752547571,2
    C,F--38884184(+) TCTCCC/TGGACT 1 -- ds50011Minor allele frequency- T:0.08WA 118
    rs1828630391,2
    C--38884302(+) ACACCA/GTGGGT 1 -- ds50010--------
    rs1381060261,2
    C--38884311(+) GTGCTA/GAAACT 1 -- ds50010--------
    rs1490848611,2
    C--38884346(+) ACCCCA/GGCGAG 1 -- ds50010--------
    rs1431527091,2
    C--38884770(+) TATGCA/GAGAAA 1 -- ut310--------
    rs1385606461,2
    --38884787(+) GGAGAC/TGATGT 1 -- ut310--------
    rs752910551,2
    C,F--38884805(+) CTGAGC/TTGGGA 1 -- ut311Minor allele frequency- T:0.14WA 118
    rs2008908761,2
    --38884828(+) AGTAG-/TGGGGC 1 -- ut310--------

    HapMap Linkage Disequilibrium report for COL9A2 (40766159 - 40783488 bp)

    Structural Variations
          Database of Genomic Variants (DGV) variations for COL9A2: --
    Human Gene Mutation Database (HGMD): COL9A2
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing COL9A2
    DNA2.0 Custom Variant and Variant Library Synthesis for COL9A2

    (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: 120260   
    OMIM disorders: 600204  603932  614284  
    UniProtKB/Swiss-Prot: CO9A2_HUMAN, Q14055
  • Multiple epiphyseal dysplasia 2 (EDM2) [MIM:600204]: 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
  • Intervertebral disc disease (IDD) [MIM:603932]: A common musculo-skeletal disorder caused by degeneration
    of intervertebral disks of the lumbar spine. It results in low-back pain and unilateral leg pain. Note=Disease
    susceptibility is associated with variations affecting the gene represented in this entry
  • Stickler syndrome 5 (STL5) [MIM:614284]: 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. STL5 is characterized by high myopia, vitreoretinal degeneration, retinal detachment,
    mild to moderate sensorineural hearing loss, short stature in childhood, and absence of cleft palate and Pierre
    Robin sequence. Note=The disease is caused by mutations affecting the gene represented in this entry

  • 17 diseases for COL9A2:    
    About MalaCards
    stickler syndrome    col9a2-related stickler syndrome    col9a2-related multiple epiphyseal dysplasia    intervertebral disc disease
    stickler syndrome, type v    degenerative disc disease    multiple epiphyseal dysplasia, dominant    hydrolethalus syndrome 1
    lumbar disc disease    hydrolethalus syndrome    multiple epiphyseal dysplasia    lumbar disc herniation
    pseudoachondroplasia    stickler syndrome, type iv    osteochondritis dissecans    spinal stenosis
    campomelic dysplasia

    7 diseases from the University of Copenhagen DISEASES database for COL9A2:
    Multiple epiphyseal dysplasia     Pseudoachondroplasia     Osteoarthritis     Diastrophic dysplasia
    Osteochondritis dissecans     Campomelic dysplasia     Stickler syndrome

    Find genes that share disorders with COL9A2           About GenesLikeMe

    5 Novoseek inferred disease relationships for COL9A2 gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    multiple epiphyseal dysplasia 97 7 8702162 (1), 16440132 (1), 9605591 (1), 8528240 (1) (see all 6)
    intervertebral disc disease 87.9 7 15167667 (3), 10411504 (2), 11118298 (1)
    psach 85.9 1 11968079 (1)
    lumbar disc disease 81.3 3 16133074 (1), 14644861 (1), 17024315 (1)
    rheumatoid arthritis 0 2 16249825 (1)

    GeneTests: COL9A2
    GeneReviews: COL9A2
    Genetic Association Database (GAD): COL9A2
    Human Genome Epidemiology (HuGE) Navigator: COL9A2 (20 documents)

    Export disorders for COL9A2 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 COL9A2 gene, integrated from 10 sources (see all 79):
    (articles sorted by number of sources associating them with COL9A2)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. An allele of COL9A2 associated with intervertebral disc disease. (PubMed id 10411504)1, 2, 4, 9 Annunen S.... Ala-Kokko L. (Science 1999)
    2. Molecular cloning of the human alpha 2(IX) collagen cDNA and assignment of the human COL9A2 gene to chromosome 1. (PubMed id 8454052)1, 2, 3, 9 Peraelae M.... Vuorio E. (FEBS Lett. 1993)
    3. Association study of COL9A2 with lumbar disc disease in the Japanese population. (PubMed id 17024315)1, 4, 9 Seki S....Ikegawa S. (J. Hum. Genet. 2006)
    4. The alpha 2 type IX collagen gene tryptophan polymorphism is not associated with rheumatoid arthritis in the Japanese population. (PubMed id 16249825)1, 4, 9 Takata Y....Yasui N. (Clin. Rheumatol. 2006)
    5. The role of collagen IX tryptophan polymorphisms in symptomatic intervertebral disc disease in Southern European patients. (PubMed id 15167667)1, 4, 9 Kales S.N....Christiani D.C. (Spine 2004)
    6. Identification of novel pro-alpha2(IX) collagen gene mutations in two families with distinctive oligo-epiphyseal forms of multiple epiphyseal dysplasia. (PubMed id 10364514)1, 2, 9 Holden P.... Briggs M.D. (Am. J. Hum. Genet. 1999)
    7. Expression of the Trp2 allele of COL9A2 is associated with alterations in the mechanical properties of human intervertebral discs. (PubMed id 18246003)1, 4, 9 Aladin D.M....Lu W.W. (Spine 2007)
    8. 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)
    9. 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)
    10. The TRP2 allele of COL9A2 is an age-dependent risk factor for the development and severity of intervertebral disc degeneration. (PubMed id 16371896)1, 4, 9 Jim J.J....Chan D. (Spine 2005)

    (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: 1298 HGNC: 2218 AceView: COL9A2 Ensembl:ENSG00000049089 euGenes: HUgn1298
    ECgene: COL9A2 Kegg: 1298 H-InvDB: COL9A2

    (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 COL9A2 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for COL9A2 Genetics and Cytogenetics in Oncology and Haematology
    GeneReviewshttp://www.ncbi.nlm.nih.gov/books/NBK1116/?term=COL9A2[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 COL9A2 gene:
    Search GeneIP for patents involving COL9A2

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



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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