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SOX9 Gene

protein-coding   GIFtS: 66
GCID: GC17P070117

SRY (Sex Determining Region Y)-Box 9

(Previous names: campomelic dysplasia, autosomal sex-reversal)
(Previous symbols: CMD1, CMPD1)
  See SOX9-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
SRY (Sex Determining Region Y)-Box 91 2     Campomelic Dysplasia, Autosomal Sex-Reversal1
CMD11 2 5     SRY (Sex-Determining Region Y)-Box 9 Protein2
CMPD11 2     SRY-Related HMG-Box, Gene 92
SRA12 5     Transcription Factor SOX-92

External Ids:    HGNC: 112041   Entrez Gene: 66622   Ensembl: ENSG000001253987   OMIM: 6081605   UniProtKB: P484363   

Export aliases for SOX9 gene to outside databases

Previous GC identifers: GC17P069873 GC17P073111 GC17P070581 GC17P070714 GC17P067628 GC17P065510


(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 SOX9 Gene:
The protein encoded by this gene recognizes the sequence CCTTGAG along with other members of the HMG-box class
DNA-binding proteins. It acts during chondrocyte differentiation and, with steroidogenic factor 1, regulates
transcription of the anti-Muellerian hormone (AMH) gene. Deficiencies lead to the skeletal malformation syndrome
campomelic dysplasia, frequently with sex reversal. (provided by RefSeq, Jul 2008)

GeneCards Summary for SOX9 Gene:
SOX9 (SRY (sex determining region Y)-box 9) is a protein-coding gene. Diseases associated with SOX9 include campomelic dysplasia with autosomal sex reversal, and pierre robin sequence. GO annotations related to this gene include protein kinase activity and sequence-specific DNA binding transcription factor activity. An important paralog of this gene is SOX13.

UniProtKB/Swiss-Prot: SOX9_HUMAN, P48436
Function: Plays an important role in the normal skeletal development. May regulate the expression of other genes
involved in chondrogenesis by acting as a transcription factor for these genes

Gene Wiki entry for SOX9 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_000017.10  NC_018928.2  NT_010783.16  
Regulatory elements:
   Regulatory transcription factor binding sites in the SOX9 gene promoter:
         PPAR-gamma1   SRY   MyoD   Sox9   Nkx2-5   PPAR-gamma2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSOX9 promoter sequence
   Search Chromatin IP Primers for SOX9

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SOX9


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

Entrez Gene cytogenetic band: 17q24.3   Ensembl cytogenetic band:  17q24.3   HGNC cytogenetic band: 17q24.3

SOX9 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SOX9 gene location

GeneLoc information about chromosome 17         GeneLoc Exon Structure

GeneLoc location for GC17P070117:  view genomic region     (about GC identifiers)

Start:
70,117,161 bp from pter      End:
70,122,561 bp from pter
Size:
5,401 bases      Orientation:
plus 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., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: SOX9_HUMAN, P48436 (See protein sequence)
Recommended Name: Transcription factor SOX-9  
Size: 509 amino acids; 56137 Da
3 PDB 3D structures from and Proteopedia for SOX9:
1S9M (3D)        1SX9 (3D)        4EUW (3D)    
Secondary accessions: Q53Y80

Explore the universe of human proteins at neXtProt for SOX9: NX_P48436

Explore proteomics data for SOX9 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys141
  • Modification sites at PhosphoSitePlus

  • See SOX9 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_000337.1  
    ENSEMBL proteins: 
     ENSP00000245479  

    SOX9 Human Recombinant Protein Products:

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    Cloud-Clone Corp. Proteins for SOX9

     
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    antibodies-online proteins for SOX9 

     
    antibodies-online peptides for SOX9

    SOX9 Antibody Products:

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    antibodies-online antibodies for SOX9 (44 products) 

    SOX9 Assay Products:

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    Cloud-Clone Corp. ELISAs for SOX9
    Cloud-Clone Corp. CLIAs for SOX9
    Search eBioscience for ELISAs for SOX9 
    antibodies-online kits for SOX9 (6 products) 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    SOX: SRY (sex determining region Y)-boxes

    2 InterPro protein domains:
     IPR009071 HMG_box_dom
     IPR022151 Sox_N

    Graphical View of Domain Structure for InterPro Entry P48436

    ProtoNet protein and cluster: P48436

    UniProtKB/Swiss-Prot: SOX9_HUMAN, P48436
    Similarity: Contains 1 HMG box DNA-binding domain


    Find genes that share domains with SOX9           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, 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: SOX9_HUMAN, P48436
    Function: Plays an important role in the normal skeletal development. May regulate the expression of other genes
    involved in chondrogenesis by acting as a transcription factor for these genes

         Genatlas biochemistry entry for SOX9:
    SRY related HMG box gene 9,expressed in the genital ridge of both sexes,in chondrocytes and in non-skeletal
    tissues,likely involved in the differentiation of Sertoli cells,potent activator of the chondrocyte-specific
    enhancer of COL2A1,required for cartilage formation,important mediator of the BMP2 and Indian hedgehog (IHH)
    sinaling pathways in osteogenic cells,modulator of LINE retroposons promoter activity

         Gene Ontology (GO): Selected molecular function terms (see all 16):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000976transcription regulatory region sequence-specific DNA binding ----
    GO:0001046core promoter sequence-specific DNA binding IDA--
    GO:0001077RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription IDA--
    GO:0001158enhancer sequence-specific DNA binding ISS--
    GO:0003677DNA binding ----
         
    Find genes that share ontologies with SOX9           About GenesLikeMe


    Phenotypes:
         1 GenomeRNAi human phenotype for SOX9:
     Increased gamma-H2AX phosphory 

         Selected MGI mutant phenotypes (inferred from 14 alleles(MGI details for Sox9) (see all 24):
     behavior/neurological  cardiovascular system  cellular  craniofacial  digestive/alimentary 
     embryogenesis  endocrine/exocrine gland  growth/size/body  hearing/vestibular/ear  hematopoietic system 
     homeostasis/metabolism  immune system  integument  limbs/digits/tail  mortality/aging 

    Find genes that share phenotypes with SOX9           About GenesLikeMe

    Animal Models:
         MGI mouse knock-outs for SOX9: Sox9tm2.1Crm Sox9tm1.1Gsr

       genOway: Develop your customized and physiologically relevant rodent model for SOX9

    miRNA
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    miRTarBase miRNAs that target SOX9:
    hsa-let-7b-5p (MIRT005049), hsa-mir-199a-5p (MIRT006193), hsa-mir-335-5p (MIRT017858), hsa-mir-1 (MIRT007222), hsa-mir-101-3p (MIRT007091)

    Block miRNA regulation of human, mouse, rat SOX9 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate SOX9 (see all 68):
    hsa-miR-582-3p hsa-miR-520f hsa-miR-300 hsa-miR-605 hsa-miR-485-3p hsa-miR-30d hsa-miR-3142 hsa-miR-30a
    SwitchGear 3'UTR luciferase reporter plasmidSOX9 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat SOX9

    Gene Editing
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    Clone
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    OriGene clones in human, mouse for SOX9 (see all 6)
    OriGene ORF clones in mouse, rat for SOX9
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector: SOX9 (NM_000346)
    Browse Sino Biological Human cDNA Clones
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for SOX9
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SOX9

    Cell Line
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    ESI BIO PureStem Progenitors for SOX9: 
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    PureStem E15, Meso-prx/latp Progenitor, PureStem MEL2, NCr-fac Progenitor,
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    In Situ Assay
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SOX9

    Flow Cytometry
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    eBioscience FlowRNA Probe Sets ( VA1-10452) for SOX9 


    (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
    SOX9_HUMAN, P48436: Nucleus (Potential)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    extracellular3
    cytoskeleton2
    plasma membrane1

    Gene Ontology (GO): 4 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA--
    GO:0005667transcription factor complex IEA--
    GO:0005730NOT nucleolus IDA--
    GO:0043234protein complex IDA--

    Find genes that share ontologies with SOX9           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 SOX9 About   (see all 7)  
    See pathways by source

    SuperPathContained pathways About
    1ERK Signaling
    Molecular Mechanisms of Cancer0.51
    2Wnt signaling pathway (KEGG)
    Wnt Signaling Pathway NetPath0.37
    3Spinal Cord Injury
    Spinal Cord Injury
    4Selected targets of ESR1
    Selected targets of ESR1
    5Selected targets of CREB1
    Selected targets of CREB1

    1 Downloadable PowerPoint Slide of GeneGlobe Pathway Central Maps for SOX9
        Molecular Mechanisms of Cancer

    4 BioSystems Pathways for SOX9
        Spinal Cord Injury
    Neural Crest Differentiation
    Endochondral Ossification
    Wnt Signaling Pathway NetPath


        Pathway & Disease-focused RT2 Profiler PCR Arrays including SOX9: 
              Osteogenesis in human mouse rat
              Notch Signaling Targets in human mouse rat
              Stem Cell Transcription Factors in human mouse rat
              WNT Signaling Targets in human mouse rat
              Mesenchymal Stem Cell in human mouse rat

    Interactions:

        GeneGlobe Interaction Network for SOX9

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

    Selected Interacting proteins for SOX9 (P484363 ENSP000002454794) via UniProtKB, MINT, STRING, and/or I2D (see all 41)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    HSPA1AP081073, ENSP000003648024I2D: score=3 STRING: ENSP00000364802
    ENSG00000212866P081073I2D: score=3 
    ENSG00000215328P081073I2D: score=3 
    ENSG00000224501P081073I2D: score=3 
    ENSG00000231555P081073I2D: score=3 
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 106):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001501skeletal system development IMP8640233
    GO:0001502cartilage condensation ISS--
    GO:0001503ossification IEA--
    GO:0001658branching involved in ureteric bud morphogenesis IEA--
    GO:0001708cell fate specification ISS--

    Find genes that share ontologies with SOX9           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 SOX9

    Selected Novoseek inferred chemical compound relationships for SOX9 gene (see all 21)    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    dmrt 70.8 2 16868052 (1), 19616114 (1)
    glycosaminoglycan 64.3 14 15639641 (2), 18163512 (1), 19096623 (1), 18985688 (1) (see all 11)
    alginate 53.1 3 19950204 (1), 15165474 (1), 17050539 (1)
    cmps 46.7 3 10213041 (1), 11076045 (1)
    testosterone 20.9 6 17234760 (2), 18190855 (2), 11097782 (1), 19535881 (1)
    ribonucleic acid 20.9 3 17518710 (1), 11710435 (1), 20157375 (1)
    chondroitin sulfate 18.3 8 18433381 (6)
    retinoic acid 16.5 17 19273910 (5), 19322650 (4), 10753864 (3), 15674337 (2) (see all 5)
    cytochalasin d 14.2 4 15665004 (1), 17050539 (1), 16565087 (1)
    dexamethasone 0.007 9 14753742 (3), 15734261 (3), 15009940 (1), 17690025 (1) (see all 5)



    Find genes that share compounds with SOX9           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 SOX9 gene: 
    NM_000346.3  

    Unigene Cluster for SOX9:

    SRY (sex determining region Y)-box 9
    Hs.647409  [show with all ESTs]
    Unigene Representative Sequence: NM_000346
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000245479(uc002jiw.3)
    miRNA
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    Selected qRT-PCR Assays for microRNAs that regulate SOX9 (see all 68):
    hsa-miR-582-3p hsa-miR-520f hsa-miR-300 hsa-miR-605 hsa-miR-485-3p hsa-miR-30d hsa-miR-3142 hsa-miR-30a
    SwitchGear 3'UTR luciferase reporter plasmidSOX9 3' UTR sequence
    Inhib. RNA
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    Primer
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      QuantiFast Probe-based Assays in human, mouse, rat SOX9
    Flow Cytometry
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    Additional mRNA sequence: 

    AK295455.1 BC007951.2 BC018276.1 BC056420.1 BT006875.1 Z46629.1 

    4 DOTS entries:

    DT.416519  DT.95288976  DT.40299601  DT.97818151 

    Selected AceView cDNA sequences (see all 205):

    BQ182292 W95308 BQ653032 AA778589 AA628091 CK570306 BE348559 AA400464 
    CA773373 BM845551 T24741 CK300183 W24710 BF343387 BQ045441 AW005563 
    BG697040 AW183687 CA773589 N92393 BC007951 AI572187 AA400739 AA983635 

    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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    SOX9 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TGTCATCCAT
    SOX9 Expression
    About this image


    SOX9 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 37) fully expand
     
     Cartilage (Muscoskeletal System)    fully expand to see all 95 entries
             Chondrocytes Nasal Capsule
             BMP2 induced Embryoid Bodies
             skeleton/cranium/viscerocranium   
     
     Bone (Muscoskeletal System)    fully expand to see all 96 entries
             Hypertrophic Chondrocytes Stylopod Growth Plate
             Endochondral Facial Bones
             HyStem+TGFbeta3+GDF5-induced SK11 cells
             sensory organ/ear/inner ear   
     
     Neural Crest (Gastrulation Derivatives)    fully expand to see all 19 entries
             Cardiac Neural Crest Cells Cardiac Neural Crest
             PureStem SK11, NCr-fac & Meso-prx Progenitor
             Neural crest-like cells
             skeleton/cranium/viscerocranium   
     
     Head Mesenchyme (Muscoskeletal System)    fully expand to see all 12 entries
             Osteochondro Progenitor Cells Branchial Arch 1
             Branchial Arch 1
     
     Epithelial Cells
             Adult Retinal Pigmented Epithelium Cells Retinal Pigmented Epithelium
    SOX9 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SOX9 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.647409
        Pathway & Disease-focused RT2 Profiler PCR Arrays including SOX9: 
              Osteogenesis in human mouse rat
              Notch Signaling Targets in human mouse rat
              Stem Cell Transcription Factors in human mouse rat
              WNT Signaling Targets in human mouse rat
              Mesenchymal Stem Cell in human mouse rat

    Primer
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    QuantiFast Probe-based Assays in human, mouse, rat SOX9
    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SOX9

    (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 SOX9 gene from Selected species (see all 15)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Sox91 , 5 SRY-box containing gene 95
    SRY (sex determining region Y)-box 91
    89.35(n)1
    92.9(a)1
      11 (77.27 cM)5
    206821  NM_011448.41  NP_035578.31 
     1127822245 
    chicken
    (Gallus gallus)
    Aves SOX91 SRY (sex determining region Y)-box 9 85.58(n)
    88.82(a)
      374148  NM_204281.1  NP_989612.1 
    lizard
    (Anolis carolinensis)
    Reptilia SOX96
    SRY (sex determining region Y)-box 9
    81(a)
    1 ↔ 1
    GL343258.1(704764-731268)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.16902 Xenopus laevis transcription factor SOX9 mRNA, complete cds less 79.19(n)    AY035397.1 
    zebrafish
    (Danio rerio)
    Actinopterygii sox9a2 SRY-box containing gene 9a 80.59(n)   60641  AF277096.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta Sox100B3 DNA bending 61(a)   100B2   --
    worm
    (Caenorhabditis elegans)
    Secernentea sox-46
    Protein SOX-4 (sox-4) mRNA, complete cds
    34(a)
    1 → many
    X(3505440-3506391) WBGene00015716


    ENSEMBL Gene Tree for SOX9 (if available)
    TreeFam Gene Tree for SOX9 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for SOX9 gene
    SOX132  SOX22  SOX42  SOX12  SOX142  SOX32  SOX122  SOX152  
    SOX182  SOX52  ENSG000002587242  SOX212  SOX172  SOX62  SOX112  SOX82  
    SRY2  SOX102  SOX72  
    3 SIMAP similar genes for SOX9 using alignment to 12 protein entries:     SOX9_HUMAN (see all proteins):
    SOX10    SOX8    FLJ00094

    Find genes that share paralogs with SOX9           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 SOX9 (see all 208)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 17 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs289402821,2,,4
    CCampomelic dysplasia (CMD1)4 pathogenic171203145(+) TGCAGC/TACAAG 2 H Y mis1 ese30--------
    VAR_0085304
    Campomelic dysplasia (CMD1)4--see VAR_0085302 A T mis40--------
    VAR_0037404
    Campomelic dysplasia (CMD1)4--see VAR_0037402 R P mis40--------
    VAR_0037364
    Campomelic dysplasia (CMD1)4--see VAR_0037362 F L mis40--------
    VAR_0037354
    Campomelic dysplasia (CMD1)4--see VAR_0037352 P L mis40--------
    VAR_0636434
    Campomelic dysplasia (CMD1)4--see VAR_0636432 M T mis40--------
    VAR_0636424
    Campomelic dysplasia (CMD1)4--see VAR_0636422 A E mis40--------
    VAR_0037384
    Campomelic dysplasia (CMD1)4--see VAR_0037382 A V mis40--------
    VAR_0636444
    Campomelic dysplasia (CMD1)4--see VAR_0636442 M V mis40--------
    VAR_0037394
    Campomelic dysplasia (CMD1)4--see VAR_0037392 W R mis40--------

    HapMap Linkage Disequilibrium report for SOX9 (70117161 - 70122561 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 1 variation for SOX9:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv833530CNV Gain+Loss17160897

    Human Gene Mutation Database (HGMD): SOX9
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing SOX9
    DNA2.0 Custom Variant and Variant Library Synthesis for SOX9

    (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: 608160   
    OMIM disorders: 114290  
    UniProtKB/Swiss-Prot: SOX9_HUMAN, P48436
  • Campomelic dysplasia (CMD1) [MIM:114290]: Rare, often lethal, dominantly inherited, congenital
    osteochondrodysplasia, associated with male-to-female autosomal sex reversal in two-thirds of the affected
    karyotypic males. A disease of the newborn characterized by congenital bowing and angulation of long bones,
    unusually small scapulae, deformed pelvis and spine and a missing pair of ribs. Craniofacial defects such as
    cleft palate, micrognathia, flat face and hypertelorism are common. Various defects of the ear are often evident,
    affecting the cochlea, malleus incus, stapes and tympanum. Most patients die soon after birth due to respiratory
    distress which has been attributed to hypoplasia of the tracheobronchial cartilage and small thoracic cage.
    Note=The disease is caused by mutations affecting the gene represented in this entry
  • 46,XX sex reversal 2 (SRXX2) [MIM:278850]: A condition in which male gonads develop in a genetic female
    (female to male sex reversal). Note=The disease is caused by mutations affecting the gene represented in this
    entry

  • 13 diseases for SOX9:    
    About MalaCards
    campomelic dysplasia with autosomal sex reversal    pierre robin sequence    campomelic dysplasia    isolated pierre robin syndrome
    inhalation anthrax    swyer syndrome    46xx sex reversal 1    chondroblastoma
    chondromyxoid fibroma    frasier syndrome    mesenchymal chondrosarcoma    mixed gonadal dysgenesis
    degenerative disc disease

    4 diseases from the University of Copenhagen DISEASES database for SOX9:
    Campomelic dysplasia     Osteoarthritis     Gonadal dysgenesis     Chondrosarcoma

    Find genes that share disorders with SOX9           About GenesLikeMe

    Selected Novoseek inferred disease relationships for SOX9 gene (see all 28)    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    campomelic dysplasia 97.1 84 10072439 (3), 8894698 (2), 10364523 (2), 16467253 (2) (see all 55)
    osteochondrodysplasias 56.9 1 11008738 (1)
    swyer syndrome 56.1 2 9002675 (1)
    skeletal dysplasia 54.3 3 20392266 (1), 9119111 (1)
    osteoarthritis 52.5 5 17935617 (2), 17968906 (1), 20196777 (1), 18550917 (1)
    virilization 48.1 1 9452059 (1)
    pierre robin sequence 45.3 3 17551083 (2), 19473998 (1)
    chondrosarcoma 44.6 7 20039424 (2), 12681949 (2), 12673561 (1), 18438857 (1) (see all 5)
    dwarfism 44.2 2 8782821 (1), 11430871 (1)
    achondroplasia 43.5 1 10980415 (1)

    GeneTests: SOX9
    GeneReviews: SOX9
    Genetic Association Database (GAD): SOX9
    Human Genome Epidemiology (HuGE) Navigator: SOX9 (5 documents)

    Export disorders for SOX9 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 SOX9 gene, integrated from 10 sources (see all 519):
    (articles sorted by number of sources associating them with SOX9)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Compound effects of point mutations causing campomelic dysplasia/autosomal sex reversal upon SOX9 structure, nuclear transport, DNA binding, and transcriptional activation. (PubMed id 11323423)1, 2, 9 Preiss S.... Harley V.R. (J. Biol. Chem. 2001)
    2. Mutations in SOX9, the gene responsible for Campomelic dysplasia and autosomal sex reversal. (PubMed id 7485151)1, 2, 9 Kwok C.... Schafer A.J. (Am. J. Hum. Genet. 1995)
    3. Mutation analysis of five candidate genes in Chinese patients with hypospadias. (PubMed id 15266301)1, 4, 9 Wang Y....Shen Y. (Eur. J. Hum. Genet. 2004)
    4. Autosomal sex reversal and campomelic dysplasia are caused by mutations in and around the SRY-related gene SOX9. (PubMed id 8001137)1, 2, 9 Wagner T.... Scherer G. (Cell 1994)
    5. Heterozygous SOX9 mutations allowing for residual DNA-binding and transcriptional activation lead to the acampomelic variant of campomelic dysplasia. (PubMed id 20513132)1, 2, 9 Staffler A.... Holzinger A. (Hum. Mutat. 2010)
    6. Mutation analysis of SOX9 and single copy number variant analysis of the upstream region in eight patients with campomelic dysplasia and acampomelic campomelic dysplasia. (PubMed id 19921652)1, 2, 9 Wada Y.... Ogata T. (Am. J. Med. Genet. A 2009)
    7. Loss of DNA-dependent dimerization of the transcription factor SOX9 as a cause for campomelic dysplasia. (PubMed id 12783851)1, 2, 9 Sock E.... Scherer G. (Hum. Mol. Genet. 2003)
    8. Acampomelic campomelic dysplasia with SOX9 mutation. (PubMed id 10951468)1, 2, 9 Thong M.-K.... Morris L. (Am. J. Med. Genet. 2000)
    9. Functional and structural studies of wild type SOX9 and mutations causing campomelic dysplasia. (PubMed id 10446171)1, 2, 9 McDowall S.... Harley V. (J. Biol. Chem. 1999)
    10. Mutational analysis of the SOX9 gene in campomelic dysplasia and autosomal sex reversal: lack of genotype/phenotype correlations. (PubMed id 9002675)1, 2, 9 Meyer J.... Scherer G. (Hum. Mol. Genet. 1997)

    (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: 6662 HGNC: 11204 AceView: SOX9 Ensembl:ENSG00000125398 euGenes: HUgn6662
    ECgene: SOX9 H-InvDB: SOX9

    (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 SOX9 Pharmacogenomics, SNPs, Pathways
    GeneReviewshttp://www.ncbi.nlm.nih.gov/books/NBK1116/?term=SOX9[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 SOX9 gene:
    Search GeneIP for patents involving SOX9

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



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