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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

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 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)
About This Section

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, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

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, and campomelic dysplasia with autosomal sex reversal, and among its related super-pathways are Rho Family GTPases and Wnt signaling pathway. 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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000017.10  NC_018928.2  NT_010783.15  
Regulatory elements:
   SABiosciences 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 SABiosciences Chromatin IP Primers for SOX9

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SOX9


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

Entrez Gene cytogenetic band: 17q23   Ensembl cytogenetic band:  17q24.3   HGNC cytogenetic band: 17q23

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 UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: SOX9_HUMAN, P48436 (See protein sequence)
Recommended Name: Transcription factor SOX-9  
Size: 509 amino acids; 56137 Da
Subcellular location: Nucleus (Potential)
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:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_P48436

  • SOX9 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    SOX9 Protein Expression
    REFSEQ proteins: NP_000337.1  
    ENSEMBL proteins: 
     ENSP00000245479  

    Human Recombinant Protein Products for SOX9: 
    Browse Purified and Recombinant Proteins at EMD Millipore
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    OriGene Protein Over-expression Lysate for SOX9
    OriGene MassSpec for SOX9 
    OriGene Custom Protein Services for SOX9
    GenScript Custom Purified and Recombinant Proteins Services for SOX9
    Novus Biologicals SOX9 Proteins
    Novus Biologicals SOX9 Lysate
    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates 
    ProSpec Recombinant Protein for SOX9
    Cloud-Clone Corp. Proteins for SOX9 

    Gene Ontology (GO): 4 cellular component terms (GO ID links to tree view):    About this table

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

    SOX9 for ontologies           About GeneDecksing



    SOX9 Antibody Products: 
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    LSBio Antibodies in human, mouse, rat for SOX9 

    Assay Products for SOX9: 
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    Browse Enzo Life Sciences for kits & assays
    Cloud-Clone Corp. ELISAs for SOX9 
    Cloud-Clone Corp. CLIAs for SOX9


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    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


    SOX9 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,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    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): 5/16 molecular function terms (GO ID links to tree view) (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 ----
         
    SOX9 for ontologies           About GeneDecksing


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

         15/24 MGI mutant phenotypes (inferred from 13 alleles(MGI details for Sox9) (see all 24):
     behavior/neurological  cardiovascular system  cellular  craniofacial  digestive/alimentary 
     embryogenesis  endocrine/exocrine gland  growth/size  hearing/vestibular/ear  hematopoietic system 
     homeostasis/metabolism  immune system  integument  limbs/digits/tail  mortality/aging 

    SOX9 for phenotypes           About GeneDecksing

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

       inGenious Targeting Laboratory - Custom generated mouse model solutions for SOX9 
       inGenious Targeting Laboratory - Custom generated inducible mouse model solutions for SOX9

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for SOX9 
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for SOX9 

    miRNA
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    miRTarBase miRNAs that target SOX9:
    hsa-let-7b (MIRT005049)

    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat SOX9
    8/68 QIAGEN miScript miRNA 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
    Products:
        
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    OriGene RNAi products in human, mouse, rat for SOX9
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    Gene Editing
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    Clone
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    Browse Sino Biological Human cDNA Clones
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SOX9
    Sirion Biotech Customized lentivirus for stable overexpression of SOX9 
                         Customized lentivirus expression plasmids for stable overexpression of SOX9 

    Cell Line
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    GenScript Custom overexpressing Cell Line Services for SOX9
    LifeMap BioReagents: cell lines associated with SOX9: PureStem 4D20.8, NCr-fac Progenitor,
    PureStem 7SMOO32, NCr-fac & Meso Progenitor, PureStem E15, Meso-prx/latp Progenitor,
    PureStem MEL2, NCr-fac Progenitor, PureStem SK11, NCr-fac & Meso-prx Progenitor,
    PureStem SM30, NCr-fac & Meso-latp Progenitor
    In Situ Assay
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SOX9


    (Pathways according to EMD Millipore, 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 SABiosciences, 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 Oct 2013 via Entrez Gene).
    About This Section

    SuperPaths for SOX9 About   (see all 7)                                                                                              See pathways by source

    SuperPathContained pathways About
    1Rho Family GTPases
    Molecular Mechanisms of Cancer0.51
    2Wnt signaling pathway
    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

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    2 EMD Millipore Pathways for SOX9
        Selected targets of CREB1
    Selected targets of ESR1

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

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



    SOX9 for pathways           About GeneDecksing

    Interactions:

        SABiosciences Gene Network CentralTM Interacting Genes and Proteins Network for SOX9

    STRING Interaction Network Preview (showing 5 interactants - click image to see 19)

    5/33 Interacting proteins for SOX9 (P484363 ENSP000002454794) via UniProtKB, MINT, STRING, and/or I2D (see all 33)
    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): 5/105 biological process terms (GO ID links to tree view) (see all 105):    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--

    SOX9 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section

    SOX9 for compounds           About GeneDecksing

    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for SOX9

    10/21 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)

    Search CenterWatch for drugs/clinical trials and news about SOX9

    (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,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    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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    8/68 QIAGEN miScript miRNA 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
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat SOX9
      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat SOX9

    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 

    24/205 AceView cDNA sequences (see all 205):

    BM762705 AA628091 AA983635 CA773373 BF343387 BU076661 AA778589 CA773589 
    AV681764 AA535677 BC007951 AA975310 AI572187 AA778708 W95308 AW183687 
    BQ774016 T24741 AA912521 BM698241 BQ182292 CK570306 BM698976 BQ045441 

    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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    SOX9 expression in normal human tissues (normalized intensities)      SOX9 embryonic expression: see
    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 
     5/50 selected tissues (see all 50) fully expand
     
     Cartilage (Muscoskeletal System)    fully expand to see all 108 entries
             Chondrocytes Nasal Capsule
             BMP2 induced Embryoid Bodies ( Generation of fibrocartilage-like constructs )
             sensory organ/nose/nasal septum   
     
     Bone (Muscoskeletal System)    fully expand to see all 105 entries
             Hypertrophic Chondrocytes Stylopod Growth Plate
             Endochondral Facial Bones
             HyStem+TGFbeta3+GDF5-induced SK11 cells
             skeleton/cranium/viscerocranium   
     
     Brain (Nervous System)    fully expand to see all 31 entries
             Oligodendrocyte Precursor Cells Spinal Cord White Matter
             Thalamus
             N2/LSB/S/F8-induced cells ( Generation of midbrain dopaminergic, forebrain and hypothalamic...
             Fetal Neuronal Stem Cells (NSC)   
             Septum   
     
     Pancreas (Endocrine System)    fully expand to see all 18 entries
             Bipotent Endocrine/Duct Progenitor Cells Dorsal Pancreatic Bud
             Posterior foregut-like cells ( A scalable, suspension protocol for derivation of...
             pancreas ; exocrine glandular cells   
     
     Neural Crest (Gastrulation Derivatives)    fully expand to see all 17 entries
             Cardiac Neural Crest Cells Cardiac Neural Crest
             PureStem SK11, NCr-fac & Meso-prx Progenitor
             skeleton/cranium/viscerocranium   

    See SOX9 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for SOX9

    SOURCE GeneReport for Unigene cluster: Hs.647409
        SABiosciences Expression via Pathway-Focused 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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    QIAGEN 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)
    About This Section

    This gene was present in the common ancestor of animals.

    Orthologs for SOX9 gene from 6/14 species (see all 14)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Sox91 , 5 SRY-box containing gene 91, 5 91.58(n)1
    97.44(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 86.4(n)
    90.06(a)
      374148  NM_204281.1  NP_989612.1 
    lizard
    (Anolis carolinensis)
    Reptilia SOX96
    Uncharacterized protein
    80(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 Sox100B1 , 3 DNA bending3
    CG15552-PA1
    61(a)3
    50.64(n)1
    38.89(a)1
      100B23
    450391  NM_143582.11  NP_651839.11 


    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)
    About This Section
    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 1 protein entry:     SOX9_HUMAN:
    SOX10    SOX8    FLJ00094

    SOX9 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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/208 SNPs in SOX9 are shown (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
    ----------
    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--------
    VAR_0636474
    Campomelic dysplasia (CMD1)4--see VAR_0636472 K E 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
    SABiosciences Cancer Mutation 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, Conferences by KenesGroup, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    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

  • 20/60 diseases for SOX9 (see all 60):    About MalaCards
    campomelic dysplasia    campomelic dysplasia with autosomal sex reversal    pierre robin sequence    mesenchymal chondrosarcoma
    46xx true true hermaphroditism    chondroblastoma    swyer syndrome    degenerative disc disease
    frasier syndrome    mobius syndrome    osteochondrodysplasia    chordoma
    hypertrichosis    achondroplasia    sertoli cell tumor    disorders of sex development
    skeletal dysplasias    dwarfism    dysgerminoma    nephrocalcinosis

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

    SOX9 for disorders           About GeneDecksing

    10/28 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)
    About This Section

    PubMed articles for SOX9 gene, integrated from 9 sources (see all 508):
    (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. (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. (1995)
    3. Mutation analysis of five candidate genes in Chinese patients with hypospadias. (PubMed id 15266301)1, 4, 9 Wang Y....Shen Y. (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. (1994)
    5. Heterozygous SOX9 mutations allowing for residual DNA -binding and transcriptional activation lead to the acampomelic variant of camp omelic dysplasia. (PubMed id 20513132)1, 2, 9 Staffler A....Holzinger A. (2010)
    6. Mutation analysis of SOX9 and single copy number vari ant 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. (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. (2003)
    8. Acampomelic campomelic dysplasia with SOX9 mutation. (PubMed id 10951468)1, 2, 9 Thong M.K....Morris L. (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. (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. (1997)

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

      Query String
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 6662 HGNC: 11204 AceView: SOX9 Ensembl:ENSG00000125398 euGenes: HUgn6662
    ECgene: SOX9 H-InvDB: SOX9

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for SOX9 Pharmacogenomics, SNPs, Pathways
    GeneReviewshttp://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/SOX9

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    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



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
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    About This Section

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     Proteins for SOX9
     Antibodies for SOX9
     ELISAs for SOX9
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     Cell Lines associated with SOX9: PureStem 4D20.8, NCr-fac Progenitor,
    PureStem 7SMOO32, NCr-fac & Meso Progenitor, PureStem E15, Meso-prx/latp Progenitor,
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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 4 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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