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SOX9 (SRY (sex determining region Y)-box 9)

Identity

Other namesCMD1
CMPD1
SRA1
HGNC (Hugo) SOX9
LocusID (NCBI) 6662
Location 17q24.3
Location_base_pair Starts at 70117161 and ends at 70122560 bp from pter ( according to hg19-Feb_2009)
Note

Non-annotated gene. Preliminary data : if you are an author
who wish to write a full paper/card on this gene, go to  How to contribute

DNA/RNA

 

External links

Nomenclature
HGNC (Hugo)SOX9   11204
Cards
Entrez_Gene (NCBI)SOX9  6662  SRY (sex determining region Y)-box 9
GeneCards (Weizmann)SOX9
Ensembl hg19 (Hinxton)ENSG00000125398 [Gene_View]  chr17:70117161-70122560 [Contig_View]  SOX9 [Vega]
Ensembl hg38 (Hinxton)ENSG00000125398 [Gene_View]  chr17:70117161-70122560 [Contig_View]  SOX9 [Vega]
ICGC DataPortalENSG00000125398
cBioPortalSOX9
AceView (NCBI)SOX9
Genatlas (Paris)SOX9
WikiGenes6662
SOURCE (Princeton)SOX9
Genomic and cartography
GoldenPath hg19 (UCSC)SOX9  -     chr17:70117161-70122560 +  17q24.3   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)SOX9  -     17q24.3   [Description]    (hg38-Dec_2013)
EnsemblSOX9 - 17q24.3 [CytoView hg19]  SOX9 - 17q24.3 [CytoView hg38]
Mapping of homologs : NCBISOX9 [Mapview hg19]  SOX9 [Mapview hg38]
OMIM114290   608160   
Gene and transcription
Genbank (Entrez)AK295455 BC007951 BC018276 BC056420 BT006875
RefSeq transcript (Entrez)NM_000346
RefSeq genomic (Entrez)AC_000149 NC_000017 NC_018928 NG_012490 NT_010783 NW_001838454 NW_004929407
Consensus coding sequences : CCDS (NCBI)SOX9
Cluster EST : UnigeneHs.647409 [ NCBI ]
CGAP (NCI)Hs.647409
Alternative Splicing : Fast-db (Paris)GSHG0012778
Alternative Splicing GalleryENSG00000125398
Gene ExpressionSOX9 [ NCBI-GEO ]     SOX9 [ SEEK ]   SOX9 [ MEM ]
SOURCE (Princeton)Expression in : [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP48436 (Uniprot)
NextProtP48436  [Medical]
With graphics : InterProP48436
Splice isoforms : SwissVarP48436 (Swissvar)
Domaine pattern : Prosite (Expaxy)HMG_BOX_2 (PS50118)   
Domains : Interpro (EBI)HMG_box_dom    Sox_N   
Related proteins : CluSTrP48436
Domain families : Pfam (Sanger)HMG_box (PF00505)    Sox_N (PF12444)   
Domain families : Pfam (NCBI)pfam00505    pfam12444   
Domain families : Smart (EMBL)HMG (SM00398)  
DMDM Disease mutations6662
Blocks (Seattle)P48436
PDB (SRS)1S9M    1SX9    4EUW   
PDB (PDBSum)1S9M    1SX9    4EUW   
PDB (IMB)1S9M    1SX9    4EUW   
PDB (RSDB)1S9M    1SX9    4EUW   
Human Protein AtlasENSG00000125398
Peptide AtlasP48436
HPRD06427
IPIIPI00009713   IPI00909150   
Protein Interaction databases
DIP (DOE-UCLA)P48436
IntAct (EBI)P48436
FunCoupENSG00000125398
BioGRIDSOX9
IntegromeDBSOX9
STRING (EMBL)SOX9
Ontologies - Pathways
QuickGOP48436
Ontology : AmiGOcore promoter sequence-specific DNA binding  RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription  enhancer sequence-specific DNA binding  skeletal system development  cartilage condensation  ossification  branching involved in ureteric bud morphogenesis  cell fate specification  epithelial to mesenchymal transition  tissue homeostasis  positive regulation of protein phosphorylation  hair follicle development  positive regulation of mesenchymal cell proliferation  negative regulation of immune system process  heart valve development  heart valve morphogenesis  heart valve formation  endocardial cushion morphogenesis  chondrocyte differentiation involved in endochondral bone morphogenesis  chondrocyte hypertrophy  chromatin binding  sequence-specific DNA binding transcription factor activity  sequence-specific DNA binding transcription factor activity  RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity  protein kinase activity  protein binding  nucleus  transcription factor complex  nucleolus  nucleosome assembly  chromatin remodeling  transcription from RNA polymerase II promoter  transcription from RNA polymerase II promoter  protein complex assembly  protein phosphorylation  signal transduction  epidermal growth factor receptor signaling pathway  spermatogenesis  beta-catenin binding  positive regulation of cell proliferation  male gonad development  male gonad development  regulation of cell cycle process  positive regulation of epithelial cell migration  neural crest cell development  positive regulation of phosphatidylinositol 3-kinase signaling  male germ-line sex determination  cAMP-mediated signaling  regulation of cell adhesion  extracellular matrix organization  negative regulation of ossification  negative regulation of bone mineralization  prostate gland development  positive regulation of epithelial cell differentiation  mammary gland development  notochord development  otic vesicle formation  endocrine pancreas development  negative regulation of chondrocyte differentiation  positive regulation of chondrocyte differentiation  positive regulation of chondrocyte differentiation  protein kinase A catalytic subunit binding  somatic stem cell maintenance  enhancer binding  intrahepatic bile duct development  regulation of cell proliferation  regulation of apoptotic process  negative regulation of apoptotic process  negative regulation of apoptotic process  protein complex  bHLH transcription factor binding  protein kinase B signaling  negative regulation of myoblast differentiation  positive regulation of protein catabolic process  negative regulation of transcription, DNA-templated  positive regulation of transcription, DNA-templated  positive regulation of transcription, DNA-templated  positive regulation of transcription from RNA polymerase II promoter  negative regulation of photoreceptor cell differentiation  oligodendrocyte differentiation  positive regulation of epithelial cell proliferation  positive regulation of epithelial cell proliferation  negative regulation of epithelial cell proliferation  cartilage development  Sertoli cell differentiation  Sertoli cell development  astrocyte fate commitment  retina development in camera-type eye  limb bud formation  retinal rod cell differentiation  epithelial cell proliferation involved in prostatic bud elongation  intestinal epithelial structure maintenance  regulation of cell proliferation involved in tissue homeostasis  positive regulation of cartilage development  morphogenesis of a branching epithelium  negative regulation of biomineral tissue development  ERK1 and ERK2 cascade  cellular response to mechanical stimulus  cellular response to retinoic acid  cellular response to interleukin-1  cellular response to epidermal growth factor stimulus  cellular response to heparin  cellular response to transforming growth factor beta stimulus  renal vesicle induction  ureter urothelium development  ureter morphogenesis  metanephric nephron tubule formation  negative regulation of canonical Wnt signaling pathway  cochlea morphogenesis  positive regulation of kidney development  positive regulation of branching involved in ureteric bud morphogenesis  positive regulation of male gonad development  positive regulation of cell proliferation involved in heart morphogenesis  positive regulation of mesenchymal stem cell differentiation  
Ontology : EGO-EBIcore promoter sequence-specific DNA binding  RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription  enhancer sequence-specific DNA binding  skeletal system development  cartilage condensation  ossification  branching involved in ureteric bud morphogenesis  cell fate specification  epithelial to mesenchymal transition  tissue homeostasis  positive regulation of protein phosphorylation  hair follicle development  positive regulation of mesenchymal cell proliferation  negative regulation of immune system process  heart valve development  heart valve morphogenesis  heart valve formation  endocardial cushion morphogenesis  chondrocyte differentiation involved in endochondral bone morphogenesis  chondrocyte hypertrophy  chromatin binding  sequence-specific DNA binding transcription factor activity  sequence-specific DNA binding transcription factor activity  RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity  protein kinase activity  protein binding  nucleus  transcription factor complex  nucleolus  nucleosome assembly  chromatin remodeling  transcription from RNA polymerase II promoter  transcription from RNA polymerase II promoter  protein complex assembly  protein phosphorylation  signal transduction  epidermal growth factor receptor signaling pathway  spermatogenesis  beta-catenin binding  positive regulation of cell proliferation  male gonad development  male gonad development  regulation of cell cycle process  positive regulation of epithelial cell migration  neural crest cell development  positive regulation of phosphatidylinositol 3-kinase signaling  male germ-line sex determination  cAMP-mediated signaling  regulation of cell adhesion  extracellular matrix organization  negative regulation of ossification  negative regulation of bone mineralization  prostate gland development  positive regulation of epithelial cell differentiation  mammary gland development  notochord development  otic vesicle formation  endocrine pancreas development  negative regulation of chondrocyte differentiation  positive regulation of chondrocyte differentiation  positive regulation of chondrocyte differentiation  protein kinase A catalytic subunit binding  somatic stem cell maintenance  enhancer binding  intrahepatic bile duct development  regulation of cell proliferation  regulation of apoptotic process  negative regulation of apoptotic process  negative regulation of apoptotic process  protein complex  bHLH transcription factor binding  protein kinase B signaling  negative regulation of myoblast differentiation  positive regulation of protein catabolic process  negative regulation of transcription, DNA-templated  positive regulation of transcription, DNA-templated  positive regulation of transcription, DNA-templated  positive regulation of transcription from RNA polymerase II promoter  negative regulation of photoreceptor cell differentiation  oligodendrocyte differentiation  positive regulation of epithelial cell proliferation  positive regulation of epithelial cell proliferation  negative regulation of epithelial cell proliferation  cartilage development  Sertoli cell differentiation  Sertoli cell development  astrocyte fate commitment  retina development in camera-type eye  limb bud formation  retinal rod cell differentiation  epithelial cell proliferation involved in prostatic bud elongation  intestinal epithelial structure maintenance  regulation of cell proliferation involved in tissue homeostasis  positive regulation of cartilage development  morphogenesis of a branching epithelium  negative regulation of biomineral tissue development  ERK1 and ERK2 cascade  cellular response to mechanical stimulus  cellular response to retinoic acid  cellular response to interleukin-1  cellular response to epidermal growth factor stimulus  cellular response to heparin  cellular response to transforming growth factor beta stimulus  renal vesicle induction  ureter urothelium development  ureter morphogenesis  metanephric nephron tubule formation  negative regulation of canonical Wnt signaling pathway  cochlea morphogenesis  positive regulation of kidney development  positive regulation of branching involved in ureteric bud morphogenesis  positive regulation of male gonad development  positive regulation of cell proliferation involved in heart morphogenesis  positive regulation of mesenchymal stem cell differentiation  
Protein Interaction DatabaseSOX9
DoCM (Curated mutations)SOX9
Wikipedia pathwaysSOX9
Gene fusion - rearrangements
Polymorphisms : SNP, variants
NCBI Variation ViewerSOX9 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SOX9
dbVarSOX9
ClinVarSOX9
1000_GenomesSOX9 
Exome Variant ServerSOX9
SNP (GeneSNP Utah)SOX9
SNP : HGBaseSOX9
Genetic variants : HAPMAPSOX9
Genomic VariantsSOX9  SOX9 [DGVbeta]
Mutations
ICGC Data PortalENSG00000125398 
Somatic Mutations in Cancer : COSMICSOX9 
CONAN: Copy Number AnalysisSOX9 
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
Diseases
DECIPHER (Syndromes)17:70117161-70122560
Mutations and Diseases : HGMDSOX9
OMIM114290    608160   
MedgenSOX9
NextProtP48436 [Medical]
GENETestsSOX9
Disease Genetic AssociationSOX9
Huge Navigator SOX9 [HugePedia]  SOX9 [HugeCancerGEM]
snp3D : Map Gene to Disease6662
DGIdb (Drug Gene Interaction db)SOX9
General knowledge
Homologs : HomoloGeneSOX9
Homology/Alignments : Family Browser (UCSC)SOX9
Phylogenetic Trees/Animal Genes : TreeFamSOX9
Chemical/Protein Interactions : CTD6662
Chemical/Pharm GKB GenePA36041
Clinical trialSOX9
Cancer Resource (Charite)ENSG00000125398
Other databases
Probes
Litterature
PubMed209 Pubmed reference(s) in Entrez
CoreMineSOX9
GoPubMedSOX9
iHOPSOX9
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

Search in all EBI   NCBI

Contributor(s)

Written09-2002Dessen P, Le Minor S
Updated12-2014Dessen P

© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Sun Dec 21 01:40:16 CET 2014

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