Atlas of Genetics and Cytogenetics in Oncology and Haematology


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SOX9 (SRY-box 9)

Identity

Other namesCMD1
CMPD1
SRA1
SRXX2
SRXY10
HGNC (Hugo) SOX9
LocusID (NCBI) 6662
Atlas_Id 43993
Location 17q24.3  [Link to chromosome band 17q24]
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

 


Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 0 ]
  Colon: Colorectal adenocarcinoma

External links

Nomenclature
HGNC (Hugo)SOX9   11204
Cards
Entrez_Gene (NCBI)SOX9  6662  SRY-box 9
AliasesCMD1; CMPD1; SRA1; SRXX2; 
SRXY10
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
TCGA 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   616425   
Gene and transcription
Genbank (Entrez)AK295455 BC007951 BC018276 BC056420 BT006875
RefSeq transcript (Entrez)NM_000346
RefSeq genomic (Entrez)NC_000017 NC_018928 NG_012490 NT_010783 NW_004929407
Consensus coding sequences : CCDS (NCBI)SOX9
Cluster EST : UnigeneHs.647409 [ NCBI ]
CGAP (NCI)Hs.647409
Alternative Splicing GalleryENSG00000125398
Gene ExpressionSOX9 [ NCBI-GEO ]   SOX9 [ EBI - ARRAY_EXPRESS ]   SOX9 [ SEEK ]   SOX9 [ MEM ]
Gene Expression Viewer (FireBrowse)SOX9 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)6662
GTEX Portal (Tissue expression)SOX9
Protein : pattern, domain, 3D structure
UniProt/SwissProtP48436 (Uniprot)
NextProtP48436  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP48436
Splice isoforms : SwissVarP48436 (Swissvar)
PhosPhoSitePlusP48436
Domaine pattern : Prosite (Expaxy)HMG_BOX_2 (PS50118)   
Domains : Interpro (EBI)HMG_box_dom    SOX-9    Sox_N   
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)SOX9
PDB (SRS)1S9M    1SX9    4EUW   
PDB (PDBSum)1S9M    1SX9    4EUW   
PDB (IMB)1S9M    1SX9    4EUW   
PDB (RSDB)1S9M    1SX9    4EUW   
Structural Biology KnowledgeBase1S9M    1SX9    4EUW   
SCOP (Structural Classification of Proteins)1S9M    1SX9    4EUW   
CATH (Classification of proteins structures)1S9M    1SX9    4EUW   
SuperfamilyP48436
Human Protein AtlasENSG00000125398
Peptide AtlasP48436
HPRD06427
IPIIPI00009713   IPI00909150   
Protein Interaction databases
DIP (DOE-UCLA)P48436
IntAct (EBI)P48436
FunCoupENSG00000125398
BioGRIDSOX9
STRING (EMBL)SOX9
ZODIACSOX9
Ontologies - Pathways
QuickGOP48436
Ontology : AmiGOnegative regulation of transcription from RNA polymerase II promoter  core promoter sequence-specific DNA binding  transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding  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  transcription factor activity, sequence-specific DNA binding  transcription factor activity, sequence-specific DNA binding  transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding  protein kinase activity  protein binding  nucleus  nucleoplasm  nucleoplasm  nucleosome assembly  chromatin remodeling  transcription from RNA polymerase II promoter  transcription from RNA polymerase II promoter  protein complex assembly  cytoskeleton organization  signal transduction  epidermal growth factor receptor signaling pathway  Notch 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  single organismal cell-cell adhesion  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  negative regulation of epithelial cell differentiation  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  protein localization to nucleus  somatic stem cell population 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  nuclear transcription factor complex  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  protein heterodimerization activity  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 tube branching involved in lung morphogenesis  lung epithelial cell differentiation  epithelial cell proliferation involved in prostatic bud elongation  bronchus cartilage development  trachea cartilage development  intestinal epithelial structure maintenance  regulation of cell proliferation involved in tissue homeostasis  positive regulation of cartilage development  regulation of branching involved in lung morphogenesis  morphogenesis of a branching epithelium  lung smooth muscle development  negative regulation of biomineral tissue development  ERK1 and ERK2 cascade  Harderian gland development  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 smooth muscle cell differentiation  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  pre-mRNA intronic binding  positive regulation of extracellular matrix assembly  positive regulation of male gonad development  positive regulation of cell proliferation involved in heart morphogenesis  positive regulation of mesenchymal stem cell differentiation  regulation of epithelial cell proliferation involved in lung morphogenesis  negative regulation of mesenchymal cell apoptotic process  
Ontology : EGO-EBInegative regulation of transcription from RNA polymerase II promoter  core promoter sequence-specific DNA binding  transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding  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  transcription factor activity, sequence-specific DNA binding  transcription factor activity, sequence-specific DNA binding  transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding  protein kinase activity  protein binding  nucleus  nucleoplasm  nucleoplasm  nucleosome assembly  chromatin remodeling  transcription from RNA polymerase II promoter  transcription from RNA polymerase II promoter  protein complex assembly  cytoskeleton organization  signal transduction  epidermal growth factor receptor signaling pathway  Notch 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  single organismal cell-cell adhesion  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  negative regulation of epithelial cell differentiation  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  protein localization to nucleus  somatic stem cell population 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  nuclear transcription factor complex  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  protein heterodimerization activity  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 tube branching involved in lung morphogenesis  lung epithelial cell differentiation  epithelial cell proliferation involved in prostatic bud elongation  bronchus cartilage development  trachea cartilage development  intestinal epithelial structure maintenance  regulation of cell proliferation involved in tissue homeostasis  positive regulation of cartilage development  regulation of branching involved in lung morphogenesis  morphogenesis of a branching epithelium  lung smooth muscle development  negative regulation of biomineral tissue development  ERK1 and ERK2 cascade  Harderian gland development  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 smooth muscle cell differentiation  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  pre-mRNA intronic binding  positive regulation of extracellular matrix assembly  positive regulation of male gonad development  positive regulation of cell proliferation involved in heart morphogenesis  positive regulation of mesenchymal stem cell differentiation  regulation of epithelial cell proliferation involved in lung morphogenesis  negative regulation of mesenchymal cell apoptotic process  
NDEx NetworkSOX9
Atlas of Cancer Signalling NetworkSOX9
Wikipedia pathwaysSOX9
Orthology - Evolution
OrthoDB6662
GeneTree (enSembl)ENSG00000125398
Phylogenetic Trees/Animal Genes : TreeFamSOX9
Homologs : HomoloGeneSOX9
Homology/Alignments : Family Browser (UCSC)SOX9
Gene fusions - Rearrangements
Polymorphisms : SNP, variants
NCBI Variation ViewerSOX9 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SOX9
dbVarSOX9
ClinVarSOX9
1000_GenomesSOX9 
Exome Variant ServerSOX9
ExAC (Exome Aggregation Consortium)SOX9 (select the gene name)
Genetic variants : HAPMAP6662
Genomic Variants (DGV)SOX9 [DGVbeta]
Mutations
ICGC Data PortalSOX9 
TCGA Data PortalSOX9 
Broad Tumor PortalSOX9
OASIS PortalSOX9 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICSOX9 
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
BioMutasearch SOX9
DgiDB (Drug Gene Interaction Database)SOX9
DoCM (Curated mutations)SOX9 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SOX9 (select a term)
intoGenSOX9
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
Diseases
DECIPHER (Syndromes)17:70117161-70122560  ENSG00000125398
CONAN: Copy Number AnalysisSOX9 
Mutations and Diseases : HGMDSOX9
OMIM114290    608160    616425   
MedgenSOX9
Genetic Testing Registry SOX9
NextProtP48436 [Medical]
TSGene6662
GENETestsSOX9
Huge Navigator SOX9 [HugePedia]
snp3D : Map Gene to Disease6662
BioCentury BCIQSOX9
ClinGenSOX9
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD6662
Chemical/Pharm GKB GenePA36041
Clinical trialSOX9
Miscellaneous
canSAR (ICR)SOX9 (select the gene name)
Probes
Litterature
PubMed252 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineSOX9
EVEXSOX9
GoPubMedSOX9
iHOPSOX9
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

Search in all EBI   NCBI

© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Mon Sep 19 19:14:30 CEST 2016

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