SOX17 (SRY-box 17)

1. Identity

Alias_names
General Information
SRY box 17
Other aliasVUR3
HGNC (Hugo) SOX17
LocusID (NCBI) 64321
Atlas_Id 50199
Location 8q11.23  [Link to chromosome band 8q11]
Location_base_pair Starts at 54457935 and ends at 54460896 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2017)		Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)

2. DNA/RNA

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

 

3. External links

Nomenclature
HGNC (Hugo)SOX17   18122
Cards
Entrez_Gene (NCBI)SOX17  64321  SRY-box 17
AliasesVUR3
GeneCards (Weizmann)SOX17
Ensembl hg19 (Hinxton)ENSG00000164736 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000164736 [Gene_View] &nbspENSG00000164736 [Sequence]  chr8:54457935-54460896 [Contig_View]  SOX17 [Vega]
ICGC DataPortalENSG00000164736
TCGA cBioPortalSOX17
AceView (NCBI)SOX17
Genatlas (Paris)SOX17
WikiGenes64321
SOURCE (Princeton)SOX17
Genetics Home Reference (NIH)SOX17
Genomic and cartography
GoldenPath hg38 (UCSC)SOX17  -     chr8:54457935-54460896 +  8q11.23   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)SOX17  -     8q11.23   [Description]    (hg19-Feb_2009)
EnsemblSOX17 - 8q11.23 [CytoView hg19]  SOX17 - 8q11.23 [CytoView hg38]
Mapping of homologs : NCBISOX17 [Mapview hg19]  SOX17 [Mapview hg38]
OMIM610928   613674   
Gene and transcription
Genbank (Entrez)AB073988 AK025905 BC030209 BC111365 BC111770
RefSeq transcript (Entrez)NM_022454
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)SOX17
Cluster EST : UnigeneHs.98367 [ NCBI ]
CGAP (NCI)Hs.98367
Alternative Splicing GalleryENSG00000164736
Gene ExpressionSOX17 [ NCBI-GEO ]   SOX17 [ EBI - ARRAY_EXPRESS ]   SOX17 [ SEEK ]   SOX17 [ MEM ]
Gene Expression Viewer (FireBrowse)SOX17 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets] &nbsp [Normal Tissue Atlas] &nbsp[carcinoma Classsification] &nbsp[NCI60]
GenevestigatorExpression in : [tissues] &nbsp[cell-lines] &nbsp[cancer] &nbsp[perturbations] &nbsp
BioGPS (Tissue expression)64321
GTEX Portal (Tissue expression)SOX17
Human Protein AtlasENSG00000164736-SOX17 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ9H6I2   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ9H6I2  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ9H6I2
Splice isoforms : SwissVarQ9H6I2
PhosPhoSitePlusQ9H6I2
Domaine pattern : Prosite (Expaxy)HMG_BOX_2 (PS50118)    SOX_C (PS51516)   
Domains : Interpro (EBI)HMG_box_dom    HMG_box_dom_sf    Sox7/17/18_central    Sox_C   
Domain families : Pfam (Sanger)HMG_box (PF00505)    Sox17_18_mid (PF12067)   
Domain families : Pfam (NCBI)pfam00505    pfam12067   
Domain families : Smart (EMBL)HMG (SM00398)  
Conserved Domain (NCBI)SOX17
DMDM Disease mutations64321
Blocks (Seattle)SOX17
PDB (RSDB)2YUL    4A3N   
PDB Europe2YUL    4A3N   
PDB (PDBSum)2YUL    4A3N   
PDB (IMB)2YUL    4A3N   
Structural Biology KnowledgeBase2YUL    4A3N   
SCOP (Structural Classification of Proteins)2YUL    4A3N   
CATH (Classification of proteins structures)2YUL    4A3N   
SuperfamilyQ9H6I2
Human Protein Atlas [tissue]ENSG00000164736-SOX17 [tissue]
Peptide AtlasQ9H6I2
HPRD18085
IPIIPI00007874   IPI00984256   
Protein Interaction databases
DIP (DOE-UCLA)Q9H6I2
IntAct (EBI)Q9H6I2
FunCoupENSG00000164736
BioGRIDSOX17
STRING (EMBL)SOX17
ZODIACSOX17
Ontologies - Pathways
QuickGOQ9H6I2
Ontology : AmiGOnegative regulation of transcription by RNA polymerase II  DNA-binding transcription factor activity, RNA polymerase II-specific  DNA-binding transcription factor activity, RNA polymerase II-specific  DNA-binding transcription factor activity, RNA polymerase II-specific  DNA-binding transcription factor activity, RNA polymerase II-specific  DNA-binding transcription factor activity, RNA polymerase II-specific  DNA-binding transcription activator activity, RNA polymerase II-specific  angiogenesis  angiogenesis  vasculogenesis  vasculogenesis  endoderm formation  inner cell mass cellular morphogenesis  heart looping  cardiogenic plate morphogenesis  embryonic heart tube morphogenesis  outflow tract morphogenesis  negative regulation of Wnt signaling pathway involved in heart development  transcription coactivator activity  protein binding  nucleus  nucleus  nucleoplasm  transcription factor complex  regulation of transcription, DNA-templated  regulation of transcription, DNA-templated  spermatogenesis  endodermal cell fate determination  beta-catenin binding  transcription factor binding  rostrocaudal neural tube patterning  signal transduction involved in regulation of gene expression  cell differentiation  negative regulation of cell growth  protein destabilization  embryonic heart tube development  cell migration involved in gastrulation  negative regulation of mesodermal cell fate specification  mRNA transcription by RNA polymerase II  sequence-specific DNA binding  transcription regulatory region DNA binding  nuclear transcription factor complex  positive regulation of cell differentiation  positive regulation of protein catabolic process  positive regulation of transcription, DNA-templated  positive regulation of transcription by RNA polymerase II  positive regulation of transcription by RNA polymerase II  regulation of embryonic development  protein heterodimerization activity  embryonic foregut morphogenesis  positive regulation of skeletal muscle tissue development  stem cell fate specification  protein stabilization  canonical Wnt signaling pathway  endocardium formation  regulation of transcription from RNA polymerase II promoter involved in definitive endodermal cell fate specification  cardiac cell fate determination  heart formation  endocardial cell differentiation  common bile duct development  gall bladder development  endodermal digestive tract morphogenesis  renal system development  regulation of stem cell proliferation  negative regulation of canonical Wnt signaling pathway  cellular response to leukemia inhibitory factor  regulation of stem cell division  regulation of cardiac cell fate specification  
Ontology : EGO-EBInegative regulation of transcription by RNA polymerase II  DNA-binding transcription factor activity, RNA polymerase II-specific  DNA-binding transcription factor activity, RNA polymerase II-specific  DNA-binding transcription factor activity, RNA polymerase II-specific  DNA-binding transcription factor activity, RNA polymerase II-specific  DNA-binding transcription factor activity, RNA polymerase II-specific  DNA-binding transcription activator activity, RNA polymerase II-specific  angiogenesis  angiogenesis  vasculogenesis  vasculogenesis  endoderm formation  inner cell mass cellular morphogenesis  heart looping  cardiogenic plate morphogenesis  embryonic heart tube morphogenesis  outflow tract morphogenesis  negative regulation of Wnt signaling pathway involved in heart development  transcription coactivator activity  protein binding  nucleus  nucleus  nucleoplasm  transcription factor complex  regulation of transcription, DNA-templated  regulation of transcription, DNA-templated  spermatogenesis  endodermal cell fate determination  beta-catenin binding  transcription factor binding  rostrocaudal neural tube patterning  signal transduction involved in regulation of gene expression  cell differentiation  negative regulation of cell growth  protein destabilization  embryonic heart tube development  cell migration involved in gastrulation  negative regulation of mesodermal cell fate specification  mRNA transcription by RNA polymerase II  sequence-specific DNA binding  transcription regulatory region DNA binding  nuclear transcription factor complex  positive regulation of cell differentiation  positive regulation of protein catabolic process  positive regulation of transcription, DNA-templated  positive regulation of transcription by RNA polymerase II  positive regulation of transcription by RNA polymerase II  regulation of embryonic development  protein heterodimerization activity  embryonic foregut morphogenesis  positive regulation of skeletal muscle tissue development  stem cell fate specification  protein stabilization  canonical Wnt signaling pathway  endocardium formation  regulation of transcription from RNA polymerase II promoter involved in definitive endodermal cell fate specification  cardiac cell fate determination  heart formation  endocardial cell differentiation  common bile duct development  gall bladder development  endodermal digestive tract morphogenesis  renal system development  regulation of stem cell proliferation  negative regulation of canonical Wnt signaling pathway  cellular response to leukemia inhibitory factor  regulation of stem cell division  regulation of cardiac cell fate specification  
Pathways : KEGGWnt signaling pathway   
NDEx NetworkSOX17
Atlas of Cancer Signalling NetworkSOX17
Wikipedia pathwaysSOX17
Orthology - Evolution
OrthoDB64321
GeneTree (enSembl)ENSG00000164736
Phylogenetic Trees/Animal Genes : TreeFamSOX17
HOGENOMQ9H6I2
Homologs : HomoloGeneSOX17
Homology/Alignments : Family Browser (UCSC)SOX17
Gene fusions - Rearrangements
Fusion : QuiverSOX17
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerSOX17 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SOX17
dbVarSOX17
ClinVarSOX17
1000_GenomesSOX17 
Exome Variant ServerSOX17
ExAC (Exome Aggregation Consortium)ENSG00000164736
GNOMAD BrowserENSG00000164736
Varsome BrowserSOX17
Genetic variants : HAPMAP64321
Genomic Variants (DGV)SOX17 [DGVbeta]
DECIPHERSOX17 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisSOX17 
Mutations
ICGC Data PortalSOX17 
TCGA Data PortalSOX17 
Broad Tumor PortalSOX17
OASIS PortalSOX17 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICSOX17  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDSOX17
intOGen PortalSOX17
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch SOX17
DgiDB (Drug Gene Interaction Database)SOX17
DoCM (Curated mutations)SOX17 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SOX17 (select a term)
intoGenSOX17
Cancer3DSOX17(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM610928    613674   
Orphanet20715   
DisGeNETSOX17
MedgenSOX17
Genetic Testing Registry SOX17
NextProtQ9H6I2 [Medical]
TSGene64321
GENETestsSOX17
Target ValidationSOX17
Huge Navigator SOX17 [HugePedia]
snp3D : Map Gene to Disease64321
BioCentury BCIQSOX17
ClinGenSOX17
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD64321
Chemical/Pharm GKB GenePA38296
Clinical trialSOX17
Miscellaneous
canSAR (ICR)SOX17 (select the gene name)
DataMed IndexSOX17
Probes
Litterature
PubMed72 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineSOX17
EVEXSOX17
GoPubMedSOX17
iHOPSOX17
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Thu Jan 17 18:39:39 CET 2019

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