Atlas of Genetics and Cytogenetics in Oncology and Haematology


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SOX1 (SRY-box 1)

Identity

Alias_namesSRY (sex determining region Y)-box 1
SRY box 1
Other alias-
HGNC (Hugo) SOX1
LocusID (NCBI) 6656
Atlas_Id 50115
Location 13q34  [Link to chromosome band 13q34]
Location_base_pair Starts at 112067599 and ends at 112071706 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)

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)SOX1   11189
Cards
Entrez_Gene (NCBI)SOX1  6656  SRY-box 1
Aliases
GeneCards (Weizmann)SOX1
Ensembl hg19 (Hinxton)ENSG00000182968 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000182968 [Gene_View]  chr13:112067599-112071706 [Contig_View]  SOX1 [Vega]
ICGC DataPortalENSG00000182968
TCGA cBioPortalSOX1
AceView (NCBI)SOX1
Genatlas (Paris)SOX1
WikiGenes6656
SOURCE (Princeton)SOX1
Genetics Home Reference (NIH)SOX1
Genomic and cartography
GoldenPath hg38 (UCSC)SOX1  -     chr13:112067599-112071706 +  13q34   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)SOX1  -     13q34   [Description]    (hg19-Feb_2009)
EnsemblSOX1 - 13q34 [CytoView hg19]  SOX1 - 13q34 [CytoView hg38]
Mapping of homologs : NCBISOX1 [Mapview hg19]  SOX1 [Mapview hg38]
OMIM602148   
Gene and transcription
Genbank (Entrez)-
RefSeq transcript (Entrez)NM_005986
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)SOX1
Cluster EST : UnigeneHs.202526 [ NCBI ]
CGAP (NCI)Hs.202526
Alternative Splicing GalleryENSG00000182968
Gene ExpressionSOX1 [ NCBI-GEO ]   SOX1 [ EBI - ARRAY_EXPRESS ]   SOX1 [ SEEK ]   SOX1 [ MEM ]
Gene Expression Viewer (FireBrowse)SOX1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)6656
GTEX Portal (Tissue expression)SOX1
Human Protein AtlasENSG00000182968-SOX1 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtO00570   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtO00570  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProO00570
Splice isoforms : SwissVarO00570
PhosPhoSitePlusO00570
Domaine pattern : Prosite (Expaxy)HMG_BOX_2 (PS50118)   
Domains : Interpro (EBI)HMG_box_dom    SOX-1    SOX_fam   
Domain families : Pfam (Sanger)HMG_box (PF00505)    SOXp (PF12336)   
Domain families : Pfam (NCBI)pfam00505    pfam12336   
Domain families : Smart (EMBL)HMG (SM00398)  
Conserved Domain (NCBI)SOX1
DMDM Disease mutations6656
Blocks (Seattle)SOX1
SuperfamilyO00570
Human Protein Atlas [tissue]ENSG00000182968-SOX1 [tissue]
Peptide AtlasO00570
HPRD03687
IPIIPI00012162   
Protein Interaction databases
DIP (DOE-UCLA)O00570
IntAct (EBI)O00570
FunCoupENSG00000182968
BioGRIDSOX1
STRING (EMBL)SOX1
ZODIACSOX1
Ontologies - Pathways
QuickGOO00570
Ontology : AmiGORNA polymerase II core promoter proximal region sequence-specific DNA binding  core promoter sequence-specific DNA binding  transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding  neuron migration  lens morphogenesis in camera-type eye  DNA binding  transcription factor activity, sequence-specific DNA binding  protein binding  nucleus  chromatin organization  regulation of transcription, DNA-templated  transcription from RNA polymerase II promoter  ventral spinal cord interneuron specification  forebrain neuron development  positive regulation of transcription from RNA polymerase II promoter  
Ontology : EGO-EBIRNA polymerase II core promoter proximal region sequence-specific DNA binding  core promoter sequence-specific DNA binding  transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding  neuron migration  lens morphogenesis in camera-type eye  DNA binding  transcription factor activity, sequence-specific DNA binding  protein binding  nucleus  chromatin organization  regulation of transcription, DNA-templated  transcription from RNA polymerase II promoter  ventral spinal cord interneuron specification  forebrain neuron development  positive regulation of transcription from RNA polymerase II promoter  
NDEx NetworkSOX1
Atlas of Cancer Signalling NetworkSOX1
Wikipedia pathwaysSOX1
Orthology - Evolution
OrthoDB6656
GeneTree (enSembl)ENSG00000182968
Phylogenetic Trees/Animal Genes : TreeFamSOX1
HOVERGENO00570
HOGENOMO00570
Homologs : HomoloGeneSOX1
Homology/Alignments : Family Browser (UCSC)SOX1
Gene fusions - Rearrangements
Tumor Fusion PortalSOX1
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerSOX1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SOX1
dbVarSOX1
ClinVarSOX1
1000_GenomesSOX1 
Exome Variant ServerSOX1
ExAC (Exome Aggregation Consortium)ENSG00000182968
GNOMAD BrowserENSG00000182968
Genetic variants : HAPMAP6656
Genomic Variants (DGV)SOX1 [DGVbeta]
DECIPHERSOX1 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisSOX1 
Mutations
ICGC Data PortalSOX1 
TCGA Data PortalSOX1 
Broad Tumor PortalSOX1
OASIS PortalSOX1 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICSOX1  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDSOX1
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch SOX1
DgiDB (Drug Gene Interaction Database)SOX1
DoCM (Curated mutations)SOX1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SOX1 (select a term)
intoGenSOX1
Cancer3DSOX1(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM602148   
Orphanet
DisGeNETSOX1
MedgenSOX1
Genetic Testing Registry SOX1
NextProtO00570 [Medical]
TSGene6656
GENETestsSOX1
Target ValidationSOX1
Huge Navigator SOX1 [HugePedia]
snp3D : Map Gene to Disease6656
BioCentury BCIQSOX1
ClinGenSOX1
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD6656
Chemical/Pharm GKB GenePA36026
Clinical trialSOX1
Miscellaneous
canSAR (ICR)SOX1 (select the gene name)
Probes
Litterature
PubMed34 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineSOX1
EVEXSOX1
GoPubMedSOX1
iHOPSOX1
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Tue Nov 21 14:36:00 CET 2017

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