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SOX5 (SRY-box 5)

Identity

Alias_namesSRY (sex determining region Y)-box 5
SRY box 5
Alias_symbol (synonym)L-SOX5
MGC35153
Other aliasL-SOX5B
L-SOX5F
LAMSHF
HGNC (Hugo) SOX5
LocusID (NCBI) 6660
Atlas_Id 49803
Location 12p12.1  [Link to chromosome band 12p12]
Location_base_pair Starts at 23685231 and ends at 24715383 bp from pter ( according to hg19-Feb_2009)
Fusion genes
(updated 2016)
AC011443.1 () / SOX5 (12p12.1)BICD1 (12p11.21) / SOX5 (12p12.1)CP (3q24) / SOX5 (12p12.1)
KIAA1535 () / SOX5 (12p12.1)KIAA1551 (12p11.21) / SOX5 (12p12.1)LRMP (12p12.1) / SOX5 (12p12.1)
SOX5 (12p12.1) / AC007621.1 ()SOX5 (12p12.1) / MANSC1 (12p13.2)SOX5 (12p12.1) / RP11-176H8.1 ()
SOX5 (12p12.1) / SOX5 (12p12.1)SOX5 (12p12.1) / TGFBR2 (3p24.1)TSPAN6 (Xq22.1) / SOX5 (12p12.1)
AC011443.1 SOX5 12p12.1BICD1 12p11.21 / SOX5 12p12.1C12orf35 SOX5 12p12.1
CP 3q24 / SOX5 12p12.1SOX5 12p12.1 AC007621.1SOX5 12p12.1 / MANSC1 12p13.2
SOX5 12p12.1 RP11-176H8.1

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)SOX5   11201
Cards
Entrez_Gene (NCBI)SOX5  6660  SRY-box 5
AliasesL-SOX5; L-SOX5B; L-SOX5F; LAMSHF
GeneCards (Weizmann)SOX5
Ensembl hg19 (Hinxton)ENSG00000134532 [Gene_View]  chr12:23685231-24715383 [Contig_View]  SOX5 [Vega]
Ensembl hg38 (Hinxton)ENSG00000134532 [Gene_View]  chr12:23685231-24715383 [Contig_View]  SOX5 [Vega]
ICGC DataPortalENSG00000134532
TCGA cBioPortalSOX5
AceView (NCBI)SOX5
Genatlas (Paris)SOX5
WikiGenes6660
SOURCE (Princeton)SOX5
Genetics Home Reference (NIH)SOX5
Genomic and cartography
GoldenPath hg19 (UCSC)SOX5  -     chr12:23685231-24715383 -  12p12.1   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)SOX5  -     12p12.1   [Description]    (hg38-Dec_2013)
EnsemblSOX5 - 12p12.1 [CytoView hg19]  SOX5 - 12p12.1 [CytoView hg38]
Mapping of homologs : NCBISOX5 [Mapview hg19]  SOX5 [Mapview hg38]
OMIM604975   
Gene and transcription
Genbank (Entrez)AB081588 AB081589 AK074317 AK096569 AK098610
RefSeq transcript (Entrez)NM_001261414 NM_001261415 NM_006940 NM_152989 NM_178010
RefSeq genomic (Entrez)NC_000012 NC_018923 NG_029612 NT_009714 NW_004929383
Consensus coding sequences : CCDS (NCBI)SOX5
Cluster EST : UnigeneHs.657542 [ NCBI ]
CGAP (NCI)Hs.657542
Alternative Splicing GalleryENSG00000134532
Gene ExpressionSOX5 [ NCBI-GEO ]   SOX5 [ EBI - ARRAY_EXPRESS ]   SOX5 [ SEEK ]   SOX5 [ MEM ]
Gene Expression Viewer (FireBrowse)SOX5 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)6660
GTEX Portal (Tissue expression)SOX5
Protein : pattern, domain, 3D structure
UniProt/SwissProtP35711   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP35711  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP35711
Splice isoforms : SwissVarP35711
PhosPhoSitePlusP35711
Domaine pattern : Prosite (Expaxy)HMG_BOX_2 (PS50118)   
Domains : Interpro (EBI)HMG_box_dom   
Domain families : Pfam (Sanger)HMG_box (PF00505)   
Domain families : Pfam (NCBI)pfam00505   
Domain families : Smart (EMBL)HMG (SM00398)  
Conserved Domain (NCBI)SOX5
DMDM Disease mutations6660
Blocks (Seattle)SOX5
SuperfamilyP35711
Human Protein AtlasENSG00000134532
Peptide AtlasP35711
HPRD18086
IPIIPI00216317   IPI00171247   IPI00221270   IPI00166143   IPI00793790   IPI01011755   IPI01010805   IPI00939555   IPI00791993   IPI01009605   IPI01015475   
Protein Interaction databases
DIP (DOE-UCLA)P35711
IntAct (EBI)P35711
FunCoupENSG00000134532
BioGRIDSOX5
STRING (EMBL)SOX5
ZODIACSOX5
Ontologies - Pathways
QuickGOP35711
Ontology : AmiGODNA binding  transcription factor activity, sequence-specific DNA binding  protein binding  nucleus  regulation of transcription, DNA-templated  transcription from RNA polymerase II promoter  positive regulation of chondrocyte differentiation  asymmetric neuroblast division  positive regulation of cartilage development  cellular response to transforming growth factor beta stimulus  positive regulation of mesenchymal stem cell differentiation  
Ontology : EGO-EBIDNA binding  transcription factor activity, sequence-specific DNA binding  protein binding  nucleus  regulation of transcription, DNA-templated  transcription from RNA polymerase II promoter  positive regulation of chondrocyte differentiation  asymmetric neuroblast division  positive regulation of cartilage development  cellular response to transforming growth factor beta stimulus  positive regulation of mesenchymal stem cell differentiation  
NDEx NetworkSOX5
Atlas of Cancer Signalling NetworkSOX5
Wikipedia pathwaysSOX5
Orthology - Evolution
OrthoDB6660
GeneTree (enSembl)ENSG00000134532
Phylogenetic Trees/Animal Genes : TreeFamSOX5
HOVERGENP35711
HOGENOMP35711
Homologs : HomoloGeneSOX5
Homology/Alignments : Family Browser (UCSC)SOX5
Gene fusions - Rearrangements
Fusion : MitelmanBICD1/SOX5 [12p11.21/12p12.1]  [t(12;12)(p11;p12)]  
Fusion : MitelmanCP/SOX5 [3q24/12p12.1]  [t(3;12)(q25;p12)]  
Fusion : MitelmanKIAA1535/12p12.1 [SOX5/t(12;12)(p11;p12)]  
Fusion : MitelmanSOX5/MANSC1 [12p12.1/12p13.2]  [t(12;12)(p12;p13)]  
Fusion: TCGAAC011443.1 SOX5 12p12.1 OV
Fusion: TCGABICD1 12p11.21 SOX5 12p12.1 LGG
Fusion: TCGAC12orf35 SOX5 12p12.1 KIRC
Fusion: TCGACP 3q24 SOX5 12p12.1 BRCA
Fusion: TCGASOX5 12p12.1 AC007621.1 LGG
Fusion: TCGASOX5 12p12.1 MANSC1 12p13.2 LGG
Fusion: TCGASOX5 12p12.1 RP11-176H8.1 BRCA
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerSOX5 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SOX5
dbVarSOX5
ClinVarSOX5
1000_GenomesSOX5 
Exome Variant ServerSOX5
ExAC (Exome Aggregation Consortium)SOX5 (select the gene name)
Genetic variants : HAPMAP6660
Genomic Variants (DGV)SOX5 [DGVbeta]
DECIPHER (Syndromes)12:23685231-24715383  ENSG00000134532
CONAN: Copy Number AnalysisSOX5 
Mutations
ICGC Data PortalSOX5 
TCGA Data PortalSOX5 
Broad Tumor PortalSOX5
OASIS PortalSOX5 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICSOX5  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDSOX5
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
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
BioMutasearch SOX5
DgiDB (Drug Gene Interaction Database)SOX5
DoCM (Curated mutations)SOX5 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SOX5 (select a term)
intoGenSOX5
Cancer3DSOX5(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM604975   
Orphanet21461    21460   
MedgenSOX5
Genetic Testing Registry SOX5
NextProtP35711 [Medical]
TSGene6660
GENETestsSOX5
Huge Navigator SOX5 [HugePedia]
snp3D : Map Gene to Disease6660
BioCentury BCIQSOX5
ClinGenSOX5
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD6660
Chemical/Pharm GKB GenePA36038
Clinical trialSOX5
Miscellaneous
canSAR (ICR)SOX5 (select the gene name)
Probes
Litterature
PubMed61 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineSOX5
EVEXSOX5
GoPubMedSOX5
iHOPSOX5
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Tue Mar 14 13:28:42 CET 2017

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