Atlas of Genetics and Cytogenetics in Oncology and Haematology

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SOX5 (SRY-box transcription factor 5)

Identity

Alias (NCBI)L-SOX5
L-SOX5B
L-SOX5F
LAMSHF
HGNC (Hugo) SOX5
HGNC Alias symbL-SOX5
MGC35153
HGNC Previous nameSRY (sex determining region Y)-box 5
 SRY-box 5
LocusID (NCBI) 6660
Atlas_Id 49803
Location 12p12.1  [Link to chromosome band 12p12]
Location_base_pair Starts at 23529504 and ends at 23584586 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)
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

 

Other Leukemias implicated (Data extracted from papers in the Atlas) [ 1 ]
  t(12;14)(p12;q32) IGH/SOX5

Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 6 ]
  inv(12)(p12q14) HMGA2/SOX5
t(2;12)(p23;p12) ASXL2/SOX5
t(3;12)(q25;p12) CP/SOX5
t(12;12)(p11;p12) BICD1/SOX5
t(12;12)(p11;p12) KIAA1551/SOX5
t(12;12)(p12;p13) SOX5/MANSC1

External links

Nomenclature
HGNC (Hugo)SOX5   11201
Cards
Entrez_Gene (NCBI)SOX5    SRY-box transcription factor 5
AliasesL-SOX5; L-SOX5B; L-SOX5F; LAMSHF
GeneCards (Weizmann)SOX5
Ensembl hg19 (Hinxton)ENSG00000134532 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000134532 [Gene_View]  ENSG00000134532 [Sequence]  chr12:23529504-23584586 [Contig_View]  SOX5 [Vega]
ICGC DataPortalENSG00000134532
TCGA cBioPortalSOX5
AceView (NCBI)SOX5
Genatlas (Paris)SOX5
SOURCE (Princeton)SOX5
Genetics Home Reference (NIH)SOX5
Genomic and cartography
GoldenPath hg38 (UCSC)SOX5  -     chr12:23529504-23584586 -  12p12.1   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)SOX5  -     12p12.1   [Description]    (hg19-Feb_2009)
GoldenPathSOX5 - 12p12.1 [CytoView hg19]  SOX5 - 12p12.1 [CytoView hg38]
ImmunoBaseENSG00000134532
genome Data Viewer NCBISOX5 [Mapview hg19]  
OMIM604975   616803   
Gene and transcription
Genbank (Entrez)AB081588 AB081589 AK074317 AK096569 AK098610
RefSeq transcript (Entrez)NM_001261414 NM_001261415 NM_001330785 NM_006940 NM_152989 NM_178010
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)SOX5
Alternative Splicing GalleryENSG00000134532
Gene ExpressionSOX5 [ NCBI-GEO ]   SOX5 [ EBI - ARRAY_EXPRESS ]   SOX5 [ SEEK ]   SOX5 [ MEM ]
Gene Expression Viewer (FireBrowse)SOX5 [ Firebrowse - Broad ]
GenevisibleExpression of SOX5 in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)6660
GTEX Portal (Tissue expression)SOX5
Human Protein AtlasENSG00000134532-SOX5 [pathology]   [cell]   [tissue]
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    HMG_box_dom_sf    SOX-5/6   
Domain families : Pfam (Sanger)HMG_box (PF00505)   
Domain families : Pfam (NCBI)pfam00505   
Domain families : Smart (EMBL)HMG (SM00398)  
Conserved Domain (NCBI)SOX5
Blocks (Seattle)SOX5
SuperfamilyP35711
Human Protein Atlas [tissue]ENSG00000134532-SOX5 [tissue]
Peptide AtlasP35711
HPRD18086
IPIIPI00216317   IPI00171247   IPI00221270   IPI00166143   IPI00793790   IPI01011755   IPI01010805   IPI00939555   IPI00791993   IPI01009605   IPI01015475   
Protein Interaction databases
DIP (DOE-UCLA)P35711
IntAct (EBI)P35711
BioGRIDSOX5
STRING (EMBL)SOX5
ZODIACSOX5
Ontologies - Pathways
QuickGOP35711
Ontology : AmiGOnuclear chromatin  transcription regulatory region sequence-specific DNA binding  transcription regulatory region sequence-specific DNA binding  DNA-binding transcription factor activity, RNA polymerase II-specific  DNA-binding transcription factor activity, RNA polymerase II-specific  cartilage condensation  chondrocyte differentiation  DNA-binding transcription factor activity  protein binding  nucleus  transcription by RNA polymerase II  positive regulation of chondrocyte differentiation  positive regulation of chondrocyte differentiation  cell fate commitment  negative regulation of transcription, DNA-templated  positive regulation of transcription by RNA polymerase II  cartilage development  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-EBInuclear chromatin  transcription regulatory region sequence-specific DNA binding  transcription regulatory region sequence-specific DNA binding  DNA-binding transcription factor activity, RNA polymerase II-specific  DNA-binding transcription factor activity, RNA polymerase II-specific  cartilage condensation  chondrocyte differentiation  DNA-binding transcription factor activity  protein binding  nucleus  transcription by RNA polymerase II  positive regulation of chondrocyte differentiation  positive regulation of chondrocyte differentiation  cell fate commitment  negative regulation of transcription, DNA-templated  positive regulation of transcription by RNA polymerase II  cartilage development  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
HOGENOMP35711
Homologs : HomoloGeneSOX5
Homology/Alignments : Family Browser (UCSC)SOX5
Gene fusions - Rearrangements
Fusion : MitelmanBICD1/SOX5 [12p11.21/12p12.1]  
Fusion : MitelmanCP/SOX5 [3q24/12p12.1]  
Fusion : MitelmanKIAA1535/12p12.1 [SOX5/t(12;12)(p11;p12)]  
Fusion : MitelmanSOX5/MANSC1 [12p12.1/12p13.2]  
Fusion PortalAC011443.1 SOX5 12p12.1 OV
Fusion PortalBICD1 12p11.21 SOX5 12p12.1 LGG
Fusion PortalC12orf35 SOX5 12p12.1 KIRC
Fusion PortalCP 3q24 SOX5 12p12.1 BRCA
Fusion PortalSOX5 12p12.1 AC007621.1 LGG
Fusion PortalSOX5 12p12.1 MANSC1 12p13.2 LGG
Fusion PortalSOX5 12p12.1 RP11-176H8.1 BRCA
Fusion : QuiverSOX5
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerSOX5 [hg38]
dbVarSOX5
ClinVarSOX5
MonarchSOX5
1000_GenomesSOX5 
Exome Variant ServerSOX5
GNOMAD BrowserENSG00000134532
Varsome BrowserSOX5
Genomic Variants (DGV)SOX5 [DGVbeta]
DECIPHERSOX5 [patients]   [syndromes]   [variants]   [genes]  
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]  
Somatic Mutations in Cancer : COSMIC3DSOX5
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] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM604975    616803   
Orphanet21461    21460   
DisGeNETSOX5
MedgenSOX5
Genetic Testing Registry SOX5
NextProtP35711 [Medical]
GENETestsSOX5
Target ValidationSOX5
Huge Navigator SOX5 [HugePedia]
ClinGenSOX5
Clinical trials, drugs, therapy
MyCancerGenomeSOX5
Protein Interactions : CTD
Pharm GKB GenePA36038
PharosP35711
Clinical trialSOX5
Miscellaneous
canSAR (ICR)SOX5 (select the gene name)
HarmonizomeSOX5
DataMed IndexSOX5
Probes
Litterature
PubMed84 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
EVEXSOX5
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 : Fri Jan 1 18:38:47 CET 2021
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