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SPDEF (SAM pointed domain containing ETS transcription factor)

Identity

Alias_namesSAM pointed domain containing ets transcription factor
Alias_symbol (synonym)PDEF
bA375E1.3
Other alias
HGNC (Hugo) SPDEF
LocusID (NCBI) 25803
Atlas_Id 42372
Location 6p21.31  [Link to chromosome band 6p21]
Location_base_pair Starts at 34537802 and ends at 34556333 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)
C6orf106 (6p21.31) / SPDEF (6p21.31)SPDEF (6p21.31) / C6orf106 (6p21.31)SPDEF 6p21.31 / C6orf106 6p21.31

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) [ 1 ]
  SPDEF/C6orf106 (6p21)


External links

Nomenclature
HGNC (Hugo)SPDEF   17257
Cards
Entrez_Gene (NCBI)SPDEF  25803  SAM pointed domain containing ETS transcription factor
AliasesPDEF; bA375E1.3
GeneCards (Weizmann)SPDEF
Ensembl hg19 (Hinxton)ENSG00000124664 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000124664 [Gene_View]  ENSG00000124664 [Sequence]  chr6:34537802-34556333 [Contig_View]  SPDEF [Vega]
ICGC DataPortalENSG00000124664
TCGA cBioPortalSPDEF
AceView (NCBI)SPDEF
Genatlas (Paris)SPDEF
WikiGenes25803
SOURCE (Princeton)SPDEF
Genetics Home Reference (NIH)SPDEF
Genomic and cartography
GoldenPath hg38 (UCSC)SPDEF  -     chr6:34537802-34556333 -  6p21.31   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)SPDEF  -     6p21.31   [Description]    (hg19-Feb_2009)
EnsemblSPDEF - 6p21.31 [CytoView hg19]  SPDEF - 6p21.31 [CytoView hg38]
Mapping of homologs : NCBISPDEF [Mapview hg19]  SPDEF [Mapview hg38]
OMIM608144   
Gene and transcription
Genbank (Entrez)AB031549 AF071538 AK301543 BC021299
RefSeq transcript (Entrez)NM_001252294 NM_012391
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)SPDEF
Cluster EST : UnigeneHs.485158 [ NCBI ]
CGAP (NCI)Hs.485158
Alternative Splicing GalleryENSG00000124664
Gene ExpressionSPDEF [ NCBI-GEO ]   SPDEF [ EBI - ARRAY_EXPRESS ]   SPDEF [ SEEK ]   SPDEF [ MEM ]
Gene Expression Viewer (FireBrowse)SPDEF [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)25803
GTEX Portal (Tissue expression)SPDEF
Human Protein AtlasENSG00000124664-SPDEF [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtO95238   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtO95238  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProO95238
Splice isoforms : SwissVarO95238
PhosPhoSitePlusO95238
Domaine pattern : Prosite (Expaxy)ETS_DOMAIN_1 (PS00345)    ETS_DOMAIN_2 (PS00346)    ETS_DOMAIN_3 (PS50061)    PNT (PS51433)   
Domains : Interpro (EBI)Ets_dom    Pointed_dom    SAM/pointed_sf    WH-like_DNA-bd_sf    WH_DNA-bd_sf   
Domain families : Pfam (Sanger)Ets (PF00178)    SAM_PNT (PF02198)   
Domain families : Pfam (NCBI)pfam00178    pfam02198   
Domain families : Smart (EMBL)ETS (SM00413)  SAM_PNT (SM00251)  
Conserved Domain (NCBI)SPDEF
DMDM Disease mutations25803
Blocks (Seattle)SPDEF
PDB (SRS)1YO5    2DKX   
PDB (PDBSum)1YO5    2DKX   
PDB (IMB)1YO5    2DKX   
PDB (RSDB)1YO5    2DKX   
Structural Biology KnowledgeBase1YO5    2DKX   
SCOP (Structural Classification of Proteins)1YO5    2DKX   
CATH (Classification of proteins structures)1YO5    2DKX   
SuperfamilyO95238
Human Protein Atlas [tissue]ENSG00000124664-SPDEF [tissue]
Peptide AtlasO95238
HPRD12176
IPIIPI00018233   IPI01011308   
Protein Interaction databases
DIP (DOE-UCLA)O95238
IntAct (EBI)O95238
FunCoupENSG00000124664
BioGRIDSPDEF
STRING (EMBL)SPDEF
ZODIACSPDEF
Ontologies - Pathways
QuickGOO95238
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 repressor activity, RNA polymerase II-specific  nucleus  regulation of transcription by RNA polymerase II  multicellular organism development  negative regulation of cell fate commitment  positive regulation of cell fate commitment  cell differentiation  positive regulation of apoptotic process  sequence-specific DNA binding  positive regulation of transcription by RNA polymerase II  lung goblet cell differentiation  intestinal epithelial cell development  
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 repressor activity, RNA polymerase II-specific  nucleus  regulation of transcription by RNA polymerase II  multicellular organism development  negative regulation of cell fate commitment  positive regulation of cell fate commitment  cell differentiation  positive regulation of apoptotic process  sequence-specific DNA binding  positive regulation of transcription by RNA polymerase II  lung goblet cell differentiation  intestinal epithelial cell development  
NDEx NetworkSPDEF
Atlas of Cancer Signalling NetworkSPDEF
Wikipedia pathwaysSPDEF
Orthology - Evolution
OrthoDB25803
GeneTree (enSembl)ENSG00000124664
Phylogenetic Trees/Animal Genes : TreeFamSPDEF
HOVERGENO95238
HOGENOMO95238
Homologs : HomoloGeneSPDEF
Homology/Alignments : Family Browser (UCSC)SPDEF
Gene fusions - Rearrangements
Fusion : MitelmanC6orf106/SPDEF [6p21.31/6p21.31]  [t(6;6)(p21;p21)]  
Fusion : MitelmanSPDEF/C6orf106 [6p21.31/6p21.31]  [t(6;6)(p21;p21)]  
Fusion PortalSPDEF 6p21.31 C6orf106 6p21.31 BRCA
Fusion : QuiverSPDEF
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerSPDEF [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SPDEF
dbVarSPDEF
ClinVarSPDEF
1000_GenomesSPDEF 
Exome Variant ServerSPDEF
ExAC (Exome Aggregation Consortium)ENSG00000124664
GNOMAD BrowserENSG00000124664
Varsome BrowserSPDEF
Genetic variants : HAPMAP25803
Genomic Variants (DGV)SPDEF [DGVbeta]
DECIPHERSPDEF [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisSPDEF 
Mutations
ICGC Data PortalSPDEF 
TCGA Data PortalSPDEF 
Broad Tumor PortalSPDEF
OASIS PortalSPDEF [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICSPDEF  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDSPDEF
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch SPDEF
DgiDB (Drug Gene Interaction Database)SPDEF
DoCM (Curated mutations)SPDEF (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SPDEF (select a term)
intoGenSPDEF
Cancer3DSPDEF(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM608144   
Orphanet
DisGeNETSPDEF
MedgenSPDEF
Genetic Testing Registry SPDEF
NextProtO95238 [Medical]
TSGene25803
GENETestsSPDEF
Target ValidationSPDEF
Huge Navigator SPDEF [HugePedia]
snp3D : Map Gene to Disease25803
BioCentury BCIQSPDEF
ClinGenSPDEF
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD25803
Chemical/Pharm GKB GenePA134993886
Clinical trialSPDEF
Miscellaneous
canSAR (ICR)SPDEF (select the gene name)
Probes
Litterature
PubMed63 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineSPDEF
EVEXSPDEF
GoPubMedSPDEF
iHOPSPDEF
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 6 11:41:30 CET 2018

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