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SPDEF (SAM pointed domain containing ETS transcription factor)

Identity

Alias (NCBI)PDEF
bA375E1.3
HGNC (Hugo) SPDEF
HGNC Alias symbPDEF
bA375E1.3
HGNC Previous nameSAM pointed domain containing ets transcription factor
LocusID (NCBI) 25803
Atlas_Id 42372
Location 6p21.31  [Link to chromosome band 6p21]
Location_base_pair Starts at 34537802 and ends at 34556329 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

 



External links

 

Nomenclature
HGNC (Hugo)SPDEF   17257
Cards
Entrez_Gene (NCBI)SPDEF    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]  chr6:34537802-34556329 [Contig_View]  SPDEF [Vega]
ICGC DataPortalENSG00000124664
TCGA cBioPortalSPDEF
AceView (NCBI)SPDEF
Genatlas (Paris)SPDEF
SOURCE (Princeton)SPDEF
Genetics Home Reference (NIH)SPDEF
Genomic and cartography
GoldenPath hg38 (UCSC)SPDEF  -     chr6:34537802-34556329 -  6p21.31   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)SPDEF  -     6p21.31   [Description]    (hg19-Feb_2009)
GoldenPathSPDEF - 6p21.31 [CytoView hg19]  SPDEF - 6p21.31 [CytoView hg38]
ImmunoBaseENSG00000124664
Genome Data Viewer NCBISPDEF [Mapview hg19]  
OMIM608144   
Gene and transcription
Genbank (Entrez)AB031549 AF071538 AK301543 BC021299
RefSeq transcript (Entrez)NM_001252294 NM_012391
Consensus coding sequences : CCDS (NCBI)SPDEF
Gene ExpressionSPDEF [ NCBI-GEO ]   SPDEF [ EBI - ARRAY_EXPRESS ]   SPDEF [ SEEK ]   SPDEF [ MEM ]
Gene Expression Viewer (FireBrowse)SPDEF [ Firebrowse - Broad ]
GenevisibleExpression of SPDEF 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
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
PDB (RSDB)1YO5    2DKX   
PDB Europe1YO5    2DKX   
PDB (PDBSum)1YO5    2DKX   
PDB (IMB)1YO5    2DKX   
Structural Biology KnowledgeBase1YO5    2DKX   
SCOP (Structural Classification of Proteins)1YO5    2DKX   
CATH (Classification of proteins structures)1YO5    2DKX   
SuperfamilyO95238
AlphaFold pdb e-kbO95238   
Human Protein Atlas [tissue]ENSG00000124664-SPDEF [tissue]
HPRD12176
Protein Interaction databases
DIP (DOE-UCLA)O95238
IntAct (EBI)O95238
BioGRIDSPDEF
STRING (EMBL)SPDEF
ZODIACSPDEF
Ontologies - Pathways
QuickGOO95238
Ontology : AmiGOnegative regulation of transcription by RNA polymerase II  chromatin  DNA-binding transcription factor activity, RNA polymerase II-specific  DNA-binding transcription factor activity, RNA polymerase II-specific  protein binding  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  sequence-specific double-stranded DNA binding  
Ontology : EGO-EBInegative regulation of transcription by RNA polymerase II  chromatin  DNA-binding transcription factor activity, RNA polymerase II-specific  DNA-binding transcription factor activity, RNA polymerase II-specific  protein binding  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  sequence-specific double-stranded DNA binding  
NDEx NetworkSPDEF
Atlas of Cancer Signalling NetworkSPDEF
Wikipedia pathwaysSPDEF
Orthology - Evolution
OrthoDB25803
GeneTree (enSembl)ENSG00000124664
Phylogenetic Trees/Animal Genes : TreeFamSPDEF
Homologs : HomoloGeneSPDEF
Homology/Alignments : Family Browser (UCSC)SPDEF
Gene fusions - Rearrangements
Fusion : MitelmanC6orf106/SPDEF [6p21.31/6p21.31]  
Fusion : MitelmanSPDEF/C6orf106 [6p21.31/6p21.31]  
Fusion : QuiverSPDEF
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerSPDEF [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SPDEF
dbVarSPDEF
ClinVarSPDEF
MonarchSPDEF
1000_GenomesSPDEF 
Exome Variant ServerSPDEF
GNOMAD BrowserENSG00000124664
Varsome BrowserSPDEF
ACMGSPDEF variants
VarityO95238
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]  
Somatic Mutations in Cancer : COSMIC3DSPDEF
Mutations and Diseases : HGMDSPDEF
LOVD (Leiden Open Variation Database)[gene] [transcripts] [variants]
BioMutaSPDEF
DgiDB (Drug Gene Interaction Database)SPDEF
DoCM (Curated mutations)SPDEF
CIViC (Clinical Interpretations of Variants in Cancer)SPDEF
Cancer3DSPDEF
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM608144   
Orphanet
DisGeNETSPDEF
MedgenSPDEF
Genetic Testing Registry SPDEF
NextProtO95238 [Medical]
GENETestsSPDEF
Target ValidationSPDEF
Huge Navigator SPDEF [HugePedia]
ClinGenSPDEF
Clinical trials, drugs, therapy
MyCancerGenomeSPDEF
Protein Interactions : CTDSPDEF
Pharm GKB GenePA134993886
PharosO95238
Clinical trialSPDEF
Miscellaneous
canSAR (ICR)SPDEF
HarmonizomeSPDEF
DataMed IndexSPDEF
Probes
Litterature
PubMed78 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
EVEXSPDEF
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Mon Oct 4 15:32:51 CEST 2021

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