Atlas of Genetics and Cytogenetics in Oncology and Haematology

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SF3B3 (splicing factor 3b subunit 3)

Identity

Alias_namessplicing factor 3b, subunit 3, 130kD
splicing factor 3b, subunit 3, 130kDa
Alias_symbol (synonym)SAP130
SF3b130
RSE1
KIAA0017
Other aliasSTAF130
HGNC (Hugo) SF3B3
LocusID (NCBI) 23450
Atlas_Id 42950
Location 16q22.1  [Link to chromosome band 16q22]
Location_base_pair Starts at 70523788 and ends at 70577668 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)
ASAH1 (8p22) / SF3B3 (16q22.1)FAM83D (20q11.23) / SF3B3 (16q22.1)SF3B3 (16q22.1) / CDH15 (16q24.3)
SF3B3 (16q22.1) / COG4 (16q22.1)SF3B3 (16q22.1) / DDX19B (16q22.1)SF3B3 (16q22.1) / ERBIN (5q12.3)
SF3B3 (16q22.1) / LOC100507217 ()SF3B3 (16q22.1) / NUP88 (17p13.2)SF3B3 (16q22.1) / SF1 (11q13.1)
SF3B3 (16q22.1) / SF3B3 (16q22.1)SF3B3 (16q22.1) / SSH2 (17q11.2)FAM83D 20q11.23 / SF3B3 16q22.1
SF3B3 16q22.1 / CDH15 16q24.3SF3B3 16q22.1 / COG4 16q22.1SF3B3 16q22.1 / DDX19B 16q22.1

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 Solid tumors implicated (Data extracted from papers in the Atlas) [ 4 ]
  SF3B3/COG4 (16q22)
SF3B3/DDX19B (16q22)
t(16;16)(q22;q24) SF3B3/CDH15
t(16;20)(q22;q11) FAM83D/SF3B3

External links

Nomenclature
HGNC (Hugo)SF3B3   10770
Cards
Entrez_Gene (NCBI)SF3B3  23450  splicing factor 3b subunit 3
AliasesRSE1; SAP130; SF3b130; STAF130
GeneCards (Weizmann)SF3B3
Ensembl hg19 (Hinxton)ENSG00000189091 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000189091 [Gene_View]  ENSG00000189091 [Sequence]  chr16:70523788-70577668 [Contig_View]  SF3B3 [Vega]
ICGC DataPortalENSG00000189091
TCGA cBioPortalSF3B3
AceView (NCBI)SF3B3
Genatlas (Paris)SF3B3
WikiGenes23450
SOURCE (Princeton)SF3B3
Genetics Home Reference (NIH)SF3B3
Genomic and cartography
GoldenPath hg38 (UCSC)SF3B3  -     chr16:70523788-70577668 +  16q22.1   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)SF3B3  -     16q22.1   [Description]    (hg19-Feb_2009)
GoldenPathSF3B3 - 16q22.1 [CytoView hg19]  SF3B3 - 16q22.1 [CytoView hg38]
ImmunoBaseENSG00000189091
Mapping of homologs : NCBISF3B3 [Mapview hg19]  SF3B3 [Mapview hg38]
OMIM605592   
Gene and transcription
Genbank (Entrez)AJ001443 AK001297 AK074933 AK291768 AL110251
RefSeq transcript (Entrez)NM_012426
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)SF3B3
Cluster EST : UnigeneHs.514435 [ NCBI ]
CGAP (NCI)Hs.514435
Alternative Splicing GalleryENSG00000189091
Gene ExpressionSF3B3 [ NCBI-GEO ]   SF3B3 [ EBI - ARRAY_EXPRESS ]   SF3B3 [ SEEK ]   SF3B3 [ MEM ]
Gene Expression Viewer (FireBrowse)SF3B3 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)23450
GTEX Portal (Tissue expression)SF3B3
Human Protein AtlasENSG00000189091-SF3B3 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ15393   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ15393  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ15393
Splice isoforms : SwissVarQ15393
PhosPhoSitePlusQ15393
Domains : Interpro (EBI)Cleavage/polyA-sp_fac_asu_C    WD40/YVTN_repeat-like_dom_sf    WD40_repeat_dom_sf   
Domain families : Pfam (Sanger)CPSF_A (PF03178)   
Domain families : Pfam (NCBI)pfam03178   
Conserved Domain (NCBI)SF3B3
DMDM Disease mutations23450
Blocks (Seattle)SF3B3
PDB (RSDB)5IFE    5O9Z   
PDB Europe5IFE    5O9Z   
PDB (PDBSum)5IFE    5O9Z   
PDB (IMB)5IFE    5O9Z   
Structural Biology KnowledgeBase5IFE    5O9Z   
SCOP (Structural Classification of Proteins)5IFE    5O9Z   
CATH (Classification of proteins structures)5IFE    5O9Z   
SuperfamilyQ15393
Human Protein Atlas [tissue]ENSG00000189091-SF3B3 [tissue]
Peptide AtlasQ15393
HPRD12027
IPIIPI00300371   IPI00179138   IPI00828110   
Protein Interaction databases
DIP (DOE-UCLA)Q15393
IntAct (EBI)Q15393
FunCoupENSG00000189091
BioGRIDSF3B3
STRING (EMBL)SF3B3
ZODIACSF3B3
Ontologies - Pathways
QuickGOQ15393
Ontology : AmiGORNA splicing, via transesterification reactions  mRNA splicing, via spliceosome  mRNA splicing, via spliceosome  mRNA splicing, via spliceosome  mRNA splicing, via spliceosome  nucleic acid binding  protein binding  nucleus  nucleus  nucleoplasm  U12-type spliceosomal complex  nucleolus  negative regulation of protein catabolic process  protein-containing complex binding  U2-type precatalytic spliceosome  catalytic step 2 spliceosome  
Ontology : EGO-EBIRNA splicing, via transesterification reactions  mRNA splicing, via spliceosome  mRNA splicing, via spliceosome  mRNA splicing, via spliceosome  mRNA splicing, via spliceosome  nucleic acid binding  protein binding  nucleus  nucleus  nucleoplasm  U12-type spliceosomal complex  nucleolus  negative regulation of protein catabolic process  protein-containing complex binding  U2-type precatalytic spliceosome  catalytic step 2 spliceosome  
Pathways : KEGGSpliceosome   
NDEx NetworkSF3B3
Atlas of Cancer Signalling NetworkSF3B3
Wikipedia pathwaysSF3B3
Orthology - Evolution
OrthoDB23450
GeneTree (enSembl)ENSG00000189091
Phylogenetic Trees/Animal Genes : TreeFamSF3B3
HOGENOMQ15393
Homologs : HomoloGeneSF3B3
Homology/Alignments : Family Browser (UCSC)SF3B3
Gene fusions - Rearrangements
Fusion : MitelmanFAM83D/SF3B3 [20q11.23/16q22.1]  [t(16;20)(q22;q11)]  
Fusion : MitelmanSF3B3/CDH15 [16q22.1/16q24.3]  [t(16;16)(q22;q24)]  
Fusion : MitelmanSF3B3/COG4 [16q22.1/16q22.1]  [t(16;16)(q22;q22)]  
Fusion : MitelmanSF3B3/DDX19B [16q22.1/16q22.1]  [t(16;16)(q22;q22)]  
Fusion PortalFAM83D 20q11.23 SF3B3 16q22.1 BRCA
Fusion PortalSF3B3 16q22.1 CDH15 16q24.3 LUAD
Fusion PortalSF3B3 16q22.1 COG4 16q22.1 BRCA
Fusion PortalSF3B3 16q22.1 DDX19B 16q22.1 BLCA GBM
Fusion : QuiverSF3B3
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerSF3B3 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SF3B3
dbVarSF3B3
ClinVarSF3B3
1000_GenomesSF3B3 
Exome Variant ServerSF3B3
ExAC (Exome Aggregation Consortium)ENSG00000189091
GNOMAD BrowserENSG00000189091
Varsome BrowserSF3B3
Genetic variants : HAPMAP23450
Genomic Variants (DGV)SF3B3 [DGVbeta]
DECIPHERSF3B3 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisSF3B3 
Mutations
ICGC Data PortalSF3B3 
TCGA Data PortalSF3B3 
Broad Tumor PortalSF3B3
OASIS PortalSF3B3 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICSF3B3  [overview]  [genome browser]  [tissue]  [distribution]  
Somatic Mutations in Cancer : COSMIC3DSF3B3
Mutations and Diseases : HGMDSF3B3
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
BioMutasearch SF3B3
DgiDB (Drug Gene Interaction Database)SF3B3
DoCM (Curated mutations)SF3B3 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SF3B3 (select a term)
intoGenSF3B3
Cancer3DSF3B3(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM605592   
Orphanet
DisGeNETSF3B3
MedgenSF3B3
Genetic Testing Registry SF3B3
NextProtQ15393 [Medical]
TSGene23450
GENETestsSF3B3
Target ValidationSF3B3
Huge Navigator SF3B3 [HugePedia]
snp3D : Map Gene to Disease23450
BioCentury BCIQSF3B3
ClinGenSF3B3
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD23450
Chemical/Pharm GKB GenePA35688
Clinical trialSF3B3
Miscellaneous
canSAR (ICR)SF3B3 (select the gene name)
DataMed IndexSF3B3
Probes
Litterature
PubMed112 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineSF3B3
EVEXSF3B3
GoPubMedSF3B3
iHOPSF3B3
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Wed Nov 13 18:07:06 CET 2019
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