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SFPQ (PTB-associated splicing factor)

Written1999-01Jean-Loup Huret
Genetics, Dept Medical Information, University of Poitiers, CHU Poitiers Hospital, F-86021 Poitiers, France

(Note : for Links provided by Atlas : click)


Other namesPSF (PTB-associated splicing factor)
SFPQ (splicing factor proline/glutamine rich)
LocusID (NCBI) 6421
Atlas_Id 167
Location 1p34.3  [Link to chromosome band 1p34]
Location_base_pair Starts at 84226164 and ends at 84230659 bp from pter ( according to hg19-Feb_2009)  [Mapping SFPQ.png]
Fusion genes
(updated 2016)
COL6A1 (21q22.3) / SFPQ (16q24.1)FTL (19q13.33) / SFPQ (16q24.1)LOC100507412 (-) / SFPQ (16q24.1)
PUM1 (1p35.2) / SFPQ (16q24.1)SFPQ (16q24.1) / ABL1 (9q34.12)SFPQ (16q24.1) / CEP95 (17q23.3)
SFPQ (16q24.1) / EIF5A (17p13.1)SFPQ (16q24.1) / FXYD5 (19q13.12)SFPQ (16q24.1) / ITGB7 (12q13.13)
SFPQ (16q24.1) / NR4A1 (12q13.13)SFPQ (16q24.1) / SFPQ (16q24.1)SFPQ (16q24.1) / SUMO3 (21q22.3)
SFPQ (16q24.1) / TBRG4 (7p13)SFPQ (16q24.1) / TEAD4 (12p13.33)SFPQ (16q24.1) / TFE3 (Xp11.23)
TFE3 (Xp11.23) / SFPQ (16q24.1)


Transcription alternative splicing; 3 kb mRNA complete cds; coding sequence: CDS 86..2209


Description 707-712 amino acids; 76 kDa; N-term proline/glutamine rich domain, a prolin rich region, 2 tandem RNA binding domains, and C-term.
Localisation nucleus
Function splicing factor required early in spliceosome formation; form a complex with the polypyrimidine tract binding protein (PTB, herein the name); involved in pre-m RNA splicing step 2 (step 1: cut after exon n, intron n is still joined to exon n+1; step 2: cut between intron n and exon n+1, join exons n and n+1); forms a heterodimer with p54nrb (nuclear RNA binbing) a protein sharing vast homologies, encoded by NONO; both form complexes with DNA topoisomerase I, which renders this enzyme much more active.
Homology with the above mentioned NONE product and with other proteins with a DBHS domain (Drosophila behaviour, human splicing) which includes the tandem RNA binding domains.

Implicated in

Entity t(X;1)(p11.2;p34) in renal cell carcinoma --> PSF/TFE3
Disease t(X;1)(p11.2;p34) has only been found in a handfull cases of papillary renal cell carcinoma
Hybrid/Mutated Gene 5' PSF- 3' TFE3
Abnormal Protein N-term PSF and most of it fused to the DNA binding domains of TFE3 (excluding the acidic transcriptional activation domain, including the C-term helix-loop-helix, and the leucine zipper); no TFE3-PSF reciprocal transcript, as the der(X) t(X;1) is missing; the normal TFE3 transcript is found.


Fusion of splicing factor genes PSF and NonO (p54nrb) to the TFE3 gene in papillary renal cell carcinoma.
Clark J, Lu YJ, Sidhar SK, Parker C, Gill S, Smedley D, Hamoudi R, Linehan WM, Shipley J, Cooper CS
Oncogene. 1997 ; 15 (18) : 2233-2239.
PMID 9393982
A novel set of spliceosome-associated proteins and the essential splicing factor PSF bind stably to pre-mRNA prior to catalytic step II of the splicing reaction.
Gozani O, Patton JG, Reed R
The EMBO journal. 1994 ; 13 (14) : 3356-3367.
PMID 8045264
The RNA-splicing factor PSF/p54 controls DNA-topoisomerase I activity by a direct interaction.
Straub T, Grue P, Uhse A, Lisby M, Knudsen BR, Tange TO, Westergaard O, Boege F
The Journal of biological chemistry. 1998 ; 273 (41) : 26261-26264.
PMID 9756848


This paper should be referenced as such :
Huret, JL
PSF (PTB-associated splicing factor)
Atlas Genet Cytogenet Oncol Haematol. 1999;3(2):59-60.
Free journal version : [ pdf ]   [ DOI ]
On line version :

Other Leukemias implicated (Data extracted from papers in the Atlas) [ 1 ]
  t(1;9)(p34;q34) SFPQ/ABL1

Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 2+1 ]
  Kidney: Renal cell carcinoma with inv(X)(p11q12) NONO/TFE3
Kidney: Renal cell carcinomas with MiT family translocation
Kidney: Renal cell carcinoma with t(X;1)(p11;p34) SFPQ/TFE3

External links

HGNC (Hugo)-   -
Entrez_Gene (NCBI)SFPQ  6421  splicing factor proline/glutamine-rich
GeneCards (Weizmann)SFPQ
Ensembl hg19 (Hinxton) [Gene_View]  chr16:84226164-84230659 [Contig_View]  SFPQ [Vega]
Ensembl hg38 (Hinxton) [Gene_View]  chr16:84226164-84230659 [Contig_View]  SFPQ [Vega]
Genatlas (Paris)SFPQ
SOURCE (Princeton)SFPQ
Genetics Home Reference (NIH)SFPQ
Genomic and cartography
GoldenPath hg19 (UCSC)SFPQ  -     chr16:84226164-84230659 -  16q24.1   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)SFPQ  -     16q24.1   [Description]    (hg38-Dec_2013)
EnsemblSFPQ - 16q24.1 [CytoView hg19]  SFPQ - 16q24.1 [CytoView hg38]
Mapping of homologs : NCBISFPQ [Mapview hg19]  SFPQ [Mapview hg38]
Gene and transcription
Genbank (Entrez)AK095331 AK123582 DQ323994
RefSeq transcript (Entrez)NM_001039504
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)SFPQ
Cluster EST : UnigeneHs.614079 [ NCBI ]
CGAP (NCI)Hs.614079
Gene ExpressionSFPQ [ NCBI-GEO ]   SFPQ [ EBI - ARRAY_EXPRESS ]   SFPQ [ SEEK ]   SFPQ [ MEM ]
Gene Expression Viewer (FireBrowse)SFPQ [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)6421
GTEX Portal (Tissue expression)SFPQ
Protein : pattern, domain, 3D structure
UniProt/SwissProtP23246 (Uniprot)
NextProtP23246  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP23246
Splice isoforms : SwissVarP23246 (Swissvar)
Domaine pattern : Prosite (Expaxy)RRM (PS50102)   
Domains : Interpro (EBI)NOPS    Nucleotide-bd_a/b_plait    RRM_dom   
Domain families : Pfam (Sanger)NOPS (PF08075)    RRM_1 (PF00076)   
Domain families : Pfam (NCBI)pfam08075    pfam00076   
Domain families : Smart (EMBL)RRM (SM00360)  
DMDM Disease mutations6421
Blocks (Seattle)SFPQ
PDB (SRS)4WII    4WIJ    4WIK   
PDB (PDBSum)4WII    4WIJ    4WIK   
PDB (IMB)4WII    4WIJ    4WIK   
PDB (RSDB)4WII    4WIJ    4WIK   
Structural Biology KnowledgeBase4WII    4WIJ    4WIK   
SCOP (Structural Classification of Proteins)4WII    4WIJ    4WIK   
CATH (Classification of proteins structures)4WII    4WIJ    4WIK   
Peptide AtlasP23246
Protein Interaction databases
IntAct (EBI)P23246
Ontologies - Pathways
Ontology : AmiGO
Ontology : EGO-EBI
NDEx NetworkSFPQ
Atlas of Cancer Signalling NetworkSFPQ
Wikipedia pathwaysSFPQ
Orthology - Evolution
Phylogenetic Trees/Animal Genes : TreeFam-
Homologs : HomoloGeneSFPQ
Homology/Alignments : Family Browser (UCSC)SFPQ
Gene fusions - Rearrangements
Fusion : MitelmanSFPQ/ABL1 [16q24.1/9q34.12]  
Fusion : MitelmanSFPQ/TFE3 [16q24.1/Xp11.23]  [t(X;1)(p11;p34)]  
Fusion : MitelmanTFE3/SFPQ [Xp11.23/16q24.1]  [t(X;1)(p11;p34)]  
Fusion : COSMICSFPQ [1p34.3]  -  TFE3 [Xp11.23]  [fusion_801]  [fusion_802]  [fusion_803]  [fusion_804]  [fusion_914]  [fusion_915]  
Fusion: TCGASFPQ 16q24.1 TFE3 Xp11.23 KIRC
Fusion: TCGATFE3 Xp11.23 SFPQ 16q24.1 KIRC
Fusion : TICdbSFPQ [1p34.3]  -  ABL1 [9q34.12]
Fusion : TICdbSFPQ [1p34.3]  -  TFE3 [Xp11.23]
Fusion Cancer (Beijing)SFPQ [16q24.1]  -  FXYD5 [19q13.12]  [FUSC002256]  [FUSC002256]  [FUSC002256]
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerSFPQ [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SFPQ
Exome Variant ServerSFPQ
ExAC (Exome Aggregation Consortium)SFPQ (select the gene name)
Genetic variants : HAPMAP6421
Genomic Variants (DGV)SFPQ [DGVbeta]
DECIPHER (Syndromes)16:84226164-84230659  
CONAN: Copy Number AnalysisSFPQ 
ICGC Data Portal- 
TCGA Data Portal- 
Broad Tumor Portal-
OASIS Portal- [ Somatic mutations - Copy number]
Cancer Gene: CensusSFPQ 
Somatic Mutations in Cancer : COSMICSFPQ 
Mutations and Diseases : HGMD-
intOGen PortalSFPQ
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch SFPQ
DgiDB (Drug Gene Interaction Database)SFPQ
DoCM (Curated mutations)SFPQ (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SFPQ (select a term)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Genetic Testing Registry SFPQ
NextProtP23246 [Medical]
Huge Navigator - [HugePedia]
snp3D : Map Gene to Disease6421
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD6421
Clinical trialSFPQ
canSAR (ICR)SFPQ (select the gene name)
PubMed1 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Mon Oct 10 11:33:44 CEST 2016

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