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SFPQ (PTB-associated splicing factor)

Identity

Other namesPSF (PTB-associated splicing factor)
SFPQ (splicing factor proline/glutamine rich)
HGNC (Hugo) SFPQ
Location 1p34
Location_base_pair Starts at 35649203 and ends at 35658743 bp from pter ( according to hg19-Feb_2009)  [Mapping]

DNA/RNA

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

Protein

 
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.
  

External links

Nomenclature
HGNC (Hugo)SFPQ   10774
Entrez_Gene (NCBI)SFPQ  6421  splicing factor proline/glutamine-rich
Cards
AtlasPSFID167
GeneCards (Weizmann)SFPQ
Ensembl (Hinxton)ENSG00000116560 [Gene_View]  SFPQ [Vega]
AceView (NCBI)SFPQ
Genatlas (Paris)SFPQ
euGene (Indiana)6421
SOURCE (Stanford)NM_005066
Gene Expression (Array Express) ENSG00000116560
Genomic and cartography
GoldenPath (UCSC)SFPQ  -  1p34   chr1:35649203-35658743 -  1p34.3   [Description]    (hg19-Feb_2009)
EnsemblSFPQ - 1p34.3 [CytoView]
Mapping of homologs : NCBISFPQ [Mapview]
OMIM605199   
Gene and transcription
Gene : Genbank (Entrez)AK307985 BC000546 BC004534 BC027708 BC027717
Reference sequence (RefSeq transcript) :SRSNM_005066
Reference transcript : EntrezNM_005066
RefSeq genomic : SRSAC_000044 AC_000133 NC_000001 NT_032977 NW_001838577 NW_921351
RefSeq genomic : EntrezAC_000044 AC_000133 NC_000001 NT_032977 NW_001838577 NW_921351
Consensus coding sequences : CCDS NCBISFPQ
Cluster EST : UnigeneHs.355934 [ SRS ] Hs.355934 [ NCBI ]
Alternative Splicing : Fast-db (Paris)13429
Protein : pattern, domain, 3D structure
Protein : UniProt/SwissProtP23246 (SRS) P23246 (Expasy) P23246 (Uniprot)
With graphics : InterProP23246
Splice isoforms : VarSplice FASTAP23246(VarSplice FASTA)
Domaine pattern : Prosite (SRS)RRM (PS50102)   
Domain pattern : Prosite (Expaxy)RRM (PS50102)   
Domains : Interpro (SRS)a_b_plait_nuc_bd    NOPS    RRM_RNP1   
Domains : Interpro (EBI)a_b_plait_nuc_bd    NOPS    RRM_RNP1   
Related proteins : CluSTrP23246
Domain families : Pfam SRSNOPS (PF08075)    RRM_1 (PF00076)   
Domain families : Pfam SangerNOPS (PF08075)    RRM_1 (PF00076)   
Domain families : Pfam NCBIpfam08075    pfam00076   
Domain families : Smart EMBLRRM (SM00360)  
Blocks (Seattle)P23246
Crystal structure of protein : PDB SRS
Crystal structure of protein : PDBSum
Crystal structure of protein : IMB
Crystal structure of protein : PDB RSDB
Human Protein AtlasENSG00000116560
HPRD07284
Protein Interaction databases
DIP (DOE-UCLA)P23246
IntAct (EBI)P23246
FunCoupENSG00000116560
Polymorphism : SNP, mutations, diseases
Single Nucleotide Polymorphism (SNP) : dbSNP NCBISFPQ
SNP : GeneSNP UtahSFPQ
SNP : HGBaseSFPQ
Genetic variants : HAPMAPSFPQ
Cancer Gene: CensusSFPQ 
Somatic Mutations in Cancer : COSMICSFPQ 
Mutations and Diseases : HGMDSFPQ
Hereditary diseases : OMIM605199   
Hereditary diseases : GENETests605199   
Diseases : Genetic AssociationSFPQ
General knowledge
Homologs : HomoloGeneSFPQ
Homology/Alignments : Family Browser UCSCSFPQ
Phylogenetic Trees/Animal Genes : TreeFamSFPQ
Chemical/Protein Interactions : CTD6421
Keywords Ontology : AmiGOnucleotide binding  alternative nuclear mRNA splicing, via spliceosome  DNA binding  RNA binding  protein binding  nucleus  nucleoplasm  DNA repair  DNA recombination  mRNA processing  RNA splicing  nuclear matrix  paraspeckles  regulation of transcription  
Keywords Ontology : EGO-EBInucleotide binding  alternative nuclear mRNA splicing, via spliceosome  DNA binding  RNA binding  protein binding  nucleus  nucleoplasm  DNA repair  DNA recombination  mRNA processing  RNA splicing  nuclear matrix  paraspeckles  regulation of transcription  
Pathways : BIOCARTARNA polymerase III transcription [Genes]   
Pathways : KEGG
Other databases
Probes
Probes : ImagenesSFPQ Related clones (RZPD - Berlin)
Literature
PubMed53 Pubmed reference(s) in Entrez
PubGeneSFPQ

Bibliography

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
 
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
 
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
 
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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Contributor(s)

Written01-1999Jean-Loup Huret

Citation

This paper should be referenced as such :
Huret JL . SFPQ (PTB-associated splicing factor). Atlas Genet Cytogenet Oncol Haematol. January 1999 .
URL : http://AtlasGeneticsOncology.org/Genes/PSFID167.html

© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Thu Jul 15 14:45:11 CEST 2010

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