PSF (PTB-associated splicing factor)

Identity

Other names	SFPQ (splicing factor proline/glutamine rich)
HGNC	SFPQ
Location	1p34

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	SFPQ   10774
Entrez_Gene	SFPQ  6421  splicing factor proline/glutamine-rich (polypyrimidine tract binding protein associated)
	Cards
Atlas	PSFID167
GeneCards	SFPQ
Ensembl	SFPQ [Search_View]   ENSG00000116560 [Gene_View]
Genatlas	SFPQ
GeneLynx	SFPQ
eGenome	SFPQ
euGene	6421
	Genomic and cartography
GoldenPath	SFPQ  -  1p34   chr1:35421788-35431322 -  1p34.3   [Description]    (hg18-Mar_2006)
Ensembl	SFPQ - 1p34.3 [CytoView]
NCBI	Mapview
OMIM	Disease map [OMIM]
HomoloGene	SFPQ
	Gene and transcription
Genbank	AK307985 [ ENTREZ ]
Genbank	BC004534 [ ENTREZ ]
Genbank	BC027708 [ ENTREZ ]
Genbank	BC027717 [ ENTREZ ]
Genbank	BC051192 [ ENTREZ ]
RefSeq	NM_005066 [ SRS ]    NM_005066 [ ENTREZ ]
RefSeq	AC_000044 [ SRS ]    AC_000044 [ ENTREZ ]
RefSeq	AC_000133 [ SRS ]    AC_000133 [ ENTREZ ]
RefSeq	NC_000001 [ SRS ]    NC_000001 [ ENTREZ ]
RefSeq	NT_032977 [ SRS ]    NT_032977 [ ENTREZ ]
RefSeq	NW_001838577 [ SRS ]    NW_001838577 [ ENTREZ ]
RefSeq	NW_921351 [ SRS ]    NW_921351 [ ENTREZ ]
AceView	SFPQ AceView - NCBI
Unigene	Hs.355934 [ SRS ]    Hs.355934 [ NCBI ]     HS355934 [ spliceNest ]
Fast-db	13429 (alternative variants)
	Protein : pattern, domain, 3D structure
SwissProt	P23246 [ SRS]    P23246 [ EXPASY ]     P23246 [ INTERPRO ]     P23246 [ UNIPROT ]
Prosite	PS50102 RRM [ SRS ]    PS50102 RRM [ Expasy ]
Interpro	IPR012677 a_b_plait_nuc_bd [ SRS ]    IPR012677 a_b_plait_nuc_bd [ EBI ]
Interpro	IPR012975 NOPS [ SRS ]    IPR012975 NOPS [ EBI ]
Interpro	IPR000504 RRM_RNP1 [ SRS ]    IPR000504 RRM_RNP1 [ EBI ]
CluSTr	P23246
Pfam	PF08075 NOPS [ SRS ]    PF08075 NOPS [ Sanger ]    pfam08075 [ NCBI-CDD ]
Pfam	PF00076 RRM_1 [ SRS ]    PF00076 RRM_1 [ Sanger ]    pfam00076 [ NCBI-CDD ]
Smart	SM00360 RRM [EMBL]
Blocks	P23246
HPRD	07284
	Protein Interaction databases
DIP	P23246
IntAct	P23246
	Polymorphism : SNP, mutations, diseases
OMIM	605199    [ map ]
GENECLINICS	605199
SNP	SFPQ [dbSNP-NCBI]
SNP	NM_005066 [SNP-NCI]
SNP	SFPQ [GeneSNPs - Utah]  SFPQ] [HGBASE - SRS]
HAPMAP	SFPQ [HAPMAP]
COSMIC	SFPQ [Somatic mutation (COSMIC-CGP-Sanger)]
HGMD	SFPQ
	General knowledge
Family Browser	SFPQ [UCSC Family Browser]
SOURCE	NM_005066
SMD	Hs.355934
SAGE	Hs.355934
GO	nucleotide binding [Amigo]  nucleotide binding
GO	DNA binding [Amigo]  DNA binding
GO	RNA binding [Amigo]  RNA binding
GO	protein binding [Amigo]  protein binding
GO	nucleus [Amigo]  nucleus
GO	DNA repair [Amigo]  DNA repair
GO	DNA recombination [Amigo]  DNA recombination
GO	transcription [Amigo]  transcription
GO	regulation of transcription, DNA-dependent [Amigo]  regulation of transcription, DNA-dependent
GO	mRNA processing [Amigo]  mRNA processing
GO	RNA splicing [Amigo]  RNA splicing
GO	nuclear matrix [Amigo]  nuclear matrix
BIOCARTA	RNA polymerase III transcription    [Genes]
PubGene	SFPQ
TreeFam	SFPQ
CTD	6421 [Comparative ToxicoGenomics Database]
	Other databases
	Probes
Probe	SFPQ Related clones (RZPD - Berlin)
	PubMed
PubMed	43 Pubmed reference(s) in LocusLink

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 articles	automatic search in PubMed
Last year publications	automatic search in PubMed

Search in all EBI   NCBI

Contributor(s)

Written	01-1999	Jean-Loup Huret

Citation

This paper should be referenced as such :

Huret JL . PSF (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 : Mon Aug 11 21:16:42 2008