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Aliases for SFPQ Gene

Aliases for SFPQ Gene

  • Splicing Factor Proline/Glutamine-Rich 2 3
  • PSF 3 4 6
  • Splicing Factor Proline/Glutamine Rich (Polypyrimidine Tract-Binding Protein-Associated) 2 3
  • Polypyrimidine Tract-Binding Protein-Associated-Splicing Factor 3 4
  • Polypyrimidine Tract Binding Protein Associated 2 3
  • DNA-Binding P52/P100 Complex, 100 KDa Subunit 3 4
  • PTB-Associated-Splicing Factor 3 4
  • 100 KDa DNA-Pairing Protein 3 4
  • HPOMp100 3 4
  • Splicing Factor Proline/Glutamine Rich (Polypyrimidine Tract Binding Protein Associated) 3
  • Polypyrimidine Tract-Binding Protein-Associated Splicing Factor 3
  • Protein Phosphatase 1, Regulatory Subunit 140 3
  • Splicing Factor, Proline- And Glutamine-Rich 3
  • PTB-Associated Splicing Factor 3
  • Regulatory Subunit 140 2
  • Protein Phosphatase 1 2
  • PPP1R140 3
  • POMP100 3

External Ids for SFPQ Gene

Summaries for SFPQ Gene

GeneCards Summary for SFPQ Gene

SFPQ (Splicing Factor Proline/Glutamine-Rich) is a Protein Coding gene. Diseases associated with SFPQ include renal cell carcinoma and translocation renal cell carcinoma. Among its related pathways are Development NOTCH1-mediated pathway for NF-KB activity modulation and mRNA Splicing - Major Pathway. GO annotations related to this gene include RNA binding and nucleotide binding. An important paralog of this gene is NONO.

UniProtKB/Swiss-Prot for SFPQ Gene

  • DNA- and RNA binding protein, involved in several nuclear processes. Essential pre-mRNA splicing factor required early in spliceosome formation and for splicing catalytic step II, probably as a heteromer with NONO. Binds to pre-mRNA in spliceosome C complex, and specifically binds to intronic polypyrimidine tracts. Involved in regulation of signal-induced alternative splicing. During splicing of PTPRC/CD45, a phosphorylated form is sequestered by THRAP3 from the pre-mRNA in resting T-cells; T-cell activation and subsequent reduced phosphorylation is proposed to lead to release from THRAP3 allowing binding to pre-mRNA splicing regulatotry elements which represses exon inclusion. Interacts with U5 snRNA, probably by binding to a purine-rich sequence located on the 3 side of U5 snRNA stem 1b. May be involved in a pre-mRNA coupled splicing and polyadenylation process as component of a snRNP-free complex with SNRPA/U1A. The SFPQ-NONO heteromer associated with MATR3 may play a role in nuclear retention of defective RNAs. SFPQ may be involved in homologous DNA pairing; in vitro, promotes the invasion of ssDNA between a duplex DNA and produces a D-loop formation. The SFPQ-NONO heteromer may be involved in DNA unwinding by modulating the function of topoisomerase I/TOP1; in vitro, stimulates dissociation of TOP1 from DNA after cleavage and enhances its jumping between separate DNA helices. The SFPQ-NONO heteromer may be involved in DNA non-homologous end joining (NHEJ) required for double-strand break repair and V(D)J recombination and may stabilize paired DNA ends; in vitro, the complex strongly stimulates DNA end joining, binds directly to the DNA substrates and cooperates with the Ku70/G22P1-Ku80/XRCC5 (Ku) dimer to establish a functional preligation complex. SFPQ is involved in transcriptional regulation. Transcriptional repression is mediated by an interaction of SFPQ with SIN3A and subsequent recruitment of histone deacetylases (HDACs). The SFPQ-NONO-NR5A1 complex binds to the CYP17 promoter and regulates basal and cAMP-dependent transcriptional avtivity. SFPQ isoform Long binds to the DNA binding domains (DBD) of nuclear hormone receptors, like RXRA and probably THRA, and acts as transcriptional corepressor in absence of hormone ligands. Binds the DNA sequence 5-CTGAGTC-3 in the insulin-like growth factor response element (IGFRE) and inhibits IGF-I-stimulated transcriptional activity. Regulates the circadian clock by repressing the transcriptional activator activity of the CLOCK-ARNTL/BMAL1 heterodimer. Required for the transcriptional repression of circadian target genes, such as PER1, mediated by the large PER complex through histone deacetylation.

Gene Wiki entry for SFPQ Gene

No data available for Entrez Gene Summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SFPQ Gene

Genomics for SFPQ Gene

Genomic Location for SFPQ Gene

Start:
35,176,378 bp from pter
End:
35,193,157 bp from pter
Size:
16,780 bases
Orientation:
Minus strand

Genomic View for SFPQ Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for SFPQ Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SFPQ Gene

Regulatory Elements for SFPQ Gene

Proteins for SFPQ Gene

  • Protein details for SFPQ Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P23246-SFPQ_HUMAN
    Recommended name:
    Splicing factor, proline- and glutamine-rich
    Protein Accession:
    P23246
    Secondary Accessions:
    • P30808
    • Q5SZ71

    Protein attributes for SFPQ Gene

    Size:
    707 amino acids
    Molecular mass:
    76149 Da
    Quaternary structure:
    • Monomer and component of the SFPQ-NONO complex, which is probably a heterotetramer of two 52 kDa (NONO) and two 100 kDa (SFPQ) subunits. SFPQ is a component of spliceosome and U5.4/6 snRNP complexes. Interacts with SNRPA/U1A. Component of a snRNP-free complex with SNRPA/U1A. Part of complex consisting of SFPQ, NONO and MATR3. Interacts with polypyrimidine tract-binding protein 1/PTB. Part of a complex consisting of SFPQ, NONO and NR5A1. Interacts with RXRA, probably THRA, and SIN3A. Interacts with TOP1. Part of a complex consisting of SFPQ, NONO and TOP1. Interacts with SNRNP70 in apoptotic cells. Interacts with PSPC1. Interacts with RNF43. Interacts with PITX3 and NR4A2/NURR1. Interacts with PTK6. Interacts with THRAP3; the interaction is dependent on SFPQ phosphorylation at Thr-687 and inhibits binding of SFPQ to a ESS1 exonic splicing silencer element-containing RNA. The large PER complex involved in the histone deacetylation is composed of at least HDAC1, PER2, SFPQ and SIN3A. Interacts with PER1 and PER2.

    Alternative splice isoforms for SFPQ Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SFPQ Gene

Proteomics data for SFPQ Gene at MOPED

Post-translational modifications for SFPQ Gene

  • Phosphorylated on multiple serine and threonine residues during apoptosis. In vitro phosphorylated by PKC. Phosphorylation stimulates binding to DNA and D-loop formation, but inhibits binding to RNA. Phosphorylation of C-terminal tyrosines promotes its cytoplasmic localization, impaired its binding to polypyrimidine RNA and led to cell cycle arrest. In resting T-cells is phosphorylated at Thr-687 by GSK3B which is proposed to promote association with THRAP and to prevent binding to PTPRC/CD45 pre-mRNA; T-cell activation leads to reduced phosphorylation at Thr-687.
  • The N-terminus is blocked
  • Modification sites at PhosphoSitePlus
  • Ubiquitination at Lys279, Lys319, Lys330, Lys338, and Lys413

Other Protein References for SFPQ Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for SFPQ Gene

Domains for SFPQ Gene

Gene Families for SFPQ Gene

HGNC:
  • RBM :RNA binding motif (RRM) containing

Protein Domains for SFPQ Gene

UniProtKB/Swiss-Prot:

SFPQ_HUMAN
Domain:
  • Contains 2 RRM (RNA recognition motif) domains.:
    • P23246
genes like me logo Genes that share domains with SFPQ: view

Function for SFPQ Gene

Molecular function for SFPQ Gene

GENATLAS Biochemistry: splicing factor proline/glutamine rich,widely expressed,interacting with polypyrimidine tract-binding protein PTB,essential factor in pre mRNA required early in spliceosome formation
UniProtKB/Swiss-Prot Function: DNA- and RNA binding protein, involved in several nuclear processes. Essential pre-mRNA splicing factor required early in spliceosome formation and for splicing catalytic step II, probably as a heteromer with NONO. Binds to pre-mRNA in spliceosome C complex, and specifically binds to intronic polypyrimidine tracts. Involved in regulation of signal-induced alternative splicing. During splicing of PTPRC/CD45, a phosphorylated form is sequestered by THRAP3 from the pre-mRNA in resting T-cells; T-cell activation and subsequent reduced phosphorylation is proposed to lead to release from THRAP3 allowing binding to pre-mRNA splicing regulatotry elements which represses exon inclusion. Interacts with U5 snRNA, probably by binding to a purine-rich sequence located on the 3 side of U5 snRNA stem 1b. May be involved in a pre-mRNA coupled splicing and polyadenylation process as component of a snRNP-free complex with SNRPA/U1A. The SFPQ-NONO heteromer associated with MATR3 may play a role in nuclear retention of defective RNAs. SFPQ may be involved in homologous DNA pairing; in vitro, promotes the invasion of ssDNA between a duplex DNA and produces a D-loop formation. The SFPQ-NONO heteromer may be involved in DNA unwinding by modulating the function of topoisomerase I/TOP1; in vitro, stimulates dissociation of TOP1 from DNA after cleavage and enhances its jumping between separate DNA helices. The SFPQ-NONO heteromer may be involved in DNA non-homologous end joining (NHEJ) required for double-strand break repair and V(D)J recombination and may stabilize paired DNA ends; in vitro, the complex strongly stimulates DNA end joining, binds directly to the DNA substrates and cooperates with the Ku70/G22P1-Ku80/XRCC5 (Ku) dimer to establish a functional preligation complex. SFPQ is involved in transcriptional regulation. Transcriptional repression is mediated by an interaction of SFPQ with SIN3A and subsequent recruitment of histone deacetylases (HDACs). The SFPQ-NONO-NR5A1 complex binds to the CYP17 promoter and regulates basal and cAMP-dependent transcriptional avtivity. SFPQ isoform Long binds to the DNA binding domains (DBD) of nuclear hormone receptors, like RXRA and probably THRA, and acts as transcriptional corepressor in absence of hormone ligands. Binds the DNA sequence 5-CTGAGTC-3 in the insulin-like growth factor response element (IGFRE) and inhibits IGF-I-stimulated transcriptional activity. Regulates the circadian clock by repressing the transcriptional activator activity of the CLOCK-ARNTL/BMAL1 heterodimer. Required for the transcriptional repression of circadian target genes, such as PER1, mediated by the large PER complex through histone deacetylation.

Gene Ontology (GO) - Molecular Function for SFPQ Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000166 nucleotide binding IEA --
GO:0000976 transcription regulatory region sequence-specific DNA binding ISS --
GO:0001047 core promoter binding ISS --
GO:0003676 nucleic acid binding --
GO:0005515 protein binding IPI 10653975
genes like me logo Genes that share ontologies with SFPQ: view
genes like me logo Genes that share phenotypes with SFPQ: view

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targeting and HOMER Transcription for SFPQ Gene

Localization for SFPQ Gene

Subcellular locations from UniProtKB/Swiss-Prot for SFPQ Gene

Nucleus matrix. Cytoplasm. Note=Predominantly in nuclear matrix.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for SFPQ Gene COMPARTMENTS Subcellular localization image for SFPQ gene
Compartment Confidence
nucleus 5

Gene Ontology (GO) - Cellular Components for SFPQ Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000785 chromatin IDA 16731528
GO:0005634 nucleus IDA 15790595
GO:0005654 nucleoplasm IDA --
GO:0005737 cytoplasm IEA --
GO:0016363 nuclear matrix IDA 19874820
genes like me logo Genes that share ontologies with SFPQ: view

Pathways for SFPQ Gene

genes like me logo Genes that share pathways with SFPQ: view

Pathways by source for SFPQ Gene

1 GeneGo (Thomson Reuters Life Sciences Research) pathway for SFPQ Gene
1 BioSystems pathway for SFPQ Gene

Gene Ontology (GO) - Biological Process for SFPQ Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription from RNA polymerase II promoter IMP 22783022
GO:0000380 alternative mRNA splicing, via spliceosome IMP 19874820
GO:0000724 double-strand break repair via homologous recombination IMP 20813759
GO:0006281 DNA repair --
GO:0006310 DNA recombination --
genes like me logo Genes that share ontologies with SFPQ: view

Compounds for SFPQ Gene

(1) HMDB Compounds for SFPQ Gene

Compound Synonyms Cas Number PubMed IDs
Cyclic AMP
  • Cyclic AMP
60-92-4

(5) Novoseek inferred chemical compound relationships for SFPQ Gene

Compound -log(P) Hits PubMed IDs
pyrimidine 49.2 4
steroid 14.1 1
progesterone 11 1
testosterone 0 3
serine 0 1
genes like me logo Genes that share compounds with SFPQ: view

Transcripts for SFPQ Gene

Unigene Clusters for SFPQ Gene

Splicing factor proline/glutamine-rich:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for SFPQ Gene

ExUns: 1 ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6 ^ 7a · 7b ^ 8 ^ 9a · 9b · 9c ^ 10 ^ 11 ^ 12 ^ 13
SP1: - -
SP2: - - -
SP3:
SP4:

Relevant External Links for SFPQ Gene

GeneLoc Exon Structure for
SFPQ
ECgene alternative splicing isoforms for
SFPQ

Expression for SFPQ Gene

mRNA expression in normal human tissues for SFPQ Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for SFPQ Gene

SOURCE GeneReport for Unigene cluster for SFPQ Gene Hs.355934

genes like me logo Genes that share expressions with SFPQ: view

Orthologs for SFPQ Gene

This gene was present in the common ancestor of animals.

Orthologs for SFPQ Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SFPQ 36
  • 99.39 (n)
  • 100 (a)
SFPQ 37
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia SFPQ 36
  • 94.49 (n)
  • 100 (a)
SFPQ 37
  • 97 (a)
OneToOne
dog
(Canis familiaris)
Mammalia -- 37
  • 98 (a)
OneToMany
-- 37
  • 87 (a)
OneToMany
-- 37
  • 90 (a)
OneToMany
SFPQ 36
  • 90.76 (n)
  • 96.39 (a)
mouse
(Mus musculus)
Mammalia Sfpq 36
  • 92.08 (n)
  • 98.35 (a)
Sfpq 16
Sfpq 37
  • 95 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SFPQ 37
  • 87 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SFPQ 37
  • 98 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Sfpq 36
  • 92.08 (n)
  • 98.35 (a)
chicken
(Gallus gallus)
Aves SFPQ 36
  • 82.46 (n)
  • 94.51 (a)
SFPQ 37
  • 81 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SFPQ 37
  • 77 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xl.1807 36
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.1954 36
zebrafish
(Danio rerio)
Actinopterygii sfpq 36
  • 67.99 (n)
  • 73.36 (a)
sfpq 37
  • 58 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta nonA 37
  • 28 (a)
ManyToMany
nonA-l 37
  • 30 (a)
ManyToMany
worm
(Caenorhabditis elegans)
Secernentea nono-1 37
  • 35 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 37
  • 44 (a)
OneToMany
Species with no ortholog for SFPQ:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for SFPQ Gene

ENSEMBL:
Gene Tree for SFPQ (if available)
TreeFam:
Gene Tree for SFPQ (if available)

Paralogs for SFPQ Gene

Paralogs for SFPQ Gene

Selected SIMAP similar genes for SFPQ Gene using alignment to 6 proteins:

Pseudogenes.org Pseudogenes for SFPQ Gene

genes like me logo Genes that share paralogs with SFPQ: view

Variants for SFPQ Gene

Sequence variations from dbSNP and Humsavar for SFPQ Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type MAF
rs11413 -- 35,178,261(-) TTAAA(A/G)AAAAT utr-variant-3-prime, intron-variant
rs14848 -- 35,177,996(-) TCATT(A/C)ACATG utr-variant-3-prime
rs1053946 -- 35,183,155(-) TGCTA(C/T)TTCTG downstream-variant-500B, utr-variant-3-prime, intron-variant
rs1053947 -- 35,182,952(-) CACCA(A/T)AAAGG utr-variant-3-prime, intron-variant
rs1136726 -- 35,177,343(-) AAGCC(A/C)CAAGC utr-variant-3-prime, intron-variant

Structural Variations from Database of Genomic Variants (DGV) for SFPQ Gene

Variant ID Type Subtype PubMed ID
nsv870757 CNV Gain 21882294
nsv508149 CNV Loss 20534489

Relevant External Links for SFPQ Gene

HapMap Linkage Disequilibrium report
SFPQ
Human Gene Mutation Database (HGMD)
SFPQ

Disorders for SFPQ Gene

UniProtKB/Swiss-Prot

SFPQ_HUMAN
  • Note=A chromosomal aberration involving SFPQ may be a cause of papillary renal cell carcinoma (PRCC). Translocation t(X;1)(p11.2;p34) with TFE3.

Relevant External Links for SFPQ

Genetic Association Database (GAD)
SFPQ
genes like me logo Genes that share disorders with SFPQ: view

Publications for SFPQ Gene

  1. Cloning and characterization of PSF, a novel pre-mRNA splicing factor. (PMID: 8449401) Patton J.G. … Nadal-Ginard B. (Genes Dev. 1993) 2 3 4 23
  2. The RNA-splicing factor PSF/p54 controls DNA-topoisomerase I activity by a direct interaction. (PMID: 9756848) Straub T. … Boege F. (J. Biol. Chem. 1998) 3 4 23
  3. The snRNP-free U1A (SF-A) complex(es): identification of the largest subunit as PSF, the polypyrimidine-tract binding protein-associated splicing factor. (PMID: 9848648) Lutz C.S. … Alwine J.C. (RNA 1998) 3 4 23
  4. Human 100-kDa homologous DNA-pairing protein is the splicing factor PSF and promotes DNA strand invasion. (PMID: 10931916) Akhmedov A.T. … Lopez B.S. (Nucleic Acids Res. 2000) 3 4 23
  5. PSF is a novel corepressor that mediates its effect through Sin3A and the DNA binding domain of nuclear hormone receptors. (PMID: 11259580) Mathur M. … Samuels H.H. (Mol. Cell. Biol. 2001) 3 4 23

Products for SFPQ Gene

  • Addgene plasmids for SFPQ

Sources for SFPQ Gene

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