Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0002649
UniProt IDP23246
Primary gene name(s)SFPQ
Synonym gene name(s)PSF
Protein nameSplicing factor, proline- and glutamine-rich
Protein functionDNA- 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(DJ 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. {ECO:0000269|PubMed:10847580, ECO:0000269|PubMed:10858305, ECO:0000269|PubMed:10931916, ECO:0000269|PubMed:11259580, ECO:0000269|PubMed:11525732, ECO:0000269|PubMed:11897684, ECO:0000269|PubMed:15590677, ECO:0000269|PubMed:20932480, ECO:0000269|PubMed:8045264, ECO:0000269|PubMed:8449401}.
Subcellular locationNucleus matrix {ECO:0000269|PubMed:10653975, ECO:0000269|PubMed:19439179, ECO:0000269|PubMed:9848648}. Cytoplasm {ECO:0000269|PubMed:19439179}. Note=Predominantly in nuclear matrix. {ECO:0000269|PubMed:19439179}.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: P23246
Gene Ontology
(Biological Process)
Complete annatation
alternative mRNA splicing, via spliceosome [GO:0000380];
chromosome organization [GO:0051276];
double-strand break repair via homologous recombination [GO:0000724];
histone H3 deacetylation [GO:0070932];
mRNA processing [GO:0006397];
negative regulation of circadian rhythm [GO:0042754];
negative regulation of transcription, DNA-templated [GO:0045892];
negative regulation of transcription from RNA polymerase II promoter [GO:0000122];
positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway [GO:1902177];
positive regulation of sister chromatid cohesion [GO:0045876];
regulation of circadian rhythm [GO:0042752];
rhythmic process [GO:0048511];
RNA splicing [GO:0008380];
transcription, DNA-templated [GO:0006351]
Gene Ontology
(Molecular Function)
Complete annatation
chromatin binding [GO:0003682];
core promoter binding [GO:0001047];
histone deacetylase binding [GO:0042826];
nucleotide binding [GO:0000166];
poly(A RNA binding [GO:0044822];
RNA polymerase II distal enhancer sequence-specific DNA binding [GO:0000980];
transcription regulatory region DNA binding [GO:0044212];
transcription regulatory region sequence-specific DNA binding [GO:0000976]
Gene Ontology
(Cellular Component)
Complete annatation
chromatin [GO:0000785];
cytoplasm [GO:0005737];
nuclear matrix [GO:0016363];
nucleoplasm [GO:0005654];
nucleus [GO:0005634];
paraspeckles [GO:0042382];
RNA polymerase II transcription factor complex [GO:0090575]
Protein-protein interaction112319
Phylogenetic treeP23246
HIV replication factor status Zhou et al., Cell. Host. Microbe., 2008
Brass et al., Science, 2008
Smith et al., J. Immunol, 2010
      Negatively associated
gene status
Lu et al., J. Virol., 2011
      Folds changes 8h: unknown; Folds changes 16h: unknown; Tested: unknown;
Schoggins JW and Rice CM, Curr. Opin. Virol., 2011
      Targeted viruses: unknown
      Viral life cycle: unknown
      Mechanism related to antiviral activity: unknown
Anti-viral restriction factor Liu et al., Retrovirology, 2011
      unknown (Triplicates)

Gene Expression Profile       top

            Up-regulated;            Down-regulated

For brief introduction to each study, please go to the help page.

Gene expression during HIV latency

(1). Mohammadi et al., PLoS Pathog., 2014

Differentially expressed transcripts (Pairwise) during latency and subsequent viral reactivation using several agents - Primary CD4+ T-cell based model

DMSO: Dimethyl suloxyde (negative control) - 0.0033% final
SAHA: Vorinostat (Histone deacetylase inhibitor) - 0.5 μM
CD3: TCR Stimulation by IL-2+ antiCD3/anti-CD28 antibodies
IL7: Interleukin-7 based stimulation
DISU: Disulfiram (alcohol dehydrogenase inhibitor) - 0.5 μM
AZA: 5-azacytidine (AZA; DNA methylation inhibitor) - 1 μM
Experimental Condition Log2 Fold Change P value Adjusted P value
AZA vs. CD31.068597987844020.001254098482298740.00443079520047036
AZA vs. DISU0.01390551171203560.9560817484678240.996649735504266
AZA vs. IL70.2661636647163630.1650999220314850.931425241577222
AZA vs. SAHA-0.1364926927669530.5751747517104770.859200187746071
DISU vs. CD3-1.067513338359580.003533489087739980.0121718040467533
DISU vs. IL70.2429245246680980.3346416992898390.714454583833189
DISU vs. SAHA-0.1484639166289020.6107446191552030.877659065018429
DMSO vs. AZA0.04680089020785270.7866050200836541
DMSO vs. CD3-1.029176038933630.001454716294003510.00473946820267364
DMSO vs. DISU0.03226088349404840.8946278589716160.988283279918411
DMSO vs. IL70.2260998437787780.2072089678690010.716699329473652
DMSO vs. SAHA-0.1906307455727880.4179925341436010.758070455123732
HIV vs. Mock in Activation0.1913833068610590.7580652195706510.999983755607037
HIV vs. Mock in Latency0.09489425560659360.5636652437778460.999834320637052
IL7 vs. CD3-0.7959573775286570.01400315204691970.0392979912126645
SAHA vs. CD3-1.228895384876970.0006356916295007230.00241428247393546
SAHA vs. IL7-0.4053567173543220.09572170828429090.280084719152395
(2). Iglesias-Ussel et al., J. Virol., 2013

Up and Downregulated transcripts during Latency (Latently infected CD4+ T cells vs Uninfected)- Primary CD4+Tcell based model
Log2 Fold Change P Value
-0.3747 0.03673

Gene expression during HIV infection and replication

(1). Imbeault et al., PloS Pathog., 2012

Transcriptomic profiling of HIV-1 infected CD4+ T cells - Primary CD4+ T cells
Experiment type Log2 Fold Change P Value Adjusted P Value
Infected vs. Mock unknown unknown unknown
Infected vs. Bystander unknown unknown unknown
(2). Lefebvre et al., J. Virol., 2011

Transcriptome analysis of T-cell line (Sup T1)
Log2 Fold Change -1.060513846
(3). Li et al., J. Immunol., 2013

Lymphatic tissue
Acute Fold Change Acute P Value Asymt Fold Change Asypt P Value AIDS Fold Change AIDS P Value
unknown unknown unknown unknown unknown unknown
(4). Chang et al., MBio., 2011

Transcriptome analysis of T-cell line (Sup T1)

Derived from Sherrill-Mix et al., BMC Retrovirol., 2015 cross validation
Up-regulated (True) FALSE
(5). Sherrill-Mix et al., BMC Retrovirol., 2015

Deep RNA-seq analysis of primary human T cell infected with low passage HIV isolate HIV89.6 - Primary CD4+ T cell based
Test Status Log2 Fold Change P Value
OK 0.231057 0.0859935
(6). Rotger et al., PLoS Pathog., 2010

Genome-wide mRNA expression of CD4+ T cells from HIV-infected patient
(Genes differentially expressed (at adjusted p<0.01) according to the empirical Bayes approach)
Log2 Fold Change P Value
unknown unknown

Proteomic/Transcriptomics studies indicating differentially expressed genes mediated by HIV

(1). Greenwood et al., Elife, 2016

Activated (CD3/CD28) Primary human CD4+ T cells infected with pNL4-3-dE-EGFP. The table shows the complete (unfiltered) TMT (tandem mass tag)-based proteomic time course dataset
6 h 24 h 48 h 72 h RTi
1.034 0.931 0.801 0.808 0.908
(2). Navare et al., Virology, 2012

SUP-T1 cell line
FC-4hpi P-value FC-8hpi P-value FC-20hpi P-value Category
unknown unknown unknown unknown unknown unknown unknown
(3). Hyrcza et al., J. Virolo., 2007

Primary human CD4+ and CD8+ T Cells
Affymetrix Prob ID Fold Change In CD8? Category
unknown unknown unknown unknown

Protein Overview       top

Drug-protein Interaction       (annotations from DrugBank)      top

not found

Protein Secondary Structure       (annotations from PDB)      top

PDB Accession Method Resolution Chain Structure Preview
4WII X-ray 2.0Å A/B=276-535.
4WIJ X-ray 3.4Å A/B=276-598.
4WIK X-ray 3.0Å A/B=369-598.

HIV-1 Interaction       (annotations from NCBI HIV-1 Interaction Database)      top

HIV Partner Interaction Type PubMed
Rev interacts with 22174317
Envelope surface glycoprotein gp120 complexes with 23125841
Gag-Pol complexes with 23125841
Rev regulated by 23158102
Pr55(Gag) complexes with 23125841
Nef complexes with 23125841

Metabolic/Signalling Pathway       (annotations from KEGG database)      top

Pathway Accession Number Description
not found