Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0002387
UniProt IDQ9UHX1
Primary gene name(s)PUF60
Synonym gene name(s)FIR, ROBPI, SIAHBP1
Protein namePoly(U-binding-splicing factor PUF60
Protein functionDNA- and RNA-binding protein, involved in several nuclear processes such as pre-mRNA splicing, apoptosis and transcription regulation. In association with FUBP1 regulates MYC transcription at the P2 promoter through the core-TFIIH basal transcription factor. Acts as a transcriptional repressor through the core-TFIIH basal transcription factor. Represses FUBP1-induced transcriptional activation but not basal transcription. Decreases ERCC3 helicase activity. Does not repress TFIIH-mediated transcription in xeroderma pigmentosum complementation group B, XPB cells. Is also involved in pre-mRNA splicing. Promotes splicing of an intron with weak 3'-splice site and pyrimidine tract in a cooperative manner with U2AF2. Involved in apoptosis induction when overexpressed in HeLa cells. Isoform 6 failed to repress MYC transcription and inhibited FIR-induced apoptosis in colorectal cancer. Isoform 6 may contribute to tumor progression by enabling increased MYC expression and greater resistance to apoptosis in tumors than in normal cells. Modulates alternative splicing of several mRNAs. Binds to relaxed DNA of active promoter regions. Binds to the pyrimidine tract and 3'-splice site regions of pre-mRNA; binding is enhanced in presence of U2AF2. Binds to Y5 RNA in association with TROVE2. Binds to poly(U RNA. {ECO:0000269|PubMed:10606266, ECO:0000269|PubMed:10882074, ECO:0000269|PubMed:11239393, ECO:0000269|PubMed:16452196, ECO:0000269|PubMed:16628215, ECO:0000269|PubMed:17579712}.
Subcellular locationNucleus {ECO:0000269|PubMed:10668799, ECO:0000269|PubMed:17579712}. Note=Colocalizes partially with TROVE2.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: Q9UHX1
Gene Ontology
(Biological Process)
Complete annatation
apoptotic process [GO:0006915];
mRNA processing [GO:0006397];
regulation of transcription, DNA-templated [GO:0006355];
RNA splicing [GO:0008380];
transcription, DNA-templated [GO:0006351]
Gene Ontology
(Molecular Function)
Complete annatation
DNA binding [GO:0003677];
identical protein binding [GO:0042802];
nucleotide binding [GO:0000166];
poly(A RNA binding [GO:0044822]
Gene Ontology
(Cellular Component)
Complete annatation
cell junction [GO:0030054];
intracellular ribonucleoprotein complex [GO:0030529];
nucleoplasm [GO:0005654]
Protein-protein interaction116502
Phylogenetic treeQ9UHX1
HIV replication factor status Zhou et al., Cell. Host. Microbe., 2008
Brass et al., Science, 2008
Smith et al., J. Immunol, 2010
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. CD31.363921538747264.33426937399561e-050.000230834303904106
AZA vs. DISU-0.1368308639314690.5888270576061280.955158276076142
AZA vs. IL70.2004579097027450.2974823862354590.999311006273513
AZA vs. SAHA-0.4094594236209690.094735832126960.388267518619303
DISU vs. CD3-1.513052889042734.33208181636058e-050.000272317770224434
DISU vs. IL70.3277907869198330.1938257231283920.568246358646541
DISU vs. SAHA-0.269989170340690.3571375406947970.734300119483122
DMSO vs. AZA0.04975872809965720.7667549227689481
DMSO vs. CD3-1.327840320332414.49774377810908e-050.000220711759013724
DMSO vs. DISU0.1842467141400130.4504837343150080.888470621945532
DMSO vs. IL70.1583326474211550.3788165646449010.832872524258073
DMSO vs. SAHA-0.4635531418545420.05037772166775210.253503386729447
HIV vs. Mock in Activation0.01804665201059370.976961776188170.999983755607037
HIV vs. Mock in Latency-0.06426459123731380.6978354207112360.999834320637052
IL7 vs. CD3-1.15767823148640.0003812470939124070.00185133294025184
SAHA vs. CD3-1.79630716330979.50144305456035e-077.72312550335623e-06
SAHA vs. IL7-0.61203571752090.01243897508819390.0730729191268258
(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
unknown unknown

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 -1.034125426
(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 -0.0859478 0.607069
(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
1.064 1.087 0.92 0.915 0.923
(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
2DNY NMR - A=454-559.
2KXF NMR - A=119-314.
2KXH NMR - A=119-314.
2QFJ X-ray 2.1Å A/B=118-316.
3DXB X-ray 2.2Å A/B/C/D/E/F/G/H=460-499.
3UE2 X-ray 1.2Å A=443-559.
3US5 X-ray 1.3Å A=443-559.
3UWT X-ray 2.5Å A=118-316.

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

not found

Metabolic/Signalling Pathway       (annotations from KEGG database)      top

Pathway Accession Number Description
hsa03040 Spliceosome - Homo sapiens (human)