Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0002019
UniProt IDO43809
Primary gene name(s)NUDT21
Synonym gene name(s)CFIM25, CPSF25, CPSF5
Protein nameCleavage and polyadenylation specificity factor subunit 5
Protein functionComponent of the cleavage factor Im, CFIm complex that plays a key role in pre-mRNA 3'-processing. Involved in association with CPSF6 or CPSF7 in pre-MRNA 3'-end poly(A site cleavage and poly(A addition. NUDT21/CPSF5 binds to cleavage and polyadenylation RNA substrates. The homodimer mediates simultaneous sequence-specific recognition of two 5'-UGUA-3' elements within the pre-mRNA. Binds to, but does not hydrolyze mono- and di-adenosine nucleotides. May have a role in mRNA export. {ECO:0000269|PubMed:14690600, ECO:0000269|PubMed:20479262, ECO:0000269|PubMed:20695905, ECO:0000269|PubMed:21295486, ECO:0000269|PubMed:8626397, ECO:0000269|PubMed:9659921}.
Subcellular locationNucleus {ECO:0000269|PubMed:15169763, ECO:0000269|PubMed:20695905, ECO:0000269|PubMed:9659921}. Note=In punctate subnuclear structures localized adjacent to nuclear speckles, called paraspeckles.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: O43809
Gene Ontology
(Biological Process)
Complete annatation
mRNA 3'-end processing [GO:0031124];
mRNA polyadenylation [GO:0006378];
mRNA processing [GO:0006397];
mRNA splicing, via spliceosome [GO:0000398];
protein tetramerization [GO:0051262];
termination of RNA polymerase II transcription [GO:0006369]
Gene Ontology
(Molecular Function)
Complete annatation
AU-rich element binding [GO:0017091];
histone deacetylase binding [GO:0042826];
hydrolase activity [GO:0016787];
mRNA binding [GO:0003729];
poly(A RNA binding [GO:0044822];
protein homodimerization activity [GO:0042803]
Gene Ontology
(Cellular Component)
Complete annatation
centrosome [GO:0005813];
microtubule organizing center [GO:0005815];
mRNA cleavage factor complex [GO:0005849];
nucleoplasm [GO:0005654];
nucleus [GO:0005634];
paraspeckles [GO:0042382]
Protein-protein interaction116237
Phylogenetic treeO43809
HIV replication factor status Zhou et al., Cell. Host. Microbe., 2008
      unknown
Brass et al., Science, 2008
      unknown
Smith et al., J. Immunol, 2010
      unknown
Interferon-stimulated
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. CD30.9798416790341130.003158113214403180.00984672783770888
AZA vs. DISU0.01819470876564310.9426934868813850.996198528027442
AZA vs. IL70.152585698592850.4268751510458790.999311006273513
AZA vs. SAHA0.01394329103553050.9543727275736650.990329939023704
DISU vs. CD3-0.9737521762930710.007718580932705050.0233587410117639
DISU vs. IL70.1254033202473620.6183404295148910.884532273158604
DISU vs. SAHA-0.003569697860560480.9902566867110130.999274089415579
DMSO vs. AZA-0.1096358238539990.5122230142316741
DMSO vs. CD3-1.099862488025150.000705304514562410.00251966149202815
DMSO vs. DISU-0.1294153489052740.5959885382080890.937098979571498
DMSO vs. IL70.2693313184693630.1338908896586760.632122723648975
DMSO vs. SAHA0.1162923720259490.6215828766672210.876193687458665
HIV vs. Mock in Activation-0.01277271509327620.9836695428755390.999983755607037
HIV vs. Mock in Latency0.05840985403123140.7230689916633040.999834320637052
IL7 vs. CD3-0.8189749902417830.01141817746025940.0332187201039356
SAHA vs. CD3-0.9907362743897630.00586001261872260.0163265650146329
SAHA vs. IL7-0.1422284865894820.559369091772960.769703776712027
(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 unknown
(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
1.9 0.000190038 1.3 0.044518008 1.4 0.079079583
(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 -0.0353244 0.848775
(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
1.07 1.074 1.099 1.089 1.017
(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
2CL3 X-ray 1.9Å A=21-227.
2J8Q X-ray 2.3Å A/B=24-227.
3BAP X-ray 1.8Å A=1-227.
3BHO X-ray 1.8Å A=20-227.
3MDG X-ray 2.2Å A/B=1-227.
3MDI X-ray 2.0Å A/B=1-227.
3N9U X-ray 1.9Å A/B=21-227.
3P5T X-ray 2.7Å A/B/C/D/E/F=34-227.
3P6Y X-ray 2.9Å A/B/E/F/I/J/M/N=34-227.
3Q2S X-ray 2.9Å A/B=21-227.
3Q2T X-ray 3.0Å A/B=21-227.

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

HIV Partner Interaction Type PubMed
Envelope surface glycoprotein gp120 complexes with 23125841
Gag-Pol complexes with 23125841
Pr55(Gag) complexes with 23125841
Nef complexes with 23125841

Metabolic/Signalling Pathway       (annotations from KEGG database)      top

Pathway Accession Number Description
hsa03015 mRNA surveillance pathway - Homo sapiens (human)
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