Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0000679
UniProt IDQ16630
Primary gene name(s)CPSF6
Synonym gene name(s)CFIM68
Protein nameCleavage and polyadenylation specificity factor subunit 6
Protein functionComponent of the cleavage factor Im complex, CFIm that plays a key role in pre-mRNA 3'-processing. Involved in association with NUDT21/CPSF5 in pre-MRNA 3'-end poly(A site cleavage and poly(A addition. CPSF6 binds to cleavage and polyadenylation RNA substrates and promotes RNA looping. {ECO:0000269|PubMed:14690600, 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: Q16630
Gene Ontology
(Biological Process)
Complete annatation
mRNA polyadenylation [GO:0006378];
mRNA processing [GO:0006397];
protein tetramerization [GO:0051262]
Gene Ontology
(Molecular Function)
Complete annatation
mRNA binding [GO:0003729];
nucleotide binding [GO:0000166];
poly(A RNA binding [GO:0044822]
Gene Ontology
(Cellular Component)
Complete annatation
intracellular ribonucleoprotein complex [GO:0030529];
membrane [GO:0016020];
mRNA cleavage factor complex [GO:0005849];
nucleoplasm [GO:0005654];
nucleus [GO:0005634];
paraspeckles [GO:0042382]
Protein-protein interaction116238
Phylogenetic treeQ16630
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. CD30.5814910619025090.07629374493740090.140763780596953
AZA vs. DISU-0.08675042149263850.7314407433641180.974560663114398
AZA vs. IL70.07478139958406470.6971225797662360.999311006273513
AZA vs. SAHA0.1306564253794030.5923058424470490.865914152139144
DISU vs. CD3-0.6808880120272360.06110451695220730.126941770746634
DISU vs. IL70.1524790853144860.5447205554501840.851296370803642
DISU vs. SAHA0.2184504241002980.45386328024030.795091653667506
DMSO vs. AZA0.03072046809139580.8544397415005951
DMSO vs. CD3-0.561523265493250.07955791597912690.141688143306011
DMSO vs. DISU0.115759210114150.6349277236393240.945993343259791
DMSO vs. IL70.05139153289888680.774868573181380.953846549996061
DMSO vs. SAHA0.09315153731350650.6927779102157450.906088335056973
HIV vs. Mock in Activation0.03041144291478750.9610442198442760.999983755607037
HIV vs. Mock in Latency0.06106492674673370.7109025432321810.999834320637052
IL7 vs. CD3-0.4991313320347630.1205806204619210.218845477690853
SAHA vs. CD3-0.4754463131451190.1790260380046650.27735805538623
SAHA vs. IL70.05228831887518790.8299845319351650.926617303687652
(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
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 0.148636 0.319558
(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
1.041 1.071 1.047 1.03 1.057
(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
3P5T X-ray 2.7Å L/M/N/O/P/Q=80-161.
3P6Y X-ray 2.9Å C/D/G/H/K/L/O/P=80-161.
3Q2S X-ray 2.9Å C/D=13-235.
3Q2T X-ray 3.0Å C/D=13-235.
4B4N X-ray 1.8Å B=276-290.
4U0A X-ray 2.0Å B=276-290.
4U0B X-ray 2.8Å M/N/O/P/Q/R/S/T/U/V/W/X=276-290.
4WYM X-ray 2.6Å M/N/O/P/Q/R/S/T/U/V/W=276-290.

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

Metabolic/Signalling Pathway       (annotations from KEGG database)      top

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