Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0000994
UniProt IDQ9NQT4
Primary gene name(s)EXOSC5
Synonym gene name(s)CML28, RRP46
Protein nameExosome complex component RRP46
Protein functionNon-catalytic component of the RNA exosome complex which has 3'->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. In the nucleus, the RNA exosome complex is involved in proper maturation of stable RNA species such as rRNA, snRNA and snoRNA, in the elimination of RNA processing by-products and non-coding 'pervasive' transcripts, such as antisense RNA species and promoter-upstream transcripts, PROMPTs, and of mRNAs with processing defects, thereby limiting or excluding their export to the cytoplasm. The RNA exosome may be involved in Ig class switch recombination, CSR and/or Ig variable region somatic hypermutation, SHM by targeting AICDA deamination activity to transcribed dsDNA substrates. In the cytoplasm, the RNA exosome complex is involved in general mRNA turnover and specifically degrades inherently unstable mRNAs containing AU-rich elements, AREs within their 3' untranslated regions, and in RNA surveillance pathways, preventing translation of aberrant mRNAs. It seems to be involved in degradation of histone mRNA. The catalytic inactive RNA exosome core complex of 9 subunits, Exo-9 is proposed to play a pivotal role in the binding and presentation of RNA for ribonucleolysis, and to serve as a scaffold for the association with catalytic subunits and accessory proteins or complexes. {ECO:0000269|PubMed:11782436, ECO:0000269|PubMed:21255825}.
Subcellular locationNucleus, nucleolus {ECO:0000269|PubMed:11812149}. Cytoplasm {ECO:0000305|PubMed:11812149}. Nucleus {ECO:0000305|PubMed:11812149}.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: Q9NQT4
Gene Ontology
(Biological Process)
Complete annatation
defense response to virus [GO:0051607];
DNA deamination [GO:0045006];
exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay [GO:0043928];
nuclear mRNA surveillance [GO:0071028];
nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5' [GO:0034427];
polyadenylation-dependent snoRNA 3'-end processing [GO:0071051];
regulation of mRNA stability [GO:0043488];
rRNA 3'-end processing [GO:0031125];
rRNA catabolic process [GO:0016075];
rRNA processing [GO:0006364];
U4 snRNA 3'-end processing [GO:0034475]
Gene Ontology
(Molecular Function)
Complete annatation
3'-5'-exoribonuclease activity [GO:0000175];
RNA binding [GO:0003723]
Gene Ontology
(Cellular Component)
Complete annatation
cytoplasm [GO:0005737];
cytoplasmic exosome, RNase complex [GO:0000177];
cytosol [GO:0005829];
exosome, RNase complex [GO:0000178];
nuclear exosome, RNase complex [GO:0000176];
nucleolus [GO:0005730];
nucleoplasm [GO:0005654];
nucleus [GO:0005634];
transcriptionally active chromatin [GO:0035327]
Protein-protein interaction121243
Phylogenetic treeQ9NQT4
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. CD30.7427921072094820.0246738931685710.0553894724213141
AZA vs. DISU-0.5962877793593040.04227244828056440.468825897555846
AZA vs. IL70.3722556958470230.05725514186010820.693178115066193
AZA vs. SAHA-0.7095529681662580.004587456551191190.0585531922545775
DISU vs. CD3-1.349774590071980.0002766315011796250.00137621889398735
DISU vs. IL70.9585159709448680.0004962289617779230.0169629287954698
DISU vs. SAHA-0.1116625851477610.7187988240704040.917103213595783
DMSO vs. AZA0.1074461780638850.531979874988451
DMSO vs. CD3-0.6486069157004640.04404382093361490.0864972184024128
DMSO vs. DISU0.7013046035435120.009147461053020560.20729659860003
DMSO vs. IL70.2724779319598140.1362897356016220.633860229772759
DMSO vs. SAHA-0.8214263418228970.0006735244981694870.0134446194859766
HIV vs. Mock in Activation-0.1266590726562950.8395100897875760.999983755607037
HIV vs. Mock in Latency0.03850718927256720.8215813187790450.999834320637052
IL7 vs. CD3-0.3645569654018370.2582925001092090.39096285971709
SAHA vs. CD3-1.475091309478594.69256478353719e-050.000246314703197163
SAHA vs. IL7-1.08375406581861.45097288377638e-050.00041424176609934
(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 -0.00360479 0.996736
(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
1.032 0.97 0.909 0.904 0.943
(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
2NN6 X-ray 3.3Å D=1-235.

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

HIV Partner Interaction Type PubMed
Pr55(Gag) cooperates with 19460752
Rev interacts with 22174317
HIV-1 virus replication enhanced by expression of human gene 19460752

Metabolic/Signalling Pathway       (annotations from KEGG database)      top

Pathway Accession Number Description
hsa03018 RNA degradation - Homo sapiens (human)