Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0002555
UniProt IDQ92600
Primary gene name(s)RQCD1
Synonym gene name(s)CNOT9, RCD1
Protein nameCell differentiation protein RCD1 homolog
Protein functionComponent of the CCR4-NOT complex which is one of the major cellular mRNA deadenylases and is linked to various cellular processes including bulk mRNA degradation, miRNA-mediated repression, translational repression during translational initiation and general transcription regulation. Additional complex functions may be a consequence of its influence on mRNA expression. Involved in down-regulation of MYB- and JUN-dependent transcription. May play a role in cell differentiation, By similarity. Can bind oligonucleotides, such as poly-G, poly-C or poly-T, in vitro, but the physiological relevance of this is not certain. Does not bind poly-A. Enhances ligand-dependent transcriptional activity of nuclear hormone receptors, including RARA, expect ESR1-mediated transcription that is not only slightly increased, if at all. {ECO:0000250, ECO:0000269|PubMed:17189474, ECO:0000269|PubMed:18180299}.
Subcellular locationNucleus {ECO:0000250|UniProtKB:Q9JKY0}. Cytoplasm, P-body {ECO:0000250|UniProtKB:Q9JKY0}. Note=NANOS2 promotes its localization to P-body. {ECO:0000250|UniProtKB:Q9JKY0}.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: Q92600
Gene Ontology
(Biological Process)
Complete annatation
cytokine-mediated signaling pathway [GO:0019221];
DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest [GO:0006977];
gene silencing by RNA [GO:0031047];
negative regulation of intracellular estrogen receptor signaling pathway [GO:0033147];
negative regulation of translation [GO:0017148];
nuclear-transcribed mRNA poly(A tail shortening [GO:0000289];
positive regulation of ligand-dependent nuclear receptor transcription coactivator activity [GO:2000327];
regulation of transcription, DNA-templated [GO:0006355];
sex differentiation [GO:0007548];
transcription, DNA-templated [GO:0006351]
Gene Ontology
(Molecular Function)
Complete annatation
protein domain specific binding [GO:0019904];
protein homodimerization activity [GO:0042803]
Gene Ontology
(Cellular Component)
Complete annatation
CCR4-NOT complex [GO:0030014];
CCR4-NOT core complex [GO:0030015];
cytoplasmic mRNA processing body [GO:0000932];
cytosol [GO:0005829];
membrane [GO:0016020];
nucleus [GO:0005634]
Protein-protein interaction114573
Phylogenetic treeQ92600
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. CD31.301406082363939.25314630515484e-050.000449882003584818
AZA vs. DISU0.01779262240861090.943904251063650.996198528027442
AZA vs. IL70.1811592153593440.3463832440929550.999311006273513
AZA vs. SAHA0.01745444056606570.9429674396544330.988407703591609
DISU vs. CD3-1.296453351109260.000431157782608160.00201153587590078
DISU vs. IL70.1543362944815590.5399609455336140.848761559408651
DISU vs. SAHA0.001252021323518350.9965699340000210.999572425883731
DMSO vs. AZA0.006761677147205990.967846026060241
DMSO vs. CD3-1.307159750732355.85015486251894e-050.000279431144590513
DMSO vs. DISU-0.01314426161924740.9570227350249930.993828264951078
DMSO vs. IL70.181784422471390.3124118338267580.794468352722399
DMSO vs. SAHA0.004636965306612120.9843056812546190.995942081836272
HIV vs. Mock in Activation0.06506231461279160.9167043078748050.999983755607037
HIV vs. Mock in Latency-0.0009224645438215810.9955490508658110.999834320637052
IL7 vs. CD3-1.112766752250430.0006157528831124410.00280400096892865
SAHA vs. CD3-1.308251057100510.0002757268974559190.00116830468603771
SAHA vs. IL7-0.1669177018180140.4932514362940930.723232558750637
(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 0.039325 0.836737
(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
0.968 1.002 0.999 0.998 0.995
(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
2FV2 X-ray 2.2Å A/B/C/D=18-285.
4CRU X-ray 1.6Å B=19-285.
4CRV X-ray 2.0Å B=19-285.
4CT6 X-ray 2.1Å B=18-285.
4CT7 X-ray 1.9Å B=16-285.

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
hsa03018 RNA degradation - Homo sapiens (human)