Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0002249
UniProt IDQ9H9Y6
Primary gene name(s)POLR1B
Synonym gene name(s)unknown
Protein nameDNA-directed RNA polymerase I subunit RPA2
Protein functionDNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Second largest core component of RNA polymerase I which synthesizes ribosomal RNA precursors. Proposed to contribute to the polymerase catalytic activity and forms the polymerase active center together with the largest subunit. Pol I is composed of mobile elements and RPA2 is part of the core element with the central large cleft and probably a clamp element that moves to open and close the cleft, By similarity. {ECO:0000250}.
Subcellular locationNucleus, nucleolus {ECO:0000269|PubMed:11250903}.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: Q9H9Y6
Gene Ontology
(Biological Process)
Complete annatation
embryo implantation [GO:0007566];
nucleologenesis [GO:0017126];
positive regulation of gene expression, epigenetic [GO:0045815];
rRNA transcription [GO:0009303];
termination of RNA polymerase I transcription [GO:0006363];
transcription elongation from RNA polymerase I promoter [GO:0006362];
transcription initiation from RNA polymerase I promoter [GO:0006361]
Gene Ontology
(Molecular Function)
Complete annatation
DNA binding [GO:0003677];
DNA-directed RNA polymerase activity [GO:0003899];
metal ion binding [GO:0046872];
ribonucleoside binding [GO:0032549]
Gene Ontology
(Cellular Component)
Complete annatation
cytoplasm [GO:0005737];
DNA-directed RNA polymerase I complex [GO:0005736];
nucleolus [GO:0005730];
nucleoplasm [GO:0005654]
Protein-protein interaction123926
Phylogenetic treeQ9H9Y6
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. CD31.33451563069546.62618158168149e-050.000334995597595102
AZA vs. DISU-0.3940343378646660.1213202166369950.681110221819761
AZA vs. IL70.4622048439105710.01680598833489680.427642929458849
AZA vs. SAHA-0.3666015624728850.1349451090061440.46805397449577
DISU vs. CD3-1.740462856105033.07435303670278e-062.60939176099424e-05
DISU vs. IL70.8470021472808890.000869398201856830.0250117898721216
DISU vs. SAHA0.02893178376404610.9213649738935870.982027592272086
DMSO vs. AZA0.05652626379016490.7375198150710341
DMSO vs. CD3-1.288844491811117.92889994858381e-050.000365622521351133
DMSO vs. DISU0.4488693275935040.06748033721496740.487969617000748
DMSO vs. IL70.4128928753654150.02232932072333470.305457812980282
DMSO vs. SAHA-0.4295820638502640.06987075837053270.308261767974912
HIV vs. Mock in Activation0.1666649440512730.7933719983786820.999983755607037
HIV vs. Mock in Latency0.02308614918616720.8898494862866880.999834320637052
IL7 vs. CD3-0.8651642045164150.007797319979379380.0243079636089318
SAHA vs. CD3-1.725280585073042.42184432863723e-061.79700610697012e-05
SAHA vs. IL7-0.8316876787912380.0007143203630535220.009040860749512
(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 0.124797 0.426896
(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
0.964 0.996 0.824 0.753 0.855
(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

not found

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
hsa00230 Purine metabolism - Homo sapiens (human)
hsa00240 Pyrimidine metabolism - Homo sapiens (human)
hsa01100 Metabolic pathways - Homo sapiens (human)
hsa03020 RNA polymerase - Homo sapiens (human)