Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0002248
UniProt IDO95602
Primary gene name(s)POLR1A
Synonym gene name(s)unknown
Protein nameDNA-directed RNA polymerase I subunit RPA1
Protein functionDNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Largest and catalytic core component of RNA polymerase I which synthesizes ribosomal RNA precursors. Forms the polymerase active center together with the second largest subunit. A single stranded DNA template strand of the promoter is positioned within the central active site cleft of Pol I. A bridging helix emanates from RPA1 and crosses the cleft near the catalytic site and is thought to promote translocation of Pol I by acting as a ratchet that moves the RNA-DNA hybrid through the active site by switching from straight to bent conformations at each step of nucleotide addition, By similarity. {ECO:0000250|UniProtKB:P10964}.
Subcellular locationNucleus, nucleolus {ECO:0000250}.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: O95602
Gene Ontology
(Biological Process)
Complete annatation
negative regulation of protein localization to nucleolus [GO:1904750];
positive regulation of gene expression, epigenetic [GO:0045815];
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];
zinc ion binding [GO:0008270]
Gene Ontology
(Cellular Component)
Complete annatation
cytoplasm [GO:0005737];
DNA-directed RNA polymerase I complex [GO:0005736];
nucleolus [GO:0005730];
nucleoplasm [GO:0005654];
nucleus [GO:0005634]
Protein-protein interaction117396
Phylogenetic treeO95602
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. CD31.3547941538740.00189099017444450.00630971970538575
AZA vs. DISU-0.2607465002665620.369189180215260.896211275303082
AZA vs. IL70.5840382955098830.004703014732635790.212878501696755
AZA vs. SAHA-0.05644556407235610.8171350451783060.953957068697164
DISU vs. CD3-1.627923748672920.0006967005650181380.00302043840008151
DISU vs. IL70.8357122508506270.003327800941505640.0590195284625854
DISU vs. SAHA0.2061105521550340.4805419436318980.811434633281613
DMSO vs. AZA0.1164766513416810.5148731863069441
DMSO vs. CD3-1.248542856491250.003136332976938270.00924454241783899
DMSO vs. DISU0.375662271948030.1591891529023150.664449187749583
DMSO vs. IL70.4748842280582010.008434111472874210.189830215695712
DMSO vs. SAHA-0.1794582158190280.4469373749854890.779048555084966
HIV vs. Mock in Activation0.2399312279979470.7907805513435990.999983755607037
HIV vs. Mock in Latency-0.08537260492874460.6071244378053490.999834320637052
IL7 vs. CD3-0.7638302700001080.07023358418017970.143874804885546
SAHA vs. CD3-1.435255156197920.0007746120829617010.00286956836043088
SAHA vs. IL7-0.6434189527591830.008479535007011930.0559634460138782
(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 0.203952 0.174511
(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
0.961 1.057 0.97 0.875 0.978
(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)
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