Protein Information (annotations from UniProt)
| Database ID | HIV0002474 |
| UniProt ID | P35251 |
| Primary gene name(s) | RFC1 |
| Synonym gene name(s) | RFC140 |
| Protein name | Replication factor C subunit 1 |
| Protein function | The elongation of primed DNA templates by DNA polymerase delta and epsilon requires the action of the accessory proteins PCNA and activator 1. This subunit binds to the primer-template junction. Binds the PO-B transcription element as well as other GA rich DNA sequences. Could play a role in DNA transcription regulation as well as DNA replication and/or repair. Can bind single- or double-stranded DNA. {ECO:0000269|PubMed:8999859}.; FUNCTION: Interacts with C-terminus of PCNA. 5' phosphate residue is required for binding of the N-terminal DNA-binding domain to duplex DNA, suggesting a role in recognition of non-primer template DNA structures during replication and/or repair. {ECO:0000269|PubMed:8999859}. |
| Subcellular location | Nucleus. |
| ECO code | Click here for more information. |
| Amino acid sequence FASTA format: P35251 |
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| Gene Ontology (Biological Process) Complete annatation | DNA damage response, detection of DNA damage [GO:0042769]; DNA-dependent DNA replication [GO:0006261]; error-free translesion synthesis [GO:0070987]; error-prone translesion synthesis [GO:0042276]; negative regulation of transcription from RNA polymerase II promoter [GO:0000122]; nucleotide-excision repair, DNA gap filling [GO:0006297]; nucleotide-excision repair, DNA incision [GO:0033683]; nucleotide-excision repair, DNA incision, 5'-to lesion [GO:0006296]; positive regulation of transcription, DNA-templated [GO:0045893]; telomere maintenance via recombination [GO:0000722]; telomere maintenance via telomerase [GO:0007004]; transcription, DNA-templated [GO:0006351]; transcription-coupled nucleotide-excision repair [GO:0006283]; translesion synthesis [GO:0019985] |
| Gene Ontology (Molecular Function) Complete annatation | ATP binding [GO:0005524]; DNA binding [GO:0003677]; DNA clamp loader activity [GO:0003689]; enzyme activator activity [GO:0008047] |
| Gene Ontology (Cellular Component) Complete annatation | DNA replication factor C complex [GO:0005663]; extracellular exosome [GO:0070062]; nucleoplasm [GO:0005654]; nucleus [GO:0005634] |
| Protein-protein interaction | 111913 |
| Phylogenetic tree | P35251 |
| 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 |
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| Experimental Condition | Log2 Fold Change | P value | Adjusted P value |
| AZA vs. CD3 | 0.420310250872582 | 0.213754724867398 | 0.321015465643824 |
| AZA vs. DISU | 0.0190127473597502 | 0.940214972602016 | 0.996198528027442 |
| AZA vs. IL7 | 0.149123124352882 | 0.438686348661311 | 0.999311006273513 |
| AZA vs. SAHA | 0.219269079293825 | 0.369364560782409 | 0.735831627566652 |
| DISU vs. CD3 | -0.412992395764304 | 0.258802454271833 | 0.386419500953596 |
| DISU vs. IL7 | 0.121167945163638 | 0.630427982857391 | 0.889574153672496 |
| DISU vs. SAHA | 0.200820115723648 | 0.493754815531261 | 0.820348233366954 |
| DMSO vs. AZA | -0.0925302336984441 | 0.581197577904556 | 1 |
| DMSO vs. CD3 | -0.523253657495298 | 0.120273846447313 | 0.198184902382696 |
| DMSO vs. DISU | -0.113047245131778 | 0.643878210176767 | 0.947456638186938 |
| DMSO vs. IL7 | 0.248620576460044 | 0.167636085732173 | 0.676241368052584 |
| DMSO vs. SAHA | 0.30427770350123 | 0.197665254386417 | 0.536372533103654 |
| HIV vs. Mock in Activation | -0.0954571334934962 | 0.90329191029663 | 0.999983755607037 |
| HIV vs. Mock in Latency | 0.0831674930485435 | 0.614592811634574 | 0.999834320637052 |
| IL7 vs. CD3 | -0.262542595726374 | 0.457512904389528 | 0.590874133138836 |
| SAHA vs. CD3 | -0.226277766263535 | 0.535278745369843 | 0.6412022018011 |
| SAHA vs. IL7 | 0.0663663869166501 | 0.786215124155738 | 0.906340355737699 |
| (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 |
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| 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 |
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| 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) |
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| Log2 Fold Change | unknown | ||||
| (3). Li et al., J. Immunol., 2013 Lymphatic tissue |
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| 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 |
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| 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 |
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| Test Status | Log2 Fold Change | P Value | |||
| OK | 0.107823 | 0.503159 | |||
| (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) |
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| 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 |
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| 6 h | 24 h | 48 h | 72 h | RTi | ||
| 0.976 | 0.919 | 0.85 | 0.777 | 0.892 | ||
| (2). Navare et al., Virology, 2012 SUP-T1 cell line |
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| 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 |
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| Affymetrix Prob ID | Fold Change | In CD8? | Category | |||
| unknown | unknown | unknown | unknown | |||
