Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0002474
UniProt IDP35251
Primary gene name(s)RFC1
Synonym gene name(s)RFC140
Protein nameReplication factor C subunit 1
Protein functionThe 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 locationNucleus.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: P35251
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 interaction111913
Phylogenetic treeP35251
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. CD30.4203102508725820.2137547248673980.321015465643824
AZA vs. DISU0.01901274735975020.9402149726020160.996198528027442
AZA vs. IL70.1491231243528820.4386863486613110.999311006273513
AZA vs. SAHA0.2192690792938250.3693645607824090.735831627566652
DISU vs. CD3-0.4129923957643040.2588024542718330.386419500953596
DISU vs. IL70.1211679451636380.6304279828573910.889574153672496
DISU vs. SAHA0.2008201157236480.4937548155312610.820348233366954
DMSO vs. AZA-0.09253023369844410.5811975779045561
DMSO vs. CD3-0.5232536574952980.1202738464473130.198184902382696
DMSO vs. DISU-0.1130472451317780.6438782101767670.947456638186938
DMSO vs. IL70.2486205764600440.1676360857321730.676241368052584
DMSO vs. SAHA0.304277703501230.1976652543864170.536372533103654
HIV vs. Mock in Activation-0.09545713349349620.903291910296630.999983755607037
HIV vs. Mock in Latency0.08316749304854350.6145928116345740.999834320637052
IL7 vs. CD3-0.2625425957263740.4575129043895280.590874133138836
SAHA vs. CD3-0.2262777662635350.5352787453698430.6412022018011
SAHA vs. IL70.06636638691665010.7862151241557380.906340355737699
(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
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 0.107823 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)
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
0.976 0.919 0.85 0.777 0.892
(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
2EBU NMR - A=392-496.
2K6G NMR - A=375-480.
2K7F NMR - A=375-480.

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

HIV Partner Interaction Type PubMed
Tat interacts with 9121429
19454010

Metabolic/Signalling Pathway       (annotations from KEGG database)      top

Pathway Accession Number Description
hsa03030 DNA replication - Homo sapiens (human)
hsa03420 Nucleotide excision repair - Homo sapiens (human)
hsa03430 Mismatch repair - Homo sapiens (human)
Menu