Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0002480
UniProt IDP48380
Primary gene name(s)RFX3
Synonym gene name(s)unknown
Protein nameTranscription factor RFX3
Protein functionTranscription factor required for ciliogenesis and islet cell differentiation during endocrine pancreas development. Essential for the differentiation of nodal monocilia and left-right asymmetry specification during embryogenesis. Required for the biogenesis of motile cilia by governing growth and beating efficiency of motile cells. Also required for ciliated ependymal cell differentiation. Regulates the expression of genes involved in ciliary assembly, DYNC2LI1, FOXJ1 and BBS4 and genes involved in ciliary motility, DNAH11, DNAH9 and DNAH5, By similarity. Together with RFX6, participates in the differentiation of 4 of the 5 islet cell types during endocrine pancreas development, with the exception of pancreatic PP, polypeptide-producing cells. Regulates transcription by forming a heterodimer with another RFX protein and binding to the X-box in the promoter of target genes, PubMed:20148032. Represses transcription of MAP1A in non-neuronal cells but not in neuronal cells, PubMed:12411430. {ECO:0000250|UniProtKB:P48381, ECO:0000269|PubMed:12411430, ECO:0000269|PubMed:20148032}.
Subcellular locationNucleus {ECO:0000305}.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: P48380
Gene Ontology
(Biological Process)
Complete annatation
cell maturation [GO:0048469];
cilium assembly [GO:0060271];
cilium-dependent cell motility [GO:0060285];
endocrine pancreas development [GO:0031018];
epithelial cilium movement involved in determination of left/right asymmetry [GO:0060287];
negative regulation of transcription, DNA-templated [GO:0045892];
positive regulation of transcription, DNA-templated [GO:0045893];
positive regulation of transcription from RNA polymerase II promoter [GO:0045944];
positive regulation of type B pancreatic cell development [GO:2000078];
regulation of insulin secretion [GO:0050796];
regulation of transcription, DNA-templated [GO:0006355];
transcription, DNA-templated [GO:0006351];
type B pancreatic cell differentiation [GO:0003309];
type B pancreatic cell maturation [GO:0072560]
Gene Ontology
(Molecular Function)
Complete annatation
DNA binding [GO:0003677];
RNA polymerase II core promoter proximal region sequence-specific DNA binding [GO:0000978];
transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding [GO:0003705];
transcription factor activity, sequence-specific DNA binding [GO:0003700];
transcription regulatory region DNA binding [GO:0044212]
Gene Ontology
(Cellular Component)
Complete annatation
nuclear chromatin [GO:0000790];
nucleus [GO:0005634];
transcription factor complex [GO:0005667]
Protein-protein interaction111923
Phylogenetic treeP48380
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. CD30.2297821844073510.4922540180008090.61008572973507
AZA vs. DISU0.793095732995040.07385710170125440.585733549466875
AZA vs. IL7-0.244991679746840.3254788719139660.999311006273513
AZA vs. SAHA1.058129464576232.86598715456554e-050.00147755383355167
DISU vs. CD30.5488972450562690.2343158316324760.358882468892821
DISU vs. IL7-1.045054394041450.01458601572196390.14748490081117
DISU vs. SAHA0.2664358505077750.540158488319320.846053687119151
DMSO vs. AZA-0.01556607603941090.9390753801322771
DMSO vs. CD3-0.2570649785831360.4289136595812430.54285342196013
DMSO vs. DISU-0.8097858883059640.0455679446370920.425733989882813
DMSO vs. IL7-0.2237185038323390.2374273850382820.743226205962435
DMSO vs. SAHA1.065325705014991.15990358851015e-050.000626555805822094
HIV vs. Mock in Activation-0.4155940258425390.5113687748012390.999983755607037
HIV vs. Mock in Latency-0.08293548813324970.6284309359473790.999834320637052
IL7 vs. CD3-0.4650664301757360.1578088468364880.269810883435389
SAHA vs. CD30.8025579755637820.02487892855327430.055290584470999
SAHA vs. IL71.299060457981692.94903206188302e-071.59905429139657e-05
(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) TRUE
(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 0.237635 0.311212
(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
1.016 1.321 1.325 1.287 1.471
(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
not found
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