Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0002427
UniProt IDQ99638
Primary gene name(s)RAD9A
Synonym gene name(s)unknown
Protein nameCell cycle checkpoint control protein RAD9A
Protein functionComponent of the 9-1-1 cell-cycle checkpoint response complex that plays a major role in DNA repair. The 9-1-1 complex is recruited to DNA lesion upon damage by the RAD17-replication factor C, RFC clamp loader complex. Acts then as a sliding clamp platform on DNA for several proteins involved in long-patch base excision repair, LP-BER. The 9-1-1 complex stimulates DNA polymerase beta, POLB activity by increasing its affinity for the 3'-OH end of the primer-template and stabilizes POLB to those sites where LP-BER proceeds; endonuclease FEN1 cleavage activity on substrates with double, nick, or gap flaps of distinct sequences and lengths; and DNA ligase I, LIG1 on long-patch base excision repair substrates. The 9-1-1 complex is necessary for the recruitment of RHNO1 to sites of double-stranded breaks, DSB occurring during the S phase. RAD9A possesses 3'->5' double stranded DNA exonuclease activity. Its phosphorylation by PRKCD may be required for the formation of the 9-1-1 complex. {ECO:0000269|PubMed:10713044, ECO:0000269|PubMed:21659603}.
Subcellular locationNucleus {ECO:0000269|PubMed:12628935}.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: Q99638
Gene Ontology
(Biological Process)
Complete annatation
cellular response to DNA damage stimulus [GO:0006974];
cellular response to ionizing radiation [GO:0071479];
DNA damage checkpoint [GO:0000077];
DNA repair [GO:0006281];
DNA replication [GO:0006260];
DNA replication checkpoint [GO:0000076];
intra-S DNA damage checkpoint [GO:0031573];
positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage [GO:1902231];
regulation of signal transduction by p53 class mediator [GO:1901796]
Gene Ontology
(Molecular Function)
Complete annatation
3'-5' exonuclease activity [GO:0008408];
enzyme binding [GO:0019899];
exodeoxyribonuclease III activity [GO:0008853];
histone deacetylase binding [GO:0042826];
protein kinase binding [GO:0019901];
SH3 domain binding [GO:0017124]
Gene Ontology
(Cellular Component)
Complete annatation
checkpoint clamp complex [GO:0030896];
cytoplasm [GO:0005737];
nucleoplasm [GO:0005654];
nucleus [GO:0005634]
Protein-protein interaction111820
Phylogenetic treeQ99638
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. CD3-0.745657716844530.02638256887386350.0584847886552243
AZA vs. DISU-0.3215904632930580.2064807606638810.796241392176044
AZA vs. IL7-0.1956296343846460.3145589398712070.999311006273513
AZA vs. SAHA0.5299704453395560.1358094750467590.469109316180418
DISU vs. CD30.4120832954454410.2653926887695050.393580114774625
DISU vs. IL70.1161266393303870.6469629211714040.897815155726679
DISU vs. SAHA0.8542674429776960.01502231280670850.135245684772941
DMSO vs. AZA0.07526164383382170.6574181679219081
DMSO vs. CD30.8069754542125640.01382645197846280.0327611668851119
DMSO vs. DISU0.3945485563508040.1081484452578810.581806680424036
DMSO vs. IL7-0.263295952901140.1478689931202430.649767945207279
DMSO vs. SAHA0.4505782578393060.1740533355429180.505181200940853
HIV vs. Mock in Activation0.1259455076593450.8618838413147110.999983755607037
HIV vs. Mock in Latency-0.04216140837078340.8008054919957450.999834320637052
IL7 vs. CD30.5552610462397870.09539442963110490.182866620606593
SAHA vs. CD31.252472095483860.009385127535891820.0243013525714587
SAHA vs. IL70.7236295833406370.04864455856953630.180474544887322
(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 0.55724 0.460746
(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
1.01 1.141 1.123 1.208 1.099
(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
3A1J X-ray 2.5Å A=1-266.
3G65 X-ray 2.9Å A=1-270.
3GGR X-ray 3.2Å A=1-270.

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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