Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0001134
UniProt IDQ9NY12
Primary gene name(s)GAR1
Synonym gene name(s)NOLA1
Protein nameH/ACA ribonucleoprotein complex subunit 1
Protein functionRequired for ribosome biogenesis and telomere maintenance. Part of the H/ACA small nucleolar ribonucleoprotein, H/ACA snoRNP complex, which catalyzes pseudouridylation of rRNA. This involves the isomerization of uridine such that the ribose is subsequently attached to C5, instead of the normal N1. Each rRNA can contain up to 100 pseudouridine, ""psi"" residues, which may serve to stabilize the conformation of rRNAs. May also be required for correct processing or intranuclear trafficking of TERC, the RNA component of the telomerase reverse transcriptase, TERT holoenzyme. {ECO:0000269|PubMed:10757788, ECO:0000269|PubMed:15044956}."
Subcellular locationNucleus, nucleolus. Nucleus, Cajal body. Note=Also localized to Cajal bodies, coiled bodies.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: Q9NY12
Gene Ontology
(Biological Process)
Complete annatation
rRNA pseudouridine synthesis [GO:0031118];
snoRNA guided rRNA pseudouridine synthesis [GO:0000454];
telomere maintenance via telomerase [GO:0007004]
Gene Ontology
(Molecular Function)
Complete annatation
box H/ACA snoRNA binding [GO:0034513];
cation channel activity [GO:0005261];
poly(A RNA binding [GO:0044822];
telomerase RNA binding [GO:0070034]
Gene Ontology
(Cellular Component)
Complete annatation
box H/ACA scaRNP complex [GO:0072589];
box H/ACA snoRNP complex [GO:0031429];
box H/ACA telomerase RNP complex [GO:0090661];
nuclear chromosome, telomeric region [GO:0000784];
nucleolus [GO:0005730];
nucleoplasm [GO:0005654];
nucleus [GO:0005634];
telomerase holoenzyme complex [GO:0005697]
Protein-protein interaction119949
Phylogenetic treeQ9NY12
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. CD32.232694739606367.53619389115556e-111.34739637399166e-09
AZA vs. DISU-0.09343471142927580.7153740205213840.973233942294547
AZA vs. IL70.5053733748971450.01010664779809720.32620450162895
AZA vs. SAHA-0.05316216757517860.8301509176929340.959664073854644
DISU vs. CD3-2.338692471330138.12926170823403e-101.65819338281353e-08
DISU vs. IL70.5895753357612870.02084110206523960.182662566065981
DISU vs. SAHA0.04136118516379990.888314364379730.971960634932983
DMSO vs. AZA0.05130695346587790.7666606346768361
DMSO vs. CD3-2.188612138664195.84714499041183e-119.63755353178931e-10
DMSO vs. DISU0.1439786675302010.559984871225190.925542552003928
DMSO vs. IL70.4606658393462960.01214653608544180.232371867370603
DMSO vs. SAHA-0.1126312151820820.6379657919278070.883919387366036
HIV vs. Mock in Activation-0.232963596926510.7093286034457880.999983755607037
HIV vs. Mock in Latency-0.02978311911357870.8612982214484020.999834320637052
IL7 vs. CD3-1.719528095799391.96333965862827e-072.25216276061674e-06
SAHA vs. CD3-2.310983917924264.90157581189976e-108.73129402899875e-09
SAHA vs. IL7-0.5616099268315310.0231383973133020.110397287876136
(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 0.362112 0.00879669
(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
0.914 0.863 0.8 0.752 0.745
(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
hsa03008 Ribosome biogenesis in eukaryotes - Homo sapiens (human)
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