Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0000946
UniProt IDQ92979
Primary gene name(s)EMG1
Synonym gene name(s)C2F
Protein nameRibosomal RNA small subunit methyltransferase NEP1
Protein functionS-adenosyl-L-methionine-dependent pseudouridine N(1-methyltransferase that methylates pseudouridine at position 1248, Psi1248 in 18S rRNA. Involved the biosynthesis of the hypermodified N1-methyl-N3-(3-amino-3-carboxypropyl pseudouridine, m1acp3-Psi conserved in eukaryotic 18S rRNA. Is not able to methylate uridine at this position, PubMed:20047967. Has also an essential role in 40S ribosomal subunit biogenesis independent on its methyltransferase activity, facilitating the incorporation of ribosomal protein S19 during the formation of pre-ribosomes, By similarity. {ECO:0000250|UniProtKB:Q06287, ECO:0000269|PubMed:20047967}.
Subcellular locationNucleus, nucleolus {ECO:0000269|PubMed:11935223}.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: Q92979
Gene Ontology
(Biological Process)
Complete annatation
maturation of SSU-rRNA from tricistronic rRNA transcript, SSU-rRNA, 5.8S rRNA, LSU-rRNA [GO:0000462];
ribosomal small subunit biogenesis [GO:0042274];
rRNA base methylation [GO:0070475];
rRNA processing [GO:0006364]
Gene Ontology
(Molecular Function)
Complete annatation
poly(A RNA binding [GO:0044822];
RNA binding [GO:0003723];
rRNA, pseudouridine methyltransferase activity [GO:0070037];
rRNA binding [GO:0019843]
Gene Ontology
(Cellular Component)
Complete annatation
cytoplasm [GO:0005737];
nucleolus [GO:0005730];
nucleoplasm [GO:0005654];
nucleus [GO:0005634];
small-subunit processome [GO:0032040]
Protein-protein interaction115703
Phylogenetic treeQ92979
HIV replication factor status Zhou et al., Cell. Host. Microbe., 2008
Brass et al., Science, 2008
Smith et al., J. Immunol, 2010
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. CD31.439987155982251.63665511472288e-059.60489972941541e-05
AZA vs. DISU-0.5087624927899530.04775215644948050.493685436024875
AZA vs. IL70.2115079014366860.2764446828140650.999311006273513
AZA vs. SAHA-0.7396696350084340.002819650784436580.0425385193160165
DISU vs. CD3-1.961260135686822.15493810351575e-072.41333855664163e-06
DISU vs. IL70.7109621176209750.005412475278301240.0787577845756672
DISU vs. SAHA-0.2293264160738520.4392969864612580.784863089819289
DMSO vs. AZA-0.08534842262644190.6162350700877051
DMSO vs. CD3-1.537301004532512.64527401294679e-061.73265447848014e-05
DMSO vs. DISU0.4213474891641510.08828154372964190.547437245510835
DMSO vs. IL70.3041294490669080.09457866577409350.56466272734434
DMSO vs. SAHA-0.6605509348617420.00576695240440450.0619484958565789
HIV vs. Mock in Activation-0.1140407742792630.8545970964225980.999983755607037
HIV vs. Mock in Latency-0.1056865829828550.5298635096020990.999834320637052
IL7 vs. CD3-1.22077730785710.0001816859295585840.00098155986245037
SAHA vs. CD3-2.203767819638052.41606978867992e-093.71238655956223e-08
SAHA vs. IL7-0.9542078602598670.0001179769028691880.00222576199480618
(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 0.448592 0.0327088
(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
1.001 0.932 0.664 0.546 0.645
(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
5FAI X-ray 1.8Å A=14-244.

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

HIV Partner Interaction Type PubMed
Rev interacts with 22174317

Metabolic/Signalling Pathway       (annotations from KEGG database)      top

Pathway Accession Number Description
hsa03008 Ribosome biogenesis in eukaryotes - Homo sapiens (human)