Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0005593
UniProt IDP62312
Primary gene name(s)LSM6
Synonym gene name(s)unknown
Protein nameU6 snRNA-associated Sm-like protein LSm6
Protein functionComponent of LSm protein complexes, which are involved in RNA processing and may function in a chaperone-like manner, facilitating the efficient association of RNA processing factors with their substrates. Component of the cytoplasmic LSM1-LSM7 complex, which is thought to be involved in mRNA degradation by activating the decapping step in the 5'-to-3' mRNA decay pathway. Component of the nuclear LSM2-LSM8 complex, which is involved in splicing of nuclear mRNAs. LSM2-LSM8 associates with multiple snRNP complexes containing the U6 snRNA, U4/U6 di-snRNP, spliceosomal U4/U6.U5 tri-snRNP, and free U6 snRNP. It binds directly to the 3'-terminal U-tract of U6 snRNA and plays a role in the biogenesis and stability of the U6 snRNP and U4/U6 snRNP complexes. LSM2-LSM8 probably also is involved degradation of nuclear pre-mRNA by targeting them for decapping, and in processing of pre-tRNAs, pre-rRNAs and U3 snoRNA, By similarity. {ECO:0000250}.
Subcellular locationCytoplasm {ECO:0000269|PubMed:12515382}. Nucleus {ECO:0000250}.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: P62312
Gene Ontology
(Biological Process)
Complete annatation
exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay [GO:0043928];
maturation of SSU-rRNA [GO:0030490];
mRNA splicing, via spliceosome [GO:0000398];
RNA splicing [GO:0008380];
tRNA processing [GO:0008033]
Gene Ontology
(Molecular Function)
Complete annatation
poly(A RNA binding [GO:0044822];
RNA binding [GO:0003723]
Gene Ontology
(Cellular Component)
Complete annatation
cytoplasmic mRNA processing body [GO:0000932];
cytosol [GO:0005829];
extracellular exosome [GO:0070062];
nucleolus [GO:0005730];
nucleoplasm [GO:0005654];
small nuclear ribonucleoprotein complex [GO:0030532];
small nucleolar ribonucleoprotein complex [GO:0005732];
spliceosomal complex [GO:0005681];
U4/U6 x U5 tri-snRNP complex [GO:0046540];
U6 snRNP [GO:0005688]
Protein-protein interaction116328
Phylogenetic treeP62312
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. CD31.258098700822550.0001805166991711850.000810469970184122
AZA vs. DISU-0.3332957082610530.1925211298217850.780368775323152
AZA vs. IL70.3673412343095450.06013689979906610.703798825350824
AZA vs. SAHA-0.2026460817134150.4117165018627480.767138931790233
DISU vs. CD3-1.602933263238841.86878630233922e-050.000129398643644747
DISU vs. IL70.6916744999518290.006706186781849420.0898629028767823
DISU vs. SAHA0.131621120567360.6539998353093770.893110282724433
DMSO vs. AZA-0.1106855453022060.5193098937857621
DMSO vs. CD3-1.376865028910462.71468209698256e-050.000140925864200697
DMSO vs. DISU0.2216309619429990.3689281398407250.85177548964527
DMSO vs. IL70.4848014888879770.008099592155742070.187621416504043
DMSO vs. SAHA-0.09969755357108320.6760158171796110.897786781843686
HIV vs. Mock in Activation-0.1652671150034740.7905989974110050.999983755607037
HIV vs. Mock in Latency-0.03832193016166720.8253063003025320.999834320637052
IL7 vs. CD3-0.8820508535628630.006771890924678230.021607263316612
SAHA vs. CD3-1.485195067862284.56912203424809e-050.000240926063877252
SAHA vs. IL7-0.5729354356669740.0201601524107350.100995060631246
(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) unknown
(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 0.140036 0.454291
(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
1.033 0.838 0.89 0.913 0.832
(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

Drugbank ID Drug Name Drug Status Pharmacological Action Drug Action
DB02745 Uridine experimental unknown unknown
DB03685 Uridine-5&,39;-Monophosphate experimental unknown unknown
DB04272 Citric Acid nutraceutical, vet_approved unknown unknown

Protein Secondary Structure       (annotations from PDB)      top

PDB Accession Method Resolution Chain Structure Preview
3JCR EM 7.0Å 6=1-80.

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
hsa03018 RNA degradation - Homo sapiens (human)
hsa03040 Spliceosome - Homo sapiens (human)
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