Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0000634
UniProt IDP54105
Primary gene name(s)CLNS1A
Synonym gene name(s)CLCI, ICLN
Protein nameMethylosome subunit pICln
Protein functionChaperone that regulates the assembly of spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins, snRNPs, the building blocks of the spliceosome. Thereby, plays an important role in the splicing of cellular pre-mRNAs. Most spliceosomal snRNPs contain a common set of Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG that assemble in a heptameric protein ring on the Sm site of the small nuclear RNA to form the core snRNP. In the cytosol, the Sm proteins SNRPD1, SNRPD2, SNRPE, SNRPF and SNRPG are trapped in an inactive 6S pICln-Sm complex by the chaperone CLNS1A that controls the assembly of the core snRNP. Dissociation by the SMN complex of CLNS1A from the trapped Sm proteins and their transfer to an SMN-Sm complex triggers the assembly of core snRNPs and their transport to the nucleus. May also indirectly participate in cellular volume control by activation of a swelling-induced chloride conductance pathway. {ECO:0000269|PubMed:10330151, ECO:0000269|PubMed:11713266, ECO:0000269|PubMed:18984161}.
Subcellular locationCytoplasm, cytosol {ECO:0000269|PubMed:18984161}. Nucleus {ECO:0000269|PubMed:18984161}. Cytoplasm, cytoskeleton {ECO:0000269|PubMed:18984161}. Note=A small fraction is also associated with the cytoskeleton.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: P54105
Gene Ontology
(Biological Process)
Complete annatation
cell volume homeostasis [GO:0006884];
chloride transport [GO:0006821];
spliceosomal snRNP assembly [GO:0000387]
Gene Ontology
(Molecular Function)
Complete annatation
poly(A RNA binding [GO:0044822];
protein heterodimerization activity [GO:0046982]
Gene Ontology
(Cellular Component)
Complete annatation
cytoplasm [GO:0005737];
cytoskeleton [GO:0005856];
cytosol [GO:0005829];
methylosome [GO:0034709];
nucleoplasm [GO:0005654];
nucleus [GO:0005634];
pICln-Sm protein complex [GO:0034715];
plasma membrane [GO:0005886]
Protein-protein interaction107617
Phylogenetic treeP54105
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. CD30.9418218329712340.004300031785491320.0127931462832462
AZA vs. DISU-0.3590771886096760.1563182989487270.738732701570578
AZA vs. IL70.08321545893924720.6655488421412780.999311006273513
AZA vs. SAHA0.03695743195109820.8796280423823280.97315727227035
DISU vs. CD3-1.312861609320110.0003600593168556760.0017230267118357
DISU vs. IL70.4331599024219260.0863666740816290.388750188670366
DISU vs. SAHA0.3970143545645610.1736476767242730.537601506966211
DMSO vs. AZA-0.09421342166805010.5745239139656481
DMSO vs. CD3-1.046845252814650.001181640734269630.00396922084110235
DMSO vs. DISU0.2631828158121480.2811746500180970.796562621733913
DMSO vs. IL70.1845216694137710.3056212342768590.788338514346039
DMSO vs. SAHA0.1240990409838820.5988391265120250.863807635037201
HIV vs. Mock in Activation-0.125954064191250.8393979547132050.999983755607037
HIV vs. Mock in Latency0.02398446631191470.8845903263618560.999834320637052
IL7 vs. CD3-0.8505464200391720.008544062663781490.0261810645519777
SAHA vs. CD3-0.9295518006646890.008996851136076960.023461247035937
SAHA vs. IL7-0.04974224084623160.8384891617644310.930814877041974
(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 -0.276278 0.042659
(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
0.944 1.032 0.761 0.673 0.913
(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

HIV Partner Interaction Type PubMed
HIV-1 virus replication enhanced by expression of human gene 18187620

Metabolic/Signalling Pathway       (annotations from KEGG database)      top

Pathway Accession Number Description
hsa03013 RNA transport - Homo sapiens (human)
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