Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0000636
UniProt IDQ92989
Primary gene name(s)CLP1
Synonym gene name(s)HEAB
Protein namePolyribonucleotide 5'-hydroxyl-kinase Clp1
Protein functionPolynucleotide kinase that can phosphorylate the 5'-hydroxyl groups of double-stranded RNA, dsRNA, single-stranded RNA, ssRNA, double-stranded DNA, dsDNA and double-stranded DNA:RNA hybrids. dsRNA is phosphorylated more efficiently than dsDNA, and the RNA component of a DNA:RNA hybrid is phosphorylated more efficiently than the DNA component. Plays a key role in both tRNA splicing and mRNA 3'-end formation. Component of the tRNA splicing endonuclease complex: phosphorylates the 5'-terminus of the tRNA 3'-exon during tRNA splicing; this phosphorylation event is a prerequisite for the subsequent ligation of the two exon halves and the production of a mature tRNA, PubMed:24766809, PubMed:24766810. Its role in tRNA splicing and maturation is required for cerebellar development, PubMed:24766809, PubMed:24766810. Component of the pre-mRNA cleavage complex II, CF-II, which seems to be required for mRNA 3'-end formation. Also phosphorylates the 5'-terminus of exogenously introduced short interfering RNAs, siRNAs, which is a necessary prerequisite for their incorporation into the RNA-induced silencing complex, RISC. However, endogenous siRNAs and microRNAs, miRNAs that are produced by the cleavage of dsRNA precursors by DICER1 already contain a 5'-phosphate group, so this protein may be dispensible for normal RNA-mediated gene silencing. {ECO:0000269|PubMed:17495927, ECO:0000269|PubMed:18648070, ECO:0000269|PubMed:24766809, ECO:0000269|PubMed:24766810}.
Subcellular locationNucleus {ECO:0000255|HAMAP-Rule:MF_03035, ECO:0000269|PubMed:11060040, ECO:0000269|PubMed:24766810}.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: Q92989
Gene Ontology
(Biological Process)
Complete annatation
cerebellar cortex development [GO:0021695];
mRNA 3'-end processing [GO:0031124];
mRNA cleavage [GO:0006379];
mRNA polyadenylation [GO:0006378];
mRNA splicing, via spliceosome [GO:0000398];
siRNA loading onto RISC involved in RNA interference [GO:0035087];
targeting of mRNA for destruction involved in RNA interference [GO:0030423];
termination of RNA polymerase II transcription [GO:0006369];
tRNA splicing, via endonucleolytic cleavage and ligation [GO:0006388]
Gene Ontology
(Molecular Function)
Complete annatation
ATP binding [GO:0005524];
ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity [GO:0046404];
ATP-dependent polyribonucleotide 5'-hydroxyl-kinase activity [GO:0051736];
polydeoxyribonucleotide kinase activity [GO:0051733]
Gene Ontology
(Cellular Component)
Complete annatation
cytoplasm [GO:0005737];
mRNA cleavage factor complex [GO:0005849];
nucleoplasm [GO:0005654];
nucleus [GO:0005634];
tRNA-intron endonuclease complex [GO:0000214]
Protein-protein interaction116174
Phylogenetic treeQ92989
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. CD30.9112057961386110.005977083747052970.0168638349373984
AZA vs. DISU0.3015162093025990.2392408071441430.824578793708559
AZA vs. IL70.05283201812731310.7885221545658450.999311006273513
AZA vs. SAHA-0.1726051478775690.4874255074912820.813308012751724
DISU vs. CD3-0.6222698659657480.08791739888060910.168535367061554
DISU vs. IL7-0.2582318940077370.3106391524368120.694377998663246
DISU vs. SAHA-0.4718143421470060.1108655087502610.42820453161845
DMSO vs. AZA-0.04092365368923910.8133529601293051
DMSO vs. CD3-0.9642307491784940.002909955954035430.00867153840387497
DMSO vs. DISU-0.3447478317728450.1630235710103830.67193445139476
DMSO vs. IL70.1011377645653980.5834541271031360.90819539448143
DMSO vs. SAHA-0.1371100005273240.5679924171254030.847965697721343
HIV vs. Mock in Activation-0.0616537139015080.9212245687368660.999983755607037
HIV vs. Mock in Latency-0.1257273032952770.4614997132708590.999834320637052
IL7 vs. CD3-0.8520344788634990.008696727064504310.0265409530356901
SAHA vs. CD3-1.107674342052220.002078237481702330.0066863874571422
SAHA vs. IL7-0.2274604073830470.3592843747844920.609824644240676
(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 0.164058 0.278663
(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
1.073 0.939 0.778 0.748 0.931
(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
hsa03015 mRNA surveillance pathway - Homo sapiens (human)
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