Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0002091
UniProt IDO95453
Primary gene name(s)PARN
Synonym gene name(s)DAN
Protein namePoly(A-specific ribonuclease PARN
Protein function3'-exoribonuclease that has a preference for poly(A tails of mRNAs, thereby efficiently degrading poly(A tails. Exonucleolytic degradation of the poly(A tail is often the first step in the decay of eukaryotic mRNAs and is also used to silence certain maternal mRNAs translationally during oocyte maturation and early embryonic development. Interacts with both the 3'-end poly(A tail and the 5'-end cap structure during degradation, the interaction with the cap structure being required for an efficient degradation of poly(A tails. Involved in nonsense-mediated mRNA decay, a critical process of selective degradation of mRNAs that contain premature stop codons. Also involved in degradation of inherently unstable mRNAs that contain AU-rich elements, AREs in their 3'-UTR, possibly via its interaction with KHSRP. Probably mediates the removal of poly(A tails of AREs mRNAs, which constitutes the first step of destabilization. {ECO:0000269|PubMed:10882133, ECO:0000269|PubMed:11359775, ECO:0000269|PubMed:12748283, ECO:0000269|PubMed:15175153, ECO:0000269|PubMed:9736620}.
Subcellular locationNucleus {ECO:0000269|PubMed:9736620}. Cytoplasm {ECO:0000269|PubMed:9736620}. Nucleus, nucleolus {ECO:0000269|PubMed:12429849}. Note=Some nuclear fraction is nucleolar.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: O95453
Gene Ontology
(Biological Process)
Complete annatation
female gamete generation [GO:0007292];
nuclear-transcribed mRNA catabolic process, nonsense-mediated decay [GO:0000184];
nuclear-transcribed mRNA poly(A tail shortening [GO:0000289];
regulation of mRNA stability [GO:0043488];
RNA modification [GO:0009451]
Gene Ontology
(Molecular Function)
Complete annatation
metal ion binding [GO:0046872];
mRNA 3'-UTR binding [GO:0003730];
nuclease activity [GO:0004518];
nucleotide binding [GO:0000166];
poly(A RNA binding [GO:0044822];
poly(A-specific ribonuclease activity [GO:0004535];
protein kinase binding [GO:0019901]
Gene Ontology
(Cellular Component)
Complete annatation
cytoplasm [GO:0005737];
cytosol [GO:0005829];
nucleolus [GO:0005730];
nucleus [GO:0005634]
Protein-protein interaction111107
Phylogenetic treeO95453
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. CD30.3769708169934750.2548631096226320.367750586919654
AZA vs. DISU-0.3892134445384670.1256029556977450.688236624568449
AZA vs. IL7-0.009499896151058480.960811440020950.999311006273513
AZA vs. SAHA-0.2175182894765290.3744970042098590.74052396041413
DISU vs. CD3-0.7780360064583480.03492820995692660.0810189513189757
DISU vs. IL70.3702308115933790.1436928683097540.493991677892125
DISU vs. SAHA0.172949761126530.5540921775736940.853246470646076
DMSO vs. AZA-0.02196166768383540.8964855588576591
DMSO vs. CD3-0.4098554234017180.204712122520490.304531265505202
DMSO vs. DISU0.3654600510483260.1359054286078050.62689888070154
DMSO vs. IL70.01954028327175850.9139627951538540.982172449135956
DMSO vs. SAHA-0.2021559024619990.3929252095290640.738076183675053
HIV vs. Mock in Activation0.04329024029062620.9445354058135660.999983755607037
HIV vs. Mock in Latency0.04486910274895060.7868854519244730.999834320637052
IL7 vs. CD3-0.3790032897172350.2413673060898570.371427198028833
SAHA vs. CD3-0.6185887557122050.08321936420021590.150239238147084
SAHA vs. IL7-0.2111319410613720.3876070449335940.637163423699999
(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 -1.429990302
(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 -0.103367 0.529828
(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
0.99 0.99 0.965 0.883 0.958
(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
203905_at 1.3 No upregulated in CD8+ cells

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
2A1R X-ray 2.6Å A/B=1-430.
2A1S X-ray 2.6Å A/B/C/D=1-430.
3CTR X-ray 2.1Å A=445-540.

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)