Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0002526
UniProt IDQ15287
Primary gene name(s)RNPS1
Synonym gene name(s)LDC2
Protein nameRNA-binding protein with serine-rich domain 1
Protein functionPart of pre- and post-splicing multiprotein mRNP complexes. Auxiliary component of the splicing-dependent multiprotein exon junction complex, EJC deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of core proteins and several peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Component of the ASAP and PSAP complexes which bind RNA in a sequence-independent manner and are proposed to be recruited to the EJC prior to or during the splicing process and to regulate specific excision of introns in specific transcription subsets. The ASAP complex can inhibit RNA processing during in vitro splicing reactions. The ASAP complex promotes apoptosis and is disassembled after induction of apoptosis. Enhances the formation of the ATP-dependent A complex of the spliceosome. Involved in both constitutive splicing and, in association with SRP54 and TRA2B/SFRS10, in distinctive modulation of alternative splicing in a substrate-dependent manner. Involved in the splicing modulation of BCL2L1/Bcl-X, and probably other apoptotic genes; specifically inhibits formation of proapoptotic isoforms such as Bcl-X(S; the activity is different from the established EJC assembly and function. Participates in mRNA 3'-end cleavage. Involved in UPF2-dependent nonsense-mediated decay, NMD of mRNAs containing premature stop codons. Also mediates increase of mRNA abundance and translational efficiency. Binds spliced mRNA 20-25 nt upstream of exon-exon junctions. {ECO:0000269|PubMed:10449421, ECO:0000269|PubMed:11546874, ECO:0000269|PubMed:12665594, ECO:0000269|PubMed:12944400, ECO:0000269|PubMed:14729963, ECO:0000269|PubMed:14752011, ECO:0000269|PubMed:15684395, ECO:0000269|PubMed:16209946, ECO:0000269|PubMed:17586820, ECO:0000269|PubMed:22203037}.
Subcellular locationNucleus. Nucleus speckle. Cytoplasm. Note=Nucleocytoplasmic shuttling protein. Colocalizes with the core EJC, ALYREF/THOC4, NXF1 and UAP56 in the nucleus and nuclear speckles.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: Q15287
Gene Ontology
(Biological Process)
Complete annatation
mRNA 3'-end processing [GO:0031124];
mRNA export from nucleus [GO:0006406];
mRNA splicing, via spliceosome [GO:0000398];
negative regulation of mRNA splicing, via spliceosome [GO:0048025];
nuclear-transcribed mRNA catabolic process, nonsense-mediated decay [GO:0000184];
positive regulation of apoptotic process [GO:0043065];
regulation of alternative mRNA splicing, via spliceosome [GO:0000381];
RNA export from nucleus [GO:0006405];
RNA splicing [GO:0008380];
termination of RNA polymerase II transcription [GO:0006369];
transcription, DNA-templated [GO:0006351]
Gene Ontology
(Molecular Function)
Complete annatation
mRNA 3'-UTR binding [GO:0003730];
nucleotide binding [GO:0000166];
poly(A RNA binding [GO:0044822];
RNA binding [GO:0003723]
Gene Ontology
(Cellular Component)
Complete annatation
ASAP complex [GO:0061574];
cytoplasm [GO:0005737];
cytosol [GO:0005829];
nuclear speck [GO:0016607];
nucleoplasm [GO:0005654];
nucleus [GO:0005634]
Protein-protein interaction116125
Phylogenetic treeQ15287
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. CD31.004774243036360.002340789705808750.00758391712079741
AZA vs. DISU0.03159455325630810.9007036087708170.993937521279788
AZA vs. IL70.1782255413680090.3538048739639910.999311006273513
AZA vs. SAHA-0.1550880889643580.5247503841691010.835690680187985
DISU vs. CD3-0.9851324841843570.007176367160038440.0220049956408502
DISU vs. IL70.1371974136141630.5859297760479190.870149874290452
DISU vs. SAHA-0.1846947900505180.5267258331570850.839577398228881
DMSO vs. AZA0.009667866105783550.9539731326205091
DMSO vs. CD3-1.006125624771920.00181648024175540.00573214806075516
DMSO vs. DISU-0.02362072130191030.9228689832623250.989539479263557
DMSO vs. IL70.1758891383956030.3276999358990150.802824414281686
DMSO vs. SAHA-0.1705159866810990.4693954083586290.795307273678797
HIV vs. Mock in Activation0.07443828844950480.904752485206060.999983755607037
HIV vs. Mock in Latency0.03982480774005180.8092985946119690.999834320637052
IL7 vs. CD3-0.8202833013426230.0111295670242990.032580299816908
SAHA vs. CD3-1.183437219205160.0009331604403427510.0033723567951955
SAHA vs. IL7-0.3359392231887970.1679840327773890.391434736448658
(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 0.243764 0.069995
(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
1.041 0.932 0.859 0.794 0.891
(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
4A8X X-ray 1.9Å A=159-244.

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 18854154

Metabolic/Signalling Pathway       (annotations from KEGG database)      top

Pathway Accession Number Description
hsa03013 RNA transport - Homo sapiens (human)
hsa03015 mRNA surveillance pathway - Homo sapiens (human)
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