Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0006718
UniProt IDQ9Y5S9
Primary gene name(s)RBM8A
Synonym gene name(s)RBM8
Protein nameRNA-binding protein 8A
Protein functionCore component of the splicing-dependent multiprotein exon junction complex, EJC deposited at splice junctions 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. The EJC marks the position of the exon-exon junction in the mature mRNA for the gene expression machinery and the core components remain bound to spliced mRNAs throughout all stages of mRNA metabolism thereby influencing downstream processes including nuclear mRNA export, subcellular mRNA localization, translation efficiency and nonsense-mediated mRNA decay, NMD. The MAGOH-RBM8A heterodimer inhibits the ATPase activity of EIF4A3, thereby trapping the ATP-bound EJC core onto spliced mRNA in a stable conformation. The MAGOH-RBM8A heterodimer interacts with the EJC key regulator PYM1 leading to EJC disassembly in the cytoplasm and translation enhancement of EJC-bearing spliced mRNAs by recruiting them to the ribosomal 48S preinitiation complex. Its removal from cytoplasmic mRNAs requires translation initiation from EJC-bearing spliced mRNAs. Associates preferentially with mRNAs produced by splicing. Does not interact with pre-mRNAs, introns, or mRNAs produced from intronless cDNAs. Associates with both nuclear mRNAs and newly exported cytoplasmic mRNAs. The MAGOH-RBM8A heterodimer is a component of the nonsense mediated decay, NMD pathway. 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 function is different from the established EJC assembly. {ECO:0000269|PubMed:12121612, ECO:0000269|PubMed:12718880, ECO:0000269|PubMed:12730685, ECO:0000269|PubMed:16209946, ECO:0000269|PubMed:19409878, ECO:0000269|PubMed:22203037}.
Subcellular locationNucleus {ECO:0000269|PubMed:19324961}. Nucleus speckle {ECO:0000269|PubMed:19324961}. Cytoplasm {ECO:0000269|PubMed:19324961}. Note=Nucleocytoplasmic shuttling protein. Travels to the cytoplasm as part of the exon junction complex, EJC bound to mRNA. 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: Q9Y5S9
Gene Ontology
(Biological Process)
Complete annatation
mRNA 3'-end processing [GO:0031124];
mRNA export from nucleus [GO:0006406];
mRNA splicing, via spliceosome [GO:0000398];
nuclear-transcribed mRNA catabolic process, nonsense-mediated decay [GO:0000184];
regulation of alternative mRNA splicing, via spliceosome [GO:0000381];
regulation of translation [GO:0006417];
RNA export from nucleus [GO:0006405];
termination of RNA polymerase II transcription [GO:0006369]
Gene Ontology
(Molecular Function)
Complete annatation
mRNA binding [GO:0003729];
nucleotide binding [GO:0000166];
poly(A RNA binding [GO:0044822];
RNA binding [GO:0003723]
Gene Ontology
(Cellular Component)
Complete annatation
catalytic step 2 spliceosome [GO:0071013];
cytoplasm [GO:0005737];
cytosol [GO:0005829];
dendrite [GO:0030425];
exon-exon junction complex [GO:0035145];
neuronal cell body [GO:0043025];
nuclear speck [GO:0016607];
nucleoplasm [GO:0005654];
nucleus [GO:0005634]
Protein-protein interaction115265
Phylogenetic treeQ9Y5S9
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. CD31.285744463500060.0001175970799116580.000557685740185047
AZA vs. DISU-0.2775371391886230.272553870035930.845804132461543
AZA vs. IL70.1846705538998470.3361720767122750.999311006273513
AZA vs. SAHA-0.3065923613663350.208823945798380.577974381507196
DISU vs. CD3-1.575346631977382.21087929538344e-050.000149716057945238
DISU vs. IL70.4527925752410820.07245126001007450.357864595233248
DISU vs. SAHA-0.02751573109953620.9246783069782980.982806795139101
DMSO vs. AZA-0.07342574543359720.6606605028803841
DMSO vs. CD3-1.368896859797282.78864738484375e-050.000144268450730326
DMSO vs. DISU0.2026048341277940.4061519878263910.868858747268752
DMSO vs. IL70.2652163947407770.1398590920158370.638901761254164
DMSO vs. SAHA-0.2400054265685760.3084864627480720.660600774393994
HIV vs. Mock in Activation0.1637129156833670.7922032763463150.999983755607037
HIV vs. Mock in Latency0.01712324772615560.917311921557860.999834320637052
IL7 vs. CD3-1.094095537584740.0007824641733307210.00344151808713568
SAHA vs. CD3-1.616332374327688.24567031376677e-065.29677116915879e-05
SAHA vs. IL7-0.4940054486382880.04270718187356180.165068733221044
(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 -0.31737 0.729943
(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
0.983 1.065 0.998 0.967 1.001
(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
1P27 X-ray 2.0Å B/D=50-155.
2HYI X-ray 2.3Å B/H=64-154.
2J0Q X-ray 3.2Å D/G=66-174.
2J0S X-ray 2.2Å D=66-154.
2XB2 X-ray 3.4Å D/Z=66-155.
3EX7 X-ray 2.3Å B/G=51-174.

HIV-1 Interaction       (annotations from NCBI HIV-1 Interaction Database)      top

HIV Partner Interaction Type PubMed
retropepsin cleaves 22944692

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)
hsa03040 Spliceosome - Homo sapiens (human)
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