Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0004505
UniProt IDQ13838
Primary gene name(s)DDX39B
Synonym gene name(s)BAT1, UAP56
Protein nameSpliceosome RNA helicase DDX39B
Protein functionInvolved in nuclear export of spliced and unspliced mRNA. Assembling component of the TREX complex which is thought to couple mRNA transcription, processing and nuclear export, and specifically associates with spliced mRNA and not with unspliced pre-mRNA. TREX is recruited to spliced mRNAs by a transcription-independent mechanism, binds to mRNA upstream of the exon-junction complex, EJC and is recruited in a splicing- and cap-dependent manner to a region near the 5' end of the mRNA where it functions in mRNA export to the cytoplasm via the TAP/NFX1 pathway. May undergo several rounds of ATP hydrolysis during assembly of TREX to drive subsequent loading of components such as ALYREF/THOC and CHTOP onto mRNA. The TREX complex is essential for the export of Kaposi's sarcoma-associated herpesvirus, KSHV intronless mRNAs and infectious virus production. Also associates with pre-mRNA independent of ALYREF/THOC4 and the THO complex. Involved in the nuclear export of intronless mRNA; the ATP-bound form is proposed to recruit export adapter ALYREF/THOC4 to intronless mRNA; its ATPase activity is cooperatively stimulated by RNA and ALYREF/THOC4 and ATP hydrolysis is thought to trigger the dissociation from RNA to allow the association of ALYREF/THOC4 and the NXF1-NXT1 heterodimer. Involved in transcription elongation and genome stability.; FUNCTION: Splice factor that is required for the first ATP-dependent step in spliceosome assembly and for the interaction of U2 snRNP with the branchpoint. Has both RNA-stimulated ATP binding/hydrolysis activity and ATP-dependent RNA unwinding activity. Even with the stimulation of RNA, the ATPase activity is weak. Can only hydrolyze ATP but not other NTPs. The RNA stimulation of ATPase activity does not have a strong preference for the sequence and length of the RNA. However, ssRNA stimulates the ATPase activity much more strongly than dsRNA. Can unwind 5' or 3' overhangs or blunt end RNA duplexes in vitro. The ATPase and helicase activities are not influenced by U2AF2; the effect of ALYREF/THOC4 is reported conflictingly with [PubMed:23299939] reporting a stimulatory effect.
Subcellular locationNucleus. Nucleus speckle. Cytoplasm. Note=Can translocate to the cytoplasm in the presence of MX1. TREX complex assembly seems to occur in regions surrounding nuclear speckles known as perispeckles.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: Q13838
Gene Ontology
(Biological Process)
Complete annatation
liver development [GO:0001889];
mRNA 3'-end processing [GO:0031124];
mRNA export from nucleus [GO:0006406];
mRNA splicing, via spliceosome [GO:0000398];
negative regulation of DNA damage checkpoint [GO:2000002];
positive regulation of cell growth involved in cardiac muscle cell development [GO:0061051];
positive regulation of DNA biosynthetic process [GO:2000573];
positive regulation of DNA-templated transcription, elongation [GO:0032786];
positive regulation of translation [GO:0045727];
positive regulation of vascular smooth muscle cell proliferation [GO:1904707];
RNA export from nucleus [GO:0006405];
RNA secondary structure unwinding [GO:0010501];
RNA splicing [GO:0008380];
spliceosomal complex assembly [GO:0000245];
termination of RNA polymerase II transcription [GO:0006369];
viral mRNA export from host cell nucleus [GO:0046784]
Gene Ontology
(Molecular Function)
Complete annatation
ATPase activity [GO:0016887];
ATP binding [GO:0005524];
ATP-dependent protein binding [GO:0043008];
ATP-dependent RNA helicase activity [GO:0004004];
poly(A RNA binding [GO:0044822];
RNA-dependent ATPase activity [GO:0008186];
U4 snRNA binding [GO:0030621];
U6 snRNA binding [GO:0017070]
Gene Ontology
(Cellular Component)
Complete annatation
cytoplasm [GO:0005737];
nuclear matrix [GO:0016363];
nuclear speck [GO:0016607];
nucleoplasm [GO:0005654];
nucleus [GO:0005634];
spliceosomal complex [GO:0005681];
transcription export complex [GO:0000346]
Protein-protein interaction113649
Phylogenetic treeQ13838
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. CD30.1858901948219660.5697584255668360.678470331843513
AZA vs. DISU0.005577208708902730.9823658892154910.998683149646457
AZA vs. IL7-0.03962064593127620.8361419314014440.999311006273513
AZA vs. SAHA-0.2644035062141710.2774763377066490.651026391193458
DISU vs. CD3-0.1936785591560920.5930413307468160.705077092439845
DISU vs. IL7-0.05451927247336550.8282684585916630.963585971081133
DISU vs. SAHA-0.2671988938508850.3585888431081350.734744671289963
DMSO vs. AZA0.1175002077367690.4811378321784691
DMSO vs. CD3-0.07949889880154230.8032727637896190.86087388393616
DMSO vs. DISU0.1104686462708210.6501246643868360.949174451880412
DMSO vs. IL7-0.1499580298039670.4026545152731360.846489249051434
DMSO vs. SAHA-0.3873719278341590.09992953998718870.373065399500919
HIV vs. Mock in Activation0.2508570821675070.6864974623243310.999983755607037
HIV vs. Mock in Latency0.1092144095055830.5061146633756580.999834320637052
IL7 vs. CD3-0.2199664199256980.493062000726040.62379751023532
SAHA vs. CD3-0.4733729368542360.1804299941586330.278994460493598
SAHA vs. IL7-0.2272550139120270.3497042935722460.599368109301652
(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 0.46173 0.00132191
(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 0.987 1.096 1.085 0.998
(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

Drugbank ID Drug Name Drug Status Pharmacological Action Drug Action
DB02325 Isopropyl Alcohol approved unknown unknown

Protein Secondary Structure       (annotations from PDB)      top

PDB Accession Method Resolution Chain Structure Preview
1T5I X-ray 1.9Å A=259-428.
1T6N X-ray 1.9Å A/B=34-251.
1XTI X-ray 1.9Å A=46-428.
1XTJ X-ray 2.7Å A=44-423.
1XTK X-ray 2.4Å A=45-428.

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

HIV Partner Interaction Type PubMed
Envelope surface glycoprotein gp120 complexes with 23125841
Gag-Pol complexes with 23125841
Rev inhibits 24753416
Pr55(Gag) complexes with 23125841
Nef complexes with 23125841

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)
hsa05164 Influenza A - Homo sapiens (human)
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