Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0000778
UniProt IDQ9NUL7
Primary gene name(s)DDX28
Synonym gene name(s)MDDX28
Protein nameProbable ATP-dependent RNA helicase DDX28
Protein functionPlays an essential role in facilitating the proper assembly of the mitochondrial large ribosomal subunit and its helicase activity is essential for this function, PubMed:25683708, PubMed:25683715. May be involved in RNA processing or transport. Has RNA and Mg(2+-dependent ATPase activity, PubMed:11350955. {ECO:0000269|PubMed:11350955, ECO:0000269|PubMed:25683708, ECO:0000269|PubMed:25683715}.
Subcellular locationNucleus {ECO:0000269|PubMed:11350955, ECO:0000269|PubMed:25683708}. Mitochondrion {ECO:0000269|PubMed:11350955}. Mitochondrion matrix, mitochondrion nucleoid {ECO:0000269|PubMed:25683715}. Mitochondrion matrix {ECO:0000269|PubMed:25683708}. Note=Transported between these two compartments. Nuclear localization depends on active RNA polymerase II transcription. Localizes to mitochondrial RNA granules found in close proximity to the mitochondrial nucleoids. {ECO:0000269|PubMed:25683708, ECO:0000269|PubMed:25683715}.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: Q9NUL7
Gene Ontology
(Biological Process)
Complete annatation
mitochondrial large ribosomal subunit assembly [GO:1902775];
RNA secondary structure unwinding [GO:0010501]
Gene Ontology
(Molecular Function)
Complete annatation
ATP binding [GO:0005524];
ATP-dependent RNA helicase activity [GO:0004004];
poly(A RNA binding [GO:0044822];
rRNA binding [GO:0019843]
Gene Ontology
(Cellular Component)
Complete annatation
cytoplasm [GO:0005737];
mitochondrial nucleoid [GO:0042645];
mitochondrion [GO:0005739];
nucleolus [GO:0005730];
nucleus [GO:0005634];
ribonucleoprotein granule [GO:0035770]
Protein-protein interaction120907
Phylogenetic treeQ9NUL7
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. CD30.851727911254110.01000494498397380.0260799949495767
AZA vs. DISU-0.3077427118612850.2295010609806190.816706641605109
AZA vs. IL7-0.07118695509298050.7162446327193080.999311006273513
AZA vs. SAHA-0.2973932353425070.2290200489185430.599154923312376
DISU vs. CD3-1.171523208738540.001456578689530420.00570001743665149
DISU vs. IL70.226744886734890.3734861926519620.746349367869539
DISU vs. SAHA0.01256349461459910.9659399193178050.992637214624418
DMSO vs. AZA-0.01268240130656860.9411280904153931
DMSO vs. CD3-0.877502821131160.006594113324514090.0173823827180761
DMSO vs. DISU0.2926418242885990.2361155179254440.753071080452157
DMSO vs. IL7-0.05092924709053180.7811447182380570.954555156022505
DMSO vs. SAHA-0.2896470232895520.2251567502663710.571251110585826
HIV vs. Mock in Activation0.001870681955219220.9976112129220980.999983755607037
HIV vs. Mock in Latency0.0009313290625607690.9956239366844810.999834320637052
IL7 vs. CD3-0.916736723932180.004761340847564630.0160697918932695
SAHA vs. CD3-1.172689190229040.001084842377632290.00383859465389026
SAHA vs. IL7-0.2283999632089510.3542525829639130.604322740076501
(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 -0.240244 0.103328
(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
1.031 1.04 0.834 0.75 0.902
(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

HIV Partner Interaction Type PubMed
capsid upregulated by 25701821
HIV-1 virus replication enhanced by expression of human gene 25701821

Metabolic/Signalling Pathway       (annotations from KEGG database)      top

Pathway Accession Number Description
not found
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