Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0000620
UniProt IDP51790
Primary gene name(s)CLCN3
Synonym gene name(s)unknown
Protein nameH(+/Cl(- exchange transporter 3
Protein functionMediates the exchange of chloride ions against protons. Functions as antiporter and contributes to the acidification of the endosome and synaptic vesicle lumen, and may thereby affect vesicle trafficking and exocytosis. May play an important role in neuronal cell function through regulation of membrane excitability by protein kinase C. It could help neuronal cells to establish short-term memory. {ECO:0000269|PubMed:11967229}.
Subcellular locationIsoform 1: Early endosome membrane {ECO:0000269|PubMed:12471024};
Multi-pass membrane protein {ECO:0000255}. Late endosome membrane {ECO:0000269|PubMed:12471024};
Multi-pass membrane protein {ECO:0000255}. Cytoplasmic vesicle, secretory vesicle membrane {ECO:0000250|UniProtKB:P51791};
Multi-pass membrane protein {ECO:0000255}. Note=Isoform 1 is localized mainly in late endosomes. {ECO:0000269|PubMed:12471024}.;
SUBCELLULAR LOCATION: Isoform 2: Golgi apparatus membrane {ECO:0000269|PubMed:12471024};
Multi-pass membrane protein {ECO:0000255}. Note=Isoform 2 is mainly enriched in the Golgi. {ECO:0000269|PubMed:12471024}.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: P51790
Gene Ontology
(Biological Process)
Complete annatation
chloride transmembrane transport [GO:1902476];
endosomal lumen acidification [GO:0048388];
negative regulation of cell volume [GO:0045794];
regulation of pH [GO:0006885];
transport [GO:0006810]
Gene Ontology
(Molecular Function)
Complete annatation
antiporter activity [GO:0015297];
ATP binding [GO:0005524];
chloride channel activity [GO:0005254];
PDZ domain binding [GO:0030165];
protein heterodimerization activity [GO:0046982];
protein homodimerization activity [GO:0042803];
voltage-gated chloride channel activity [GO:0005247];
volume-sensitive chloride channel activity [GO:0072320]
Gene Ontology
(Cellular Component)
Complete annatation
apical plasma membrane [GO:0016324];
cell surface [GO:0009986];
cytoplasmic vesicle [GO:0031410];
early endosome [GO:0005769];
early endosome membrane [GO:0031901];
external side of plasma membrane [GO:0009897];
Golgi apparatus [GO:0005794];
Golgi membrane [GO:0000139];
integral component of membrane [GO:0016021];
late endosome [GO:0005770];
late endosome membrane [GO:0031902];
membrane [GO:0016020];
phagocytic vesicle [GO:0045335];
plasma membrane [GO:0005886];
secretory granule [GO:0030141];
specific granule [GO:0042581];
synaptic vesicle [GO:0008021];
transport vesicle membrane [GO:0030658];
vesicle membrane [GO:0012506]
Protein-protein interaction107596
Phylogenetic treeP51790
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. CD3-0.188616195670040.564367884975080.673455842316698
AZA vs. DISU0.1129460323494370.6558079228521220.960323430331341
AZA vs. IL7-0.09848256314742270.6084935552588440.999311006273513
AZA vs. SAHA0.4428267380985830.06987329991960420.325824926864318
DISU vs. CD30.2881683525951490.4269601615795790.558892009195314
DISU vs. IL7-0.2201601149098790.3834906685224360.753121417320375
DISU vs. SAHA0.3305782559585020.2568535946974370.634850298482705
DMSO vs. AZA-0.0231112868313570.8902846797925261
DMSO vs. CD30.1526268418508570.6329188761580090.725001454354835
DMSO vs. DISU-0.1383708757737630.5713983859267810.930312627043711
DMSO vs. IL7-0.06795671161462280.7054893209644040.939646666682909
DMSO vs. SAHA0.4586075566722820.05211027158260060.258680468715868
HIV vs. Mock in Activation0.1071220686729410.8640164683390470.999983755607037
HIV vs. Mock in Latency0.03173030437013880.8478511628263130.999834320637052
IL7 vs. CD30.0988226367684470.758252059182310.839328287291985
SAHA vs. CD30.6050805527855810.08750986287807430.156530995082799
SAHA vs. IL70.5366217852675270.02798479764976550.124308703868351
(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) TRUE
(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 -0.213633 0.121655
(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
1.097 1.278 1.222 1.431 1.227
(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

not found

Metabolic/Signalling Pathway       (annotations from KEGG database)      top

Pathway Accession Number Description
not found