Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0000627
UniProt IDQ96DZ5
Primary gene name(s)CLIP3
Synonym gene name(s)CLIPR59
Protein nameCAP-Gly domain-containing linker protein 3
Protein functionFunctions as a cytoplasmic linker protein. Involved in TGN-endosome dynamics. May modulate the cellular compartmentalization of AKT kinase family and promote its cell membrane localization, thereby playing a role in glucose transport in adipocytes. {ECO:0000269|PubMed:19139280}.
Subcellular locationCell membrane {ECO:0000269|PubMed:24001771};
Lipid-anchor {ECO:0000269|PubMed:24001771}. Cytoplasm {ECO:0000269|PubMed:24001771}. Golgi apparatus, Golgi stack {ECO:0000269|PubMed:24001771}. Note=Localized to Golgi stacks as well as on tubulovesicular elements juxtaposed to Golgi cisternae.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: Q96DZ5
Gene Ontology
(Biological Process)
Complete annatation
chaperone-mediated protein transport [GO:0072321];
fat cell differentiation [GO:0045444];
membrane biogenesis [GO:0044091];
negative regulation of microtubule polymerization [GO:0031115];
peptidyl-L-cysteine S-palmitoylation [GO:0018230];
positive regulation of apoptotic process [GO:0043065];
positive regulation of endocytosis [GO:0045807];
positive regulation of establishment of protein localization to plasma membrane [GO:0090004];
positive regulation of glucose transport [GO:0010828];
positive regulation of protein phosphorylation [GO:0001934];
regulation of tumor necrosis factor-mediated signaling pathway [GO:0010803]
Gene Ontology
(Molecular Function)
Complete annatation
ganglioside binding [GO:0035594];
microtubule binding [GO:0008017]
Gene Ontology
(Cellular Component)
Complete annatation
cytosol [GO:0005829];
early endosome membrane [GO:0031901];
Golgi stack [GO:0005795];
membrane raft [GO:0045121];
plasma membrane [GO:0005886];
recycling endosome membrane [GO:0055038];
trans-Golgi network [GO:0005802];
trans-Golgi network membrane [GO:0032588]
Protein-protein interaction117475
Phylogenetic treeQ96DZ5
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. CD3-0.5727938940324260.09889179386583050.174408742937725
AZA vs. DISU0.2026611716313220.4547249840692210.921997150117399
AZA vs. IL7-0.3452986922945160.120104221907710.882657697130628
AZA vs. SAHA0.229768873708170.3858327940280640.748644001723269
DISU vs. CD30.7646806224095860.04336184923789340.09617959320365
DISU vs. IL7-0.5566584539219280.0402827998151920.265064691058062
DISU vs. SAHA0.02659190006371810.9306670240258010.984054479085387
DMSO vs. AZA-0.03105937113996350.8759684080121571
DMSO vs. CD30.5260093518562450.1191113122632590.196669434375932
DMSO vs. DISU-0.2369877962004050.3646112257997190.84938803104062
DMSO vs. IL7-0.304702346180190.1450085817056660.646627282384002
DMSO vs. SAHA0.2540673723117560.3193287814611870.672433151516214
HIV vs. Mock in Activation0.05871792164501110.9281251486741490.999983755607037
HIV vs. Mock in Latency-0.3193921921637540.08771315969433560.999834320637052
IL7 vs. CD30.2373169754536090.4861682482363730.617458500365545
SAHA vs. CD30.7769238483025810.03586965930117960.0754018364721406
SAHA vs. IL70.5679970396132550.03236912549836210.13752258385242
(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 -0.990646 0.000305467
(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
unknown unknown unknown unknown unknown
(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
2CP0 NMR - A=285-366.

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
not found
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