Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0002602
UniProt IDO75056
Primary gene name(s)SDC3
Synonym gene name(s)KIAA0468
Protein nameSyndecan-3
Protein functionCell surface proteoglycan that may bear heparan sulfate, By similarity. May have a role in the organization of cell shape by affecting the actin cytoskeleton, possibly by transferring signals from the cell surface in a sugar-dependent mechanism. {ECO:0000250, ECO:0000269|PubMed:11527150}.
Subcellular locationMembrane;
Single-pass type I membrane protein.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: O75056
Gene Ontology
(Biological Process)
Complete annatation
cell migration [GO:0016477];
glycosaminoglycan biosynthetic process [GO:0006024];
glycosaminoglycan catabolic process [GO:0006027];
glycosaminoglycan metabolic process [GO:0030203];
retinoid metabolic process [GO:0001523]
Gene Ontology
(Molecular Function)
Complete annatation
Gene Ontology
(Cellular Component)
Complete annatation
axon [GO:0030424];
cell surface [GO:0009986];
Golgi lumen [GO:0005796];
integral component of membrane [GO:0016021];
lysosomal lumen [GO:0043202];
membrane [GO:0016020];
plasma membrane [GO:0005886];
protein complex [GO:0043234]
Protein-protein interaction115027
Phylogenetic treeO75056
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. CD3-0.04227254605013960.9217562845818240.949928938202889
AZA vs. DISU-0.4846124799734070.1076901358604640.653579050610225
AZA vs. IL7-0.2062684053511190.4954926451117730.999311006273513
AZA vs. SAHA0.2460990445789210.3711668831951030.737927934223554
DISU vs. CD3-0.4557877136920160.3131106223975770.445392990659723
DISU vs. IL70.2705376604742860.3978620905306270.761911968337042
DISU vs. SAHA0.7324108842521520.02200845260506650.17248538180497
DMSO vs. AZA0.1218794140273420.6804796549262631
DMSO vs. CD30.1437435378794560.7372313712374660.809914021303167
DMSO vs. DISU0.6028493976940940.05114302898056070.445067187377236
DMSO vs. IL7-0.32001918153990.3050361155533650.788338514346039
DMSO vs. SAHA0.11965074923720.6533606173941450.889342292697539
HIV vs. Mock in Activation-0.3101205778867980.7190786686486560.999983755607037
HIV vs. Mock in Latency-0.2756374361859420.5692204613265630.999834320637052
IL7 vs. CD3-0.1591456158963480.7246484118492050.814634957622544
SAHA vs. CD30.2624212274762880.5222959958666090.629277315135098
SAHA vs. IL70.4504747471974840.1029749805091450.292490080308055
(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
NOTEST 0.165615 1
(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

not found

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

HIV Partner Interaction Type PubMed
Nef inhibits 22721673
Tat binds 7690138
Envelope surface glycoprotein gp120 binds 16157597
Envelope transmembrane glycoprotein gp41 downregulates 23383108

Metabolic/Signalling Pathway       (annotations from KEGG database)      top

Pathway Accession Number Description
hsa04514 Cell adhesion molecules (CAMs) - Homo sapiens (human)