Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0007011
UniProt IDP55735
Primary gene name(s)SEC13
Synonym gene name(s)D3S1231E, SEC13L1, SEC13R
Protein nameProtein SEC13 homolog
Protein functionFunctions as a component of the nuclear pore complex, NPC and the COPII coat. At the endoplasmic reticulum, SEC13 is involved in the biogenesis of COPII-coated vesicles. {ECO:0000269|PubMed:8972206}.; FUNCTION: As a component of the GATOR subcomplex GATOR2, functions within the amino acid-sensing branch of the TORC1 signaling pathway. Indirectly activates mTORC1 and the TORC1 signaling pathway through the inhibition of the GATOR1 subcomplex, PubMed:23723238. It is negatively regulated by the upstream amino acid sensors SESN2 and GATSL3, PubMed:25457612, PubMed:27487210. {ECO:0000269|PubMed:23723238, ECO:0000269|PubMed:25457612, ECO:0000269|PubMed:27487210}.
Subcellular locationCytoplasmic vesicle, COPII-coated vesicle membrane;
Peripheral membrane protein;
Cytoplasmic side. Endoplasmic reticulum membrane;
Peripheral membrane protein;
Cytoplasmic side. Nucleus, nuclear pore complex. Note=In interphase, localizes at both sides of the NPC.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: P55735
Gene Ontology
(Biological Process)
Complete annatation
antigen processing and presentation of exogenous peptide antigen via MHC class II [GO:0019886];
antigen processing and presentation of peptide antigen via MHC class I [GO:0002474];
COPII vesicle coating [GO:0048208];
intracellular protein transport [GO:0006886];
mRNA transport [GO:0051028];
positive regulation of TOR signaling [GO:0032008];
sister chromatid cohesion [GO:0007062]
Gene Ontology
(Molecular Function)
Complete annatation
unknown
Gene Ontology
(Cellular Component)
Complete annatation
cytosol [GO:0005829];
endoplasmic reticulum membrane [GO:0005789];
ER to Golgi transport vesicle membrane [GO:0012507];
extracellular exosome [GO:0070062];
GATOR2 complex [GO:0061700];
Golgi membrane [GO:0000139];
intracellular membrane-bounded organelle [GO:0043231];
nuclear envelope [GO:0005635];
nuclear pore outer ring [GO:0031080];
nucleoplasm [GO:0005654]
Protein-protein interaction112296
Phylogenetic treeP55735
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. CD30.9575716242132750.003752224310093370.0113881443418702
AZA vs. DISU0.1112226109822220.6606003645888180.961362166066015
AZA vs. IL70.1396269365040470.4687266151122360.999311006273513
AZA vs. SAHA-0.1248310839277450.6094936409278750.871897540037369
DISU vs. CD3-0.858909759398730.0189123775626810.0489752927984632
DISU vs. IL70.01909935301891530.9396198602369280.988709793931654
DISU vs. SAHA-0.2335865412386470.4239505032839010.776161082967889
DMSO vs. AZA-0.01532137316215840.9274145988246841
DMSO vs. CD3-0.9859392657497960.002265546312961280.00694979743530067
DMSO vs. DISU-0.128826260629620.5979058137645370.937098979571498
DMSO vs. IL70.1625232478129250.3672846304249510.826760609773948
DMSO vs. SAHA-0.1145898231317330.6275764623053390.878362264431999
HIV vs. Mock in Activation-0.003192718026086320.9959032574562780.999983755607037
HIV vs. Mock in Latency-0.07513774523958990.6502124494374860.999834320637052
IL7 vs. CD3-0.8116149393544640.0120773011682480.0347469076468646
SAHA vs. CD3-1.105898251530650.001960406583934260.00636472870222888
SAHA vs. IL7-0.2666878658339030.2743965868519160.5215490393141
(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 0.135079 0.389456
(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
0.993 0.95 1.016 1.051 0.962
(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
207707_s_at 1.33 No upregulated in CD8+ cells

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
3BG0 X-ray 3.1Å A/D/E/H=1-316.
3BG1 X-ray 3.0Å A/D/E/H=1-316.
5A9Q EM 23.0Å 6/F/O/X=1-322.

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

HIV Partner Interaction Type PubMed
Envelope surface glycoprotein gp120 co-localizes with 24825317

Metabolic/Signalling Pathway       (annotations from KEGG database)      top

Pathway Accession Number Description
hsa03013 RNA transport - Homo sapiens (human)
hsa04141 Protein processing in endoplasmic reticulum - Homo sapiens (human)
hsa04150 mTOR signaling pathway - Homo sapiens (human)
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