Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0002646
UniProt IDQ12874
Primary gene name(s)SF3A3
Synonym gene name(s)SAP61
Protein nameSplicing factor 3A subunit 3
Protein functionSubunit of the splicing factor SF3A required for 'A' complex assembly formed by the stable binding of U2 snRNP to the branchpoint sequence, BPS in pre-mRNA. Sequence independent binding of SF3A/SF3B complex upstream of the branch site is essential, it may anchor U2 snRNP to the pre-mRNA. May also be involved in the assembly of the 'E' complex.
Subcellular locationNucleus speckle.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: Q12874
Gene Ontology
(Biological Process)
Complete annatation
mRNA 3'-splice site recognition [GO:0000389];
mRNA processing [GO:0006397];
mRNA splicing, via spliceosome [GO:0000398];
RNA splicing [GO:0008380];
RNA splicing, via transesterification reactions [GO:0000375]
Gene Ontology
(Molecular Function)
Complete annatation
poly(A RNA binding [GO:0044822];
RNA binding [GO:0003723];
zinc ion binding [GO:0008270]
Gene Ontology
(Cellular Component)
Complete annatation
catalytic step 2 spliceosome [GO:0071013];
nuclear speck [GO:0016607];
nucleoplasm [GO:0005654];
spliceosomal complex [GO:0005681]
Protein-protein interaction116146
Phylogenetic treeQ12874
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. CD31.152933034395960.0005003245292454220.00199073160105253
AZA vs. DISU0.07434126257969040.7686171612704310.976327198566393
AZA vs. IL70.1812811986150830.3455160578301650.999311006273513
AZA vs. SAHA-0.2952547385350110.2263084903921860.59609623825128
DISU vs. CD3-1.09098827647610.00288947476410140.0102364142406732
DISU vs. IL70.09774741176142090.6977037409004690.922418222091218
DISU vs. SAHA-0.3680777599344070.206682072491280.580548911402724
DMSO vs. AZA-0.04755334395358790.7764641296070331
DMSO vs. CD3-1.21068624541370.0001854464824315730.000777337578695504
DMSO vs. DISU-0.123335906276920.6129004360133770.939289650701039
DMSO vs. IL70.2359172497851370.189419309279970.700391485748232
DMSO vs. SAHA-0.2544511493928930.2804893546696040.629336767042669
HIV vs. Mock in Activation0.07405068807994920.905132013308420.999983755607037
HIV vs. Mock in Latency0.03466547182192310.8337737623693030.999834320637052
IL7 vs. CD3-0.964475424444990.002884778650485980.0105232983056087
SAHA vs. CD3-1.472418851502644.35964979930148e-050.000230687930040285
SAHA vs. IL7-0.479591754859770.04924720820130790.182261825786034
(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 -0.9804257
(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 -0.0190345 0.925287
(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
1.048 0.942 0.832 0.755 0.868
(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
2DT7 NMR - A=71-107.

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

HIV Partner Interaction Type PubMed
Rev interacts with 22174317
retropepsin interacts with 22190034

Metabolic/Signalling Pathway       (annotations from KEGG database)      top

Pathway Accession Number Description
hsa03040 Spliceosome - Homo sapiens (human)
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