Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0007051
UniProt IDQ15427
Primary gene name(s)SF3B4
Synonym gene name(s)SAP49
Protein nameSplicing factor 3B subunit 4
Protein functionSubunit of the splicing factor SF3B 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. SF3B4 has been found in complex 'B' and 'C' as well. Belongs also to the minor U12-dependent spliceosome, which is involved in the splicing of rare class of nuclear pre-mRNA intron.
Subcellular locationNucleus {ECO:0000250}.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: Q15427
Gene Ontology
(Biological Process)
Complete annatation
mRNA processing [GO:0006397];
mRNA splicing, via spliceosome [GO:0000398];
positive regulation of mRNA splicing, via spliceosome [GO:0048026];
RNA splicing [GO:0008380];
RNA splicing, via transesterification reactions [GO:0000375]
Gene Ontology
(Molecular Function)
Complete annatation
nucleotide binding [GO:0000166];
poly(A RNA binding [GO:0044822]
Gene Ontology
(Cellular Component)
Complete annatation
nucleoplasm [GO:0005654];
spliceosomal complex [GO:0005681];
U12-type spliceosomal complex [GO:0005689]
Protein-protein interaction115554
Phylogenetic treeQ15427
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. CD31.322692110179237.24087892952641e-050.000361612084909947
AZA vs. DISU0.1571792584918250.5349787234411960.940988247042308
AZA vs. IL70.1780158929992770.3567649806721290.999311006273513
AZA vs. SAHA0.1010164840155910.6796274216765990.906724266704883
DISU vs. CD3-1.177725501335090.001352970849290310.0053644239733401
DISU vs. IL70.01129018708885380.9643243635281680.994460945401169
DISU vs. SAHA-0.05354958026981430.8543143634072550.961063803158225
DMSO vs. AZA0.02445817218572690.8846404332527351
DMSO vs. CD3-1.310350942736355.822155089652e-050.000278270198050785
DMSO vs. DISU-0.1348391314431090.5811797815470490.932784987235767
DMSO vs. IL70.1611282492813220.372108399375190.830213976027877
DMSO vs. SAHA0.07171448205778490.7618282952627020.931289292684464
HIV vs. Mock in Activation0.0998966106386180.8723482480617090.999983755607037
HIV vs. Mock in Latency-0.05371795630872760.7464777635491280.999834320637052
IL7 vs. CD3-1.138926156102730.0004933751682900670.00231815583280429
SAHA vs. CD3-1.244700901674930.0005133500338171390.00200211827371229
SAHA vs. IL7-0.07873976672514010.7476266087196730.885775642524589
(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 0.261616 0.0512964
(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
1.026 1.156 1.127 1.156 0.965
(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
1X5T NMR - A=102-184.
1X5U NMR - A=5-96.

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

HIV Partner Interaction Type PubMed
Envelope surface glycoprotein gp120 complexes with 23125841
Gag-Pol complexes with 23125841
Vpr inhibits 16923959
19275585
2001252917347016
19275585
20012529
Pr55(Gag) complexes with 23125841
Nef complexes with 23125841

Metabolic/Signalling Pathway       (annotations from KEGG database)      top

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