Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0007896
UniProt IDQ9HCS7
Primary gene name(s)XAB2
Synonym gene name(s)HCNP, KIAA1177, SYF1
Protein namePre-mRNA-splicing factor SYF1
Protein functionInvolved in transcription-coupled repair, TCR, transcription and pre-mRNA splicing. {ECO:0000269|PubMed:10944529, ECO:0000269|PubMed:17981804}.
Subcellular locationNucleus {ECO:0000250}. Note=Detected in the splicing complex carrying pre-mRNA. {ECO:0000250}.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: Q9HCS7
Gene Ontology
(Biological Process)
Complete annatation
blastocyst development [GO:0001824];
cerebral cortex development [GO:0021987];
generation of catalytic spliceosome for first transesterification step [GO:0000349];
mRNA splicing, via spliceosome [GO:0000398];
transcription, DNA-templated [GO:0006351];
transcription-coupled nucleotide-excision repair [GO:0006283]
Gene Ontology
(Molecular Function)
Complete annatation
Gene Ontology
(Cellular Component)
Complete annatation
catalytic step 1 spliceosome [GO:0071012];
catalytic step 2 spliceosome [GO:0071013];
membrane [GO:0016020];
nucleoplasm [GO:0005654];
nucleus [GO:0005634];
post-mRNA release spliceosomal complex [GO:0071014];
prespliceosome [GO:0071010];
Prp19 complex [GO:0000974]
Protein-protein interaction121273
Phylogenetic treeQ9HCS7
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. CD3-0.02449540000582570.9407627497256380.961952249922987
AZA vs. DISU0.3701819129664720.1452253215819870.718797155225174
AZA vs. IL7-0.1473800198964420.445174379182640.999311006273513
AZA vs. SAHA-0.1916129241947730.433175421472080.782318188498334
DISU vs. CD30.3820503374724580.3012303985883610.432474398856177
DISU vs. IL7-0.5272036013133710.03716491218892120.252939526522793
DISU vs. SAHA-0.5590834791300130.05643237831653870.298315805279824
DMSO vs. AZA0.04219757983367160.8020722131032821
DMSO vs. CD30.05402289409980840.8672005107320930.908510131723156
DMSO vs. DISU-0.3302047103210350.1770449671543070.690311335740057
DMSO vs. IL7-0.1819359470371640.3134239257029970.795175691304346
DMSO vs. SAHA-0.2386015195237060.3126853284155070.663962137427825
HIV vs. Mock in Activation0.2077399722737390.7400184818636470.999983755607037
HIV vs. Mock in Latency0.06521286964573360.694242150055980.999834320637052
IL7 vs. CD3-0.1176756690515910.7172611399929840.809287908010648
SAHA vs. CD3-0.1898942960842250.5935328788567330.692301211322222
SAHA vs. IL7-0.04664977997015410.8484269074036540.936165774492104
(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 -0.245998 0.125263
(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
1.002 0.969 0.909 0.806 0.941
(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
HIV-1 virus replication enhanced by expression of human gene 18854154

Metabolic/Signalling Pathway       (annotations from KEGG database)      top

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