Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0007195
UniProt IDP09012
Primary gene name(s)SNRPA
Synonym gene name(s)unknown
Protein nameU1 small nuclear ribonucleoprotein A
Protein functionComponent of the spliceosomal U1 snRNP, which is essential for recognition of the pre-mRNA 5' splice-site and the subsequent assembly of the spliceosome. U1 snRNP is the first snRNP to interact with pre-mRNA. This interaction is required for the subsequent binding of U2 snRNP and the U4/U6/U5 tri-snRNP. SNRPA binds stem loop II of U1 snRNA. In a snRNP-free form, SF-A may be involved in coupled pre-mRNA splicing and polyadenylation process. May bind preferentially to the 5'-UGCAC-3' motif on RNAs. {ECO:0000269|PubMed:9848648}.
Subcellular locationNucleus.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: P09012
Gene Ontology
(Biological Process)
Complete annatation
mRNA splicing, via spliceosome [GO:0000398];
regulation of mRNA polyadenylation [GO:1900363]
Gene Ontology
(Molecular Function)
Complete annatation
nucleotide binding [GO:0000166];
poly(A RNA binding [GO:0044822];
RNA binding [GO:0003723];
snRNA stem-loop binding [GO:0035614];
U1 snRNA binding [GO:0030619]
Gene Ontology
(Cellular Component)
Complete annatation
cytoplasm [GO:0005737];
nucleolus [GO:0005730];
nucleoplasm [GO:0005654];
spliceosomal complex [GO:0005681];
U1 snRNP [GO:0005685]
Protein-protein interaction112510
Phylogenetic treeP09012
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. CD31.017926556421110.002126921286479840.00697561378349699
AZA vs. DISU-0.2745240450189120.2811392859326260.851448190328572
AZA vs. IL70.1031873030121350.6418662566584390.999311006273513
AZA vs. SAHA-0.1608141830635690.5125660443317630.828748316234795
DISU vs. CD3-1.303439347992050.0004256683800271110.00199108391780774
DISU vs. IL70.3680577235239670.1487473652675850.501498696298822
DISU vs. SAHA0.1155984171706090.6927983129397690.909285722039125
DMSO vs. AZA-0.09550111605740980.5740808737643311
DMSO vs. CD3-1.124187747755390.0005238636189147660.001943843699249
DMSO vs. DISU0.1772531826096930.4706588586259040.896463712752207
DMSO vs. IL70.2060498143560510.3660459886248290.82594517618926
DMSO vs. SAHA-0.07091548206536540.7650706783588980.93257158786482
HIV vs. Mock in Activation0.08285555799440850.8941357701572060.999983755607037
HIV vs. Mock in Latency0.03335106192260060.8414874882791620.999834320637052
IL7 vs. CD3-0.9085607231577940.005041915538439360.0168806736807855
SAHA vs. CD3-1.201658325473850.0008224568756692860.00302376802057481
SAHA vs. IL7-0.2663951370095110.2787667802144350.526146040477362
(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
-0.2824 0.04401

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 0.43014 0.00221059
(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
1.107 0.934 0.883 0.868 0.905
(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

Drugbank ID Drug Name Drug Status Pharmacological Action Drug Action
DB02175 Malonic acid experimental unknown unknown

Protein Secondary Structure       (annotations from PDB)      top

PDB Accession Method Resolution Chain Structure Preview
1AUD NMR - A=2-102.
1DRZ X-ray 2.3Å A=2-98.
1DZ5 NMR - A/B=2-102.
1FHT NMR - A=2-117.
1M5K X-ray 2.4Å C/F=1-100.
1M5O X-ray 2.2Å C/F=1-100.
1M5P X-ray 2.6Å C/F=1-100.
1M5V X-ray 2.4Å C/F=1-100.
1NU4 X-ray 1.8Å A/B=2-98.
1OIA X-ray 2.4Å A/B=1-95.
1SJ3 X-ray 2.2Å P=1-100.
1SJ4 X-ray 2.7Å P=1-100.
1SJF X-ray 2.7Å A=1-100.
1U6B X-ray 3.1Å A=1-98.
1URN X-ray 1.9Å A/B/C=2-98.
1VBX X-ray 2.7Å A=1-100.
1VBY X-ray 2.9Å A=1-100.
1VBZ X-ray 2.8Å A=1-100.
1VC0 X-ray 2.5Å A=1-100.
1VC5 X-ray 3.4Å A=1-100.
1VC6 X-ray 2.8Å A=1-100.
1ZZN X-ray 3.3Å A=1-98.
2A3J NMR - A=3-80.
2NZ4 X-ray 2.5Å A/B/C/D=5-98.
2OIH X-ray 2.4Å A=2-100.
2OJ3 X-ray 2.9Å A=2-100.
2U1A NMR - A=195-282.
3BO2 X-ray 3.3Å A=4-98.
3BO3 X-ray 3.4Å A=4-98.
3BO4 X-ray 3.3Å A=4-98.
3CUL X-ray 2.8Å A/B=1-96.
3CUN X-ray 3.0Å A/B=1-98.
3EGZ X-ray 2.2Å A=1-98.
3G8S X-ray 3.1Å A/B/C/D=1-98.
3G8T X-ray 3.0Å A/B/C/D=1-98.
3G96 X-ray 3.0Å A/B/C/D=1-98.
3G9C X-ray 2.9Å A/B/C/D=1-98.
3HHN X-ray 2.9Å B/D=2-98.
3IIN X-ray 4.1Å A=4-98.
3IRW X-ray 2.7Å P=1-98.
3IWN X-ray 3.2Å C/D=6-96.
3K0J X-ray 3.1Å A/B/C/D=2-97.
3L3C X-ray 2.8Å A/B/C/D=7-96.
3MUM X-ray 2.9Å P=1-98.
3MUR X-ray 3.0Å P=1-98.
3MUT X-ray 3.0Å P=1-98.
3MUV X-ray 3.2Å P=1-98.
3MXH X-ray 2.3Å P=1-98.
3P49 X-ray 3.5Å B=1-98.
3PGW X-ray 4.4Å A/P=1-282.
3R1H X-ray 3.1Å A/D=1-98.
3R1L X-ray 3.1Å A/D=1-98.
3UCU X-ray 2.8Å P=1-98.
3UCZ X-ray 2.8Å P=1-98.
3UD3 X-ray 3.1Å P=1-98.
3UD4 X-ray 2.7Å P=1-98.
3UTR Model - B/D=1-98.
4C4W X-ray 2.9Å A/B/E/F=1-102.
4PR6 X-ray 2.3Å A=4-96.
4PRF X-ray 2.4Å A=1-100.
4W90 X-ray 3.1Å B=6-96.
4W92 X-ray 3.2Å B=6-96.
4YB1 X-ray 2.0Å P=7-97.
5DDO X-ray 3.1Å C/G=2-98.
5DDP X-ray 2.3Å C/D=2-98.
5DDQ X-ray 2.4Å C/D=2-98.
5DDR X-ray 2.6Å C/D=2-98.
5FJ4 X-ray 2.9Å A/B/E/F=1-102.

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

HIV Partner Interaction Type PubMed
Tat downregulates 23166591
HIV-1 virus replication enhanced by expression of human gene 18854154
Nef upregulates 11420046
Tat interacts with 25496916

Metabolic/Signalling Pathway       (annotations from KEGG database)      top

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