Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0001338
UniProt IDP17096
Primary gene name(s)HMGA1
Synonym gene name(s)HMGIY
Protein nameHigh mobility group protein HMG-I/HMG-Y
Protein functionHMG-I/Y bind preferentially to the minor groove of A+T rich regions in double-stranded DNA. It is suggested that these proteins could function in nucleosome phasing and in the 3'-end processing of mRNA transcripts. They are also involved in the transcription regulation of genes containing, or in close proximity to A+T-rich regions.
Subcellular locationNucleus. Chromosome.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: P17096
Gene Ontology
(Biological Process)
Complete annatation
base-excision repair [GO:0006284];
DNA unwinding involved in DNA replication [GO:0006268];
establishment of integrated proviral latency [GO:0075713];
negative regulation of cell proliferation [GO:0008285];
negative regulation of chromatin silencing [GO:0031936];
negative regulation of transcription, DNA-templated [GO:0045892];
nuclear transport [GO:0051169];
nucleosome disassembly [GO:0006337];
oncogene-induced cell senescence [GO:0090402];
positive regulation of cellular senescence [GO:2000774];
positive regulation of transcription, DNA-templated [GO:0045893];
positive regulation of transcription from RNA polymerase II promoter [GO:0045944];
protein complex assembly [GO:0006461];
regulation of transcription, DNA-templated [GO:0006355];
response to virus [GO:0009615];
senescence-associated heterochromatin focus assembly [GO:0035986]
Gene Ontology
(Molecular Function)
Complete annatation
5'-deoxyribose-5-phosphate lyase activity [GO:0051575];
AT DNA binding [GO:0003680];
chromatin binding [GO:0003682];
DNA-(apurinic or apyrimidinic site lyase activity [GO:0003906];
DNA binding [GO:0003677];
enzyme binding [GO:0019899];
ligand-dependent nuclear receptor transcription coactivator activity [GO:0030374];
peroxisome proliferator activated receptor binding [GO:0042975];
retinoic acid receptor binding [GO:0042974];
retinoid X receptor binding [GO:0046965];
transcriptional activator activity, RNA polymerase II distal enhancer sequence-specific binding [GO:0001205];
transcription factor activity, sequence-specific DNA binding [GO:0003700];
transcription factor binding [GO:0008134]
Gene Ontology
(Cellular Component)
Complete annatation
cytosol [GO:0005829];
focal adhesion [GO:0005925];
nucleoplasm [GO:0005654];
nucleus [GO:0005634];
RNA polymerase II transcription factor complex [GO:0090575];
senescence-associated heterochromatin focus [GO:0035985];
transcription factor complex [GO:0005667]
Protein-protein interaction109402
Phylogenetic treeP17096
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. CD31.343738952289820.008412108616951630.0225760863736992
AZA vs. DISU0.1431065745331590.5717607974781140.954304256505839
AZA vs. IL7-0.187298897335320.453818332961650.999311006273513
AZA vs. SAHA0.4084934413942540.09498266064097270.388750645262564
DISU vs. CD3-1.213185062618790.01653327074745370.043962343137611
DISU vs. IL7-0.338905532629170.1793641656042170.548239009830407
DISU vs. SAHA0.265985737906650.3624211885994780.736837586251643
DMSO vs. AZA-0.09495423182944190.6757502873874521
DMSO vs. CD3-1.458110952245530.004398446063258230.0123027459975836
DMSO vs. DISU-0.242318758025940.3213055704246020.822419732079662
DMSO vs. IL7-0.08383086484068790.7536450056151680.951631847120623
DMSO vs. SAHA0.4982460767809720.03512500555290070.203967844270333
HIV vs. Mock in Activation-0.1336431476837320.9007868673098620.999983755607037
HIV vs. Mock in Latency-0.2788734195550440.1446979191323690.999834320637052
IL7 vs. CD3-1.521707360459550.005155570663095350.0171973229840485
SAHA vs. CD3-0.9609177684410940.04507058601162470.0910840460232244
SAHA vs. IL70.5915525685260510.01609226408683990.0873981723592222
(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
1.9 0.000292953 1.4 0.034494806 1.5 0.263741025
(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 0.200039 0.149218
(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
1.039 0.921 0.77 0.835 0.821
(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
2EZD NMR - A=51-71.
2EZE NMR - A=51-75.
2EZF NMR - A=80-89.
2EZG NMR - A=80-89.

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

HIV Partner Interaction Type PubMed
Tat competes with 23392246
matrix associates with 9188609
integrase stimulated by 9038339
Tat interacts with 19454010

Metabolic/Signalling Pathway       (annotations from KEGG database)      top

Pathway Accession Number Description
not found