Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0000662
UniProt IDP02452
Primary gene name(s)COL1A1
Synonym gene name(s)unknown
Protein nameCollagen alpha-1(I chain
Protein functionType I collagen is a member of group I collagen, fibrillar forming collagen.
Subcellular locationSecreted, extracellular space, extracellular matrix {ECO:0000255|PROSITE-ProRule:PRU00793}.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: P02452
Gene Ontology
(Biological Process)
Complete annatation
blood coagulation [GO:0007596];
blood vessel development [GO:0001568];
bone trabecula formation [GO:0060346];
cartilage development involved in endochondral bone morphogenesis [GO:0060351];
cellular response to amino acid stimulus [GO:0071230];
cellular response to epidermal growth factor stimulus [GO:0071364];
cellular response to fibroblast growth factor stimulus [GO:0044344];
cellular response to fluoride [GO:1902618];
cellular response to mechanical stimulus [GO:0071260];
cellular response to retinoic acid [GO:0071300];
cellular response to transforming growth factor beta stimulus [GO:0071560];
cellular response to tumor necrosis factor [GO:0071356];
cellular response to vitamin E [GO:0071306];
collagen biosynthetic process [GO:0032964];
collagen catabolic process [GO:0030574];
collagen fibril organization [GO:0030199];
embryonic skeletal system development [GO:0048706];
endochondral ossification [GO:0001958];
extracellular matrix organization [GO:0030198];
face morphogenesis [GO:0060325];
intramembranous ossification [GO:0001957];
leukocyte migration [GO:0050900];
negative regulation of cell-substrate adhesion [GO:0010812];
osteoblast differentiation [GO:0001649];
platelet activation [GO:0030168];
positive regulation of canonical Wnt signaling pathway [GO:0090263];
positive regulation of cell migration [GO:0030335];
positive regulation of epithelial to mesenchymal transition [GO:0010718];
positive regulation of transcription, DNA-templated [GO:0045893];
protein heterotrimerization [GO:0070208];
protein localization to nucleus [GO:0034504];
protein transport [GO:0015031];
regulation of immune response [GO:0050776];
response to cAMP [GO:0051591];
response to corticosteroid [GO:0031960];
response to drug [GO:0042493];
response to estradiol [GO:0032355];
response to hydrogen peroxide [GO:0042542];
response to hyperoxia [GO:0055093];
response to peptide hormone [GO:0043434];
sensory perception of sound [GO:0007605];
skeletal system development [GO:0001501];
skin morphogenesis [GO:0043589];
tooth eruption [GO:0044691];
tooth mineralization [GO:0034505];
visual perception [GO:0007601]
Gene Ontology
(Molecular Function)
Complete annatation
extracellular matrix structural constituent [GO:0005201];
identical protein binding [GO:0042802];
metal ion binding [GO:0046872];
platelet-derived growth factor binding [GO:0048407]
Gene Ontology
(Cellular Component)
Complete annatation
collagen type I trimer [GO:0005584];
endoplasmic reticulum lumen [GO:0005788];
extracellular matrix [GO:0031012];
extracellular region [GO:0005576];
extracellular space [GO:0005615];
Golgi apparatus [GO:0005794];
secretory granule [GO:0030141]
Protein-protein interaction107674
Phylogenetic treeP02452
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. CD3unknownunknownunknown
AZA vs. DISUunknownunknownunknown
AZA vs. IL7unknownunknownunknown
AZA vs. SAHA3.644348176490100
DISU vs. CD3unknownunknownunknown
DISU vs. IL7unknownunknownunknown
DISU vs. SAHA3.4329866664577800
DMSO vs. AZAunknownunknownunknown
DMSO vs. CD3unknownunknownunknown
DMSO vs. DISUunknownunknownunknown
DMSO vs. IL7unknownunknownunknown
DMSO vs. SAHA3.5721305694851500
HIV vs. Mock in Activationunknownunknownunknown
HIV vs. Mock in Latencyunknownunknownunknown
IL7 vs. CD3unknownunknownunknown
SAHA vs. CD32.68252486764935.5068184134921e-074.77215373728154e-06
SAHA vs. IL73.8623289339857700
(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 4.173164701
(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) TRUE
(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
NOTEST -0.685132 1
(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
unknown unknown unknown unknown unknown
(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
DB00048 Collagenase clostridium histolyticum approved, investigational unknown unknown
DB04866 Halofuginone investigational, vet_approved unknown unknown

Protein Secondary Structure       (annotations from PDB)      top

PDB Accession Method Resolution Chain Structure Preview
1Q7D X-ray 1.8Å A/B/C=677-685.
2LLP NMR - A/B/C=949-965.
3EJH X-ray 2.1Å E/F=956-977.
3GXE X-ray 2.6Å E/F=254-275.
5CTD X-ray 1.6Å A=572-583# C=554-583.
5CTI X-ray 1.9Å A=572-583# C=554-583# C=611-665.
5CVA X-ray 2.1Å B/C/E/F=554-583# B/E=593-629.
5CVB X-ray 2.2Å A/D=572-583# B/C/E/F=554-583# B/E=593-606.

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

HIV Partner Interaction Type PubMed
Tat inhibits 8552450
Vpu upregulates 24551192
matrix upregulates 24736615
Tat upregulates 1409674
11311202
Envelope surface glycoprotein gp120 upregulates 22479424

Metabolic/Signalling Pathway       (annotations from KEGG database)      top

Pathway Accession Number Description
hsa04151 PI3K-Akt signaling pathway - Homo sapiens (human)
hsa04510 Focal adhesion - Homo sapiens (human)
hsa04512 ECM-receptor interaction - Homo sapiens (human)
hsa04611 Platelet activation - Homo sapiens (human)
hsa04933 AGE-RAGE signaling pathway in diabetic complications - Homo sapiens (human)
hsa04974 Protein digestion and absorption - Homo sapiens (human)
hsa05146 Amoebiasis - Homo sapiens (human)
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