RegulonDB RegulonDB 11.1: Operon Form
   

dgkA operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: dgkA
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit          
Name: dgkA
Gene(s): dgkA   Genome Browser M3D Gene expression COLOMBOS
Note(s): A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for dgkA . This structure could regulate the expression of the gene, as observed for hemL gene expression Shao X, Zhang W, Umar MI, Wong HY, Seng Z, Xie Y, Zhang Y, Yang L, Kwok CK, Deng X,2020.
Promoter
Name: dgkAp1
+1: 4256457
Distance from start of the gene: 180
Sequence: acttgctttttaccaggatgcttaatggtaaattcagtaatttgtagtaaattcgtggccAgccggacataaacgatgtaa
Evidence: [COMP-HINF]
[EXP-IEP]
[RS-EPT-CBR]
Reference(s): [1] Salgado H, et al., 2012
[2] Wahl A., et al., 2011
TF binding sites (TFBSs)
[BasR,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal BasR-phosphorylated activator dgkAp1 4256417 4256436 -30.5 taccaggatgCTTAATGGTAAATTCAGTAAtttgtagtaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [2]


Transcription unit       
Name: dgkA
Gene(s): dgkA   Genome Browser M3D Gene expression COLOMBOS
Note(s): A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for dgkA . This structure could regulate the expression of the gene, as observed for hemL gene expression Shao X, Zhang W, Umar MI, Wong HY, Seng Z, Xie Y, Zhang Y, Yang L, Kwok CK, Deng X,2020.
Evidence: [COMP-AINF] Inferred computationally without human oversight
Promoter
Name: dgkAp2
+1: 4256608
Distance from start of the gene: 29
Sequence: tcatgtttcgcgcggcgctacgcaaacccgaatcatcggatttaacggtacactgatattGacgctcataatgtaaaaagg
Evidence: [EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP]
Reference(s): [3] Mendoza-Vargas A., et al., 2009


Evidence    

 [COMP-HINF] Inferred by a human based on computational evidence

 [EXP-IEP] Inferred from expression pattern

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis

 [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins

 [EXP-IMP-SITE-MUTATION] Site mutation

 [EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP] High-throughput transcription initiation mapping


Reference(s)    

 [1] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

 [2] Wahl A., My L., Dumoulin R., Sturgis JN., Bouveret E., 2011, Antagonistic regulation of dgkA and plsB genes of phospholipid synthesis by multiple stress responses in Escherichia coli., Mol Microbiol 80(5):1260-75

 [3] Mendoza-Vargas A., Olvera L., Olvera M., Grande R., Vega-Alvarado L., Taboada B., Jimenez-Jacinto V., Salgado H., Juarez K., Contreras-Moreira B., Huerta AM., Collado-Vides J., Morett E., 2009, Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli., PLoS One 4(10):e7526

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