RegulonDB RegulonDB 10.10: Operon Form
   

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




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


Transcription unit          
Name: yqjI
Gene(s): nfeR   Genome Browser M3D Gene expression COLOMBOS
Evidence: [AISGDTU] Automated inference that a single-gene directon is a transcription unit
Promoter
Name: yqjIp
+1: 3216753
Distance from start of the gene: 26
Sequence: cacgtttaaaaatcatttttacacttgcaagaacgctcatatcagatataaattagatatAtctaattaagcaaaaggagg
Evidence: [HTTIM]    
[RS-EPT-CBR]
Reference(s): [1] Mendoza-Vargas A., et al., 2009
[2] Salgado H, et al., 2012
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd FNR activator yqjIp nd nd nd nd nd [GEA], [BPP] [5]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal NfeR repressor yqjIp 3216731 3216762 -7.0 aagaacgctcATATCAGATATAAATTAGATATATCTAATTAAgcaaaaggag nd [GEA], [APIORCISFBSCS], [BPP], [SM] [3], [4]




Reference(s)    

 [1] 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

 [2] 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.

 [3] Wang S., Blahut M., Wu Y., Philipkosky KE., Outten FW., 2014, Communication between binding sites is required for YqjI regulation of target promoters within the yqjH-yqjI intergenic region., J Bacteriol 196(17):3199-207

 [4] Wang S., Wu Y., Outten FW., 2011, Fur and the novel regulator YqjI control transcription of the ferric reductase gene yqjH in Escherichia coli., J Bacteriol 193(2):563-74

 [5] Constantinidou C., Hobman JL., Griffiths L., Patel MD., Penn CW., Cole JA., Overton TW., 2006, A reassessment of the FNR regulon and transcriptomic analysis of the effects of nitrate, nitrite, NarXL, and NarQP as Escherichia coli K12 adapts from aerobic to anaerobic growth., J Biol Chem 281(8):4802-15


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