RegulonDB RegulonDB 10.8: Operon Form
   

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




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


Transcription unit          
Name: pepT
Gene(s): pepT   Genome Browser M3D Gene expression COLOMBOS
Evidence: [AISDTU] Automated inference that a single-gene directon is a transcription unit
Promoter
Name: pepTp
+1: 1185823
Distance from start of the gene: 21
Sequence: gcaggggtaaaagtgacctgacgcaatatttgtcttttcttgcttcttaataatgttgtcAcaaaaagtgagggtgactac
Evidence: [CV(RS-EPT-CBR/TA)]
[HTIM]
[RS-EPT-CBR]
Reference(s): [1] Mendoza-Vargas A., et al., 2009
[2] Salgado H, et al., 2012
TF binding sites (TFBSs)
[FNR,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd FNR1 activator pepTp nd nd nd nd nd [AIBSCS], [CV(GEA/ROMA)], [GEA] [3]
Note(s): 1By making use of microarray analyses, Constantinidou et al. Constantinidou C,2006 concluded that FNR activates pepT gene expression. They also identified a putative FNR-binding site upstream of the pepT gene, but the sequence was not shown.1By making use of microarray analyses, Constantinidou et al. Constantinidou C,2006 concluded that FNR activates pepT gene expression. They also identified a putative FNR-binding site upstream of the pepT gene, but the sequence was not shown.


Evidence    

 [CV(RS-EPT-CBR/TA)] cross validation(RS-EPT-CBR/TA)

 [HTIM] High-throughput transcription initiation mapping

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

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [CV(GEA/ROMA)] cross validation(GEA/ROMA)

 [GEA] Gene expression analysis


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] 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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