RegulonDB RegulonDB 10.8: Operon Form
   

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




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


Transcription unit          
Name: ydfH
Gene(s): ydfH   Genome Browser M3D Gene expression COLOMBOS
Evidence: [ICWHO] Inferred computationally without human oversight
Promoter
Name: ydfHp
+1: 1628326
Distance from start of the gene: 26
Sequence: tttatacccggcgtaactgccgggttattgcttgtcacaaaaaagtggtagactcatgcaGttaactcactcacaagcaag
Evidence: [CV(RS-EPT-CBR)]
[HTIM]
[RS-EPT-CBR]
Reference(s): [1] Mendoza-Vargas A., et al., 2009
[2] Salgado H, et al., 2012
TF binding sites (TFBSs)
[PhoB,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal PhoB-Phosphorylated activator ydfHp 1628297 1628315 -20.0 gggttattgcTTGTCACAAAAAAGTGGTAgactcatgca nd [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [3]


Evidence    

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

 [HTIM] High-throughput transcription initiation mapping

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

 [APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [BPP] Binding of purified proteins

 [CV(GEA)] cross validation(GEA)

 [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] Yang C., Huang TW., Wen SY., Chang CY., Tsai SF., Wu WF., Chang CH., 2012, Genome-wide PhoB binding and gene expression profiles reveal the hierarchical gene regulatory network of phosphate starvation in Escherichia coli., PLoS One 7(10):e47314

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