RegulonDB RegulonDB 10.8: Operon Form
   

pth-ychF operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit          
Name: ychF
Gene(s): ychF   Genome Browser M3D Gene expression COLOMBOS
Note(s): Overexpression of YchF results in H2 O2 hypersensitivity Wenk M,2012
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [1] Cruz-Vera LR., et al., 2002
Promoter
Name: ychFp
+1: 1257882
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 70
Sequence: ttaaagcgcaataagtcgttgtctgcggcatttttgccgagtgccgtgtataataggcaaAgttatttccatttctgcaat
                       -35                       -10        +1                   
Evidence: [CV(RS-EPT-CBR)]
[CV(TIM)]
[HIPP]
[RS-EPT-CBR]
[TIM]
Reference(s): [1] Cruz-Vera LR., et al., 2002
[2] Salgado H, et al., 2012
TF binding sites (TFBSs)
[OxyR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote OxyR repressor ychFp 1257843 1257859 31.5 tctgcaatctGTTAGCAATAACAGGTTgattattaag nd [APIORCISFBSCS], [BPP] [3]
proximal OxyR repressor ychFp 1257865 1257881 9.5 aataggcaaaGTTATTTCCATTTCTGCaatctgttag nd [APIORCISFBSCS], [BPP] [3]


Transcription unit       
Name: pth-ychF
Gene(s): ychF, pth   Genome Browser M3D Gene expression COLOMBOS
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [1] Cruz-Vera LR., et al., 2002
Promoter
Name: pthp
+1: 1258542
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 29
Sequence: tatctgcatttgatacgcagttttttgtcaagcggggccgcaaccagtaaactacgcgccAgttatgtacacactcaggac
                         -35                    -10         +1                   
Evidence: [HIPP]
[TIM]
Reference(s): [1] Cruz-Vera LR., et al., 2002


Evidence    

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

 [CV(TIM)] cross validation(TIM)

 [HIPP] Human inference of promoter position

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

 [TIM] Transcription initiation mapping

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

 [BPP] Binding of purified proteins


Reference(s)    

 [1] Cruz-Vera LR., Galindo JM., Guarneros G., 2002, Transcriptional analysis of the gene encoding peptidyl-tRNA hydrolase in Escherichia coli., Microbiology 148(Pt 11):3457-66

 [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] Wenk M., Ba Q., Erichsen V., Macinnes K., Wiese H., Warscheid B., Koch HG., 2012, A Universally Conserved ATPase Regulates the Oxidative Stress Response in Escherichia coli., J Biol Chem 287(52):43585-98

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