RegulonDB RegulonDB 10.8: Operon Form
   

rnc-era-recO-pdxJ-acpS operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: rnc-era-recO-pdxJ-acpS
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit       
Name: pdxJ-acpS
Gene(s): acpS, pdxJ   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
[CV(LTED/PM)] cross validation(LTED/PM)
[CV(PM)] cross validation(PM)
[LTED] Length of transcript experimentally determined
[PM] Polar mutation
Reference(s): [1] Matsunaga J., et al., 1996
Promoter
Name: pdxJp
+1: 2701813
Distance from start of the gene: 84
Sequence: agacacactgcgcgccgcgaaacgctttacccgcatggcgcttaagccgtatcttggcggTaaacctttaaagagcaggga
Evidence: [CV(RS-EPT-CBR)]
[CV(TIM)]
[RS-EPT-CBR]
[TIM]
Reference(s): [1] Matsunaga J., et al., 1996
[2] Salgado H, et al., 2012


Transcription unit       
Name: rnc-era-recO-pdxJ-acpS
Gene(s): acpS, pdxJ, recO, era, rnc   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
[CV(LTED/PM)] cross validation(LTED/PM)
[CV(PM)] cross validation(PM)
[LTED] Length of transcript experimentally determined
[PM] Polar mutation
Reference(s): [1] Matsunaga J., et al., 1996
Promoter
Name: rncp
+1: 2704223
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 160
Sequence: atgagataaatctcccgtggctaacgacatcccccgtcgttgtgtatagaatattcccccGaagtttaaggttggcacctc
                     -35                       -10          +1                   
Evidence: [HIPP]
[TIM]
Reference(s): [1] Matsunaga J., et al., 1996


Transcription unit       
Name: rnc-era
Gene(s): era, rnc   Genome Browser M3D Gene expression COLOMBOS
Note(s): The stability of the mRNA containing rnc and era genes is negatively affected by RNAse III Matsunaga J,1996.
Evidence: [CV(LTED/PM)] cross validation(LTED/PM)
[CV(PM)] cross validation(PM)
[LTED] Length of transcript experimentally determined
[PM] Polar mutation
Reference(s): [1] Matsunaga J., et al., 1996
[3] Regnier P., et al., 1990
Promoter
Name: rncp
+1: 2704223
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 160
Sequence: atgagataaatctcccgtggctaacgacatcccccgtcgttgtgtatagaatattcccccGaagtttaaggttggcacctc
                     -35                       -10          +1                   
Evidence: [HIPP]
[TIM]
Reference(s): [1] Matsunaga J., et al., 1996


Evidence    

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

 [CV(TIM)] cross validation(TIM)

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

 [TIM] Transcription initiation mapping

 [HIPP] Human inference of promoter position


Reference(s)    

 [1] Matsunaga J., Dyer M., Simons EL., Simons RW., 1996, Expression and regulation of the rnc and pdxJ operons of Escherichia coli., Mol Microbiol 22(5):977-89

 [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] Regnier P., Grunberg-Manago M., 1990, RNase III cleavages in non-coding leaders of Escherichia coli transcripts control mRNA stability and genetic expression., Biochimie 72(11):825-34

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