RegulonDB RegulonDB 11.0: 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)
[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: [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
Note(s): A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for rnc. This structure could regulate the expression of the gene, as observed for hemL gene expression Shao X, Zhang W, Umar MI, Wong HY, Seng Z, Xie Y, Zhang Y, Yang L, Kwok CK, Deng X,2020.
Evidence: [BTEI] Boundaries of transcription experimentally identified
[CV(LTED/PM)] cross validation(LTED/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]
[ICWHO]
[TIM]
Reference(s): [3] Huerta AM., et al., 2003
[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.
A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for rnc. This structure could regulate the expression of the gene, as observed for hemL gene expression Shao X, Zhang W, Umar MI, Wong HY, Seng Z, Xie Y, Zhang Y, Yang L, Kwok CK, Deng X,2020.
Evidence: [CV(LTED/PM)] cross validation(LTED/PM)
[LTED] Length of transcript experimentally determined
[PM] Polar mutation
Reference(s): [1] Matsunaga J., et al., 1996
[4] 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]
[ICWHO]
[TIM]
Reference(s): [3] Huerta AM., et al., 2003
[1] Matsunaga J., et al., 1996


Evidence    

 [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

 [ICWHO] Inferred computationally without human oversight


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] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

 [4] 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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