RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit       
Name: yabI
Gene(s): yabI   Genome Browser M3D Gene expression COLOMBOS
Note(s): The transcript of yabI is increased after σE induction, as observed in high-throughput analysis of gene expression Lacoux C,2020.
Evidence: [COMP-AINF] Inferred computationally without human oversight
Promoter
Name: yabIp
+1: 71271
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 80
Sequence: gtttcgtgccggttgtgaagaaaaagtgaatgatgtagccgtcaagttgtcataattggtAacgaatcagacaattgacgg
                                                -10         +1                   
Note(s): The yabIp promoter is significantly affected by ectopic production of a nanoRNase during stationary-phase growth Vvedenskaya IO,2012
This promoter appears to be induced in two phases after σE induction. It is induced during the first 5 minutes following σE induction, decreased from 5 to 10 minutes, induced from 10 to 15 minutes, and decreased from 15 to 20 minutes Lacoux C,2020.
Evidence: [COMP-HINF]
[EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [1] Mendoza-Vargas A., et al., 2009
[2] Salgado H, et al., 2012
[3] Vvedenskaya IO., et al., 2012


Evidence    

 [COMP-HINF] Inferred by a human based on computational evidence

 [EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP] High-throughput transcription initiation mapping

 [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] Transcription initiation mapping

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


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] Vvedenskaya IO., Sharp JS., Goldman SR., Kanabar PN., Livny J., Dove SL., Nickels BE., 2012, Growth phase-dependent control of transcription start site selection and gene expression by nanoRNAs., Genes Dev 26(13):1498-507

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