RegulonDB RegulonDB 11.1: Operon Form
   

bepA-yfgD operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit       
Name: bepA-yfgD
Gene(s): bepA, yfgD   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IEP-COREGULATION] Inferred through co-regulation
Reference(s): [1] Rhodius VA., et al., 2005
Promoter
Name: bepAp2
+1: 2616026
Distance from start of the gene: 68
Sequence: ggattcaggaaactgaaaagtcatttgagtgggctaatcttcgccgttacactcaaaggcGgcgcggtgggaacgatattt
Evidence: [EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP]
Reference(s): [2] Mendoza-Vargas A., et al., 2009


Transcription unit       
Name: bepA-yfgD
Synonym(s): yfgCD
Gene(s): bepA, yfgD   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IEP-COREGULATION] Inferred through co-regulation
Reference(s): [1] Rhodius VA., et al., 2005
Promoter
Name: bepAp1
+1: 2616068
Sigma Factor: Sigma24 Sigmulon
Distance from start of the gene: 26
Sequence: gccgttacactcaaaggcggcgcggtgggaacgatatttcacagtatcggtcaaatgactAtctccagaaatacaggatag
                             -35                   -10      +1                   
Note(s): 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, and induced from 10 to 20 minutes Lacoux C,2020.
Evidence: [COMP-AINF]
[COMP-AINF-POSITIONAL-IDENTIFICATION]
[COMP-AINF-SIMILAR-TO-CONSENSUS]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [3] Huerta AM., et al., 2003
[1] Rhodius VA., et al., 2005


Evidence    

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

 [COMP-AINF] Inferred computationally without human oversight

 [COMP-AINF-POSITIONAL-IDENTIFICATION] Automated inference of promoter position

 [COMP-AINF-SIMILAR-TO-CONSENSUS] Automated inference based on similarity to consensus sequences

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


Reference(s)    

 [1] Rhodius VA., Suh WC., Nonaka G., West J., Gross CA., 2005, Conserved and variable functions of the sigmaE stress response in related genomes., PLoS Biol 4(1):e2

 [2] 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

 [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

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