RegulonDB RegulonDB 11.1: Operon Form
   

ynfB-speG operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit          
Name: ynfB-speG
Gene(s): ynfB, speG   Genome Browser M3D Gene expression COLOMBOS
Evidence: [COMP-AINF] Inferred computationally without human oversight
Promoter
Name: ynfBp
+1: 1655709
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 99
Sequence: aaaatagtaacgttgttttaatcatctttgtctcttattgacatcatgtatagttataggGcgacataatatcatcaatat
Evidence: [EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP]
[EXP-IEP]
[EXP-IPI]
Reference(s): [1] Mendoza-Vargas A., et al., 2009
[2] Seo SW., et al., 2015
TF binding sites (TFBSs)
[GadX,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote GadX repressor ynfBp 1655605 1655624 -94.5 ttaaccacaaCCAGGGCAGAAAGCATCCAAtaatttcaca nd [EXP-IEP-RNA-SEQ], [COMP-HINF], [EXP-CHIP-EXO-MANUAL] S [2]


Evidence    

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

 [EXP-IEP] Inferred from expression pattern

 [EXP-IPI] Inferred from physical interaction

 [EXP-IEP-RNA-SEQ] high throughput RNA-seq evidence

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

 [EXP-CHIP-EXO-MANUAL] ChIP-exo evidence used in manual assertion


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] Seo SW., Kim D., O'Brien EJ., Szubin R., Palsson BO., 2015, Decoding genome-wide GadEWX-transcriptional regulatory networks reveals multifaceted cellular responses to acid stress in Escherichia coli., Nat Commun 6:7970

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