RegulonDB RegulonDB 11.2: Operon Form
   

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




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


Transcription unit          
Name: nepI
Gene(s): nepI   Genome Browser M3D Gene expression COLOMBOS
Evidence: [COMP-AINF] Inferred computationally without human oversight
[EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Gronskiy SV., et al., 2005
Promoter
Name: nepIp
+1: 3841771
Distance from start of the gene: 32
Sequence: acaccgtaaaagttgcaaaaacgttaaatgcgtcacacatttcaatgttaaagtggtcggCttttcccctgaaacatgcca
Evidence: [COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] Gronskiy SV., et al., 2005
TF binding sites (TFBSs)
[SoxS,+] 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
proximal SoxS activator nepIp 3841756 3841775 6.0 gttaaagtggTCGGCTTTTCCCCTGAAACAtgccacgggt nd [EXP-IEP-RNA-SEQ], [COMP-HINF], [EXP-CHIP-EXO-MANUAL] S [2]


Evidence    

 [COMP-HINF-POSITIONAL-IDENTIFICATION] Human inference of promoter position

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

 [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] Gronskiy SV., Zakataeva NP., Vitushkina MV., Ptitsyn LR., Altman IB., Novikova AE., Livshits VA., 2005, The yicM (nepI) gene of Escherichia coli encodes a major facilitator superfamily protein involved in efflux of purine ribonucleosides., FEMS Microbiol Lett 250(1):39-47

 [2] Seo SW., Kim D., Szubin R., Palsson BO., 2015, Genome-wide Reconstruction of OxyR and SoxRS Transcriptional Regulatory Networks under Oxidative Stress in Escherichia coli K-12 MG1655., Cell Rep 12(8):1289-99

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