RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: ridA
Gene(s): ridA   Genome Browser M3D Gene expression COLOMBOS
Note(s): ridA is indirectly regulated by BglG through the transcriptional regulator Lrp in stationary phase and under conditions where leucine antagonizes the effect of Lrp Shukla S,2019
Evidence: [COMP-AINF] Inferred computationally without human oversight
Promoter
Name: ridAp
+1: 4470946
Distance from start of the gene: 33
Sequence: aatgtggtgctggccaattaattgcggttggtaataaaagtctggctccctataatgagcCagactttttaccgctgtaat
Evidence: [EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP]
Reference(s): [1] Mendoza-Vargas A., et al., 2009
TF binding sites (TFBSs)
[Lrp,+] 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 Lrp activator ridAp 4470995 4471009 -56.0 agagttttccCATAATGTGGTGCTGgccaattaat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-CHIP], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [2]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: reverse
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -15.2 4470936 4470967 ggtaataaaaGTCTGGCTCCCTATAATGAGCCAGACTTTTTaccgctgtaa
  anti-terminator -9.1 4470958 4471001 cccataatgtGGTGCTGGCCAATTAATTGCGGTTGGTAATAAAAGTCTGGCTCcctataatga
  anti-anti-terminator -4.94 4470993 4471043 atgatatcgcGCTCAAATGCAAATACTGTGAAAAAGAGTTTTCCCATAATGTGGTGCTGGccaattaatt
Notes: "The provided "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appear as the reverse complement of the sequence delimited by LeftPos-RigtPos"


Evidence    

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

 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis

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

 [EXP-CHIP-CHIP] high throughput ChIP-chip evidence

 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins


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] Shukla S., Mahadevan S., 2019, The ridA gene of E. coli is indirectly regulated by BglG through the transcriptional regulator Lrp in stationary phase., Microbiology 165(6):683-696

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