RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: decR
Gene(s): decR   Genome Browser M3D Gene expression COLOMBOS
Evidence: [COMP-AINF] Inferred computationally without human oversight
Promoter
Name: decRp
+1: 468352
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 31
Sequence: tgccgtggtgtttaaaccgcacagaataaattgtcgtgatttcacctttaaaataaaattAaaagagaaaaaaattctctg
                               -35                    -10   +1                   
Note(s): We assigned a putative transcriptional start site to this promoter based on the observation that the majority of the promoters, whose transcriptional start sites were determined experimentally, present a distance of 6 nucleotides between the transcriptional start site and the -10 box Harley CB, Reynolds RP,1987.
Evidence: [COMP-AINF]
[COMP-AINF-POSITIONAL-IDENTIFICATION]
Reference(s): [1] Huerta AM., et al., 2003
TF binding sites (TFBSs)
[MarA,+] 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 MarA activator decRp 468277 468296 -65.0 tttttgcgttGAATTTGTCATTTTGTGCCGtggtgtttaa nd [COMP-AINF-SIMILAR-TO-CONSENSUS] nd [2]
[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 decRp 468279 468298 -63.0 tttgcgttgaATTTGTCATTTTGTGCCGTGgtgtttaaac nd [EXP-IEP-RNA-SEQ], [COMP-HINF], [EXP-CHIP-EXO-MANUAL] S [3]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: forward
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -13.6 468247 468292 ccttccagcaCCGGGCAATTGCCCGGTTTTTTTTGCGTTGAATTTGTCATTTTGTgccgtggtgt
  anti-terminator -15.7 468188 468253 ctatttgacgCACTGGCTGGACTATCCACATCTACCTTATTCCCCCGAATAACGAGATCCCTTCCAGCACCGGGCaattgcccgg
  anti-anti-terminator -13.7 468146 468210 tttaccggtgATTGGACATTGCCGAAATCAGGCTGTCTCTCACTATTTGACGCACTGGCTGGACTATCCACATCtaccttattc
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    

 [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-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] 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

 [2] Rodionov DA., Gelfand MS., Mironov AA., Rakhmaninova AB., 2001, Comparative approach to analysis of regulation in complete genomes: multidrug resistance systems in gamma-proteobacteria., J Mol Microbiol Biotechnol 3(2):319-24

 [3] 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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