RegulonDB RegulonDB 10.8: Operon Form
   

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




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


Transcription unit          
Name: yecR
Gene(s): yecR   Genome Browser M3D Gene expression COLOMBOS
Promoter
Name: yecRp
+1: 1988200
Distance from start of the gene: 22
Sequence: gcctgccaggcgtcttttccggccattgtcgcagcactgtaacgcgtaaaatagtgctttCtcttactcttctggctggac
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.
Evidence: [HIPP]
Reference(s): [1] Stafford GP., et al., 2005
TF binding sites (TFBSs)
[FNR,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd FNR1 activator yecRp nd nd nd nd nd [AIBSCS], [CV(GEA)], [GEA] [2]
[FlhDC,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal FlhDC activator yecRp 1988124 1988140 -68.0 gacacctacaGATGGCAAGAAATAGCGcctgccaggc nd [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [1]
proximal FlhDC activator yecRp 1988151 1988167 -41.0 cctgccaggcGTCTTTTCCGGCCATTGtcgcagcact nd [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [1]
Note(s): 1By making use of microarray analyses, Constantinidou et al. Constantinidou C,2006 concluded that FNR activates yecR gene expression. They also identified a putative FNR-binding site upstream of the gene, but the sequence was not shown.3By making use of microarray analyses, Constantinidou et al. Constantinidou C,2006 concluded that FNR activates yecR gene expression. They also identified a putative FNR-binding site upstream of the gene, but the sequence was not shown.


Evidence    

 [HIPP] Human inference of promoter position

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [CV(GEA)] cross validation(GEA)

 [GEA] Gene expression analysis

 [APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [BPP] Binding of purified proteins


Reference(s)    

 [1] Stafford GP., Ogi T., Hughes C., 2005, Binding and transcriptional activation of non-flagellar genes by the Escherichia coli flagellar master regulator FlhD2C2., Microbiology 151(Pt 6):1779-88

 [2] Constantinidou C., Hobman JL., Griffiths L., Patel MD., Penn CW., Cole JA., Overton TW., 2006, A reassessment of the FNR regulon and transcriptomic analysis of the effects of nitrate, nitrite, NarXL, and NarQP as Escherichia coli K12 adapts from aerobic to anaerobic growth., J Biol Chem 281(8):4802-15

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