RegulonDB RegulonDB 10.8: Operon Form
   

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




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


Transcription unit          
Name: ychO
Gene(s): ychO   Genome Browser M3D Gene expression COLOMBOS
Evidence: [AISDTU] Automated inference that a single-gene directon is a transcription unit
Promoter
Name: ychOp
+1: 1273760
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 24
Sequence: cgcgagaaaatacgacaaaagttgccagtaatcgttattctttaaggctatggtttttcaTtattaccggaagttaccgac
                      -35                        -10        +1                   
Evidence: [AIPP]
Reference(s): [1] Huerta AM., et al., 2003
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 repressor ychOp nd nd nd nd nd [AIBSCS], [CV(GEA)], [GEA] [2]
Note(s): 1By making use of microarray analyses, Constantinidou et al. Constantinidou C,2006 concluded that FNR represses ychO gene expression. They also identified a putative FNR-binding site upstream of the gene, but the sequence was not shown.1By making use of microarray analyses, Constantinidou et al. Constantinidou C,2006 concluded that FNR represses ychO gene expression. They also identified a putative FNR-binding site upstream of the gene, but the sequence was not shown.


Evidence    

 [AIPP] Automated inference of promoter position

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [CV(GEA)] cross validation(GEA)

 [GEA] Gene expression analysis


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] 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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