RegulonDB RegulonDB 10.9: Operon Form
   

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




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


Transcription unit          
Name: plaR
Synonym(s): yiaJ
Gene(s): plaR   Genome Browser M3D Gene expression COLOMBOS
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [1] Ibanez E., et al., 2000
Promoter
Name: plaRp
+1: 3742618
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 86
Sequence: aaacttgatttcaaatatatcgatcactttttaacaaggcaatctgattgatgaatttcaAaagacataaaaatcaattgg
                               -35                    -10   +1                   
Evidence: [ICWHO]
[TIM]
Reference(s): [2] Huerta AM., et al., 2003
[1] Ibanez E., et al., 2000
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote CRP-cAMP repressor plaRp 3742558 3742579 50.5 ttatctgtcgAGATCGTGAACTACGGCACACTTtgcgctacca nd [APIORCISFBSCS], [BPP], [GEA] [1]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal IHF1 repressor plaRp 3742616 3742628 -4.0 caatctgattGATGAATTTCAAAAgacataaaaa nd [APIORCISFBSCS], [BPP] [1]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal YiaJ1 repressor plaRp 3742663 3742683 -55.0 aaaatttcaaTATGCGAAACTTGATTTCAAATatatcgatca nd [BCE], [GEA] [1]
Note(s): 1The regulatory effect of IHF on the promoter yiaJp is not yet known. However, we assigned a negative effect to this regulatory interaction based on the fact that the protein-binding site is very close to the promoter (4 bp upstream from the transcription start site).1In 2000, Ibanez et al showed that transcription of the divergent operon yiaJ-yiaKLMNO-lyxK-sgbHUE depends on the YiaJ repressor. However, the authors suggested that this regulator binds a long region of 35 bp Ibanez E,2000. The alignment of this region with the orthologous sequence of Klebsiella pneumoniae showed a conserved palindrome of 21 bp 18708499. The position and length of the YiaJ binding site have been changed to reflect this.1In 2000, Ibanez et al showed that transcription of the divergent operon yiaJ-yiaKLMNO-lyxK-sgbHUE depends on the YiaJ repressor. However, the authors suggested that this regulator binds a long region of 35 bp Ibanez E,2000. The alignment of this region with the orthologous sequence of Klebsiella pneumoniae showed a conserved palindrome of 21 bp 18708499. The position and length of the YiaJ binding site have been changed to reflect this.
2The regulatory effect of IHF on the promoter yiaJp is not yet known. However, we assigned a negative effect to this regulatory interaction based on the fact that the protein-binding site is very close to the promoter (4 bp upstream from the transcription start site).





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