RegulonDB RegulonDB 10.9: Operon Form
   

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




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


Transcription unit          
Name: gadY
Synonym(s): IS183
Gene(s): gadY   Genome Browser M3D Gene expression COLOMBOS
Note(s): The transcription of gadY appears to be increased under acidic growth conditions during the exponential phase in a RcsB-dependent manner, but not during stationary phase Johnson MD,2011
The RNA produced by the gadY gene has been observed mainly in the poles of the cell 31540875.
Evidence: [AISGDTU] Automated inference that a single-gene directon is a transcription unit
[BTEI] Boundaries of transcription experimentally identified
[LTED] Length of transcript experimentally determined
Reference(s): [1] Opdyke JA., et al., 2004
[2] Tramonti A., et al., 2008
Promoter
Name: gadYp
+1: 3664864
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 0
Sequence: atagcttatgtttataaaaaaatggctgatcttatttccagtaaaagttatatttaacttActgagagcacaaagtttccc
                          -35               -10             +1                   
Note(s): Three alternative 5' ends of GadY (105, 90, and 59 nucleotides) were identified by primer extension. gadY (90) and gadY (59) are believed to be processed forms of the full-length 105-nucleotide transcript due to the fact that the expression of all three forms was eliminated when Opdyke et al. (2004) mutated the promoter of the full-length RNA.
Evidence: [AIPP]
[ICWHO]
[IMP]
[TIM]
Reference(s): [3] Huerta AM., et al., 2003
[1] Opdyke JA., et al., 2004
Terminator(s)
Type: rho-independent
Sequence: ctatcctcttCCCGGTCCCCTATGCCGGGttttttttat
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
proximal GadW repressor gadYp 3664804 3664823 -50.5 cgcacagcgtATAGCTTATGTTTATAAAAAAatggctgatc nd [GEA] [2]
proximal GadW repressor gadYp 3664825 3664844 -29.5 ttataaaaaaATGGCTGATCTTATTTCCAGTaaaagttata nd [GEA] [2]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal GadX activator gadYp 3664804 3664823 -50.5 cgcacagcgtATAGCTTATGTTTATAAAAAAatggctgatc nd [GEA] [2]
proximal GadX activator gadYp 3664825 3664844 -29.5 ttataaaaaaATGGCTGATCTTATTTCCAGTaaaagttata nd [GEA] [2]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd RcsB-Pasp56 activator gadYp nd nd nd nd nd [BPP], [GEA], [IGI] [4]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd SdiA activator gadYp nd nd nd nd nd [BPP], [GEA], [IGI] [5]





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