RegulonDB RegulonDB 10.6.3: Operon Form
   

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




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


Transcription unit       
Name: yciE
Gene(s): yciE   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Stoltzfus A., et al., 1988
Promoter
Name: yciEp
+1: 1315396
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 172
Sequence: agcacagaaagtcgagcattatgagattgccagttacgggacattagcgacgctggctgaAcaattaggttaccgtaaagc
                           -10                   -35        +1                   
Evidence: [HIPP]
Reference(s): [1] Stoltzfus A., et al., 1988
Terminator(s)
Type: rho-independent
Sequence: attccgcacaAAAACGACCCCGTAATATACGGGGTCAATAAggacatggta
Reference(s): [1] Stoltzfus A., et al., 1988


Transcription unit          
Name: yciG
Gene(s): yciG   Genome Browser M3D Gene expression COLOMBOS
Note(s): Induction of the expression of the yciG gene was observed when cells were exposed to a sudden transition from glucose limitation to a high concentration of glucose in an experiment in a bioreactor |CITS:[ 23376621]|.
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Stoltzfus A., et al., 1988
Promoter
Name: yciGp
+1: 1316092
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 57
Sequence: ccctctatcttctcgttgcgcttaatttgactaattctcattagcgactaattttaatgaGtgtcgacacacaacactcat
                           -10              -35             +1                   
Evidence: [AIPP]
[HIPP]
Reference(s): [2] Huerta AM., et al., 2003
[1] Stoltzfus A., et al., 1988
Terminator(s)
Type: rho-independent
Sequence: ttctccagtgAAATCACTGCGAGCCATACGGCCCGCAGATGcaattatctt
Reference(s): [1] Stoltzfus A., et al., 1988
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 H-NS repressor yciGp 1316153 1316163 -65.5 atgttcctcaAAATATATTTTccctctatct nd [BPP], [GEA], [HIBSCS] [3], [5]
proximal H-NS repressor yciGp 1316176 1316186 -88.5 aggtaattgtTAATATATCCAgaatgttcct nd [BPP], [GEA], [HIBSCS] [3], [5]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal McbR activator yciGp 1316149 1316170 -67.5 atccagaatgTTCCTCAAAATATATTTTCCCTctatcttctc nd [BPP], [GEA] [3], [4]
proximal McbR2 activator yciGp 1316170 1316191 -88.5 tcctcaggtaATTGTTAATATATCCAGAATGTtcctcaaaat nd [BPP], [GEA] [3], [4]
Note(s): 2McbR activates σS-dependent transcription at yciGp by countering the negative effect of H-NS Beraud M,2010 i.e., σS induces expression of the yciGFE operon only when H-NS-mediated repression is relieved. Repression of yciGFE by H-NS is inversely correlated with σS levels Beraud M,20101McbR activates σS-dependent transcription at yciGp by countering the negative effect of H-NS Beraud M,2010 i.e., σS induces expression of the yciGFE operon only when H-NS-mediated repression is relieved. Repression of yciGFE by H-NS is inversely correlated with σS levels Beraud M,2010


Transcription unit          
Name: yciGFE
Gene(s): yciE, yciF, yciG   Genome Browser M3D Gene expression COLOMBOS
Note(s): The yciGFE operon is poorly expressed |CITS:[20713450]|.
Evidence: [BTEI] Boundaries of transcription experimentally identified
[ITCR] Inferred through co-regulation
Reference(s): [5] Yoshida T., et al., 1993
Promoter
Name: yciGp
+1: 1316092
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 57
Sequence: ccctctatcttctcgttgcgcttaatttgactaattctcattagcgactaattttaatgaGtgtcgacacacaacactcat
                           -10              -35             +1                   
Evidence: [AIPP]
[HIPP]
Reference(s): [2] Huerta AM., et al., 2003
[1] Stoltzfus A., et al., 1988
Terminator(s)
Type: rho-independent
Sequence: attccgcacaAAAACGACCCCGTAATATACGGGGTCAATAAggacatggta
Reference(s): [1] Stoltzfus A., et al., 1988
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 H-NS repressor yciGp 1316153 1316163 -65.5 atgttcctcaAAATATATTTTccctctatct nd [BPP], [GEA], [HIBSCS] [3], [5]
proximal H-NS repressor yciGp 1316176 1316186 -88.5 aggtaattgtTAATATATCCAgaatgttcct nd [BPP], [GEA], [HIBSCS] [3], [5]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal McbR activator yciGp 1316149 1316170 -67.5 atccagaatgTTCCTCAAAATATATTTTCCCTctatcttctc nd [BPP], [GEA] [3], [4]
proximal McbR2 activator yciGp 1316170 1316191 -88.5 tcctcaggtaATTGTTAATATATCCAGAATGTtcctcaaaat nd [BPP], [GEA] [3], [4]
Note(s): 2McbR activates σS-dependent transcription at yciGp by countering the negative effect of H-NS Beraud M,2010 i.e., σS induces expression of the yciGFE operon only when H-NS-mediated repression is relieved. Repression of yciGFE by H-NS is inversely correlated with σS levels Beraud M,20101McbR activates σS-dependent transcription at yciGp by countering the negative effect of H-NS Beraud M,2010 i.e., σS induces expression of the yciGFE operon only when H-NS-mediated repression is relieved. Repression of yciGFE by H-NS is inversely correlated with σS levels Beraud M,2010


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Translational
Strand: reverse
Evidence: [ICA] Inferred by computational analysis
Reference(s): [6] null null
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -16.3 1315789 1315815 aagataattgCATCTGCGGGCCGTATGGCTCGCAGTgatttcactg
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"





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