RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: ycdZ
Gene(s): ycdZ   Genome Browser M3D Gene expression COLOMBOS
Note(s): The functions of the CRP and CytR transcriptional regulator (CRP-CytR-CRP system) were added based on the behavior of this system in Escherichia coli Sernova NV,2012
Evidence: [COMP-AINF] Inferred computationally without human oversight
Promoter
Name: ycdZp4
+1: 1100252
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 44
Sequence: taagtgtgatctacgtcactcataactgcaacggataatttgttgttgcataaaatgtgtGctcgatctcattcatggccg
                          -35                      -10      +1                   
Evidence: [COMP-AINF]
Reference(s): [1] Huerta AM., et al., 2003
TF binding sites (TFBSs)
[CRP,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CRP-cyclic-AMP activator ycdZp4 1100193 1100215 -48.0 tctgaagaatAAGTGTGATCTACGTCACTCATAactgcaacgg nd [COMP-AINF-SIMILAR-TO-CONSENSUS] nd [2]
proximal CRP-cyclic-AMP activator ycdZp4 1100244 1100266 4.0 ttgttgcataAAATGTGTGCTCGATCTCATTCAtggccgcgtt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [2], [3]
[CRP,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CRP-cyclic-AMP repressor ycdZp4 1100193 1100215 -48.0 tctgaagaatAAGTGTGATCTACGTCACTCATAactgcaacgg nd [COMP-AINF-SIMILAR-TO-CONSENSUS] nd [2]
proximal CRP-cyclic-AMP repressor ycdZp4 1100244 1100266 4.0 ttgttgcataAAATGTGTGCTCGATCTCATTCAtggccgcgtt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [2], [3]
[CytR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CytR repressor ycdZp4 1100216 1100244 -22.0 gtcactcataACTGCAACGGATAATTTGTTGTTGCATAAaatgtgtgct nd [COMP-AINF-SIMILAR-TO-CONSENSUS] nd [2]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Translational
Strand: forward
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -12.92 1100265 1100298 gatctcattcATGGCCGCGTTTTCTGCTATCATGCGCGGCATGaacatacttc
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"


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [COMP-AINF-SIMILAR-TO-CONSENSUS] Automated inference based on similarity to consensus sequences

 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] 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] Sernova NV., Gelfand MS., 2012, Comparative genomics of CytR, an unusual member of the LacI family of transcription factors., PLoS One 7(9):e44194

 [3] Tsai MJ., Wang JR., Yang CD., Kao KC., Huang WL., Huang HY., Tseng CP., Huang HD., Ho SY., 2018, PredCRP: predicting and analysing the regulatory roles of CRP from its binding sites in Escherichia coli., Sci Rep 8(1):951

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