RegulonDB RegulonDB 11.1: Operon Form
   

yfiR-dgcN-yfiB operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: yfiR-dgcN-yfiB
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit          
Name: yfiR-dgcN-yfiB
Gene(s): yfiR, dgcN, yfiB   Genome Browser M3D Gene expression COLOMBOS
Evidence: [COMP-AINF] Inferred computationally without human oversight
Promoter
Name: yfiRp
+1: 2741824
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 51
Sequence: cattgtgttttatttctcacattgatgacggtcgcatgaaaaaatgatattttaatgagcAttctgaaaaaatatcgatgc
                         -35                    -10         +1                   
Evidence: [COMP-HINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[IC]
[RS-EPT-CBR]
Reference(s): [1] Salgado H, et al., 2012
[2] Wiebe H., et al., 2015
Terminator(s)
Type: rho-independent
Sequence: taaaacaccaGCAAACAGATAAAAAAGGGCCAGCCAATTGGCCAGCCCTTCTTAACAGGATGTCGcttaagcgaa
Reference(s): [3] Feng CQ., et al., 2019
[4] Lesnik EA., et al., 2001
TF binding sites (TFBSs)
[YjjQ,-] 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 YjjQ repressor yfiRp 2741752 2741766 -65.0 aaattaaacaTAAGATTTTACTCATtgtgttttat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [2]


Transcription unit       
Name: yfiRN
Gene(s): yfiR, dgcN   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IMP-POLAR-MUTATION] Polar mutation
Reference(s): [5] Sommerfeldt N., et al., 2009


Evidence    

 [COMP-HINF] Inferred by a human based on computational evidence

 [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] Transcription initiation mapping

 [IC] Inferred by curator

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis

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


Reference(s)    

 [1] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

 [2] Wiebe H., Gurlebeck D., Gross J., Dreck K., Pannen D., Ewers C., Wieler LH., Schnetz K., 2015, YjjQ Represses Transcription of flhDC and Additional Loci in Escherichia coli., J Bacteriol 197(16):2713-20

 [3] Feng CQ., Zhang ZY., Zhu XJ., Lin Y., Chen W., Tang H., Lin H., 2019, iTerm-PseKNC: a sequence-based tool for predicting bacterial transcriptional terminators., Bioinformatics 35(9):1469-1477

 [4] Lesnik EA., Sampath R., Levene HB., Henderson TJ., McNeil JA., Ecker DJ., 2001, Prediction of rho-independent transcriptional terminators in Escherichia coli., Nucleic Acids Res 29(17):3583-94

 [5] Sommerfeldt N., Possling A., Becker G., Pesavento C., Tschowri N., Hengge R., 2009, Gene expression patterns and differential input into curli fimbriae regulation of all GGDEF/EAL domain proteins in Escherichia coli., Microbiology 155(Pt 4):1318-31

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