RegulonDB RegulonDB 11.1: Operon Form
   

yefM-yoeB operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit          
Name: yefM-yoeB
Gene(s): yoeB, yefM   Genome Browser M3D Gene expression COLOMBOS
Evidence: [COMP-AINF] Inferred computationally without human oversight
Promoter
Name: yefMp
+1: 2089733
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 20
Sequence: ccttgatctacaaactaattaataaatagttaattaacgctcatcattgtacaatgaactGtacaaaagaggagattgaca
                                  -35                  -10  +1                   
Evidence: [COMP-AINF]
[COMP-HINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [1] Huerta AM., et al., 2003
[2] Kedzierska B., et al., 2007
[3] Salgado H, et al., 2012
TF binding sites (TFBSs)
[YefM,-] 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 YefM repressor yefMp 2089725 2089739 2.5 cattgtacaaTGAACTGTACAAAAGaggagattga nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [2], [4]
proximal YefM repressor yefMp 2089737 2089751 -10.5 attaacgctcATCATTGTACAATGAactgtacaaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2]
[YefM-YoeB,-] 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 YefM-YoeB repressor yefMp 2089725 2089738 2.5 attgtacaatGAACTGTACAAAAGaggagattga nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [2], [4]
proximal YefM-YoeB repressor yefMp 2089737 2089750 -10.5 ttaacgctcaTCATTGTACAATGAactgtacaaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [2], [4]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

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

 [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-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] Binding of cellular extracts

 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins


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] Kedzierska B., Lian LY., Hayes F., 2007, Toxin-antitoxin regulation: bimodal interaction of YefM-YoeB with paired DNA palindromes exerts transcriptional autorepression., Nucleic Acids Res 35(1):325-39

 [3] 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.

 [4] Kedzierska B., Potrykus K., Szalewska-Palasz A., Wodzikowska B., 2020, Insights into Transcriptional Repression of the Homologous Toxin-Antitoxin Cassettes yefM-yoeB and axe-txe., Int J Mol Sci 21(23)

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