RegulonDB RegulonDB 11.1: Operon Form
   

ybeZYX-lnt operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit       
Name: ybeZYX-lnt
Gene(s): lnt, ybeX, ybeY, ybeZ   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IEP-COREGULATION] Inferred through co-regulation
Reference(s): [1] Nonaka G., et al., 2006
Promoter
Name: ybeZp
+1: 693469
Sigma Factor: Sigma32 Sigmulon
Distance from start of the gene: 91
Sequence: tctcaggcctgccgttccggtgggccttgttttttctctctttatccccatctttattgcAatgcttgcgcctttttcctg
                                -35                -10      +1                   
Evidence: [COMP-AINF]
[COMP-AINF-POSITIONAL-IDENTIFICATION]
[COMP-AINF-SIMILAR-TO-CONSENSUS]
[EXP-IDA]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IEP]
[RS-EPT-CBR]
Reference(s): [2] Huerta AM., et al., 2003
[1] Nonaka G., et al., 2006
[3] Salgado H, et al., 2012
[4] Wade JT., et al., 2006


Transcription unit       
Name: ybeX-lnt
Gene(s): lnt, ybeX   Genome Browser M3D Gene expression COLOMBOS
Evidence: [COMP-AINF] Inferred computationally without human oversight


Transcription unit       
Name: ybeZY
Gene(s): ybeY, ybeZ   Genome Browser M3D Gene expression COLOMBOS
Evidence: [COMP-AINF] Inferred computationally without human oversight


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: reverse
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -16.0 693493 693525 cgtaattctcAGGCCTGCCGTTCCGGTGGGCCTTGTTTTTTCtctctttatc
  anti-terminator -11.6 693514 693560 caaagaaaacGACCTTGGCGTGGGTTATTATCAGCCGTAATTCTCAGGCCTGCCGTtccggtgggc
  anti-anti-terminator -12.6 693540 693587 accggaatcaGTGATTGCCCGTACCCGCAAAGAAAACGACCTTGGCGTGGGTTATTAtcagccgtaa
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-POSITIONAL-IDENTIFICATION] Automated inference of promoter position

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

 [EXP-IDA] Inferred from direct assay

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

 [EXP-IEP] Inferred from expression pattern

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


Reference(s)    

 [1] Nonaka G., Blankschien M., Herman C., Gross CA., Rhodius VA., 2006, Regulon and promoter analysis of the E. coli heat-shock factor, sigma32, reveals a multifaceted cellular response to heat stress., Genes Dev 20(13):1776-89

 [2] 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

 [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] Wade JT., Roa DC., Grainger DC., Hurd D., Busby SJ., Struhl K., Nudler E., 2006, Extensive functional overlap between sigma factors in Escherichia coli., Nat Struct Mol Biol 13(9):806-14

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