RegulonDB RegulonDB 10.8: Operon Form
   

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




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


Transcription unit       
Name: shiA
Gene(s): shiA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [ICWHO] Inferred computationally without human oversight
Promoter
Name: shiAp
+1: 2053566
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 77
Sequence: ttgccgctaatcagccataaaatcatttgcagatgcgctctgtcgaggtagtctcataagGttcgtttatagatcgacggc
                           -35                   -10        +1                   
Evidence: [CV(RS-EPT-CBR)]
[CV(TIM)]
[HTIM]
[RS-EPT-CBR]
[TIM]
Reference(s): [1] Liu F., et al., 2018
[2] Prevost K., et al., 2007
[3] Salgado H, et al., 2012


Regulation by sRNA    
  Small RNA name (Regulator) Regulation type Mechanism Function Binding Sites Evidence Reference
LeftPos RightPos Sequence (RNA-strand)
  ryhB antisense translational regulation activator       [GEA]
[HIFS]
[IMP]		 [2]
Notes: "The provided sequence is that of the RNA strand,i.e. 'U's are showed instead the 'T'"


Evidence    

 [CV(RS-EPT-CBR)] cross validation(RS-EPT-CBR)

 [CV(TIM)] cross validation(TIM)

 [HTIM] High-throughput transcription initiation mapping

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

 [TIM] Transcription initiation mapping


Reference(s)    

 [1] Liu F., Zheng K., Chen HC., Liu ZF., 2018, Capping-RACE: a simple, accurate, and sensitive 5' RACE method for use in prokaryotes., Nucleic Acids Res 46(21):e129

 [2] Prevost K., Salvail H., Desnoyers G., Jacques JF., Phaneuf E., Masse E., 2007, The small RNA RyhB activates the translation of shiA mRNA encoding a permease of shikimate, a compound involved in siderophore synthesis., Mol Microbiol 64(5):1260-73

 [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.

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