RegulonDB RegulonDB 11.1: Gene Form
   

rybA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

opgE mntR rybA yliL mntS ybiR MntR MntR TSS_979 TSS_979 mntRp4 mntRp4 mntRp mntRp mntRp5 mntRp5 mntRp6 mntRp6 rybAp rybAp TSS_978 TSS_978 ybiPp5 ybiPp5

Gene      
Name: rybA    Texpresso search in the literature
Synonym(s): ECK0806, G0-8881, b4416
Genome position(nucleotides): 852725 <-- 853064
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 46.76
Reference(s): [1] Gerstle K., et al., 2012
[2] Wassarman KM., et al., 2001
External database links:  
ASAP:
 ABE-0047240
ECHOBASE:
 EB4505
ECOLIHUB:
 rybA
COLOMBOS: rybA


Product      
Name: small RNA RybA
Synonym(s): RybA
Type: small RNA
Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.2 - RNA related
Gene Ontology Terms (GO)  
biological_process GO:0042542 - response to hydrogen peroxide
Note(s): Note(s): ...[more].
Evidence: [EXP-IMP] Inferred from mutant phenotype
Reference(s): [1] Gerstle K., et al., 2012
[3] PLOS Genetics Staff. 2015
External database links:  
ECOCYC:
 RYBA-RNA
ECOLIWIKI:
 b4416


Operon      
Name: rybA-mntS         
Operon arrangement:
Transcription unit        Promoter
rybA-mntS


Transcriptional Regulation      
Display Regulation             
Repressed by: MntR


Elements in the selected gene context region unrelated to any object in RegulonDB      

  Type Name Post Left Post Right Strand Notes Evidence (Confirmed, Strong, Weak) References
  promoter ybiPp5 852626 reverse nd [COMP-AINF] [4]
  promoter TSS_978 853047 reverse nd [RS-EPT-CBR] [5]
  promoter mntRp6 853080 forward nd [COMP-AINF] [4]
  promoter mntRp5 853083 forward nd [COMP-AINF] [4]
  promoter mntRp4 853135 forward nd [COMP-AINF] [4]
  promoter TSS_979 853137 forward nd [RS-EPT-CBR] [5]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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


Reference(s)    

 [1] Gerstle K., Klatschke K., Hahn U., Piganeau N., 2012, The small RNA RybA regulates key-genes in the biosynthesis of aromatic amino acids under peroxide stress in E. coli., RNA Biol 9(4):458-68

 [2] Wassarman KM., Repoila F., Rosenow C., Storz G., Gottesman S., 2001, Identification of novel small RNAs using comparative genomics and microarrays., Genes Dev 15(13):1637-51

 [3] PLOS Genetics Staff., 2015, Correction: The Escherichia coli Small Protein MntS and Exporter MntP Optimize the Intracellular Concentration of Manganese., PLoS Genet 11(6):e1005322

 [4] 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

 [5] 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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