RegulonDB RegulonDB 10.9: Gene Form
   

rirA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

waaA waaQ rirA waaG Cis-reg waaAp1 waaAp1 waaAp2 waaAp2 rirAp rirAp waaQp waaQp TSS_4211 TSS_4211

Gene      
Name: rirA    Texpresso search in the literature
Synonym(s): ECK4617, G0-16662, b4760
Genome position(nucleotides): 3808166 <-- 3808238 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
46.58


Product      
Name: small regulatory RNA RirA
Synonym(s): RirA
Type: small RNA
Classification:
Multifun Terms (GenProtEC)  
  3 - regulation --> 3.1 - type of regulation --> 3.1.3 - posttranscriptional
Gene Ontology Terms (GO)  
molecular_function GO:0005515 - protein binding
biological_process GO:2000142 - regulation of DNA-templated transcription, initiation
Note(s): Note(s): ...[more].
Evidence: [IMP] Inferred from mutant phenotype
[IPI] Inferred from physical interaction
Reference(s): [1] Klein G., et al., 2016
External database links:  
ECOCYC:
RNA0-390


Operon      
Name: rirA-waaQGPSBOJYZU         
Operon arrangement:
Transcription unit        Promoter
rfaYZ
rfaQGPSBIJYZ-waaU
rirA-rfaQGPSBIJYZ-waaU
rfaZ-waaU


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 TSS_4211 3807069 reverse nd [RS-EPT-CBR] [2]


Evidence    

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



Reference(s)    

 [1] Klein G., Stupak A., Biernacka D., Wojtkiewicz P., Lindner B., Raina S., 2016, Multiple Transcriptional Factors Regulate Transcription of the rpoE Gene in Escherichia coli under Different Growth Conditions and When the Lipopolysaccharide Biosynthesis Is Defective., J Biol Chem 291(44):22999-23019

 [2] 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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