RegulonDB RegulonDB 11.0: Gene Form

omrA gene in Escherichia coli K-12 genome

Gene local context to scale (view description)

aas omrA omrB lplT OmpR anti-anti-terminator anti-terminator terminator omrBp omrBp omrAp omrAp TSS_3137 TSS_3137 TSS_3136 TSS_3136 lplTp3 lplTp3

Name: omrA    Texpresso search in the literature
Synonym(s): ECK2833, G0-8868, PAIR2a, b4444, psrA12, rygA, sraE, t59
Genome position(nucleotides): 2976102 <-- 2976189
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
Reference(s): [1] Argaman L., et al., 2001
External database links:  

Name: small regulatory RNA OmrA
Synonym(s): OmrA, PAIR2a, PsrA12, RygA, SraE, T59
Type: small RNA
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.2 - RNA related --> 2.2.4 - RNA degradation
  2 - information transfer --> 2.2 - RNA related --> 2.2.7 - antisense RNA
Gene Ontology Terms (GO)  
molecular_function GO:0005515 - protein binding
GO:0003729 - mRNA binding
biological_process GO:0040033 - RNA-mediated gene silencing by inhibition of translation
GO:1900191 - negative regulation of single-species biofilm formation
GO:1902201 - negative regulation of bacterial-type flagellum-dependent cell motility
Note(s): Note(s): ...[more].
Evidence: [IDA] Inferred from direct assay
[IMP] Inferred from mutant phenotype
Reference(s): [2] Guillier M., et al., 2006
[3] Guillier M., et al., 2008
[4] Holmqvist E., et al., 2010
[5] Moon K., et al., 2011
[6] Rivas E., et al., 2001
[7] Romilly C., et al., 2020
External database links:  

Name: omrA         
Operon arrangement:
Transcription unit        Promoter

Transcriptional Regulation      
Display Regulation             
Activated by: OmpR

RNA cis-regulatory element    
Attenuation: Transcriptional

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 lplTp3 2973939 reverse nd [ICWHO] [8]
  promoter TSS_3136 2975992 reverse nd [RS-EPT-CBR] [9]
  promoter TSS_3137 2976050 reverse nd [RS-EPT-CBR] [9]


 [ICWHO] Inferred computationally without human oversight

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


 [1] Argaman L., Hershberg R., Vogel J., Bejerano G., Wagner EG., Margalit H., Altuvia S., 2001, Novel small RNA-encoding genes in the intergenic regions of Escherichia coli., Curr Biol 11(12):941-50

 [2] Guillier M., Gottesman S., 2006, Remodelling of the Escherichia coli outer membrane by two small regulatory RNAs., Mol Microbiol 59(1):231-47

 [3] Guillier M., Gottesman S., 2008, The 5' end of two redundant sRNAs is involved in the regulation of multiple targets, including their own regulator., Nucleic Acids Res 36(21):6781-94

 [4] Holmqvist E., Reimegard J., Sterk M., Grantcharova N., Romling U., Wagner EG., 2010, Two antisense RNAs target the transcriptional regulator CsgD to inhibit curli synthesis., EMBO J 29(11):1840-50

 [5] Moon K., Gottesman S., 2011, Competition among Hfq-binding small RNAs in Escherichia coli., Mol Microbiol 82(6):1545-62

 [6] Rivas E., Klein RJ., Jones TA., Eddy SR., 2001, Computational identification of noncoding RNAs in E. coli by comparative genomics., Curr Biol 11(17):1369-73

 [7] Romilly C., Hoekzema M., Holmqvist E., Wagner EGH., 2020, Small RNAs OmrA and OmrB promote class III flagellar gene expression by inhibiting the synthesis of anti-Sigma factor FlgM., RNA Biol 17(6):872-880

 [8] 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

 [9] 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.