RegulonDB

Gene
Name:	omrA
Synonym(s):	ECK2833, G0-8868, PAIR2a, b4444, psrA12, rygA, sraE, t59
Genome position(nucleotides):	2976102 <-- 2976189 Genome Browser
Strand:	reverse
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	50.0
Reference(s):	[1] Argaman L., et al., 2001
External database links:

ASAP:	ABE-0047264
ECHOBASE:	EB4530
ECOLIHUB:	omrA
COLOMBOS:	omrA

Product

Name:

small regulatory RNA OmrA

Synonym(s):

OmrA, PAIR2a, PsrA12, RygA, SraE, T59

Type:

small RNA

Classification:

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 - negative regulation of translation, ncRNA-mediated 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:

ECOCYC:

SRAE-RNA

ECOLIWIKI:

b4444

Operon

Name:

omrA

Operon arrangement:

Transcription unit	Promoter
omrA	omrAp

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	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]

Evidence
[ICWHO] Inferred computationally without human oversight
[RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

Reference(s)
[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.