RegulonDB

Gene
Name:	mcaS
Synonym(s):	ECK1336, G0-8899, IS061, b4426, isrA
Genome position(nucleotides):	1405658 <-- 1405751 Genome Browser
Strand:	reverse
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	51.06
Reference(s):	[1] Jorgensen MG., et al., 2012
External database links:

ASAP:	ABE-0047247
ECHOBASE:	EB4510
ECOLIHUB:	isrA
COLOMBOS:	mcaS

Product

Name:

small regulatory RNA McaS

Synonym(s):

IS061, IsrA, McaS

Type:

small RNA

Classification:

Multifun Terms (GenProtEC)
		2 - information transfer --> 2.2 - RNA related --> 2.2.7 - antisense RNA
		3 - regulation --> 3.1 - type of regulation --> 3.1.3 - posttranscriptional --> 3.1.3.1 - translation attenuation and efficiency
		3 - regulation --> 3.1 - type of regulation --> 3.1.3 - posttranscriptional --> 3.1.3.3 - inhibition / activation of enzymes
		3 - regulation --> 3.1 - type of regulation --> 3.1.3 - posttranscriptional --> 3.1.3.6 - antisense RNA
Gene Ontology Terms (GO)
	molecular_function	GO:0005515 - protein binding GO:0048027 - mRNA 5'-UTR binding GO:0001000 - bacterial-type RNA polymerase core enzyme binding
	biological_process	GO:0045947 - negative regulation of translational initiation GO:0051100 - negative regulation of binding GO:0045948 - positive regulation of translational initiation GO:0070928 - regulation of mRNA stability, ncRNA-mediated GO:1900191 - negative regulation of single-species biofilm formation GO:1902021 - 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] Andreassen PR., et al., 2019
[3] Boehm A., et al., 2012
[1] Jorgensen MG., et al., 2012
[4] Mihailovic MK., et al., 2018
[5] Thomason MK., et al., 2012

External database links:

ECOCYC:

IS061-RNA

ECOLIWIKI:

b4426

Operon

Name:

mcaS

Operon arrangement:

Transcription unit	Promoter
mcaS	mcaSp

Transcriptional Regulation
	Display Regulation
Activated by:	CRP

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	TSS_1761	1405810	reverse	nd	[RS-EPT-CBR]	[6]
promoter	smrAp1	1405936	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: poor homology. Score: -2.43. P-value: 3.908e-5 Read more >	[ICWHO]	[7]
promoter	TSS_1762	1405955	forward	nd	[RS-EPT-CBR]	[6]

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

Reference(s)
[1] Jorgensen MG., Nielsen JS., Boysen A., Franch T., Moller-Jensen J., Valentin-Hansen P., 2012, Small regulatory RNAs control the multi-cellular adhesive lifestyle of Escherichia coli., Mol Microbiol 84(1):36-50
[2] Andreassen PR., Pettersen JS., Jorgensen M., 2019, Site-Directed Mutagenesis for In Vitro and In Vivo Experiments Exemplified with RNA Interactions in Escherichia Coli., J Vis Exp (144)
[3] Boehm A., Vogel J., 2012, The csgD mRNA as a hub for signal integration via multiple small RNAs., Mol Microbiol 84(1):1-5
[4] Mihailovic MK., Vazquez-Anderson J., Li Y., Fry V., Vimalathas P., Herrera D., Lease RA., Powell WB., Contreras LM., 2018, High-throughput in vivo mapping of RNA accessible interfaces to identify functional sRNA binding sites., Nat Commun 9(1):4084
[5] Thomason MK., Fontaine F., De Lay N., Storz G., 2012, A small RNA that regulates motility and biofilm formation in response to changes in nutrient availability in Escherichia coli., Mol Microbiol 84(1):17-35
[6] 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.
[7] 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