RegulonDB

Gene
Name:	micF
Synonym(s):	ECK2208, EG30063, b4439, stc
Genome position(nucleotides):	2313084 --> 2313176 Genome Browser
Strand:	forward
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	35.48
External database links:

ASAP:	ABE-0047259
CGSC:	18157
ECHOBASE:	EB4226
PortEco:	micF
COLOMBOS:	micF

Product

Name:

MicF

Synonym(s):

Stc, small regulatory RNA MicF, stc

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 --> 3.1.3.6 - antisense RNA
		5 - cell processes --> 5.10 - defense/survival
		5 - cell processes --> 5.5 - adaptations
		5 - cell processes --> 5.6 - protection --> 5.6.4 - drug resistance/sensitivity
Gene Ontology Terms (GO)
	molecular_function	GO:0000900 - translation repressor activity, mRNA regulatory element binding GO:0005515 - protein binding GO:0003729 - mRNA binding GO:0048027 - mRNA 5'-UTR binding
	biological_process	GO:0006979 - response to oxidative stress GO:0042493 - response to drug GO:0040033 - negative regulation of translation, ncRNA-mediated GO:0034605 - cellular response to heat GO:0071474 - cellular hyperosmotic response

Note(s):

Note(s): ...[more].

Evidence:

[IDA] Inferred from direct assay
[IE] Inferred from experiment

Reference(s):

[1] Andersen J., et al., 1987
[2] Andersen J., et al., 1989
[3] Chen S., et al., 2002
[4] Delihas N. 1997
[5] Komatsu T., et al., 1990
[6] Kumar A., et al., 2016
[7] Mihailovic MK., et al., 2018
[8] Tkachenko AG., et al., 2006
[9] Urban JH., et al., 2007

External database links:

ECOCYC:

MICF-RNA

ECOLIWIKI:

b4439

Operon

Name:

micF

Operon arrangement:

Transcription unit	Promoter
micF	micFp

Transcriptional Regulation

Display Regulation

Activated by:

MarA, OmpR, Rob, HU, SoxS

Repressed by:

H-NS, IHF, Lrp, AcrR

Growth Conditions:

[1]	C: Escherichia coli\| protox assay E: Escherichia coli\| chenodeoxycholate; protox assay
[2]	C: Escherichia coli\| protox assay E: Escherichia coli\| protox assay; ursodeoxycholate
[3]	C: Escherichia coli\| protox assay E: Escherichia coli\| glycocholate; protox assay
[4]	C: Escherichia coli\| protox assay E: Escherichia coli\| deoxycholate; protox assay

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_2484	2311836	reverse	nd	[RS-EPT-CBR]	[10]
promoter	TSS_2485	2312187	reverse	nd	[RS-EPT-CBR]	[10]
promoter	TSS_2486	2312511	forward	nd	[RS-EPT-CBR]	[10]
promoter	TSS_2487	2312654	forward	nd	[RS-EPT-CBR]	[10]
promoter	TSS_2488	2312657	reverse	nd	[RS-EPT-CBR]	[10]
promoter	TSS_2489 (cluster)	2316062	forward	For this promoter, there is a cluster of 2 transcription start sites,in the interval 2316062 to 2316063, where the highest frequency is at position 2314084. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[10]

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

Reference(s)
[1] Andersen J., Delihas N., Ikenaka K., Green PJ., Pines O., Ilercil O., Inouye M., 1987, The isolation and characterization of RNA coded by the micF gene in Escherichia coli., Nucleic Acids Res 15(5):2089-101
[2] Andersen J., Forst SA., Zhao K., Inouye M., Delihas N., 1989, The function of micF RNA. micF RNA is a major factor in the thermal regulation of OmpF protein in Escherichia coli., J Biol Chem 264(30):17961-70
[3] Chen S., Lesnik EA., Hall TA., Sampath R., Griffey RH., Ecker DJ., Blyn LB., 2002, A bioinformatics based approach to discover small RNA genes in the Escherichia coli genome., Biosystems 65(2-3):157-77
[4] Delihas N., 1997, Antisense micF RNA and 5'-UTR of the target ompF RNA: phylogenetic conservation of primary and secondary structures., Nucleic Acids Symp Ser (36):33-5
[5] Komatsu T., Ohta M., Kido N., Arakawa Y., Ito H., Mizuno T., Kato N., 1990, Molecular characterization of an Enterobacter cloacae gene (romA) which pleiotropically inhibits the expression of Escherichia coli outer membrane proteins., J Bacteriol 172(7):4082-9
[6] Kumar A., Beloglazova N., Bundalovic-Torma C., Phanse S., Deineko V., Gagarinova A., Musso G., Vlasblom J., Lemak S., Hooshyar M., Minic Z., Wagih O., Mosca R., Aloy P., Golshani A., Parkinson J., Emili A., Yakunin AF., Babu M., 2016, Conditional Epistatic Interaction Maps Reveal Global Functional Rewiring of Genome Integrity Pathways in Escherichia coli., Cell Rep 14(3):648-61
[7] 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
[8] Tkachenko AG., Pozhidaeva ON., Shumkov MS., 2006, Role of polyamines in formation of multiple antibiotic resistance of Escherichia coli under stress conditions., Biochemistry (Mosc) 71(9):1042-9
[9] Urban JH., Vogel J., 2007, Translational control and target recognition by Escherichia coli small RNAs in vivo., Nucleic Acids Res 35(3):1018-37
[10] 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.