Gene
Name:	frsA
Synonym(s):	ECK0240, EG11091, b0239, yafA
Genome position(nucleotides):	256527 --> 257771 Genome Browser
Strand:	forward
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	53.65
External database links:

ASAP:	ABE-0000817
ECHOBASE:	EB1083
ECOLIHUB:	frsA
OU-MICROARRAY:	b0239
STRING:	511145.b0239
COLOMBOS:	frsA

Type	Name	Post Left	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
promoter	TSS_455	256509	forward	nd	[RS-EPT-CBR]	[3]
promoter	crlp1	257810	forward	Zaslaver et al. demonstrated in 2006, by means of a library of fluorescent transcription fusions, that this promoter can be transcribed in vitro Zaslaver A,2006. Read more >	[HTTIM], [IEP], [IHBCE], [IPI], [RS-EPT-CBR], [TIM]	[3], [4], [5], [6], [7], [8]
promoter	crlp1	257810	forward	This promoter initiates the expression of crl and is recognized by σ⁷⁰, and it appears to be occluded by the overlapped promoter activated by σ⁵⁴ to produce a transcript that is not translated because the ribosome-binding site (RBS) is located upstream of the transcriptional start site Zafar MA,2014. Zaslaver et al. demonstrated in 2006, by means of a library of fluorescent transcription fusions, that this promoter can be transcribed in vitro Zaslaver A,2006. Read more >	[HTTIM], [IEP], [IPI], [RS-EPT-CBR], [TIM]	[3], [4], [5], [6], [8]
promoter	crlp2	257824	forward	The crlp2 promoter appears to be functional under nitrogen limitation conditions and positively regulated by NtrC Zafar MA,2014. This promoter produces a transcript that is not translated because the ribosome-binding site (RBS) is located upstream of the transcriptional start site. It was suggested that it is a negative regulatory system to inhibit the expression of crl, because this promoter overlaps with another σ⁷⁰ promoter that produces a transcript with the RBS, therefore producing the protein Crl Zafar MA,2014. This promoter was identified by microarray and ChIP assays with a mutant σ⁵⁴ strain and a σ⁵⁴-overexpressing strain, and by σ⁵⁴-related promoter element identification Zhao K,2010 We assigned a putative transcription start site to this promoter based on the observation that the majority of the σ⁵⁴-dependent promoters, whose transcription start sites were determined experimentally, present a distance of 11 nucleotides between the transcription start site and the -12 box Barrios H,1999. Read more >	[HIPP], [ICWHO], [IEP], [IHBCE], [IMP]	[9], [10], [11]

Evidence
[RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates
[HTTIM] High-throughput transcription initiation mapping
[IEP] Inferred from expression pattern
[IHBCE] Inferred by a human based on computational evidence
[IPI] Inferred from physical interaction
[TIM] Transcription initiation mapping
[HIPP] Human inference of promoter position
[ICWHO] Inferred computationally without human oversight
[IMP] Inferred from mutant phenotype

Reference(s)
[1] Koo BM., Yoon MJ., Lee CR., Nam TW., Choe YJ., Jaffe H., Peterkofsky A., Seok YJ., 2004, A novel fermentation/respiration switch protein regulated by enzyme IIAGlc in Escherichia coli., J Biol Chem 279(30):31613-21
[2] Kuznetsova E., Proudfoot M., Sanders SA., Reinking J., Savchenko A., Arrowsmith CH., Edwards AM., Yakunin AF., 2005, Enzyme genomics: Application of general enzymatic screens to discover new enzymes., FEMS Microbiol Rev 29(2):263-79
[3] 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.
[4] Arnqvist A., Olsen A., Pfeifer J., Russell DG., Normark S., 1992, The Crl protein activates cryptic genes for curli formation and fibronectin binding in Escherichia coli HB101., Mol Microbiol 6(17):2443-52
[5] Mendoza-Vargas A., Olvera L., Olvera M., Grande R., Vega-Alvarado L., Taboada B., Jimenez-Jacinto V., Salgado H., Juarez K., Contreras-Moreira B., Huerta AM., Collado-Vides J., Morett E., 2009, Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli., PLoS One 4(10):e7526
[6] Peano C., Wolf J., Demol J., Rossi E., Petiti L., De Bellis G., Geiselmann J., Egli T., Lacour S., Landini P., 2015, Characterization of the Escherichia coli σ(S) core regulon by Chromatin Immunoprecipitation-sequencing (ChIP-seq) analysis., Sci Rep 5:10469
[7] Sabina RL., Magill JM., Magill CW., 1976, Regulation of hypoxanthine transport in Neurospora crassa., J Bacteriol 128(2):598-603
[8] Zaslaver A., Bren A., Ronen M., Itzkovitz S., Kikoin I., Shavit S., Liebermeister W., Surette MG., Alon U., 2006, A comprehensive library of fluorescent transcriptional reporters for Escherichia coli., Nat Methods 3(8):623-8
[9] 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
[10] Zafar MA., Carabetta VJ., Mandel MJ., Silhavy TJ., 2014, Transcriptional occlusion caused by overlapping promoters., Proc Natl Acad Sci U S A 111(4):1557-61
[11] Zhao K., Liu M., Burgess RR., 2010, Promoter and regulon analysis of nitrogen assimilation factor, sigma54, reveal alternative strategy for E. coli MG1655 flagellar biosynthesis., Nucleic Acids Res 38(4):1273-83

RNA cis-regulatory element

Attenuation:	Transcriptional