Gene
Name:	rlmN
Synonym(s):	ECK2513, EG12401, b2517, yfgB
Genome position(nucleotides):	2643129 <-- 2644283 Genome Browser
Strand:	reverse
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	52.99
External database links:

ASAP:	ABE-0008287
ECHOBASE:	EB2301
OU-MICROARRAY:	b2517
PortEco:	rlmN
STRING:	511145.b2517
COLOMBOS:	rlmN

Type	Name	Post Left	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
promoter	ispGp1	2641880	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: poor homology. Score: -0.33. P-value: 4.644e-6 Read more >	[ICWHO]	[4]
promoter	TSS_2810	2641922	reverse	nd	[RS-EPT-CBR]	[5]
promoter	TSS_2811 (cluster)	2641929	reverse	For this promoter, there is a cluster of 2 transcription start sites,in the interval 2641928 to 2641929, where the highest frequency is at position 2639951. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[5]
promoter	TSS_2812	2641933	reverse	nd	[RS-EPT-CBR]	[5]
promoter	ispGp4	2641950	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 5.09. P-value: 2.761e-6 Read more >	[ICWHO]	[4]
promoter	ispGp5	2641954	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 6.606. P-value: 2.005e-6 Read more >	[ICWHO]	[4]
promoter	TSS_2813 (cluster)	2641985	reverse	For this promoter, there is a cluster of 2 transcription start sites,in the interval 2641984 to 2641985, where the highest frequency is at position 2640007. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[5]
promoter	TSS_2814 (cluster)	2641990	reverse	For this promoter, there is a cluster of 2 transcription start sites,in the interval 2641989 to 2641990, where the highest frequency is at position 2640012. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[5]
promoter	TSS_2815	2641997	reverse	nd	[RS-EPT-CBR]	[5]
promoter	TSS_2816	2642045	reverse	nd	[RS-EPT-CBR]	[5]
promoter	rodZp1	2642932	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 3.284. P-value: 9.142e-5 Read more >	[ICWHO]	[4]
promoter	rodZp2	2642934	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 5.548. P-value: 4.330e-6 Read more >	[ICWHO]	[4]
promoter	TSS_2817	2644379	reverse	nd	[RS-EPT-CBR]	[5]

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] Atkinson GC., Hansen LH., Tenson T., Rasmussen A., Kirpekar F., Vester B., 2013, Distinction between the Cfr methyltransferase conferring antibiotic resistance and the housekeeping RlmN methyltransferase., Antimicrob Agents Chemother 57(8):4019-26
[2] Lanz ND., Grove TL., Gogonea CB., Lee KH., Krebs C., Booker SJ., 2012, RlmN and AtsB as models for the overproduction and characterization of radical SAM proteins., Methods Enzymol 516:125-52
[3] Stojkovic V., Fujimori DG., 2015, Radical SAM-Mediated Methylation of Ribosomal RNA., Methods Enzymol 560:355-76
[4] 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
[5] 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.

RNA cis-regulatory element

Attenuation:	Translational