RegulonDB RegulonDB 10.8: Operon Form
   

folD-ybcJ operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: folD-ybcJ
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit       
Name: folD-ybcJ
Gene(s): ybcJ, folD   Genome Browser M3D Gene expression COLOMBOS
Note(s): Putative promoter islands, which are regions of DNA containing multiple transcription start sites, were found by computational prediction methods in the intergenic region of the folD and sfmA genes in E. coli. These promoter islands are associated with genes acquired horizontally, and they are absent in the same region in Salmonella 23717391 In addition, some sites that bind HNS have been predicted in this intergenic region. This protein appears to inactivate the promoter islands 23717391
Evidence: [ICWHO] Inferred computationally without human oversight
Promoter
Name: folDp
+1: 557781
Distance from start of the gene: 40
Sequence: tcacgcgataaatctgaaacgaaacctgacagcgcgccccgcttctgacaaaataggcgcAtccccttcgatctacgtaac
Evidence: [CV(RS-EPT-CBR)]
[HTIM]
[RS-EPT-CBR]
Reference(s): [1] Mendoza-Vargas A., et al., 2009
[2] Salgado H, et al., 2012


Evidence    

 [CV(RS-EPT-CBR)] cross validation(RS-EPT-CBR)

 [HTIM] High-throughput transcription initiation mapping

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


Reference(s)    

 [1] 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

 [2] 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.

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