RegulonDB RegulonDB 10.8: Operon Form
   

pykA operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit       
Name: pykA
Gene(s): pykA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [ICWHO] Inferred computationally without human oversight
Promoter
Name: pykAp2
+1: 1937494
Sigma Factor: Sigma70, Sigma38
Distance from start of the gene: 155
Sequence: attcagagataacttgaagcgggtcaaagaagcgctgaaggaatcgcgttttgataagcaGttacttaatttaagtgacga
                                                 -10        +1                   
Evidence: [CV(RS-EPT-CBR)]
[HTIM]
[RS-EPT-CBR]
Reference(s): [1] Mendoza-Vargas A., et al., 2009
[2] Olvera L., et al., 2009
[3] Salgado H, et al., 2012


Transcription unit       
Name: pykA
Gene(s): pykA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [ICWHO] Inferred computationally without human oversight
Promoter
Name: pykAp1
+1: 1937544
Sigma Factor: Sigma70, Sigma38
Distance from start of the gene: 105
Sequence: ttgataagcagttacttaatttaagtgacgatcgctaaaaacgactgtcactgtcctaatCttatacgacatccgaatgag
                                                -10         +1                   
Evidence: [CV(RS-EPT-CBR)]
[HTIM]
[RS-EPT-CBR]
Reference(s): [1] Mendoza-Vargas A., et al., 2009
[2] Olvera L., et al., 2009
[3] 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] Olvera L., Mendoza-Vargas A., Flores N., Olvera M., Sigala JC., Gosset G., Morett E., Bolivar F., 2009, Transcription analysis of central metabolism genes in Escherichia coli. Possible roles of sigma38 in their expression, as a response to carbon limitation., PLoS One 4(10):e7466

 [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.

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