RegulonDB RegulonDB 10.8: Operon Form
   

ybgI-pxpBCA-nei operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: ybgI-pxpBCA-nei
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit       
Name: ybgIJKL-nei
Gene(s): ybgI, pxpB, pxpC, pxpA, nei   Genome Browser M3D Gene expression COLOMBOS
Note(s): Downstream of the nei gene, there are two putative rho-dependent terminators of transcription Gifford CM,2000.
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [1] Gifford CM., et al., 2000
Promoter
Name: ybgIp1
+1: 742619
Distance from start of the gene: 208
Sequence: taattccacaattgacggcaacgtcacgtaatagttgcgcggcgtgcttgtgtttccttaAagttaaaactttgatacaga
Evidence: [TIM]
Reference(s): [1] Gifford CM., et al., 2000


Transcription unit       
Name: ybgIJKL-nei
Gene(s): ybgI, pxpB, pxpC, pxpA, nei   Genome Browser M3D Gene expression COLOMBOS
Note(s): Downstream of the nei gene, there are two putative rho-dependent terminators of transcription Gifford CM,2000.
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [1] Gifford CM., et al., 2000
Promoter
Name: ybgIp2
+1: 742798
Distance from start of the gene: 29
Sequence: tcttaatatgtcaaaagattggctatcgacgaactggcgaggtaacgctatgttaacggtGtagctatcagaatacggaag
Evidence: [CV(RS-EPT-CBR)]
[CV(TIM)]
[RS-EPT-CBR]
[TIM]
Reference(s): [1] Gifford CM., et al., 2000
[2] Salgado H, et al., 2012


Transcription unit       
Name: nei
Gene(s): nei   Genome Browser M3D Gene expression COLOMBOS
Evidence: [IEP] Inferred from expression pattern
Reference(s): [3] Li Z., et al., 2019
Promoter
Name: neip
+1: 745904
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 31
Sequence: tcgcccgccgactacgctctgcatttgccgaaaaggggattgttgtcgcagcataaccccGattaataaagaatgaaaaaa
                         -35                        -10     +1                   
Evidence: [RE]
[TIM]
Reference(s): [3] Li Z., et al., 2019


Evidence    

 [TIM] Transcription initiation mapping

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

 [CV(TIM)] cross validation(TIM)

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

 [RE] RNA-seq evidence


Reference(s)    

 [1] Gifford CM., Wallace SS., 2000, The genes encoding endonuclease VIII and endonuclease III in Escherichia coli are transcribed as the terminal genes in operons., Nucleic Acids Res 28(3):762-9

 [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.

 [3] Li Z., Pan Q., Xiao Y., Fang X., Shi R., Fu C., Danchin A., You C., 2019, Deciphering global gene expression and regulation strategy in Escherichia coli during carbon limitation., Microb Biotechnol 12(2):360-376

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