RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit       
Name: panBC
Gene(s): panC, panB   Genome Browser M3D Gene expression COLOMBOS
Note(s): A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for panC . This structure could regulate the expression of the gene, as observed for hemL gene expression Shao X, Zhang W, Umar MI, Wong HY, Seng Z, Xie Y, Zhang Y, Yang L, Kwok CK, Deng X,2020.
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Jones CE., et al., 1993
[2] Merkel WK., et al., 1996
[3] Vallari DS., et al., 1985
Promoter
Name: panBp
+1: 149630
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 29
Sequence: tggcagtgctgctacggataaatcattgcccccaccaatgtgactgataaaatgccagacAgcacaacatcaatttatcag
                               -35                   -10    +1                   
Note(s): We assigned a putative transcriptional start site to this promoter based on the observation that the majority of the promoters, whose transcriptional start sites were determined experimentally, present a distance of 6 nucleotides between the transcriptional start site and the -10 box Harley CB, Reynolds RP,1987.
Evidence: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[RS-EPT-CBR]
Reference(s): [4] Huerta AM., et al., 2003
[1] Jones CE., et al., 1993
[5] Salgado H, et al., 2012


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [COMP-HINF] Inferred by a human based on computational evidence

 [COMP-HINF-POSITIONAL-IDENTIFICATION] Human inference of promoter position

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


Reference(s)    

 [1] Jones CE., Brook JM., Buck D., Abell C., Smith AG., 1993, Cloning and sequencing of the Escherichia coli panB gene, which encodes ketopantoate hydroxymethyltransferase, and overexpression of the enzyme., J Bacteriol 175(7):2125-30

 [2] Merkel WK., Nichols BP., 1996, Characterization and sequence of the Escherichia coli panBCD gene cluster., FEMS Microbiol Lett 143(2-3):247-52

 [3] Vallari DS., Rock CO., 1985, Isolation and characterization of Escherichia coli pantothenate permease (panF) mutants., J Bacteriol 164(1):136-42

 [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.

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