RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit       
Name: frsA
Gene(s): frsA   Genome Browser M3D Gene expression COLOMBOS
Note(s): The -35 region of the frsA gene overlaps with the gpt terminator. Here, RNA polymerase could be controlling the positive or negative effect on frsA gene transcription Nuesch J,1984.
Evidence: [COMP-AINF] Inferred computationally without human oversight
[EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Nuesch J., et al., 1984
Promoter
Name: frsAp
+1: 256502
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 25
Sequence: caacgcctggcactgccgggcgttgttctttttaacttcaggcgggttacaatagtttccAgtaagtattctggaggctgc
                       -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): [2] Huerta AM., et al., 2003
[1] Nuesch J., et al., 1984
[3] Salgado H, et al., 2012


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: forward
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -18.8 256442 256475 taatcttttcAACGCCTGGCACTGCCGGGCGTTGTTCTTTTTAacttcaggcg
  anti-terminator -4.14 256426 256456 gccaatctccGGTCGCTAATCTTTTCAACGCCTGGCACTGccgggcgttg
  anti-anti-terminator -17.4 256387 256429 gattgaacagCCGTGGGATATGGGCGTCGTATTCGTCCCGCCAATCTCCGGTcgctaatctt
Notes: "The provided "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appear as the reverse complement of the sequence delimited by LeftPos-RigtPos"


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] Nuesch J., Schumperli D., 1984, Structural and functional organization of the gpt gene region of Escherichia coli., Gene 32(1-2):243-9

 [2] 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

 [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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