RegulonDB RegulonDB 10.10: Operon Form
   

menA-rraA operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit       
Name: rraA
Gene(s): rraA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
[LTED] Length of transcript experimentally determined
Reference(s): [1] Zhao M., et al., 2006
Promoter
Name: rraAp
+1: 4119358
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 28
Sequence: caaatatcaattaacaattgatgattttgccaacagcccacatagcgcgatatactgaaaAttctcgcagcaactgaatgt
                           -35              -10             +1                   
Evidence: [HTTIM]    
[ICWHO]
[RS-EPT-CBR]
[TIM]
Reference(s): [2] Huerta AM., et al., 2003
[3] Mendoza-Vargas A., et al., 2009
[4] Salgado H, et al., 2012
[1] Zhao M., et al., 2006


Transcription unit       
Name: menA-rraA
Gene(s): rraA, menA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [IC] Inferred by curator
Promoter
Name: menAp1
+1: 4120398
Distance from start of the gene: 49
Sequence: tgcgttggtggcagatgaagatctgagccgttttatcctataatcgcgttcaatcattttCatcattgtttgatggggctg
Evidence: [HTTIM]
Reference(s): [3] Mendoza-Vargas A., et al., 2009


Transcription unit       
Name: menA-rraA
Gene(s): rraA, menA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [1] Zhao M., et al., 2006
Promoter
Name: menAp2
+1: 4120406
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 57
Sequence: catctggatgcgttggtggcagatgaagatctgagccgttttatcctataatcgcgttcaAtcattttcatcattgtttga
                       -35                     -10          +1                   
Evidence: [HIPP]
[ICWHO]
[TIM]
Reference(s): [2] Huerta AM., et al., 2003
[5] Suvarna K., et al., 1998


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: reverse
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -16.6 4120360 4120387 atcattgtttGATGGGGCTGAAAGGCCCCATTTTTATtggcgcgtat
  anti-terminator -8.0 4120377 4120405 tcgcgttcaaTCATTTTCATCATTGTTTGATGGGGCTGaaaggcccca
  anti-anti-terminator -13.2 4120390 4120448 tgcgttggtgGCAGATGAAGATCTGAGCCGTTTTATCCTATAATCGCGTTCAATCATTTTCATCATTGtttgatgggg
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    

 [HTTIM] High-throughput transcription initiation mapping

 [ICWHO] Inferred computationally without human oversight

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

 [TIM] Transcription initiation mapping

 [HIPP] Human inference of promoter position


Reference(s)    

 [1] Zhao M., Zhou L., Kawarasaki Y., Georgiou G., 2006, Regulation of RraA, a protein inhibitor of RNase E-mediated RNA decay., J Bacteriol 188(9):3257-63

 [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] 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

 [4] 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.

 [5] Suvarna K., Stevenson D., Meganathan R., Hudspeth ME., 1998, Menaquinone (vitamin K2) biosynthesis: localization and characterization of the menA gene from Escherichia coli., J Bacteriol 180(10):2782-7

RegulonDB