RegulonDB RegulonDB 10.9: Operon Form
   

rapA-rluA operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit       
Name: rapA-rluA
Gene(s): rluA, rapA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [ICWHO] Inferred computationally without human oversight
Promoter
Name: rapAp
+1: 63358
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 94
Sequence: gagttcgccagataccattttgatgcgtgacgaatgctttgccatccagtaccatagcgcCctttccattcctggacctga
                       -35                        -10       +1                   
Evidence: [AIPP]
[HIPP]
[ICWHO]
[TIM]
Reference(s): [1] Cabrera JE., et al., 2001
[2] Huerta AM., et al., 2003
[3] O'Neill MC. 1991


Transcription unit       
Name: hepA
Gene(s): rapA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [IEP] Inferred from expression pattern
Reference(s): [4] Nonaka G., et al., 2006
Promoter
Name: rapAp2
+1: 63588
Sigma Factor: Sigma32 Sigmulon
Distance from start of the gene: 324
Sequence: agaaaaccaaaagcgtggtcgccccttgcaatatcagaatcgcggcaccattaagtacgtAtggaccaccaacggcccgga
                          -35                 -10           +1                   
Evidence: [HIPP]
[ICWHO]
[IDA]
[IEP]
[RS-EPT-CBR]
[TIM]
Reference(s): [2] Huerta AM., et al., 2003
[4] Nonaka G., et al., 2006
[5] Salgado H, et al., 2012
[6] Wade JT., et al., 2006


Transcription unit       
Name: hepA
Gene(s): rapA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [IEP] Inferred from expression pattern
Reference(s): [4] Nonaka G., et al., 2006
Promoter
Name: hepAp2
+1: 63588
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 324
Sequence: agaaaaccaaaagcgtggtcgccccttgcaatatcagaatcgcggcaccattaagtacgtAtggaccaccaacggcccgga
                         -35                  -10           +1                   
Evidence: [HIPP]
[ICWHO]
[IDA]
[IEP]
[RS-EPT-CBR]
[TIM]
Reference(s): [2] Huerta AM., et al., 2003
[4] Nonaka G., et al., 2006
[5] Salgado H, et al., 2012
[6] Wade JT., et al., 2006


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Translational
Strand: reverse
Evidence: [ICA] Inferred by computational analysis
Reference(s): [7] Merino E, et al., 2005
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -7.5 63291 63309 aagcacggtaGCGGGTGGTTATTGCCTGcaattaaaga
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"




Reference(s)    

 [1] Cabrera JE., Jin DJ., 2001, Growth phase and growth rate regulation of the rapA gene, encoding the RNA polymerase-associated protein RapA in Escherichia coli., J Bacteriol 183(20):6126-34

 [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] O'Neill MC., 1991, Training back-propagation neural networks to define and detect DNA-binding sites., Nucleic Acids Res 19(2):313-8

 [4] Nonaka G., Blankschien M., Herman C., Gross CA., Rhodius VA., 2006, Regulon and promoter analysis of the E. coli heat-shock factor, sigma32, reveals a multifaceted cellular response to heat stress., Genes Dev 20(13):1776-89

 [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.

 [6] Wade JT., Roa DC., Grainger DC., Hurd D., Busby SJ., Struhl K., Nudler E., 2006, Extensive functional overlap between sigma factors in Escherichia coli., Nat Struct Mol Biol 13(9):806-14

 [7] Merino E, Yanofsky C., 2005, Transcription attenuation: a highly conserved regulatory strategy used by bacteria., Trends Genet. 2005 May;21(5):260-4.


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