RegulonDB RegulonDB 10.8: Operon Form
   

ybgA-phr operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit       
Name: ybgA-phr
Gene(s): ybgA, phr   Genome Browser M3D Gene expression COLOMBOS
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [1] Ma C., et al., 1995
Promoter
Name: ybgAp2
+1: 738920
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 81
Sequence: cagctatggttagaaactacctgacgtcagtccttgcggggagcaggctttcgtaaatttGtcctgctacaacaggattaa
                                  -35             -10       +1                   
Evidence: [TIM]
Reference(s): [2] Lacour S., et al., 2004


Transcription unit       
Name: ybgA-phr
Synonym(s): orf169-phr, ybgA-phrB
Gene(s): ybgA, phr   Genome Browser M3D Gene expression COLOMBOS
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [1] Ma C., et al., 1995
Promoter
Name: ybgAp1
+1: 738980
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 21
Sequence: gtcctgctacaacaggattaacttcacaaatatcatttctcaacgtctacacttactcctGtaaaccgctcaggagcagta
                       -35                 -10              +1                   
Evidence: [CV(RS-EPT-CBR)]
[CV(TIM)]
[RS-EPT-CBR]
[TIM]
Reference(s): [2] Lacour S., et al., 2004
[1] Ma C., et al., 1995
[3] Salgado H, et al., 2012


Transcription unit          
Name: phr
Synonym(s): phrB
Gene(s): phr   Genome Browser M3D Gene expression COLOMBOS
Reference(s): [1] Ma C., et al., 1995
Promoter
Name: phrp
+1: 739421
Distance from start of the gene: 86
Sequence: agttatcgccgtggcgagcaaccacttcttgcgccgctgatgcgtatcaaacactatatgGcgctttatcctgacgcctgg
Note(s):
Evidence: [TIM]
Reference(s): [1] Ma C., et al., 1995
TF binding sites (TFBSs)
[LexA,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal LexA repressor phrp 739345 739364 -66.5 gccagcagctGGCTGCGCTTATCGACAGTTatcgccgtgg nd [APIORCISFBSCS] [4], [5]
proximal LexA repressor phrp 739436 739455 25.5 ttatcctgacGCCTGGCTTTCAGGGCAGCGttatttcgaa nd [APIORCISFBSCS], [CV(GEA)], [GEA] [1]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Translational
Strand: forward
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -7.6 738970 738999 aacgtctacaCTTACTCCTGTAAACCGCTCAGGAGCAGTaatgaatcta
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    

 [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

 [APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [CV(GEA)] cross validation(GEA)

 [GEA] Gene expression analysis


Reference(s)    

 [1] Ma C., Rupert CS., 1995, Promoters of the phr gene in Escherichia coli K-12., Mol Gen Genet 248(1):52-8

 [2] Lacour S., Landini P., 2004, SigmaS-dependent gene expression at the onset of stationary phase in Escherichia coli: function of sigmaS-dependent genes and identification of their promoter sequences., J Bacteriol 186(21):7186-95

 [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.

 [4] Lewis LK., Harlow GR., Gregg-Jolly LA., Mount DW., 1994, Identification of high affinity binding sites for LexA which define new DNA damage-inducible genes in Escherichia coli., J Mol Biol 241(4):507-23

 [5] Payne NS., Sancar A., 1989, The LexA protein does not bind specifically to the two SOS box-like sequences immediately 5' to the phr gene., Mutat Res 218(3):207-10

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