RegulonDB RegulonDB 10.8: Operon Form
   

pyrG-eno operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit       
Name: eno
Gene(s): eno   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Shimada T., et al., 2005
Promoter
Name: enop4
+1: 2907968
Sigma Factor: Sigma70, Sigma38
Distance from start of the gene: 27
Sequence: gtaaaaaagttagagcggcaacgcgtaccctgggtacgcgttgtttgtctggagtttcagTttaactagtgacttgaggaa
                                                 -10        +1                   
Evidence: [CV(RS-EPT-CBR)]
[HTIM]
[RS-EPT-CBR]
Reference(s): [2] Olvera L., et al., 2009
[3] Salgado H, et al., 2012


Transcription unit       
Name: eno
Gene(s): eno   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
[IC] Inferred by curator
Reference(s): [1] Shimada T., et al., 2005
Promoter
Name: enop6
+1: 2908018
Distance from start of the gene: 77
Sequence: caggctttgtgaaagccgccagcgagttccagaaacgtcaggcgaagtaagtaaaaaagtTagagcggcaacgcgtaccct
Evidence: [HTIM]
Reference(s): [4] Mendoza-Vargas A., et al., 2009
[2] Olvera L., et al., 2009


Transcription unit       
Name: eno
Gene(s): eno   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Shimada T., et al., 2005
Promoter
Name: enop7
+1: 2908152
Sigma Factor: Sigma70, Sigma38
Distance from start of the gene: 211
Sequence: tctgcgcgttgcgggccgttccggggatgatcagttggtcgagatcatcgaagttccgaaTcacccgtggttcgtggcttg
                                               -10          +1                   
Evidence: [HTIM]
Reference(s): [2] Olvera L., et al., 2009


Transcription unit          
Name: eno
Gene(s): eno   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Shimada T., et al., 2005
Promoter
Name: enop1
+1: 2908674
Distance from start of the gene: 733
Sequence: actgaaacacggtgggctgaagaatcgtgtcagcgtcaacatcaaactgatcgattcacaAgatgttgaaacgcgcggcgt
Evidence: [TIM]
Reference(s): [1] Shimada T., et al., 2005
TF binding sites (TFBSs)
[Cra,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Cra repressor enop1 2908674 2908691 -8.5 cgtcaacatcAAACTGATCGATTCACAAgatgttgaaa nd [BPP], [GEA] [1]
remote Cra repressor enop1 2908871 2908888 -205.5 gacgattataTTTGTAAACGATTCAGCTtaaactgccc nd [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [1]


Transcription unit          
Name: eno
Gene(s): eno   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Shimada T., et al., 2005
Promoter
Name: enop2
+1: 2908702
Distance from start of the gene: 761
Sequence: cggatgcttataaatcagtgatcgaagcactgaaacacggtgggctgaagaatcgtgtcaGcgtcaacatcaaactgatcg
Evidence: [TIM]
Reference(s): [1] Shimada T., et al., 2005
TF binding sites (TFBSs)
[Cra,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Cra repressor enop2 2908674 2908691 20.5 cgtcaacatcAAACTGATCGATTCACAAgatgttgaaa nd [BPP], [GEA] [1]
remote Cra repressor enop2 2908871 2908888 -177.5 gacgattataTTTGTAAACGATTCAGCTtaaactgccc nd [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [1]


Transcription unit          
Name: eno
Gene(s): eno   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Shimada T., et al., 2005
Promoter
Name: enop3
+1: 2908846
Distance from start of the gene: 905
Sequence: aggggctggacgattatatttgtaaacgattcagcttaaactgcccggaagcgaatctgtCcgaatgggaacaggttatct
Evidence: [TIM]
Reference(s): [1] Shimada T., et al., 2005
TF binding sites (TFBSs)
[Cra,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote Cra repressor enop3 2908674 2908691 164.5 cgtcaacatcAAACTGATCGATTCACAAgatgttgaaa nd [BPP], [GEA] [1]
proximal Cra repressor enop3 2908871 2908888 -33.5 gacgattataTTTGTAAACGATTCAGCTtaaactgccc nd [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [1]


Transcription unit       
Name: pyrG-eno
Gene(s): eno, pyrG   Genome Browser M3D Gene expression COLOMBOS
Evidence: [ICWHO] Inferred computationally without human oversight
Promoter
Name: pyrGp
+1: 2909713
Distance from start of the gene: 47
Sequence: cgaagaggagggataatgaaagtttgtggcacaggtcatgttcgggtatactgctttcccGtcttggttattccatcgtct
Evidence: [HTIM]
Reference(s): [4] Mendoza-Vargas A., et al., 2009


Transcription unit       
Name: pyrG-eno
Gene(s): eno, pyrG   Genome Browser M3D Gene expression COLOMBOS
Evidence: [ICWHO] Inferred computationally without human oversight
Promoter
Name: pyrGp2
+1: 2909717
Distance from start of the gene: 51
Sequence: ctggcgaagaggagggataatgaaagtttgtggcacaggtcatgttcgggtatactgcttTcccgtcttggttattccatc
Evidence: [TIM]
Reference(s): [5] Weng M., et al., 1986


Transcription unit       
Name: pyrG-eno
Gene(s): eno, pyrG   Genome Browser M3D Gene expression COLOMBOS
Evidence: [ICWHO] Inferred computationally without human oversight
Promoter
Name: pyrGp1
+1: 2909797
Distance from start of the gene: 131
Sequence: ttaaatgacaagcgcttgatttgcgtcaaaaacatttaccccaaaggggctattttctcaCtcctgatttcaatagtgcgc
Evidence: [TIM]
Reference(s): [5] Weng M., et al., 1986


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: reverse
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -11.5 2907983 2908007 agagcggcaaCGCGTACCCTGGGTACGCGTTGTTtgtctggagt
  anti-terminator -8.99 2907996 2908041 tccagaaacgTCAGGCGAAGTAAGTAAAAAAGTTAGAGCGGCAACGCGTACCCTGggtacgcgtt
  anti-anti-terminator -8.2 2908010 2908064 ctttgtgaaaGCCGCCAGCGAGTTCCAGAAACGTCAGGCGAAGTAAGTAAAAAAGTTAGAGCGGcaacgcgtac
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    

 [CV(RS-EPT-CBR)] cross validation(RS-EPT-CBR)

 [HTIM] High-throughput transcription initiation mapping

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

 [TIM] Transcription initiation mapping

 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis

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

 [CV(GEA)] cross validation(GEA)


Reference(s)    

 [1] Shimada T., Fujita N., Maeda M., Ishihama A., 2005, Systematic search for the Cra-binding promoters using genomic SELEX system., Genes Cells 10(9):907-18

 [2] Olvera L., Mendoza-Vargas A., Flores N., Olvera M., Sigala JC., Gosset G., Morett E., Bolivar F., 2009, Transcription analysis of central metabolism genes in Escherichia coli. Possible roles of sigma38 in their expression, as a response to carbon limitation., PLoS One 4(10):e7466

 [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] 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

 [5] Weng M., Makaroff CA., Zalkin H., 1986, Nucleotide sequence of Escherichia coli pyrG encoding CTP synthetase., J Biol Chem 261(12):5568-74

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