RegulonDB RegulonDB 11.2: Operon Form
   

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




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


Transcription unit          
Name: ribA
Gene(s): ribA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Koh YS., et al., 1996
[2] Richter G., et al., 1993
Promoter
Name: ribAp1
+1: 1339190
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 30
Sequence: cgtgaacgatcgacgcgtcgtgattaggtgaaccccttctcgttatggcaaaataagccaAtacagaaccagcattatctg
                             -35                      -10   +1                   
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [3] Huerta AM., et al., 2003
[1] Koh YS., et al., 1996
[4] Salgado H, et al., 2012
Terminator(s)
Type: rho-independent
Sequence: agtaacaactATTTGCTTGCCGGTTATTTTGCTTCCGGCAAGCAAATgaattacaca
Reference(s): [2] Richter G., et al., 1993
TF binding sites (TFBSs)
[SoxS,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal SoxS activator ribAp1 1339249 1339268 -69.0 aggaaaaattGACAGATTTGTGCCATTCCGtgaacgatcg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-RNA-SEQ], [COMP-HINF], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO-MANUAL], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [1], [5], [6], [7]


Transcription unit       
Name: ribA
Gene(s): ribA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Koh YS., et al., 1996
[2] Richter G., et al., 1993
Promoter
Name: ribAp2
+1: 1339234
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 74
Sequence: tgaaaacgccagttccaggaaaaattgacagatttgtgccattccgtgaacgatcgacgcGtcgtgattaggtgaacccct
                              -35                     -10   +1                   
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [3] Huerta AM., et al., 2003
[1] Koh YS., et al., 1996
Terminator(s)
Type: rho-independent
Sequence: agtaacaactATTTGCTTGCCGGTTATTTTGCTTCCGGCAAGCAAATgaattacaca
Reference(s): [2] Richter G., et al., 1993


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [COMP-HINF-POSITIONAL-IDENTIFICATION] Human inference of promoter position

 [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] Transcription initiation mapping

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

 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis

 [EXP-IEP-RNA-SEQ] high throughput RNA-seq evidence

 [COMP-HINF] Inferred by a human based on computational evidence

 [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [EXP-CHIP-EXO-MANUAL] ChIP-exo evidence used in manual assertion

 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins


Reference(s)    

 [1] Koh YS., Choih J., Lee JH., Roe JH., 1996, Regulation of the ribA gene encoding GTP cyclohydrolase II by the soxRS locus in Escherichia coli., Mol Gen Genet 251(5):591-8

 [2] Richter G., Ritz H., Katzenmeier G., Volk R., Kohnle A., Lottspeich F., Allendorf D., Bacher A., 1993, Biosynthesis of riboflavin: cloning, sequencing, mapping, and expression of the gene coding for GTP cyclohydrolase II in Escherichia coli., J Bacteriol 175(13):4045-51

 [3] 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

 [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] Koh YS., Chung WH., Lee JH., Roe JH., 1999, The reversed SoxS-binding site upstream of the ribA promoter in Escherichia coli., Mol Gen Genet 261(2):374-80

 [6] Martin RG., Gillette WK., Rhee S., Rosner JL., 1999, Structural requirements for marbox function in transcriptional activation of mar/sox/rob regulon promoters in Escherichia coli: sequence, orientation and spatial relationship to the core promoter., Mol Microbiol 34(3):431-41

 [7] Seo SW., Kim D., Szubin R., Palsson BO., 2015, Genome-wide Reconstruction of OxyR and SoxRS Transcriptional Regulatory Networks under Oxidative Stress in Escherichia coli K-12 MG1655., Cell Rep 12(8):1289-99

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