RegulonDB RegulonDB 11.1: Operon Form
   

ubiT-yhbS operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit          
Name: ubiT-yhbS
Gene(s): yhbS, ubiT   Genome Browser M3D Gene expression COLOMBOS
Evidence: [COMP-AINF] Inferred computationally without human oversight
Promoter
Name: ubiTp2
+1: 3301301
Distance from start of the gene: 25
Sequence: tcatatggaattgttgatttataccgctatgttatttttctgatatggcaaaataggatgAttgttgaaacagggagtaaa
Evidence: [EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP]
[RS-EPT-CBR]
Reference(s): [1] Mendoza-Vargas A., et al., 2009
[2] Salgado H, et al., 2012
TF binding sites (TFBSs)
[CsgD,-] 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 CsgD repressor ubiTp2 3301280 3301294 15.5 atgattgttgAAACAGGGAGTAAAActcgtgttgg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [3]
proximal CsgD repressor ubiTp2 3301307 3301321 -12.5 gttatttttcTGATATGGCAAAATAggatgattgt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [3]


Transcription unit       
Name: ubiT-yhbS
Gene(s): yhbS, ubiT   Genome Browser M3D Gene expression COLOMBOS
Evidence: [COMP-AINF] Inferred computationally without human oversight
Promoter
Name: ubiTp1
+1: 3301368
Distance from start of the gene: 92
Sequence: tagttaaccttgctgcgacaatttttgatttaaggcagttaaagttgtattggtggtagcAgcaatttcatatggaattgt
Evidence: [EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP]
Reference(s): [1] Mendoza-Vargas A., et al., 2009


Evidence    

 [EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP] High-throughput 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

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

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


Reference(s)    

 [1] 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

 [2] 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.

 [3] Ogasawara H., Yamamoto K., Ishihama A., 2011, Role of the biofilm master regulator CsgD in cross-regulation between biofilm formation and flagellar synthesis., J Bacteriol 193(10):2587-97

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