RegulonDB RegulonDB 11.1: Operon Form
   

yobF-cspC operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit       
Name: yobF-cspC
Gene(s): cspC, yobF   Genome Browser M3D Gene expression COLOMBOS
Note(s): The mRNA that contains the cspC gene has been observed mainly in the poles of the cell Kannaiah S, Livny J, Amster-Choder O,2019.
Evidence: [COMP-AINF] Inferred computationally without human oversight
Promoter
Name: yobFp2
+1: 1907617
Distance from start of the gene: 26
Sequence:
Note(s): This promoter appears to have more transcriptional sites at positions 1907615/6/7/8, as determined by high-throughput screening of maps of promoters Lacoux C,2020.
Evidence: [EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [1] Hemm MR., et al., 2010
[2] Mendoza-Vargas A., et al., 2009
[3] Salgado H, et al., 2012


Transcription unit          
Name: yobF-cspC
Gene(s): cspC, yobF   Genome Browser M3D Gene expression COLOMBOS
Note(s): The mRNA that contains the cspC gene has been observed mainly in the poles of the cell Kannaiah S, Livny J, Amster-Choder O,2019.
Promoter
Name: yobFp1
+1: 1907793
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 202
Sequence: atgtaataacttctcccactggcctggaacaactgaacttattgaactatgttagaaaatAcgccagtttaagtatctgcc
                             -35                     -10    +1                   
Evidence: [COMP-AINF]
[COMP-HINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] Hemm MR., et al., 2010
[4] Huerta AM., et al., 2003
TF binding sites (TFBSs)
[BtsR,-] 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
remote BtsR-Phosphorylated repressor yobFp1 1907926 1907937 -138.0 gggtaattaaTAGCCGTTAACTgactgtttta nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-PATTERN-DISCOVERY], [EXP-GSELEX] S [5]
remote BtsR-Phosphorylated repressor yobFp1 1907962 1907973 -174.0 aaatttacaaTCCCTTTGGGGAttgacttctc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-PATTERN-DISCOVERY], [EXP-GSELEX] S [5]
remote BtsR-Phosphorylated repressor yobFp1 1907995 1908006 -207.0 tttttttgctCATTCATCAATTtttcttattt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-PATTERN-DISCOVERY], [EXP-GSELEX] S [5]


Evidence    

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

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

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

 [COMP-AINF] Inferred computationally without human oversight

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

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

 [COMP-AINF-PATTERN-DISCOVERY] Automated inference based on sequence pattern discovery

 [EXP-GSELEX] high throughput Genomic SELEX-chip evidence


Reference(s)    

 [1] Hemm MR., Paul BJ., Miranda-Rios J., Zhang A., Soltanzad N., Storz G., 2010, Small stress response proteins in Escherichia coli: proteins missed by classical proteomic studies., J Bacteriol 192(1):46-58

 [2] 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

 [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] 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

 [5] Ogasawara H., Ishizuka T., Yamaji K., Kato Y., Shimada T., Ishihama A., 2019, Regulatory role of pyruvate-sensing BtsSR in biofilm formation by Escherichia coli K-12., FEMS Microbiol Lett 366(24)

 [6] Wright PR., Richter AS., Papenfort K., Mann M., Vogel J., Hess WR., Backofen R., Georg J., 2013, Comparative genomics boosts target prediction for bacterial small RNAs., Proc Natl Acad Sci U S A 110(37):E3487-96

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