RegulonDB RegulonDB 10.9: Operon Form
   

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




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


Transcription unit          
Name: sohB
Gene(s): sohB   Genome Browser M3D Gene expression COLOMBOS
Reference(s): [1] Talukder AA., et al., 1996
Promoter
Name: sohBp
+1: 1329284
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 48
Sequence: aaatggatactttgtcatactttcgctgcaataacatctctgcgagacggcttaacatgcCtgttgtaaactgtgagccaa
                      -35              -10                  +1                   
Note(s): We assigned a putative transcription start site to this promoter based on the observation that the majority of the promoters, whose transcription start sites were determined experimentally, present a distance of 6 nucleotides between the transcription start site and the -10 box.
Evidence: [HIPP]
[ICWHO]
Reference(s): [2] Huerta AM., et al., 2003
[1] Talukder AA., et al., 1996
TF binding sites (TFBSs)
[CRP,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CRP-cAMP repressor sohBp 1329292 1329313 19.5 gcctgttgtaAACTGTGAGCCAAAGCGTTGTTTaaccaaggtg nd [AIBSCS] nd


Transcription unit          
Name: sohB
Gene(s): sohB   Genome Browser M3D Gene expression COLOMBOS
Reference(s): [1] Talukder AA., et al., 1996
Promoter
Name: sohBp1
+1: 1329284
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 48
Sequence: aaatggatactttgtcatactttcgctgcaataacatctctgcgagacggcttaacatgcCtgttgtaaactgtgagccaa
                               -35                   -10    +1                   
Note(s): We assigned a putative transcription start site to this promoter based on the observation that the majority of the promoters, whose transcription start sites were determined experimentally, present a distance of 6 nucleotides between the transcription start site and the -10 box.
Evidence: [HIPP]
[ICWHO]
Reference(s): [2] Huerta AM., et al., 2003
[1] Talukder AA., et al., 1996
TF binding sites (TFBSs)
[CRP,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CRP-cAMP repressor sohBp1 1329292 1329313 19.5 gcctgttgtaAACTGTGAGCCAAAGCGTTGTTTaaccaaggtg nd [AIBSCS] nd


Transcription unit          
Name: sohB
Gene(s): sohB   Genome Browser M3D Gene expression COLOMBOS
Reference(s): [1] Talukder AA., et al., 1996
Promoter
Name: sohBp2
+1: 1329301
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 31
Sequence: tactttcgctgcaataacatctctgcgagacggcttaacatgcctgttgtaaactgtgagCcaaagcgttgtttaaccaag
                       -35                        -10       +1                   
Note(s): We assigned a putative transcription start site to this promoter based on the observation that the majority of the promoters, whose transcription start sites were determined experimentally, present a distance of 6 nucleotides between the transcription start site and the -10 box.
Evidence: [HIPP]
[ICWHO]
[RS-EPT-CBR]
Reference(s): [2] Huerta AM., et al., 2003
[3] Salgado H, et al., 2012
[1] Talukder AA., et al., 1996
TF binding sites (TFBSs)
[CRP,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CRP-cAMP repressor sohBp2 1329291 1329312 2.0 tgcctgttgtAAACTGTGAGCCAAAGCGTTGTTtaaccaaggt nd [AIBSCS] nd


Evidence    

 [HIPP] Human inference of promoter position

 [ICWHO] Inferred computationally without human oversight

 [AIBSCS] Automated inference based on similarity to consensus sequences

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


Reference(s)    

 [1] Talukder AA., Yanai S., Nitta T., Kato A., Yamada M., 1996, RpoS-dependent regulation of genes expressed at late stationary phase in Escherichia coli., FEBS Lett 386(2-3):177-80

 [2] 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

 [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.

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