RegulonDB RegulonDB 11.0: Operon Form
   

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




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


Transcription unit          
Name: nfsB
Synonym(s): nfnB
Gene(s): nfsB   Genome Browser M3D Gene expression COLOMBOS
Evidence: [ICWHO] Inferred computationally without human oversight
Promoter
Name: nfsBp
+1: 605453
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 29
Sequence: gaaatctatagcgcatttttctcgcttaccatttctcgttgaaccttgtaatctgctggcAcgcaaaattactttcacatg
                          -35                    -10        +1                   
Evidence: [HIPP]
[ICWHO]
[RS-EPT-CBR]
Reference(s): [1] Barbosa TM., et al., 2002
[2] Huerta AM., et al., 2003
[3] Salgado H, et al., 2012
TF binding sites (TFBSs)
[MarA,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal MarA activator nfsBp 605487 605507 -43.5 gcggaaatctATAGCGCATTTTTCTCGCTTaccatttctc nd [GEA], [APIORCISFBSCS], [BPP] [1], [4]
[Rob,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Rob activator nfsBp 605487 605507 -43.5 gcggaaatctATAGCGCATTTTTCTCGCTTaccatttctc nd [GEA], [APIORCISFBSCS], [BPP] [4]
[SoxS,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal SoxS activator nfsBp 605487 605507 -43.5 gcggaaatctATAGCGCATTTTTCTCGCTTaccatttctc nd [GEA], [APIORCISFBSCS], [BPP] [4], [5]


Evidence    

 [HIPP] Human inference of promoter position

 [ICWHO] Inferred computationally without human oversight

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

 [GEA] Gene expression analysis

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

 [BPP] Binding of purified proteins


Reference(s)    

 [1] Barbosa TM., Levy SB., 2002, Activation of the Escherichia coli nfnB gene by MarA through a highly divergent marbox in a class II promoter., Mol Microbiol 45(1):191-202

 [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.

 [4] Martin RG., Rosner JL., 2002, Genomics of the marA/soxS/rob regulon of Escherichia coli: identification of directly activated promoters by application of molecular genetics and informatics to microarray data., Mol Microbiol 44(6):1611-24

 [5] Martin RG., Rosner JL., 2011, Promoter discrimination at class I MarA regulon promoters mediated by glutamic acid 89 of the MarA transcriptional activator of Escherichia coli., J Bacteriol 193(2):506-15

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