RegulonDB RegulonDB 11.2: Operon Form
   

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




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


Transcription unit          
Name: caiF
Gene(s): caiF   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Eichler K., et al., 1996
Promoter
Name: caiFp
+1: 34218
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 82
Sequence: gatgacataagcaggatttagctcacacttatcgacggtgaagttgcatactatcgatatAtccacaattttaatatggcc
                      -35                        -10        +1                   
Evidence: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [1] Eichler K., et al., 1996
[2] Huerta AM., et al., 2003
[3] Salgado H, et al., 2012
TF binding sites (TFBSs)
[CRP,+] 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 CRP-cyclic-AMP activator caiFp 34166 34187 -41.5 ttgatgacatAAGCAGGATTTAGCTCACACTTatcgacggtg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] W [1]
[FNR,+] 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 FNR activator caiFp 34156 34169 -55.5 atcgatatttTTGATGACATAAGCaggatttagc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] S [1]
[H-NS,-] 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
nd H-NS repressor caiFp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [1]
[NarL,-] 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
nd NarL-phosphorylated repressor caiFp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [1]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

 [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-IDA-BINDING-OF-CELLULAR-EXTRACTS] Binding of cellular extracts

 [EXP-CHIP-SEQ] high throughput ChIP-seq evidence


Reference(s)    

 [1] Eichler K., Buchet A., Lemke R., Kleber HP., Mandrand-Berthelot MA., 1996, Identification and characterization of the caiF gene encoding a potential transcriptional activator of carnitine metabolism in Escherichia coli., J Bacteriol 178(5):1248-57

 [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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