RegulonDB RegulonDB 11.2: Operon Form
   

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




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


Transcription unit          
Name: agaR
Gene(s): agaR   Genome Browser M3D Gene expression COLOMBOS
Evidence: [COMP-AINF-SINGLE-DIRECTON] Automated inference that a single-gene directon is a transcription unit
Promoter
Name: agaRp
+1: 3278703
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 38
Sequence: agcttgcgtcaatgggcaaggtgggcttgcatttgcttaatagaaaggcgttaataggcaAaacgaaatgaaacgaaagtt
                                      -35                   +10                  
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] Huerta AM., et al., 2003
[2] Ray WK., et al., 2004
TF binding sites (TFBSs)
[AgaR,-] 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 AgaR repressor agaRp 3278686 3278705 8.5 cgttaataggCAAAACGAAATGAAACGAAAgttttacgaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [2]
proximal AgaR repressor agaRp 3278713 3278732 -19.5 tgggcttgcaTTTGCTTAATAGAAAGGCGTtaataggcaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [2]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [COMP-HINF-POSITIONAL-IDENTIFICATION] Human inference of promoter position

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

 [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-DAP-SEQ] high throughput DNA Affinity Purification (DAP) Sequencing

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


Reference(s)    

 [1] 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

 [2] Ray WK., Larson TJ., 2004, Application of AgaR repressor and dominant repressor variants for verification of a gene cluster involved in N-acetylgalactosamine metabolism in Escherichia coli K-12., Mol Microbiol 51(3):813-26

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