RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: rutR
Gene(s): rutR   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Shimada T., et al., 2007
Promoter
Name: rutRp2
+1: 1074113
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 129
Sequence: ccagtttttaaaaagttaatgttattaatctgttaacattacgttatctaaaatatctggTaaaaagtggactaaacggtc
                      -35                        -10        +1                   
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-RNA-POLYMERASE-FOOTPRINTING]
Reference(s): [2] Huerta AM., et al., 2003
[1] Shimada T., et al., 2007
TF binding sites (TFBSs)
[RutR,-] 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 RutR repressor rutRp2 1074120 1074138 16.5 tggtaaaaagTGGACTAAACGGTCAAAACagttgcacat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1], [3]


Transcription unit       
Name: rutR
Synonym(s): ycdC
Gene(s): rutR   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
[EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Shimada T., et al., 2007
Promoter
Name: rutRp1
+1: 1074134
Sigma Factor: Sigma24 Sigmulon
Distance from start of the gene: 108
Sequence: ttattaatctgttaacattacgttatctaaaatatctggtaaaaagtggactaaacggtcAaaacagttgcacataaaaca
                             -35                  -10       +1                   
Evidence: [COMP-AINF]
[COMP-AINF-POSITIONAL-IDENTIFICATION]
[COMP-AINF-SIMILAR-TO-CONSENSUS]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Huerta AM., et al., 2003
[4] Rhodius VA., et al., 2005


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: forward
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -8.8 1074027 1074062 ttcagccgcgTATTGGCTTGTTTGCAAAGCGGATGCCAGTTTTTAaaaagttaat
  anti-terminator -16.02 1073984 1074036 gtaaagtgaaAGTCAGACGGGGCGCTGCATCCTGCATATCCTTTTCAGCCGCGTATTGGCTTgtttgcaaag
  anti-anti-terminator -9.6 1073969 1073998 acctctcttcGTCTCGTAAAGTGAAAGTCAGACGGGGCGctgcatcctg
Notes: "The provided "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appear as the reverse complement of the sequence delimited by LeftPos-RigtPos"


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

 [EXP-IDA-RNA-POLYMERASE-FOOTPRINTING] RNA polymerase footprinting

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

 [COMP-AINF-SIMILAR-TO-CONSENSUS] Automated inference based on similarity to consensus sequences

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

 [EXP-IMP-SITE-MUTATION] Site mutation

 [COMP-AINF-POSITIONAL-IDENTIFICATION] Automated inference of promoter position

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


Reference(s)    

 [1] Shimada T., Hirao K., Kori A., Yamamoto K., Ishihama A., 2007, RutR is the uracil/thymine-sensing master regulator of a set of genes for synthesis and degradation of pyrimidines., Mol Microbiol 66(3):744-57

 [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] Shimada T., Ishihama A., Busby SJ., Grainger DC., 2008, The Escherichia coli RutR transcription factor binds at targets within genes as well as intergenic regions., Nucleic Acids Res 36(12):3950-5

 [4] Rhodius VA., Suh WC., Nonaka G., West J., Gross CA., 2005, Conserved and variable functions of the sigmaE stress response in related genomes., PLoS Biol 4(1):e2

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