RegulonDB RegulonDB 10.9: Operon Form
   

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




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


Transcription unit       
Name: idnR
Gene(s): idnR   Genome Browser M3D Gene expression COLOMBOS
Note(s): The idnR gene is the last of the idnDOTR operon. The whole operon is transcribed from a single promoter. However, most of the expression of idnR comes from its own internal promoter, idnRp, which is constitutive.
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [1] Bausch C., et al., 2004
[2] Tsunedomi R., et al., 2003
Promoter
Name: idnRp
+1: 4491182
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 43
Sequence: gctgggcgtgttagccattaacgccgtattgcactgaaagaataaaatattgtgatgtagTttcgggggaagattgaagat
                             -35                   -10      +1                   
Note(s): A possible promoter, TTGCACX16TGTGAT, corresponding to -35 and -10 sequences, exists at position
48 upstream of the initiation codon (Tsunedomi Y, 2003).
Evidence: [AIPP]
Reference(s): [2] Tsunedomi R., et al., 2003


Transcription unit          
Name: idnDOTR
Synonym(s): idnD
Gene(s): idnR, idnT, idnO, idnD   Genome Browser M3D Gene expression COLOMBOS
Note(s): The idnR gene is the last of the idnDOTR operon. The whole operon is transcribed from a single promoter. However, most of the expression of idnR comes from its own internal promoter, idnRp, which is constitutive.
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [1] Bausch C., et al., 2004
Promoter
Name: idnDp
+1: 4494435
Distance from start of the gene: 29
Sequence: caattttctgacgtgatcttcatcacaaataatgacagttaaaaccgcttaaatgcttccGaggtgtctacctgaccagtg
Evidence: [TIM]
Reference(s): [1] Bausch C., et al., 2004
[3] Tsunedomi R., et al., 2003
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CRP-cAMP activator idnDp 4494466 4494488 -41.5 taacaattttCTGACGTGATCTTCATCACAAATaatgacagtt nd [AIBSCS], [APIORCISFBSCS], [GEA] [3], [5]
proximal CRP-cAMP activator idnDp 4494516 4494537 -91.5 ctactgataaGAATTACAAGGCACATCACGTTAtgcgtaacat nd [APIORCISFBSCS], [GEA] [3]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal GntR repressor idnDp 4494484 4494503 -58.5 gcgtaacataGTAATGTAACAATTTTCTGACgtgatcttca nd [APIORCISFBSCS], [GEA] [3]
proximal GntR repressor idnDp 4494504 4494523 -78.5 tacaaggcacATCACGTTATGCGTAACATAGtaatgtaaca nd [AIBSCS], [APIORCISFBSCS], [GEA] [3]
remote GntR repressor idnDp 4494534 4494553 -108.5 tcacgtttttTTATTTCTACTGATAAGAATTacaaggcaca nd [AIBSCS], [APIORCISFBSCS], [GEA] [3]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal IdnR-5-ketogluconate activator idnDp 4494506 4494521 -78.5 caaggcacatCACGTTATGCGTAACATagtaatgtaa nd [AIBSCS], [GEA] [3], [4]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: reverse
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -16.4 4492549 4492572 ccccctacgtGCAGCGCGAAAGCGCTGCTTTTCtggcactaat
  terminator -16.1 4491149 4491185 tattgtgatgTAGTTTCGGGGGAAGATTGAAGATTCCCCCGACGTTgggagaagtt
  anti-terminator -18.2 4492565 4492611 tgtttgttgaTGGCGGCATGTTAGTGGCTGTTTAACAGCCCCCCTACGTGCAGCGCgaaagcgctg
  anti-anti-terminator -19.71 4492588 4492636 tctgatttcgTAAACGGCCACCTGTTGTTTGTTGATGGCGGCATGTTAGTGGCTGTTTaacagccccc
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"





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