RegulonDB RegulonDB 10.8: Operon Form
   

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




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


Transcription unit          
Name: dinI
Gene(s): dinI   Genome Browser M3D Gene expression COLOMBOS
Evidence: [ICWHO] Inferred computationally without human oversight
Promoter
Name: dinIp
+1: 1121509
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 22
Sequence: aaacaataaaaatcgtagcttcctgttgtcattaggttattttacctgtataaataaccaGtatattcaacagggggctat
                                                 -10        +1                   
Evidence: [HTIM]
[IHBCE]
Reference(s): [1] Maciag A., et al., 2011
[2] Yasuda T., et al., 1996
TF binding sites (TFBSs)
[LexA,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal LexA repressor dinIp 1121507 1121526 -7.5 aggttattttACCTGTATAAATAACCAGTAtattcaacag nd [AIBSCS], [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [IHBCE], [SM] [2], [4], [5], [6], [7]
[NagC,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal NagC1 repressor dinIp 1121512 1121534 -14.0 ttgtcattagGTTATTTTACCTGTATAAATAACcagtatattc nd [AIBSCS] [3]
Note(s): 1This binding site was determined from a computational prediction based on different statistical methods Oberto J.,2010 The function of the binding site was assigned according to the distance from the transcription start, with NagC as the transcriptional repressor.1This binding site was determined from a computational prediction based on different statistical methods Oberto J.,2010 The function of the binding site was assigned according to the distance from the transcription start, with NagC as the transcriptional repressor.


Evidence    

 [HTIM] High-throughput transcription initiation mapping

 [IHBCE] Inferred by a human based on computational evidence

 [AIBSCS] Automated inference based on similarity to consensus sequences

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

 [BPP] Binding of purified proteins

 [CV(GEA)] cross validation(GEA)

 [CV(GEA/SM)] cross validation(GEA/SM)

 [CV(SM)] cross validation(SM)

 [GEA] Gene expression analysis

 [SM] Site mutation


Reference(s)    

 [1] Maciag A., Peano C., Pietrelli A., Egli T., De Bellis G., Landini P., 2011, In vitro transcription profiling of the σS subunit of bacterial RNA polymerase: re-definition of the σS regulon and identification of σS-specific promoter sequence elements., Nucleic Acids Res 39(13):5338-55

 [2] Yasuda T., Nagata T., Ohmori H., 1996, Multicopy suppressors of the cold-sensitive phenotype of the pcsA68 (dinD68) mutation in Escherichia coli., J Bacteriol 178(13):3854-9

 [3] Oberto J., 2010, FITBAR: a web tool for the robust prediction of prokaryotic regulons., BMC Bioinformatics 11:554

 [4] Fernandez De Henestrosa AR., Ogi T., Aoyagi S., Chafin D., Hayes JJ., Ohmori H., Woodgate R., 2000, Identification of additional genes belonging to the LexA regulon in Escherichia coli., Mol Microbiol 35(6):1560-72

 [5] Kaleta C., Gohler A., Schuster S., Jahreis K., Guthke R., Nikolajewa S., 2010, Integrative inference of gene-regulatory networks in Escherichia coli using information theoretic concepts and sequence analysis., BMC Syst Biol 4:116

 [6] Lewis LK., Harlow GR., Gregg-Jolly LA., Mount DW., 1994, Identification of high affinity binding sites for LexA which define new DNA damage-inducible genes in Escherichia coli., J Mol Biol 241(4):507-23

 [7] Wade JT., Reppas NB., Church GM., Struhl K., 2005, Genomic analysis of LexA binding reveals the permissive nature of the Escherichia coli genome and identifies unconventional target sites., Genes Dev 19(21):2619-30

RegulonDB