RegulonDB RegulonDB 10.9: Operon Form
   

dinB-yafNOP operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit          
Name: dinB-yafNOP
Gene(s): dinB, yafN, yafO, yafP   Genome Browser M3D Gene expression COLOMBOS
Evidence: [CV(LTED/PM)] cross validation(LTED/PM)
[LTED] Length of transcript experimentally determined
[PM] Polar mutation
Reference(s): [1] McKenzie GJ., et al., 2003
Promoter
Name: dinBp
+1: 250880
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 18
Sequence: cgcgttaaatgctgaatctttacgcatttctcaaaccctgaaatcactgtatactttaccAgtgttgagaggtgagcaatg
                            -35                   -10       +1                   
Evidence: [AIPP]
[ICWHO]
Reference(s): [2] Huerta AM., 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 LexA repressor dinBp 250864 250883 -6.5 accctgaaatCACTGTATACTTTACCAGTGTtgagaggtga nd [AIBSCS], [APIORCISFBSCS], [ICWHO] [3], [4]


Transcription unit          
Name: dinB-yafNOP
Gene(s): dinB, yafN, yafO, yafP   Genome Browser M3D Gene expression COLOMBOS
Evidence: [CV(LTED/PM)] cross validation(LTED/PM)
[LTED] Length of transcript experimentally determined
[PM] Polar mutation
Reference(s): [1] McKenzie GJ., et al., 2003
Promoter
Name: dinBp2
+1: 250880
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 18
Sequence: cgcgttaaatgctgaatctttacgcatttctcaaaccctgaaatcactgtatactttaccAgtgttgagaggtgagcaatg
                            -35              -10            +1                   
Evidence: [AIPP]
[ICWHO]
Reference(s): [2] Huerta AM., 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 LexA repressor dinBp2 250864 250883 -6.5 accctgaaatCACTGTATACTTTACCAGTGTtgagaggtga nd [AIBSCS], [APIORCISFBSCS], [ICWHO] [3], [4]


Transcription unit          
Name: yafNOP
Gene(s): yafN, yafO, yafP   Genome Browser M3D Gene expression COLOMBOS
Evidence: [ICWHO] Inferred computationally without human oversight
Promoter
Name: yafNp
+1: 251969
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 36
Sequence: ttgcttgacccgcaaatggaaagacaactggtgctgggattatgatgtatactattatgtAtattctggtgtgcattatta
                               -35                   -10    +1                   
Note(s): Zaslaver et al. demonstrated in 2006, by means of a library of fluorescent transcription fusions, that this promoter can be transcribed in vitro Zaslaver A,2006.
There are two transcription start sites (TSSs) for the yafN promoter. Here we associated the TTS more upstream to this promoter. In addition, Christensen-Dalsgaard et al. (2009) showed -10 and -35 boxes which are far from the normal position 19763168 However, the -10 box associated with the yafN promoter also shows an unusual distance Christensen-Dalsgaard M,2010
Evidence: [ICWHO]
[IEP]
[TIM]
Reference(s): [5] Christensen-Dalsgaard M., et al., 2010
[2] Huerta AM., et al., 2003
[6] Zaslaver A., et al., 2006
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 LexA repressor yafNp 251958 251977 -1.5 ttatgatgtaTACTATTATGTATATTCTGGTgtgcattatt nd [APIORCISFBSCS] [5]





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