RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit       
Name: yafDE
Gene(s): yafD, yafE   Genome Browser M3D Gene expression COLOMBOS
Note(s): By using ChIP-Seq analysis, it was observed that the protein PdeL binds in the intergenic region of yafC and yafD Sellner B,2021.
Evidence: [COMP-AINF] Inferred computationally without human oversight
[EXP-IEP-COREGULATION] Inferred through co-regulation
Reference(s): [1] Nonaka G., et al., 2006
Promoter
Name: yafDp
+1: 231064
Sigma Factor: Sigma32 Sigmulon
Distance from start of the gene: 58
Sequence: gcacttgcttacataacaatatacaattgctcgttgaaagagtgagctaaaatccctataAcagtagaaccctcccgagtg
                                  -35                 -10   +1                   
Evidence: [COMP-AINF]
[COMP-AINF-POSITIONAL-IDENTIFICATION]
[COMP-AINF-SIMILAR-TO-CONSENSUS]
[EXP-IDA]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IEP]
Reference(s): [2] Huerta AM., et al., 2003
[1] Nonaka G., et al., 2006
[3] Wade JT., et al., 2006


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

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

 [EXP-IDA] Inferred from direct assay

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

 [EXP-IEP] Inferred from expression pattern


Reference(s)    

 [1] Nonaka G., Blankschien M., Herman C., Gross CA., Rhodius VA., 2006, Regulon and promoter analysis of the E. coli heat-shock factor, sigma32, reveals a multifaceted cellular response to heat stress., Genes Dev 20(13):1776-89

 [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] Wade JT., Roa DC., Grainger DC., Hurd D., Busby SJ., Struhl K., Nudler E., 2006, Extensive functional overlap between sigma factors in Escherichia coli., Nat Struct Mol Biol 13(9):806-14

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