RegulonDB RegulonDB 11.0: Operon Form
   

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




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


Transcription unit       
Name: rne
Gene(s): rne   Genome Browser M3D Gene expression COLOMBOS
Evidence: [AISGDTU] Automated inference that a single-gene directon is a transcription unit
Promoter
Name: rnep4
+1: 1144421
Distance from start of the gene: 54
Sequence: cgataaccgtgaggttggcgacgcgactagacacgaggccatcggttcacacccggaaagGcgttactttgcccgcagctt
Evidence: [HTTIM]
Reference(s): [1] Mendoza-Vargas A., et al., 2009


Transcription unit       
Name: rne
Gene(s): rne   Genome Browser M3D Gene expression COLOMBOS
Evidence: [AISGDTU] Automated inference that a single-gene directon is a transcription unit
[LTED] Length of transcript experimentally determined
Reference(s): [2] Ow MC., et al., 2002
Promoter
Name: rnep1
+1: 1144728
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 361
Sequence: gggtgataaatggtaaaagtcatcttgctataacaaggcttgcagtggaataatgaggccGtttccgtgtccatccttgtt
                         -35                     -10        +1                   
Evidence: [HIPP]
[ICWHO]
[TIM]
Reference(s): [3] Claverie-Martin F., et al., 1991
[4] Huerta AM., et al., 2003
[2] Ow MC., et al., 2002


Transcription unit       
Name: rne
Gene(s): rne   Genome Browser M3D Gene expression COLOMBOS
Evidence: [AISGDTU] Automated inference that a single-gene directon is a transcription unit
[LTED] Length of transcript experimentally determined
Reference(s): [2] Ow MC., et al., 2002
Promoter
Name: rnep2
+1: 1144762
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 395
Sequence: tcaccagcaagaagtgaaaaaactgtgagtaagcgggtgataaatggtaaaagtcatcttGctataacaaggcttgcagtg
                         -35                    -10         +1                   
Evidence: [ICWHO]
[TIM]
Reference(s): [4] Huerta AM., et al., 2003
[2] Ow MC., et al., 2002


Transcription unit       
Name: rne
Gene(s): rne   Genome Browser M3D Gene expression COLOMBOS
Evidence: [AISGDTU] Automated inference that a single-gene directon is a transcription unit
[LTED] Length of transcript experimentally determined
Reference(s): [2] Ow MC., et al., 2002
Promoter
Name: rnep3
+1: 1144873
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 506
Sequence: cgattctaattagccaacaggattcgcgccactcatttttctatgcttatatttacttttGcaccttattacttcactgcg
                       -35                      -10         +1                   
Evidence: [ICWHO]
[TIM]
Reference(s): [4] Huerta AM., et al., 2003
[2] Ow MC., et al., 2002


Evidence    

 [HTTIM] High-throughput transcription initiation mapping

 [HIPP] Human inference of promoter position

 [ICWHO] Inferred computationally without human oversight

 [TIM] Transcription initiation mapping


Reference(s)    

 [1] Mendoza-Vargas A., Olvera L., Olvera M., Grande R., Vega-Alvarado L., Taboada B., Jimenez-Jacinto V., Salgado H., Juarez K., Contreras-Moreira B., Huerta AM., Collado-Vides J., Morett E., 2009, Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli., PLoS One 4(10):e7526

 [2] Ow MC., Liu Q., Mohanty BK., Andrew ME., Maples VF., Kushner SR., 2002, RNase E levels in Escherichia coli are controlled by a complex regulatory system that involves transcription of the rne gene from three promoters., Mol Microbiol 43(1):159-71

 [3] Claverie-Martin F., Diaz-Torres MR., Yancey SD., Kushner SR., 1991, Analysis of the altered mRNA stability (ams) gene from Escherichia coli. Nucleotide sequence, transcriptional analysis, and homology of its product to MRP3, a mitochondrial ribosomal protein from Neurospora crassa., J Biol Chem 266(5):2843-51

 [4] 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

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