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| Operon |  |
|---|---|
| Name: | rnlAB |
| This page displays every known transcription unit of this operon and their known regulation. | |
| Name: | rnlAB |
| Synonym(s): | rnlA-yfjO |
| Gene(s): | rnlA, rnlB Genome Browser M3D Gene expression COLOMBOS |
| Note(s): | That the rnlA and rnlB genes are located together in the genome, such that the terminal region of the first gene overlaps the start region of the second one, that there is not a terminator sequence of transcription at the end of rnlA, and that both genes encode a toxin-antitoxin system, suggest that they are transcribed as an operon Koga M,2011 |
| Evidence: | [PAGTSBP] Products of adjacent genes in the same biological process |
| Reference(s): | [1] Koga M., et al., 2011 |
| Promoter | |
| Name: | rnlAp2 |
| +1: | 2765894 |
| Sigma Factor: | Sigma70 Sigmulon |
| Distance from start of the gene: | 24 |
| Sequence: |
caggtggctaaatttagcaaatcaatacacttcaggggggtattattgtagagtttccccAtatgtttctatgggatccag -35 -10 +1 |
| Note(s): | Base on primer extension analysis, four 52'-termini specific to rnlA transcripts were identified 65, 46, 32, and 24 bp upstream of the initiation codon; however, only a strong signal for the last site was detected Otsuka Y,2010 rnlA promoter activity is much weaker than from the rnlB promoter Otsuka Y,2010 |
| Evidence: |
[CV(RS-EPT-CBR)] [CV(TIM)] [RS-EPT-CBR] [TIM] |
| Reference(s): |
[2] Otsuka Y., et al., 2010 [3] Salgado H, et al., 2012 |
| Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
|---|---|---|---|---|---|---|---|---|---|---|
| LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
| proximal | IscR | repressor | rnlAp2 | 2765852 | 2765876 | -29.5 | taaatttagcAAATCAATACACTTCAGGGGGGTATtattgtagag | nd | [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] | [2] |
| Name: | rnlA |
| Gene(s): | rnlA Genome Browser M3D Gene expression COLOMBOS |
| Evidence: | [IEP] Inferred from expression pattern |
| Reference(s): | [4] Nonaka G., et al., 2006 |
| Promoter | |
| Name: | rnlAp |
| +1: | 2765906 |
| Sigma Factor: | Sigma32 Sigmulon |
| Distance from start of the gene: | 12 |
| Sequence: |
tttagcaaatcaatacacttcaggggggtattattgtagagtttccccatatgtttctatGggatccaggaaatgacaatc -35 -10 +1 |
| Evidence: |
[AIPP] [IDA] |
| Reference(s): | [4] Nonaka G., et al., 2006 |
| Name: | rnlB |
| Synonym(s): | yfjO |
| Gene(s): | rnlB Genome Browser M3D Gene expression COLOMBOS |
| Note(s): | Otsuka et al. in 2010 reported that there is a terminator sequence of transcription just downstream of the rnlB gene Otsuka Y,2010 but the sequence was not reported. Therefore, we have not added this terminator to the database. |
| Evidence: | [BTEI] Boundaries of transcription experimentally identified |
| Reference(s): | [5] Rhodius VA., et al., 2005 |
| Promoter | |
| Name: | rnlBp |
| +1: | 2766707 |
| Sigma Factor: | Sigma24 Sigmulon |
| Distance from start of the gene: | 277 |
| Sequence: |
cctgactactgtatgttactttatcctgaactacgcaccattgaaggtgtcttaaaaagtAagatgagtgggttaggcatg -35 -10 +1 |
| Note(s): | This promoter appears to be induced in two phases after σE induction. It is induced in a delayed way during the first 10 minutes following σE induction, decreased from 10 to 15 minutes, and induced from 15 to 20 minutes Lacoux C,2020. |
| Evidence: |
[AIPP] [CV(RS-EPT-CBR)] [CV(TIM)] [RS-EPT-CBR] [TIM] |
| Reference(s): |
[5] Rhodius VA., et al., 2005 [3] Salgado H, et al., 2012 |
| Name: | rnlB |
| Synonym(s): | yfjO |
| Gene(s): | rnlB Genome Browser M3D Gene expression COLOMBOS |
| Note(s): | Otsuka et al. in 2010 reported that there is a terminator sequence of transcription just downstream of the rnlB gene Otsuka Y,2010 but the sequence was not reported. Therefore, we have not added this terminator to the database. |
| Evidence: | [BTEI] Boundaries of transcription experimentally identified |
| Reference(s): | [2] Otsuka Y., et al., 2010 |
| Promoter | |
| Name: | rnlBp2 |
| +1: | 2766860 |
| Sigma Factor: | Sigma70 Sigmulon |
| Distance from start of the gene: | 124 |
| Sequence: |
tttgcagctactcttagaccggaacagattaacatcatcagcacagcctatactttttttAatgtggaacgtcattctctg -35 -10 +1 |
| Note(s): | Two transcriptional start site (TSS) rnlB transcripts were also detected 123 and 124 bp upstream of the initiation codon Otsuka Y,2010 Expression of the rnlB promoter was much higher than from the rnlA promoter, indicating that high rnlB activity is important for cell viability, because RnlA in the absence of RnlB induces cell death Otsuka Y,2010 rnlB can be transcribed from rnlA promoters as polycistronic mRNA (there is not a transcription terminator-like sequence upstream of the rnlB promoter) and from its own promoter as monocistronic mRNA Otsuka Y,2010 |
| Evidence: | [TIM] |
| Reference(s): | [2] Otsuka Y., et al., 2010 |
| Reference(s) |
|
|---|---|
[CV(RS-EPT-CBR)] cross validation(RS-EPT-CBR)