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|
| Operon |  |
|---|---|
| Name: | rplKAJL-rpoBC |
| This page displays every known transcription unit of this operon and their known regulation. | |
| Name: | rplKAJL-rpoBC |
| Gene(s): | rplK, rplA, rplJ, rplL, rpoB, rpoC Genome Browser M3D Gene expression COLOMBOS |
| Note(s): | There has been identified an attenuator that stops 70% of the transcription starts. It is located between the rplL and rpoB genes Post LE,1979. Ralling G,1984. A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for rpoB. This structure could regulate the expression of the gene, as observed for hemL gene expression Shao X, Zhang W, Umar MI, Wong HY, Seng Z, Xie Y, Zhang Y, Yang L, Kwok CK, Deng X,2020. |
| Evidence: | [PM] Polar mutation |
| Reference(s): | [1] Steward KL., et al., 1991 |
| Promoter | |
| Name: | rplKp |
| +1: | 4178354 |
| Distance from start of the gene: | 93 |
| Sequence: |
cgatcaaaaaagcggcgatttaatcgttgcacaaggcgtgagattggaatacaatttcgcGccttttgtttttatgggcct |
| Note(s): | Promoters rplJp and rplKp were identified in in vitro experiments that assigned possible start sites Post LE,1979. They appear to be the major promoters within the rplKLJL-rpoBC operon, although rplKp is 35% stronger than rplJp Ralling G,1984. |
| Evidence: |
[HIPP] [IMP] [TIM] |
| Reference(s): |
[2] Post LE., et al., 1979 [3] Yamamoto M., et al., 1979 |
| Terminator(s) | |
| Type: | rho-independent |
| Sequence: | taacgtaaaaACCCGCTTCGGCGGGtttttttatg |
| Reference(s): | [4] Squires C., et al., 1981 |
| Evidence: |
[APPH] Assay of protein purified to homogeneity [GEA] Gene expression analysis [IMP] Inferred from mutant phenotype |
| Reference(s): | [5] Lemke JJ., et al., 2011 |
| Name: | rplJL-rpoBC |
| Gene(s): | rplJ, rplL, rpoB, rpoC Genome Browser M3D Gene expression COLOMBOS |
| Note(s): | There has been identified an attenuator that stops 70% of the transcription starts. It is located between the rplL and rpoB genes Post LE,1979. Ralling G,1984. A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for rpoB. This structure could regulate the expression of the gene, as observed for hemL gene expression Shao X, Zhang W, Umar MI, Wong HY, Seng Z, Xie Y, Zhang Y, Yang L, Kwok CK, Deng X,2020. |
| Evidence: | [PM] Polar mutation |
| Reference(s): |
[6] Barry G., et al., 1980 [7] Hui I., et al., 1982 |
| Promoter | |
| Name: | rplJp |
| +1: | 4179623 |
| Distance from start of the gene: | 373 |
| Sequence: |
ctgagcgcttctgtaaactaatgcctttacgtgggcggtgattttgtctacaatcttaccCccacgtataatgcttaatgc |
| Note(s): | Promoters rplJp and rplKp were identified using in vitro experiments that assign possible start sites Post LE,1979. They appear to be the major promoters within the rplKLJL-rpoBC operon, although rplKp is 35 % stronger than rplJp Ralling G,1984. |
| Evidence: |
[HIPP] [IMP] [TIM] |
| Reference(s): | [2] Post LE., et al., 1979 |
| Terminator(s) | |
| Type: | rho-independent |
| Sequence: | taacgtaaaaACCCGCTTCGGCGGGtttttttatg |
| Reference(s): | [4] Squires C., et al., 1981 |
| Evidence: |
[APPH] Assay of protein purified to homogeneity [GEA] Gene expression analysis [IMP] Inferred from mutant phenotype |
| Reference(s): | [5] Lemke JJ., et al., 2011 |
| Name: | rpoBC |
| Gene(s): | rpoB, rpoC Genome Browser M3D Gene expression COLOMBOS |
| Note(s): | A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for rpoB. This structure could regulate the expression of the gene, as observed for hemL gene expression Shao X, Zhang W, Umar MI, Wong HY, Seng Z, Xie Y, Zhang Y, Yang L, Kwok CK, Deng X,2020. |
| Evidence: | [LTED] Length of transcript experimentally determined |
| Reference(s): |
[6] Barry G., et al., 1980 [8] Fukuda R., et al., 1983 |
| Promoter | |
| Name: | rpoBp |
| +1: | 4181063 |
| Distance from start of the gene: | 182 |
| Sequence: |
aaggcgccagtagcgtttcacactgtttgactactgctgtgcctttcaatgcttgtttctAtcgacgacttaatatactgc |
| Note(s): | The rpoBp promoter is very weak; as a matter of fact, Ralling and Linn Ralling G,1984did not find evidence for it. Therefore, it can be concluded that even if it does exist, it might not be very efficient. |
| Evidence: |
[NTAS] [TIM] |
| Reference(s): |
[9] Bass IA., et al., null [8] Fukuda R., et al., 1983 |
| Terminator(s) | |
| Type: | rho-independent |
| Sequence: | taacgtaaaaACCCGCTTCGGCGGGtttttttatg |
| Reference(s): | [4] Squires C., et al., 1981 |
| Name: | rplL |
| Gene(s): | rplL Genome Browser M3D Gene expression COLOMBOS |
| Note(s): | Due to the attenuator identified between the rplL and rpoB genes, and its weak promoter, rplLp, the transcription rate of this transciption unit (rpoBC) is very low Ralling G,1984. |
| Evidence: | [BTEI] Boundaries of transcription experimentally identified |
| Reference(s): | [10] Ralling G., et al., 1984 |
| Promoter | |
| Name: | rplLp |
| +1: | Unknown |
| Note(s): | rplLp is a weak promoter; it is only 8% as effective as the rplJp promoter Ralling G,1984 |
| Evidence: |
[IEP] [IMP] |
| Reference(s): |
[10] Ralling G., et al., 1984 [11] Zaslaver A., et al., 2006 |
| RNA cis-regulatory element | |
|---|
| Regulation, transcriptional elongation | |
| Attenuator type: | Transcriptional |
| Strand: | forward |
| Structure type | Energy | LeftPos | RightPos | Sequence (RNA-strand) | |
|---|---|---|---|---|---|
| terminator | -21.6 | 4178323 | 4178368 | taatcgttgcACAAGGCGTGAGATTGGAATACAATTTCGCGCCTTTTGTTTTTATgggccttgcc | |
| terminator | -6.2 | 4180484 | 4180510 | tgcgaaagaaGCTGCTTAATCGCAGTTATCTTTTTAacgcattcgc | |
| terminator | -12.4 | 4185317 | 4185351 | aacccggcagCGGATTGTGCTAACTCCGACGGGAGCAAATCCGTgaaagattta | |
| anti-terminator | -8.13 | 4178294 | 4178339 | ctaacccagcGATCAAAAAAGCGGCGATTTAATCGTTGCACAAGGCGTGAGATTGgaatacaatt | |
| anti-terminator | -7.3 | 4180460 | 4180490 | tcgtactctgGCTGCTGTACGCGATGCGAAAGAAGCTGCTtaatcgcagt | |
| anti-anti-terminator | -18.6 | 4178238 | 4178313 | tctatcttcgGTCGTGCGACCCCGGTAGAGCTGGACTTCAGCCAGGTTGAAAAAGCCTAACCCAGCGATCAAAAAAGCGGCGATTtaatcgttgc | |
| anti-anti-terminator | -3.6 | 4180452 | 4180471 | aaactggttcGTACTCTGGCTGCTGTACGcgatgcgaaa |
| Notes: "The provided "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appear as the reverse complement of the sequence delimited by LeftPos-RigtPos" |
| Reference(s) |
|
|---|---|
[HIPP] Human inference of promoter position