Interspersed Palindromic Repeats and Short Repeats inRickettsia conorii
| Name | Total number | Size (bp)[i] | RNA 2-D structure | G + C | Full length repeat[ii] | Partial repeat[ii] | Distribution in other species | Number in R. prowazekii | |||||||||
| Number | Within gene | Number | Within gene | ||||||||||||||
| Rickettsiapalindromic elements (RPEs) | |||||||||||||||||
| RPE-1 | 52 | 141 (25–150) | hairpin | 42% | 45 | 24[iii] | 7 | 3 | Rickettsiaspp. | 10 | |||||||
| RPE-2 | 7 | 105 (76–105) | hairpin | 43% | 7 | 5 | — | — | — | — | |||||||
| RPE-3 | 12 | 116 (28–122) | hairpin | 40% | 4 | 4 | 8 | 2 | Rickettsiaspp. | 4[v] | |||||||
| RPE-4 | 94 | 95 (20–103) | hairpin | 43% | 19 | 2 | 75 | 11 | Rickettsiaspp. | 15 | |||||||
| RPE-5 | 55 | 115 (22–130) | hairpin | 40% | 26 | 2[iv] | 29 | 3 | Rickettsiaspp. | 11[vi] | |||||||
| RPE-6 | 168 | 136 (20–141) | clover leaf, | 39% | 23 | 1 | 145 | 26 | Rickettsiaspp. | 3 | |||||||
| (RS3-like) | Y-shape | Neisseriaspp. | |||||||||||||||
| RPE-7 | 223 | 99 (20–136) | clover leaf, hairpin | 43% | 36 | 1 | 187 | 26 | Rickettsiaspp. | 14 | |||||||
| RPE-8 | 31 | 149 (30–172) | hairpin | 22% | 15 | — | 16 | — | Rickettsiaspp. | 17 | |||||||
| Rickettsia repeats (RRs) | |||||||||||||||||
| RR-1 | 5 | 27 (19–27) | — | 49% | 5 | 1 | — | — | — | — | |||||||
| RR-2 | 9 | 25 (22–39) | — | 47% | 8 | — | 1 | — | — | — | |||||||
[i] Sizes of the consensus sequences. The lengths for the smallest and the largest copies are shown in parentheses.
[ii] See text for the definition of the “full size” repeat and the “partial” repeats.
[iii] One of the repeats is within the tmRNA gene (ssrA) of R. conorii.
[iv] One of the repeats is within the M1 RNA gene (rnpB) of R. conorii.
[v] Three copies are within the ORFs (RP037, RP012, RP707) ofR. prowazekii.
[vi] One of the repeats is within the tmRNA gene of R. prowazekii.