Table 2.
All annotated small RNA features. Coordinates shown in boldface represent small RNA features not previously reported in S. pneumoniae
| D39V coordinates | Locus | Old locus | Gene name | Product | Note | Literaturec |
|---|---|---|---|---|---|---|
| 23967-24065 (+) | SPV_2078 | ccnC | Small regulatory RNA csRNA3 | (53,54,56) | ||
| 24632-24707 (+) | SPV_0026 | SPD_0026 | scRNA | scRNA | RNA component of signal recognition particle | (112) |
| 29658-29873 (+) | SPV_2081 | srf-01 | ncRNA of unknown function | |||
| 39980-40186 (+) | SPV_2084 | srf-02 | ncRNA of unknown function | (53,55) | ||
| 41719-41886 (+) | SPV_2086 | srf-03 | ncRNA of unknown function | Contains BOX element | (18,114) | |
| 132229-132308 (+) | SPV_2107 | srf-04 | ncRNA of unknown function | (52,57) | ||
| 149645-149877 (+)b | SPV_2119 | srf-05 | ncRNA of unknown function | (52,57) | ||
| 150711-150914 (-) | SPV_2120 | srf-06 | ncRNA of unknown function | Antisense to mutR1 (SPV_0144) | ||
| 212734-212881 (+) | SPV_2125 | ccnE | Small regulatory RNA csRNA5 | Involved in stationary phase autolysis | (53,54,55,56) | |
| 231599-231691 (+) | SPV_2129 | ccnA | Small regulatory RNA csRNA1 | (52,53,55,56,57) | ||
| 231786-231883 (+) | SPV_2130 | ccnB | Small regulatory RNA csRNA2 | (53,56) | ||
| 232279-232354 (+)b | SPV_2131 | srf-07 | Type I addiction module antitoxin, Fst family | (55,58) | ||
| 234171-234264 (+) | SPV_2133 | ccnD | Small regulatory RNA csRNA4 | Involved in stationary phase autolysis | (53,56) | |
| 282194-282479 (+) | SPV_2139 | srf-08 | ncRNA of unknown function | (54,55) | ||
| 344607-345007 (+) | SPV_0340 | SPD_0340 | rnpB | Ribonuclease P RNA component | (115) | |
| 508697-508842 (+) | SPV_2185 | srf-10 | ncRNA of unknown function | (55) | ||
| 587896-587989 (+) | SPV_2200 | srf-11 | ncRNA of unknown function | (53,54,55) | ||
| 742022-742141 (-)a | SPV_2226 | srf-12 | ncRNA of unknown function | Implicated in competence | (54) | |
| 781595-781939 (+) | SPV_0769 | SPD_0769 | ssrA | tmRNA | (53,54,55,112) | |
| 826260-826587 (+) | SPV_2247 | srf-13 | ncRNA of unknown function | (53,54,55) | ||
| 1037649-1037755 (-) | SPV_2291 | srf-16 | ncRNA of unknown function | (55) | ||
| 1051910-1052049 (-) | SPV_2292 | srf-17 | asd RNA motif | (52,54,55,57,116) | ||
| 1079561-1079658 (-) | SPV_2300 | srf-18 | ncRNA of unknown function | Similar to S. aureus RsaK | (113) | |
| 1170746-1170923 (+)b | SPV_2317 | srf-19 | ncRNA of unknown function | (55) | ||
| 1528520-1528643 (-) | SPV_2378 | srf-21 | ncRNA of unknown function | |||
| 1548804-1549088 (-) | SPV_2383 | srf-22 | ncRNA of unknown function | (55) | ||
| 1598326-1598522 (+) | SPV_2392 | ssrS | 6S RNA | (53,54) | ||
| 1873736-1873781 (-) | SPV_2433 | srf-24 | ncRNA of unknown function | (54) | ||
| 1892857-1893007 (-) | SPV_2436 | srf-25 | ncRNA of unknown function | (53,54) | ||
| 1949385-1949547 (+) | SPV_2442 | srf-26 | ncRNA of unknown function | |||
| 1973172-1973570 (-)a | SPV_2447 | srf-27 | Type I addiction module antitoxin, Fst family | Not detected in this study due to its size; annotation based on sequence similarity | (58) | |
| 1973509-1973913 (-) | SPV_2449 | srf-28 | Type I addiction module antitoxin, Fst family | (58) | ||
| 2008242-2008356 (-) | SPV_2454 | srf-29 | ncRNA of unknown function | Similar to L. welshimeri LhrC | ||
| 2020587-2020685 (-) | SPV_2458 | srf-30 | ncRNA of unknown function |
aNot detected in this study, exact coordinates uncertain.
bAlternative terminator present.
cStudies containing Northern blot validation are highlighted in boldface.