Table 2 Top 20 highest-scoring putative sRNA genes predicted by the global scoring procedure as independent transcriptional units in chromosomal IgRs of S. meliloti 1021.
From: Prediction of Sinorhizobium meliloti sRNA genes and experimental detection in strain 2011
Gene or Designation1 | IgR length | Upstream ORF | Orientation Up sRNA Dn | Promoter2 | Predicted 5'-end3 | Predicted 3'-end4 | Blast score | Qrna score | Global score | Length (nt)5 | SP6 | Microarray detection7 | ||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
smrC15 ( sm3 ) smrC16 ( sm3' ) | 652 | SMc01226 | < < | < < | < < | NN, s70 PhoB | 1698732 1698968 * | 1698618 1698820 | 6 | 2 | 98 | 114 151 | y | <, C (1698954-1698905) |
sm4 | 541 | SMc01844 | > | > | < | NN, s70 | 2371490, 2371606 | 2371852 | 1 | 1 | 82 | 256–362 | n | >, S (2371745–2371696 2371735–2371784) |
sm5 | 384 | SMc03856 | < | > | > | s70 | 3522121, 3522271 | 3522379 | 12 | 8 | 80 | 108–258 | y | >, A, B, O, S (3522279–3522328) |
sm6 | 491 | SMc01202 | < | < | < | NN, s70 | 1728153, 1728196, 1728269 | 1728021 | 1 | 1 | 62 | 120–248 | n | - |
smrC14 ( sm7 ) sm7' | 922 | SMc02051 | < < | < < | < < | NN, s70 NN | 1667614 1667983 | 1667488 1667769 | 3 | 5 | 58 | 126 214 | n | <, S (1667516-1667467) |
sm8 | 301 | SMc04042 | < | > | < | NN, s70 | 3046713 | 3046789 | 9 | 4 | 53 | 76 | y | - |
sm9 | 470 | SMc02080 | > | < | > | NN, s70 | 1635343, 1635411, 1635564 | 1635217 | 1 | 1 | 52 | 126–347 | n | <, B, H, O (*) (1635305–1635354 1635259-1635210) |
sm10 | 405 | SMc00057 | > | > | > | NN, s70 | 1091047, 1091106 | 1091343 | 1 | 1 | 52 | 237–296 | n | - |
smrC9 ( sm12 ) | 710 | SMc01933 | < | < | > | NN, s70 | 1398427, 1398584 | 1398279 | 4 | 3 | 47 | 148–305 | y | <, A, C, H, S (1398340–1398389 1398389-1398340) |
smrC7 ( sm13 ) | 472 | SMc02850 | < | > | > | NN, s70 | 201682 | 201829 | 4 | 3 | 47 | 147 | y | - |
sm11 | 1101 | SMc01671 | < | > | < | NN, s70 | 2475717, 2475862 | 2475961 | 5 | 2 | 47 | 99–244 | y | - |
sm14 | 410 | SMc02139 | < | > | > | NN, PhoB | 573816, 573830 * | 574040 | 4 | 1 | 45 | 210 | y | - |
sra12 ( sm17 ) | 829 | SMc02151 | < | > | < | NN, s70 | 560780, 560916, 561000 | 561258 | 1 | 1 | 42 | 258–478 | n | >, S (*) (560802–560753) |
sm16 | 902 | SMc02597 | > | < | > | NN, s70 | 1198309, 1198440, 1198508 | 1198093 | 1 | 1 | 42 | 212–416 | n | - |
sm18 | 277 | SMc01425 | < | > | > | s70 | 2270996, 2271068 | 2271224 | 1 | 1 | 42 | 156–228 | n | - |
sm23 | 292 | SMc01218 | < | < | > | NN | 1706863 | 1706715 | 1 | 3 | 34 | 148 | n | - |
sm25 | 396 | SMc04289 | < | > | > | s70, PhoB | 2210185, 2210260 * | 2210322 | 1 | 2 | 33 | 62–137 | n | - |
sm26 | 1270 | SMc04453 | < | < | > | NN | 2321447 | 2321055 | 2 | 1 | 33 | 392 | y | <, A, C, O, S (2321429–2321478) |
sm28 | 826 | SMc03014 | > | < | > | NN, s70 | 713461, 713680, 713763 | 713290 | 1 | 1 | 32 | 170–463 | n | - |
sm30 | 644 | SMc01257 | < | > | > | NN, s70, PhoB | 1518613, 1518748 * | 1518988 | 1 | 1 | 32 | 234–375 | n | - |