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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 -
  1. 1 sRNA candidates reported in contemporary studies retain their original notation (smrC# or sra#) [26, 27]. Otherwise, the designation sm# corresponds to the full list of sRNA predictions obtained in this work by the global scoring procedure (Additional file 17). Candidate IgRs are sorted according to its descending global score (GS). Bolded candidates have been verified experimentally ([26, 27]; this work).
  2. 2 NN, neural network promoter prediction; s70, σ70-dependent promoter; s54, RpoN (σ54)-dependent promoter promoter; PhoB, putative PhoB binding site.
  3. 3 The coordinates of all putative promoters and/or transcription factor binding sites within an IgR are presented. The position given for NN is the 3' end of the identified sequence. For σ70 the position given is 7 bases downstream of the 3' end of the -10 hexamer. The 3' end of the predicted binding site for σ54 and PhoB is indicated with an asterisk.
  4. 4 Given is the position of the last uridine at the end of the terminator sequence.
  5. 5 Range of possible lengths based on putative 5' and 3' ends.
  6. 6 y, candidate present in sRNAPredictHT search (Additional file 4); n, candidate absent in sRNAPredictHT output.
  7. 7 As described in Table 1.