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Table 4 Putative sRNA genes predicted as independent transcriptional units in IgRs of S. meliloti 1021 megaplasmids pSymA (smA#) and pSymB (smB#).

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
Length
(nt)5
Microarray
detection6
smA1 719 SMa0450 > > > s70 241667 241961 294 >, C, O (*)
(241991-241942)
smA2a
smA2b
smA2c
817 SMa0585 <
<
<
<
<
>
>
>
<
s54
s70
NN
313672 *
313772
313667
313529
313529
314181
143–243
444
>, A, B, C, H, S
(314210-314161 313991–314040 314162–314211 313784–313833)
smA3a
smA3b
1007 SMa0922 > < < NN
s70
512362
512439
512154 208–285 <, A, C
(512371–512420)
smA4a
smA4b
714 SMa0995 <
<
>
>
>
>
NN
NN
552600
552853
552980 127–280 >, A, B, C, H, O, S
(552880–552929 552801-552752 552954-552905)
smA5 292 SMa1024 < > > PhoB 567336 * 567465 129 >, H, S
(567397-567348)
smA6 624 SMa1245 < < < NN 682304 682237 67 <, O
(682278-682229)
smA7 879 SMa1644 >
>
>
>
<
<
s70
NN, s70
916928
917145
917238 93–310 -
smA8 1124 SMa2165 > > > NN 1220442 1220807 365 >, A, H, O, S
(1220782–1220831)
smB1 282 SMb20203 > > > NN 213506 213617 111 -
smB2 495 SMb20366 > > < NN 379143 379269 126 >, H, S
(379180–379131)
smB3a
smB3b
smB3c
750 SMb20516 >
>
>
<
<
<
<
<
<
NN
NN
s70
541963
541911
541833
541769 64–194 <, H
(541835–541884)
smB4a
smB4b
592 SMb20543 < < < NN, s70
s70
571374
571340
571217 123–157 <, A, C
(571271-571222 571222–571271)
smB5a
smB5b
1623 SMb20548 >
>
>
>
>
>
NN
NN, s70
574477
574621
574763 142–286 >, A, sB, C, H, O, S
(574671-574622)
smrB35 (smB6) 751 SMb20551 < > > s70 577731 577869 138 >, O, S
(577781-577732)
smB7 196 SMb21316 < > > s70 983786 983878 92 >, S (*)
(983845-983796)
smB8 767 SMb20872 < < < NN, s70
s70
1279964
1281110
1279836 128–274 <, A, O
(1279979–1280028 1280182-1280231)
smB9 1014 SMb20916 < > > s70 1325140 1325588 448 >, H
(1325459–1325508)
smB10 506 SMb20748 < < > NN 1537794 1537673 121 -
  1. 1 sRNA candidates verified experimentally retain their original notation [26].
  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 As described in Table 1.