Table 3.
Candidate new brassica-specific miRNAs
|
miRNA |
miR sequence (5'→3') |
miR length (nt) |
Reads |
Precursor from EST |
Mature miRNA position |
Stem-loop position |
||
|---|---|---|---|---|---|---|---|---|
| miR start | miR end | Precursor start | Precursor end | |||||
| Bna-miRC1 |
CCATACTAAATCTGGATCATTT |
22 |
115 |
CU943501 |
519 |
540 |
519 |
634 |
| Bna-miRC2 |
ATAAATCCCAAGCATCATCCA |
21 |
1011 |
EV202910 |
179 |
199 |
173 |
261 |
| Bna-miRC3 |
TGGGATTGGCTTTGGGCTTTTC |
22 |
12 |
CU940792 |
108 |
129 |
82 |
281 |
| Bna-miRC4 |
TTTCAGTCGTCATAGGTTAGT |
21 |
11 |
GT084890 |
55 |
75 |
51 |
158 |
| Bna-miRC5-1 |
TGTGTTGTGATGATAATCCGA |
21 |
306 |
CU971106 |
285 |
305 |
132 |
350 |
| Bna-miRC5-1* |
AATCGGATTATCATCACAACA |
21 |
7 |
CU971106 |
93 |
113 |
29 |
291 |
| Bna-miRC5-2 |
TCAACCAAATACACATTGTGG |
21 |
4 |
CU971106 |
52 |
72 |
35 |
306 |
| Bna-miRC5-3 |
TTATCATCACAACACTAGATC |
21 |
536 |
CU971106 |
76 |
96 |
19 |
281 |
| Bna-miRC5-3* |
TCTTGTGTTGTGATGATAATC |
21 |
216 |
CU971106 |
288 |
308 |
136 |
349 |
| Bna-miRC5-4 |
TGATAATCCGACTTCTATGAC |
21 |
29 |
CU971106 |
272 |
292 |
122 |
356 |
| Bna-miRC5-5 |
TTGGTTTGGATCTTGGAAATC |
21 |
8 |
CU971106 |
123 |
143 |
42 |
304 |
| Bna-miRC5-6 |
TCGGATTATCATCACAACACT |
21 |
182 |
CU971106 |
89 |
109 |
27 |
289 |
| Bna-miRC6 |
ATAGATCCTTCTGATGACGCA |
21 |
16 |
DU099814 |
306 |
326 |
254 |
327 |
| Bna-miRC7 |
CAAATCCTGTCATCCCTACCA |
21 |
89 |
GT079632 |
102 |
122 |
102 |
229 |
| Bna-miRC8 |
CAGGAGAGATTGTTGGATCCA |
21 |
3 |
CU931338 |
337 |
357 |
337 |
443 |
| Bna-miRC9 |
TGCCTGGCTCCCTGTATACCA |
21 |
118 |
EV193539 |
387 |
407 |
380 |
474 |
| Bna-miRC10 |
TCAATGTTGGCTCAATTATGT |
21 |
12 |
CU934632 |
731 |
751 |
666 |
751 |
| Bna-miRC11 |
GGCGAGTCACCGGTGTCGGTC |
21 |
6 |
FP328714 |
415 |
435 |
406 |
534 |
| Bna-miRC12 |
GGGTCGATATGAGAACACATG |
21 |
15 |
EE426846 |
15 |
35 |
1 |
123 |
| Bna-miRC13 |
ACCCTGTTGAGCTTGTCTCTA |
21 |
3 |
CU980942 |
490 |
510 |
449 |
524 |
| Bna-miRC14 |
CAGCTGGACGACTTAGTAGAC |
21 |
7 |
CU943399 |
123 |
143 |
103 |
229 |
| Bna-miRC15-1 |
ACATTGGACTACATATATTAC |
21 |
8 |
ES901619 |
392 |
412 |
299 |
430 |
| Bna-miRC15-2 |
TCAATACATTGGACTACATAT |
21 |
9 |
ES901619 |
387 |
407 |
299 |
430 |
| Bna-miRC16 |
GTTTTGAGAGATTGGGAAGCT |
21 |
3 |
EV146378 |
77 |
97 |
58 |
216 |
| Bna-miRC17a-1 |
TTTCCAAATGTAGACAAAGCA |
21 |
7132 |
ES913560 |
96 |
116 |
31 |
137 |
| Bna-miRC17a-1* |
CTTTGTCTATCGTTTGGAAAAG |
22 |
782 |
ES913560 |
53 |
74 |
31 |
137 |
| Bna-miRC18 |
TCGCGATCTTAGATCCTCTAA |
21 |
41 |
EV179238 |
441 |
461 |
288 |
564 |
| Bna-miRC19 |
CGAGTTGGTCGGGAAAGACGG |
21 |
12 |
DU102764 |
104 |
124 |
35 |
128 |
| Bna-miRC20 |
CTCTCGTGGAGCGTCTCGAGG |
21 |
3 |
EV192419 |
700 |
720 |
567 |
746 |
| Bna-miRC21 |
GGAGGCAGCGGTTGATCGATC |
21 |
7 |
DY025212 |
429 |
449 |
420 |
523 |
| Bna-miRC22a-1 |
CAAGTAGACGACTTTCCAGAC |
21 |
10 |
CU945922 |
359 |
379 |
298 |
403 |
| Bna-miRC22a-2 |
CGTGGTCGTCCAAGTAGACGA |
21 |
13 |
CU945922 |
363 |
383 |
292 |
397 |
| Bna-miRC22a-3 |
TTGGACGACTTTGTAGACGAC |
21 |
9 |
CU945922 |
303 |
323 |
297 |
402 |
| Bna-miRC23a-1 |
TCAGAACCAAACCCAGAACAAG |
22 |
54 |
CU958057 |
25 |
46 |
3 |
241 |
| Bna-miRC23a-2 |
TTACAGAACAGCAACAAGCTGT |
22 |
150 |
CU958057 |
47 |
68 |
7 |
238 |
| Bna-miRC23a-3 |
TATCTACTGCTTATGCCACCA |
21 |
65 |
CU958057 |
54 |
74 |
1 |
215 |
| Bna-miRC23a-3* |
GATGCATAACCACTAGATACG |
21 |
8 |
CU958057 |
140 |
160 |
1 |
215 |
| Bna-miRC24 |
TTAGGATTGAGATCTTAGCGA |
21 |
7 |
EV176533 |
225 |
245 |
214 |
395 |
| Bna-miRC25 |
TTGGACTGAAGGGAACTCCCT |
21 |
23719 |
FP023833 |
319 |
339 |
168 |
343 |
| Bna-miRC25* |
AGAGTTTCCTTAAGTCCATTC |
21 |
34 |
FP023833 |
173 |
193 |
167 |
343 |
| Bna-miRC26 |
TGAGCCAAAGATGACTTGTCG |
21 |
45 |
BZ021311 |
68 |
88 |
66 |
323 |
| Bna-miRC27 |
TAAGATGATGGAACACTGGCC |
21 |
25 |
EE438385 |
18 |
38 |
14 |
279 |
| Bna-miRC28 |
ATGGATCCGCCGGATAAGGAT |
21 |
6 |
CU965419 |
466 |
486 |
350 |
511 |
| Bna-miRC29 |
TTGAGGTTTTGAGGACTGGCC |
21 |
6 |
EV093069 |
644 |
664 |
564 |
668 |
| Bna-miRC30 |
TCCTGGACGACTTTCAAGTAAG |
22 |
9 |
CZ888137 |
161 |
182 |
20 |
250 |
| Bna-miRC31 |
AGATCATCCTGCGGCTTCATT |
21 |
26 |
EV134163 |
290 |
310 |
233 |
335 |
| Bna-miRC32 |
GCAAGTTGACTTTGGCTCCGT |
21 |
51 |
BZ021311 |
52 |
72 |
13 |
184 |
| Bna-miRC33 |
TTTTGCCTACTCCTCCCATACC |
22 |
268 |
CU981257 |
103 |
124 |
95 |
223 |
| Bna-miRC34 |
ATCCTCGGGACACAGATTACC |
21 |
113 |
EV076017 |
357 |
377 |
339 |
459 |
| Bna-miRC35 |
ATGGTGTAGGTACTGAGCAGA |
21 |
13 |
EV194620 |
298 |
318 |
294 |
400 |
| Bna-miRC36 |
CGTCCGGGGAAAGCAAAGTCG |
21 |
11 |
EV088144 |
141 |
161 |
64 |
186 |
| Bna-miRC37 |
TGATTTATCCAAGGGTTCAGG |
21 |
31 |
DU101557 |
509 |
529 |
367 |
608 |
| Bna-miRC38 |
CAAGTAGACTACTTTCCAGACG |
22 |
9 |
GT084321 |
52 |
73 |
1 |
92 |
| Bna-miRC39 |
TAAGATGATGGGACGTTGGATC |
22 |
11 |
DY002174 |
42 |
63 |
40 |
306 |
| Bna-miRC40 |
CGCTCACAGCATCTGAACTCT |
21 |
21 |
CD842549 |
99 |
119 |
78 |
243 |
| Bna-miRC41 |
TTTTGGAGAAGGCTGTAGGCA |
21 |
13 |
DU109430 |
791 |
811 |
780 |
890 |
| Bna-miRC42 |
TTCCCCGGACGACTTTAAATT |
21 |
15 |
EV088144 |
90 |
110 |
3 |
125 |
| Bna-miRC43 |
TGTGAATGATGCGGGAGATGT |
21 |
15 |
CN829704 |
219 |
239 |
69 |
315 |
| Bna-miRC44 |
TTGGCCACAACGGATTTAACA |
21 |
9 |
EV006438 |
66 |
86 |
66 |
141 |
| Bna-miRC45 |
TTTCATCTTAGAGAATGTTGTC |
22 |
42 |
EV178795 |
578 |
599 |
478 |
617 |
| Bna-miRC46 |
ACTTGTCTCACTCATCAGTT |
20 |
7 |
EV063926 |
5 |
24 |
3 |
215 |
| Bna-miRC47 | CAAATGTAGACAAAGCAAAAC | 21 | 4 | ES913560 | 100 | 120 | 31 | 137 |