Table 2.
Novel miRNAs identified in Thellungiella
| Novel miRNA | Novel miRNA sequence | Length |
miRNA count |
Genomic location of pre-miRNA | MFE | miR* |
miR* count |
||
|---|---|---|---|---|---|---|---|---|---|
| CL | TL | CL | TL | ||||||
| tsa-miRn1 |
GGAGGAUGAUACAAGCUCUCAUA |
23 |
24 |
0 |
scaffold_10:7369671:7369761:+ |
-18.5 |
CUUCAACAUUAGAAUGCAUGUAUC |
1 |
0 |
| tsa-miRn2 |
UAGGAAUCUGUGCUCAAACCAC |
22 |
18 |
22 |
scaffold_11:1867622:1867724:+ |
-57.1 |
UUGAGCACAGAUUUCUACA |
1 |
1 |
| tsa-miRn3-5p |
UUGGGGGUAAGAGUAUUAUAC |
21 |
78 |
72 |
scaffold_13:6097671:6097798:- |
-46.1 |
UAUAAUACCCUUAAACCCAAU |
10 |
10 |
| tsa-miRn3-3p |
UAUAAUACCCUUAAACCCAAU |
21 |
10 |
10 |
UUGGGGGUAAGAGUAUUAUAC |
78 |
72 |
||
| tsa-miRn4 |
UGUUCGCCGGAAAAUAACCAG |
21 |
47 |
55 |
scaffold_15:2449702:2449784:+ |
-48.2 |
GGUUAUUUUCCGGCGAAGCAGA |
1 |
0 |
| tsa-miRn5 |
UUUUAAAACUGAAAACGUAAU |
21 |
92 |
77 |
scaffold_15:2733677:2733793:+ |
-45.3 |
UACGUUAUCAGUUUUAAAACA |
1 |
1 |
| tsa-miRn6 |
AUUGGAGUUGAUAUAAUGCAG |
21 |
0 |
10 |
scaffold_9:4431521:4431709:+ |
-71.2 |
CAACCUGCAUUAUAUCAACUC |
0 |
1 |
| tsa-miRn7 |
CAAGGCAGAAGAAGGCUGUUU |
21 |
1927 |
0 |
scaffold_19:2418388:2418480:+ |
-63.1 |
ACAGCCUCUUCUUCCUUGUU |
1 |
0 |
| tsa-miRn8-5p |
AAUGAAUGAUGCGGUAGACAAAU |
23 |
123 |
71 |
scaffold_1:6999873:6999998:- |
-36 |
UAGCUUCCGACUCAUUCAUCCA |
13 |
9 |
| tsa-miRn8-3p |
UAGCUUCCGACUCAUUCAUCCA |
22 |
13 |
9 |
AAUGAAUGAUGCGGUAGACAAAU |
123 |
71 |
||
| tsa-miRn9 |
AGGAGAGUUUUGGUGUAGCAA |
21 |
21 |
23 |
scaffold_229:434:568:- |
-30.7 |
UUCUAUGCUCAGAACUCCUUCUU |
0 |
1 |
| tsa-miRn10 |
UGAAUUUGAUUUUAGACAGGA |
21 |
26 |
0 |
scaffold_2:7409777:7409908:+ |
-57.1 |
UGUCUGAAAUCAGGUUCAGGUA |
1 |
0 |
| tsa-miRn11-3p |
UGAGUCGUCAAUCAGUAAGGU |
21 |
228 |
247 |
scaffold_2:8810421:8810518:+ |
-34.9 |
AUUACUUGUUGACGAUUCCUU |
252 |
133 |
| tsa-miRn11-5p |
AUUACUUGUUGACGAUUCCUU |
21 |
252 |
133 |
scaffold_2:8810421:8810518:+ |
UGAGUCGUCAAUCAGUAAGGU |
228 |
247 |
|
| tsa-miRn12 |
UGAUAGCAGUAGUUUCGUCUA |
21 |
192 |
172 |
scaffold_2:856191:856302:- |
-23.5 |
AGAGAUCGGAGCUUUGUUGG |
1 |
0 |
| tsa-miRn13 |
UAGUGAAAUUGGAAAGUUGCC |
21 |
3777 |
2846 |
scaffold_2:6151436:6151550:- |
-49 |
AACGACAGCUUUCCUGAUUCCA |
2 |
1 |
| tsa-miRn14 |
UCAUGAAGGAUCUGAGAUUGA |
21 |
78 |
0 |
scaffold_2:18154827:18154925:- |
-48.1 |
CUCCAGUCUCAUACUCUUCAU |
2 |
0 |
| tsa-miRn15 |
CUAGGGUUCCAGAAUUGAGGCUA |
23 |
57 |
32 |
scaffold_3:8786082:8786170:+ |
-26.4 |
GCUUUAAUUCGGAGUUGGUCGGC |
1 |
1 |
| tsa-miRn16 |
UGUGAUCCUCAGAUAGACGUACA |
23 |
4 |
10 |
scaffold_3:10218595:10218739:+ |
-38.3 |
AGUUGUCAUUAUAUCUCUGAUCGC |
0 |
2 |
| tsa-miRn17 |
ACCCCAAACCAGCUCAGACAA |
21 |
142 |
263 |
scaffold_3:2561950:2562105:- |
-67.7 |
CAGCUUAUUUGGGAUUGGAGGUC |
0 |
3 |
| tsa-miRn18 |
UGGAUUUAGAAUAAUGGUGGCUA |
23 |
127 |
118 |
scaffold_4:1893254:1893541:+ |
-47.63 |
AUCAUUGCUCUGAUACCAUGUUGA |
2 |
3 |
| tsa-miRn19 |
AAGGCUGUGAAUUGUUUUGGC |
21 |
167 |
116 |
scaffold_7:7785014:7785113:- |
-57.26 |
CGAAACAAUUCACAGUCUUGA |
0 |
1 |
| tsa-miRn20-3p |
AAAGCAUGUGAGUACUUCGUA |
21 |
639 |
523 |
scaffold_9:9328524:9328666:- |
-71.2 |
UGAAAUAUUCACAUGCUUUCG |
357 |
439 |
| |
|
|
|
|
scaffold_9:9328524:9328666:- |
-71.2 |
|
|
|
| tsa-miRn20-5p |
UGAAAUAUUCACAUGCUUUCG |
21 |
357 |
439 |
|
AAAGCAUGUGAGUACUUCGUA |
639 |
523 |
|
| tsa-miRn21 |
UGAAAGGAAACAUUGAUGUUU |
21 |
0 |
82 |
scaffold_15:1338317:1338445:- |
-50.1 |
ACAACAGUGUUUUCUUUCACA |
0 |
9 |
| tsa-miRn22 | UUGUGCAAGACUGAGAAGCAA | 21 | 0 | 10 | scaffold_5:15200075:15200174:+ | -57.5 | UCUUCUUCCUCUUGCACAACC | 0 | 1 |
Novel miRNA is the name of detected novel miRNAs. -5p and -3p means the novel miRNA and miR*. Genomic locations of pre-miRNA are listed: The T. salsuginea genome sequence was downloaded from the T. salsuginea Sequencing Resource: website ftp://ftp.jgi-psf.org/pub/compgen/phytozome/v9.0/Thalophila/assembly/). +, sense strand. -, anti-sense strand.