Table 2.
Illumina sequencing identifies novel miRNAs
|
miRNA |
Chr |
miRNA Start |
miRNA End |
Mature Sequence |
miRNA* |
miRNA previoulsy reported |
miRNA located in |
| miR5640 |
1(−) |
1653540 |
1653560 |
AUGAGAGAAGGAAUUAGAUUC |
YES |
ath-miR5640 [47] |
AT1G05570.1 intron |
| ath-MIR472-5p |
1(−) |
4182266 |
4182286 |
AUGGUCGAAGUAGGCAAAAUC |
NO |
Novel |
ath-MIR472 stem loop |
| ath-MIR8166 |
1(−) |
4525316 |
4525337 |
AGAGAGUGUAGAAAGUUUCUCA |
NO |
Novel |
Intergenic region AT1G13240-AT1G13245 |
| miR5654-3p |
1(+) |
11786350 |
11786371 |
GAAGAUGCUUUGGGAUUUAUUU |
NO |
miR5654-3p [47,63] |
AT1G32583.1, 5'UTR |
| ath-MIR829-5p |
1(−) |
11834153 |
11834173 |
ACUUUGAAGCUUUGAUUUGAA |
YES |
Novel |
ath-MIR829 stem loop |
| miR5014a |
1(+) |
24554009 |
24554029 |
UGUUGUACAAAUUUAAGUGUA |
YES |
ath-miR5014a [47,60] |
AT1G65960.1 intron |
| ath-MIR840-3p |
1(−) |
771385 |
771405 |
UUGUUUAGGUCCCUUAGUUUC |
YES |
Novel |
ath-MIR840 stem loop |
| ath-MIR398a-3p |
2(+) |
1040948 |
1040968 |
AAGGAGUGGCAUGUGAACACA |
YES |
Novel |
ath-MIR398a stem loop |
| ath-MIR8180 |
2(+) |
2063980 |
2063998 |
UGCGGUGCGGGAGAAGUGC |
NO |
Novel |
Intergenic region AT2G05580-AT2G05590 |
| ath-MIR8175 |
2(+) |
3740938 |
3740957 |
GAUCCCCGGCAACGGCGCCA |
NO |
Novel |
Intergenic region AT2G09880-AT2G09890 |
| ath-MIR396a-3p |
2(−) |
4142331 |
4142351 |
GUUCAAUAAAGCUGUGGGAAG |
YES |
Novel |
ath-MIR396a stem loop |
| ath-MIR8168 |
2(+) |
5080690 |
5080710 |
AGGUGCUGAGUGUGCUAGUGC |
NO |
Novel |
Intergenic region AT2G12490-AT2G12500 |
| ath-MIR5632-5p |
2(−) |
8392588 |
8392608 |
UUGAUUCUCUUAUCCAACUGU |
YES |
Novel |
ath-MIR5632 stem loop |
| ath-MIR8167a |
2(+) |
8894985 |
8895006 |
AGAUGUGGAGAUCGUGGGGAUG |
NO |
Novel |
Intergenic region AT2G20620-AT2G20625 |
| miR5995b |
2(−) |
10026977 |
10026997 |
AAAGAUGCAGAUCAUAUGUCC |
YES |
ath-miR5995b [63]) |
Intergenic region AT2G23540-AT2G23550 |
| ath-MIR831-5p |
2(+) |
10247259 |
10247280 |
AGAAGCGUACAAGGAGAUGAGG |
NO |
Novel |
ath-MIR831 stem loop |
| miR5637 |
2(−) |
12270195 |
12270216 |
UAGAGGAAAAUAUAGAGUUGGG |
NO |
ath-miR5637 [47] |
Intergenic region AT2G28620-AT2G28625 |
| ath-MIR8170.1 |
2(+) |
14100020 |
14100040 |
AUAGCAAAUCGAUAAGCAAUG |
YES |
Novel |
AT2G33255.1 intron |
| ath-MIR8170.2 |
2(+) |
14100079 |
14100099 |
UUGCUUAAAGAUUUUCUAUGU |
YES |
Novel |
AT2G33255.1 intron |
| ath-MIR160a-3p |
2(+) |
16340342 |
16340362 |
GCGUAUGAGGAGCCAUGCAUA |
YES |
Novel |
ath-MIR160a stem loop |
| ath-MIR8171 |
2(+) |
16890466 |
16890486 |
AUAGGUGGGCCAGUGGUAGGA |
NO |
Novel |
AT2G40440.1 intron |
| ath-MIR166a-5p |
2(+) |
19176128 |
19176148 |
GGACUGUUGUCUGGCUCGAGG |
YES |
Novel |
ath-MIR166 stem loop |
| ath-MIR408-5p |
2(+) |
19319866 |
19319886 |
ACAGGGAACAAGCAGAGCAUG |
YES |
Novel |
ath-MIR408 stem loop |
| miR5650 |
2(+) |
19686959 |
19686979 |
UUGUUUUGGAUCUUAGAUACA |
YES |
ath-miR5650 [47] |
AT2G48140.1 intron |
| miR173-5p |
3(+) |
8236161 |
8236182 |
UUCGCUUGCAGAGAGAAAUCAC |
YES |
ath-miR173-5p [62,63] |
ath-miR173-5p stem loop |
| ath-MIR8169 |
3(+) |
8836359 |
8836379 |
AUAGACAGAGUCACUCACAGA |
NO |
Novel |
Intergenic region AT3G24340-AT3G24350 |
| ath-MIR8183 |
3(−) |
11747799 |
11747819 |
UUUAGUUGACGGAAUUGUGGC |
NO |
Novel |
AT3G30110.1, pseudogene |
| ath-MIR8165 |
3(−) |
16538510 |
16538530 |
AAUGGAGGCAAGUGUGAAGGA |
NO |
Novel |
Intergenic region AT3G45170-AT3G45180 |
| ath-MIR8174 |
3(−) |
16589431 |
16589451 |
AUGUGUAUAGGGAAGCUAAUC |
NO |
Novel |
Intergenic region AT5G38460-AT5G38470 |
| miR5651 |
3(+) |
17178489 |
17178509 |
UUGUGCGGUUCAAAUAGUAAC |
YES |
ath-miR5651 [47] |
Intergenic region AT3G46616-AT3G46620 |
| ath-MIR8167b |
3(−) |
8894985 |
8895006 |
AGAUGUGGAGAUCGUGGGGAUG |
NO |
Novel |
Intergenic region AT3G47410-AT3G47420 |
| ath-MIR8167c |
3(−) |
17469946 |
17469967 |
AGAUGUGGAGAUCGUGGGGAUG |
NO |
Novel |
Intergenic region AT3G50700-AT3G50710 |
| miR5633 |
3(+) |
19544786 |
19544807 |
AUGAUCAUCAGAAAACAGUGAU |
NO |
ath-miR5633 [47]) |
Intergenic region AT3G52730-AT3G52740 |
| ath-MIR393b-3p |
3(+) |
20691778 |
20691798 |
AUCAUGCGAUCUCUUUGGAUU |
YES |
Novel |
ath-MIR393 stem loop |
| ath-MIR8182 |
3(+) |
22678166 |
22678187 |
UUGUGUUGCGUUUCUGUUGAUU |
NO |
Novel |
AT3G61270.1, 5'UTR |
| ath-MIR166b-5p |
3(+) |
22922212 |
22922232 |
GGACUGUUGUCUGGCUCGAGG |
YES |
Novel |
ath-MIR166 stem loop |
| ath-MIR8172 |
4(−) |
7102572 |
7102592 |
AUGGAUCAUCUAGAUGGAGAU |
YES |
Novel |
Intergenic region AT4G11800-AT4G11810 |
| ath-MIR8179 |
4(−) |
7161930 |
7161950 |
UGACUGCAUUAACUUGAUCGU |
NO |
Novel |
AT4G1192.1 intron |
| ath-MIR8176 |
4(+) |
11795199 |
11795219 |
GGCCGGUGGUCGCGAGAGGGA |
NO |
Novel |
Intergenic region AT4G22320-AT4G22330 |
| ath-MIR8178 |
4(+) |
18087285 |
18087305 |
UAACAGAGUAAUUGUACAGUG |
NO |
Novel |
AT4G38760.1 intron |
| ath-MIR8184 |
5(−) |
3311974 |
3311994 |
UUUGGUCUGAUUACGAAUGUA |
NO |
Novel |
Intergenic region AT5G10504-AT5G10510 |
| miR5629 |
5(+) |
3802933 |
3802954 |
UUAGGGUAGUUAACGGAAGUUA |
NO |
ath-miR5629 [47] |
Intergenic region AT5G11790-AT5G11800 |
| ath-MIR865.2 |
5(+) |
5169992 |
5170011 |
UCUGGGAUGAAUUUGGAUCU |
NO |
Novel |
ath-MIR865 stem loop |
| miR1888 |
5(+) |
7168879 |
7168899 |
UAAGUUAAGAUUUGUGAAGAA |
NO |
ath-miR1888 [61,62] |
AT5G21100.1 intron |
| ath-MIR8173 |
5(−) |
7478572 |
7478592 |
AUGUGCUGAUUCGAGGUGGGA |
NO |
Novel |
Intergenic region AT5G22510-AT5G22520 |
| ath-MIR8177 |
5(−) |
9362634 |
9362655 |
GUGUGAUGAUGUGUCAUUUAUA |
NO |
Novel |
Intergenic region AT5G26617-AT5G26620 |
| miR5638b |
5(+) |
14100017 |
14100037 |
ACAGUGGUCAUCUGGUGGGCU |
NO |
ath-miR5638b [47] |
Intergenic region AT5G35945-AT5G35950 |
| ath-MIR160c-3p |
5(−) |
19009095 |
19009115 |
CGUACAAGGAGUCAAGCAUGA |
YES |
Novel |
ath-MIR160c stem loop |
| ath-MIR870-5p.1 |
5(−) |
21395592 |
21395612 |
UUAGAAUGUGAUGCAAAACUU |
NO |
Novel |
ath-MIR870 stem loop |
| ath-MIR870-5p.2 |
5(−) |
21395604 |
21395624 |
AAGAACAUCAAAUUAGAAUGU |
NO |
Novel |
ath-MIR870 stem loop |
| ath-MIR8181 | 5(−) | 21641289 | 21641308 | UGGGGGUGGGGGGGUGACAG | NO | Novel | AT5G5333.1, intron |
Sequences from the Illumina libraries were queried for sequences representing putative new miRNAs with the miRCat program from the UEA sRNA toolkit. We show the genomic location and sequences of these miRNAs. Presence of reads corresponding to miRNA* are indicated (Yes or No). miRNAs that are not included in miRBase 17 but that have been cross-validated by other groups are indicated.
The name of mature sequences derived from the same arm of known hairpin precursor were named with the suffix .1 or .2. If the sequences derive from the opposite arm from the previously annotated sequence,were named with the suffix -5p, -3p.