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Tomato miRNA M00055
| sequence | Length | miRNA family | sRNA ID | target |
|---|---|---|---|---|
| UUCCACAGCUUUCUUGAAC | 19 | miR396 | S25045575 | click here |
Digital expression
| Sample | No. raw reads | RPM | |||
|---|---|---|---|---|---|
| ID | Organism | Cultivar | Tissue | ||
| S0739 | Solanum lycopersicum | Ailsa Craig | fruit, red ripe (52 days after anthesis) | 17 | 1.66 |
| S0738 | Solanum lycopersicum | Ailsa Craig | fruit, breaker (42 days after anthesis) | 6 | 0.8 |
| S0737 | Solanum lycopersicum | Ailsa Craig | fruit, mature green (39 days after anthesis) | 30 | 3.5 |
| S0736 | Solanum lycopersicum | Ailsa Craig | fruit, immature (17 days after anthesis) | 5 | 1.08 |
| S0735 | Solanum lycopersicum | Sunny | leaf , TSWV-infected | 392 | 28.91 |
| S0734 | Solanum lycopersicum | IL8-3-1 | seedlings, two-week-old | 501 | 386.08 |
| S0733 | Solanum lycopersicum | IL8-3 | seedlings, two-week-old | 713 | 540.89 |
| S0732 | Solanum lycopersicum | IL8-2-1 | seedlings, two-week-old | 809 | 576.36 |
| S0731 | Solanum lycopersicum | IL8-2 | seedlings, two-week-old | 339 | 249.67 |
| S0730 | Solanum lycopersicum | IL8-1-3 | seedlings, two-week-old | 961 | 600.05 |
| S0729 | Solanum lycopersicum | IL8-1D | seedlings, two-week-old | 632 | 402.61 |
| S0728 | Solanum lycopersicum | IL8-1-1 | seedlings, two-week-old | 549 | 361.82 |
| S0727 | Solanum lycopersicum | IL2-5 | seedlings, two-week-old | 465 | 284.28 |
| S0726 | Solanum lycopersicum | IL1-1 | seedlings, two-week-old | 467 | 279.55 |
| S0725 | Solanum lycopersicum x S. pennellii | M82 x LA716 (F2) | seedlings, two-week-old , replicate3 | 1802 | 1758.21 |
| S0724 | Solanum lycopersicum x S. pennellii | M82 x LA716 (F2) | seedlings, two-week-old , replicate2 | 1451 | 847.05 |
| S0723 | Solanum lycopersicum x S. pennellii | M82 x LA716 (F2) | seedlings, two-week-old , replicate1 | 1950 | 1912.82 |
| S0722 | Solanum lycopersicum x S. pennellii | M82 x LA716 (F1) | seedlings, two-week-old , replicate2 | 2413 | 1706.55 |
| S0721 | Solanum lycopersicum x S. pennellii | M82 x LA716 (F1) | seedlings, two-week-old , replicate1 | 228 | 248.2 |
| S0720 | Solanum pennellii | LA716 | seedlings, two-week-old , replicate2 | 302 | 288.55 |
| S0719 | Solanum pennellii | LA716 | seedlings, two-week-old , replicate1 | 293 | 846.4 |
| S0718 | Solanum lycopersicum | M82 | seedlings, two-week-old , replicate2 | 232 | 161.62 |
| S0717 | Solanum lycopersicum | M82 | seedlings, two-week-old , replicate1 | 174 | 232.19 |
| S0716 | Solanum lycopersicum | MicroTom | fruit , 7 days post breaker | 9 | 3.76 |
| S0715 | Solanum lycopersicum | MicroTom | fruit , 5 days post breaker | 1 | 1.02 |
| S0714 | Solanum lycopersicum | MicroTom | fruit , 3 days post breaker | 104 | 26.18 |
| S0713 | Solanum lycopersicum | MicroTom | fruit , breaker stage | 29 | 8.22 |
| S0712 | Solanum lycopersicum | MicroTom | fruit , mature green | 335 | 85.71 |
| S0711 | Solanum lycopersicum | MicroTom | fruit , 11mm to 14mm in diameter | 266 | 128.13 |
| S0710 | Solanum lycopersicum | MicroTom | fruit , 5mm to 7mm in diameter | 42 | 34.89 |
| S0709 | Solanum lycopersicum | MicroTom | fruit , 1mm to 3mm in diameter | 103 | 58.4 |
| S0708 | Solanum lycopersicum | MicroTom | flower, open | 29 | 8.95 |
| S0707 | Solanum lycopersicum | MicroTom | flower bud, closed bud before flower blooming | 85 | 22.31 |
| S0373 | Solanum lycopersicum | Heinz 1706 | fruit | 267 | 79.92 |
| S0372 | Solanum lycopersicum | Heinz 1706 | flower | 149 | 45.09 |
| S0371 | Solanum lycopersicum | Heinz 1706 | leaf | 191 | 57.56 |
Hits on known miRNAs
| hit miRNA | alignment |
|---|---|
| aau-miR396 | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTG |
| aly-miR396a-5p | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTG |
| aly-miR396b-5p | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTT |
| amg-miR396 | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTG |
| aqc-miR396a | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTG |
| aqc-miR396b | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTT |
| ath-miR396a | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTG |
| ath-miR396b | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTT |
| bcy-miR396a | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTG |
| bcy-miR396b | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTT |
| bdi-miR396c | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTG |
| bdi-miR396d | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTG |
| bdi-miR396e | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTT |
| bgy-miR396a | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTG |
| bgy-miR396b | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTT |
| bna-miR396a | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTT |
| cca-miR396a-5p | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTT |
| ccl-miR396 | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTT |
| cme-miR396a | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTT |
| cme-miR396b | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTG |
| cme-miR396c | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTT |
| cme-miR396d | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTT |
| csi-miR396a | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTG |
| csi-miR396b | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTG |
| dpr-miR396 | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTG |
| ghr-miR396a | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTG |
| ghr-miR396b | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTG |
| gma-miR396a-5p | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTG |
| gma-miR396b-5p | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTT |
| gma-miR396c | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTT |
| gma-miR396e | TTCCACAGCTTTCTTGAAC--- |||||||||||||||||||xxx TTCCACAGCTTTCTTGAACTGT |
| gma-miR396i-5p | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTG |
| hbr-miR396b | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTG |
| lja-miR396 | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTG |
| mdm-miR396a | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACAG |
| mdm-miR396b | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTG |
| mdm-miR396c | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTT |
| mdm-miR396d | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTT |
| mdm-miR396e | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTT |
| mtr-miR396a-5p | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTT |
| mtr-miR396b | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTG |
| nta-miR396a | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTG |
| nta-miR396b | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTT |
| nta-miR396c | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTT |
| osa-miR396a-5p | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTG |
| osa-miR396b-5p | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTG |
| osa-miR396c-5p | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTT |
| pab-miR396a | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTA |
| pta-miR396 | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTT |
| ptc-miR396a | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTG |
| ptc-miR396b | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTG |
| ptc-miR396c | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTT |
| ptc-miR396d | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTT |
| ptc-miR396e-5p | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTT |
| rco-miR396 | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTT |
| sbi-miR396a | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTG |
| sbi-miR396b | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTG |
| sbi-miR396c | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTT |
| sof-miR396 | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTG |
| ssl-miR396 | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTG |
| ssp-miR396 | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTG |
| tcc-miR396a | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTG |
| tcc-miR396b | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTG |
| tcc-miR396c | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTT |
| tcc-miR396e | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTT |
| vvi-miR396a | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTA |
| vvi-miR396b | TTCCACAGCTTTCTTGAAC- |||||||||||||||||||x TTCCACAGCTTTCTTGAACT |
| vvi-miR396c | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTG |
| vvi-miR396d | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTG |
| zma-miR396a-5p | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTG |
| zma-miR396b-5p | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTG |
| zma-miR396e-5p | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTT |
| zma-miR396f-5p | TTCCACAGCTTTCTTGAAC-- |||||||||||||||||||xx TTCCACAGCTTTCTTGAACTT |
Precursor of miRNA M00055
| genome hit of precursor | precursor | ||||||
|---|---|---|---|---|---|---|---|
| sequence ID | start | end | strand | sequence | folding energy | miRNA* | structure |
| SL2.40ch00 | 12537520 | 12537617 | + | UUCCACAGCUUUCUUGAACU GCAUCUACAAUUUCAAUUCA UUAUUGAAAAAGAAAAAAUU GAUUCAUAUUGUUGUUGCGG UUCAAUAAAGCUGUGGGA |
-40.30 | miRNA* | structure |
| SL2.40ch12 | 2905790 | 2905661 | - | UUCCACAGCUUUCUUGAACU GCAUACAUAUAACAAAAAAA UCUGAUUUUUUUUUGAUUUU UUUUUACUUUUAUAAAGAAA AAAUUUAGAUGGAAAGAAUU AAAUUGUUGCGGUUCAAUAA AGCUGUGGGA |
-42.20 | miRNA* | structure |
| SL2.40ch07 | 2628873 | 2628773 | - | UUCCACAGCUUUCUUGAACU UCUUCUUGCUAAAUUUUGAU CUCUAAAUUGAUAAUUUUGA GAUGAGAUUUGAAGCUAUGA AAGUCCAAGAAAGCUGUGGG A |
-40.20 | NA | structure |
