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Tomato miRNA M00059
| sequence | Length | miRNA family | sRNA ID | target |
|---|---|---|---|---|
| UUCCACAGCUUUCUUGAACU | 20 | miR396 | S25045576 | 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) | 576 | 56.13 |
| S0738 | Solanum lycopersicum | Ailsa Craig | fruit, breaker (42 days after anthesis) | 264 | 34.99 |
| S0737 | Solanum lycopersicum | Ailsa Craig | fruit, mature green (39 days after anthesis) | 830 | 96.96 |
| S0736 | Solanum lycopersicum | Ailsa Craig | fruit, immature (17 days after anthesis) | 4179 | 899.92 |
| S0735 | Solanum lycopersicum | Sunny | leaf , TSWV-infected | 55 | 4.06 |
| S0734 | Solanum lycopersicum | IL8-3-1 | seedlings, two-week-old | 8 | 6.16 |
| S0733 | Solanum lycopersicum | IL8-3 | seedlings, two-week-old | 9 | 6.83 |
| S0732 | Solanum lycopersicum | IL8-2-1 | seedlings, two-week-old | 3 | 2.14 |
| S0731 | Solanum lycopersicum | IL8-2 | seedlings, two-week-old | 14 | 10.31 |
| S0730 | Solanum lycopersicum | IL8-1-3 | seedlings, two-week-old | 18 | 11.24 |
| S0729 | Solanum lycopersicum | IL8-1D | seedlings, two-week-old | 12 | 7.64 |
| S0728 | Solanum lycopersicum | IL8-1-1 | seedlings, two-week-old | 24 | 15.82 |
| S0727 | Solanum lycopersicum | IL2-5 | seedlings, two-week-old | 8 | 4.89 |
| S0726 | Solanum lycopersicum | IL1-1 | seedlings, two-week-old | 5 | 2.99 |
| S0725 | Solanum lycopersicum x S. pennellii | M82 x LA716 (F2) | seedlings, two-week-old , replicate3 | 24 | 23.42 |
| S0724 | Solanum lycopersicum x S. pennellii | M82 x LA716 (F2) | seedlings, two-week-old , replicate2 | 27 | 15.76 |
| S0723 | Solanum lycopersicum x S. pennellii | M82 x LA716 (F2) | seedlings, two-week-old , replicate1 | 35 | 34.33 |
| S0722 | Solanum lycopersicum x S. pennellii | M82 x LA716 (F1) | seedlings, two-week-old , replicate2 | 29 | 20.51 |
| S0721 | Solanum lycopersicum x S. pennellii | M82 x LA716 (F1) | seedlings, two-week-old , replicate1 | 17 | 18.51 |
| S0720 | Solanum pennellii | LA716 | seedlings, two-week-old , replicate2 | 18 | 17.2 |
| S0719 | Solanum pennellii | LA716 | seedlings, two-week-old , replicate1 | 5 | 14.44 |
| S0718 | Solanum lycopersicum | M82 | seedlings, two-week-old , replicate2 | 9 | 6.27 |
| S0717 | Solanum lycopersicum | M82 | seedlings, two-week-old , replicate1 | 5 | 6.67 |
| S0716 | Solanum lycopersicum | MicroTom | fruit , 7 days post breaker | 8 | 3.35 |
| S0715 | Solanum lycopersicum | MicroTom | fruit , 5 days post breaker | 6 | 6.14 |
| S0714 | Solanum lycopersicum | MicroTom | fruit , 3 days post breaker | 11 | 2.77 |
| S0713 | Solanum lycopersicum | MicroTom | fruit , breaker stage | 14 | 3.97 |
| S0712 | Solanum lycopersicum | MicroTom | fruit , mature green | 34 | 8.7 |
| S0711 | Solanum lycopersicum | MicroTom | fruit , 11mm to 14mm in diameter | 36 | 17.34 |
| S0710 | Solanum lycopersicum | MicroTom | fruit , 5mm to 7mm in diameter | 6 | 4.98 |
| S0709 | Solanum lycopersicum | MicroTom | fruit , 1mm to 3mm in diameter | 12 | 6.8 |
| S0708 | Solanum lycopersicum | MicroTom | flower, open | 27 | 8.33 |
| S0707 | Solanum lycopersicum | MicroTom | flower bud, closed bud before flower blooming | 20 | 5.25 |
| S0373 | Solanum lycopersicum | Heinz 1706 | fruit | 23 | 6.88 |
| S0372 | Solanum lycopersicum | Heinz 1706 | flower | 21 | 6.36 |
| S0371 | Solanum lycopersicum | Heinz 1706 | leaf | 19 | 5.73 |
Hits on known miRNAs
| hit miRNA | alignment |
|---|---|
| aau-miR396 | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTG |
| aly-miR396a-5p | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTG |
| aly-miR396b-5p | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTT |
| amg-miR396 | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTG |
| aqc-miR396a | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTG |
| aqc-miR396b | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTT |
| ath-miR396a | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTG |
| ath-miR396b | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTT |
| bcy-miR396a | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTG |
| bcy-miR396b | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTT |
| bdi-miR396c | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTG |
| bdi-miR396d | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTG |
| bdi-miR396e | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTT |
| bgy-miR396a | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTG |
| bgy-miR396b | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTT |
| bna-miR396a | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTT |
| cca-miR396a-5p | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTT |
| ccl-miR396 | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTT |
| cme-miR396a | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTT |
| cme-miR396b | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTG |
| cme-miR396c | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTT |
| cme-miR396d | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTT |
| csi-miR396a | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTG |
| csi-miR396b | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTG |
| dpr-miR396 | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTG |
| ghr-miR396a | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTG |
| ghr-miR396b | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTG |
| gma-miR396a-5p | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTG |
| gma-miR396b-5p | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTT |
| gma-miR396c | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTT |
| gma-miR396e | TTCCACAGCTTTCTTGAACT-- ||||||||||||||||||||xx TTCCACAGCTTTCTTGAACTGT |
| gma-miR396i-5p | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTG |
| hbr-miR396b | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTG |
| lja-miR396 | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTG |
| mdm-miR396b | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTG |
| mdm-miR396c | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTT |
| mdm-miR396d | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTT |
| mdm-miR396e | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTT |
| mtr-miR396a-5p | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTT |
| mtr-miR396b | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTG |
| nta-miR396a | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTG |
| nta-miR396b | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTT |
| nta-miR396c | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTT |
| osa-miR396a-5p | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTG |
| osa-miR396b-5p | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTG |
| osa-miR396c-5p | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTT |
| pab-miR396a | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTA |
| pta-miR396 | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTT |
| ptc-miR396a | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTG |
| ptc-miR396b | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTG |
| ptc-miR396c | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTT |
| ptc-miR396d | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTT |
| ptc-miR396e-5p | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTT |
| rco-miR396 | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTT |
| sbi-miR396a | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTG |
| sbi-miR396b | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTG |
| sbi-miR396c | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTT |
| sof-miR396 | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTG |
| ssl-miR396 | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTG |
| ssp-miR396 | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTG |
| tcc-miR396a | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTG |
| tcc-miR396b | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTG |
| tcc-miR396c | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTT |
| tcc-miR396e | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTT |
| vvi-miR396a | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTA |
| vvi-miR396b | TTCCACAGCTTTCTTGAACT |||||||||||||||||||| TTCCACAGCTTTCTTGAACT |
| vvi-miR396c | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTG |
| vvi-miR396d | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTG |
| zma-miR396a-5p | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTG |
| zma-miR396b-5p | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTG |
| zma-miR396e-5p | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTT |
| zma-miR396f-5p | TTCCACAGCTTTCTTGAACT- ||||||||||||||||||||x TTCCACAGCTTTCTTGAACTT |
Precursor of miRNA M00059
| 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 |
