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Tomato miRNA M00063
| sequence | Length | miRNA family | sRNA ID | target |
|---|---|---|---|---|
| UUCCACAGCUUUCUUGAACUG | 21 | miR396 | S25045577 | 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) | 8555 | 833.64 |
| S0738 | Solanum lycopersicum | Ailsa Craig | fruit, breaker (42 days after anthesis) | 3913 | 518.65 |
| S0737 | Solanum lycopersicum | Ailsa Craig | fruit, mature green (39 days after anthesis) | 442097 | 51646.7 |
| S0736 | Solanum lycopersicum | Ailsa Craig | fruit, immature (17 days after anthesis) | 65614 | 14129.5 |
| S0735 | Solanum lycopersicum | Sunny | leaf , TSWV-infected | 1379 | 101.71 |
| S0734 | Solanum lycopersicum | IL8-3-1 | seedlings, two-week-old | 110 | 84.77 |
| S0733 | Solanum lycopersicum | IL8-3 | seedlings, two-week-old | 129 | 97.86 |
| S0732 | Solanum lycopersicum | IL8-2-1 | seedlings, two-week-old | 49 | 34.91 |
| S0731 | Solanum lycopersicum | IL8-2 | seedlings, two-week-old | 56 | 41.24 |
| S0730 | Solanum lycopersicum | IL8-1-3 | seedlings, two-week-old | 128 | 79.92 |
| S0729 | Solanum lycopersicum | IL8-1D | seedlings, two-week-old | 78 | 49.69 |
| S0728 | Solanum lycopersicum | IL8-1-1 | seedlings, two-week-old | 139 | 91.61 |
| S0727 | Solanum lycopersicum | IL2-5 | seedlings, two-week-old | 163 | 99.65 |
| S0726 | Solanum lycopersicum | IL1-1 | seedlings, two-week-old | 83 | 49.68 |
| S0725 | Solanum lycopersicum x S. pennellii | M82 x LA716 (F2) | seedlings, two-week-old , replicate3 | 187 | 182.46 |
| S0724 | Solanum lycopersicum x S. pennellii | M82 x LA716 (F2) | seedlings, two-week-old , replicate2 | 282 | 164.62 |
| S0723 | Solanum lycopersicum x S. pennellii | M82 x LA716 (F2) | seedlings, two-week-old , replicate1 | 210 | 206 |
| S0722 | Solanum lycopersicum x S. pennellii | M82 x LA716 (F1) | seedlings, two-week-old , replicate2 | 182 | 128.72 |
| S0721 | Solanum lycopersicum x S. pennellii | M82 x LA716 (F1) | seedlings, two-week-old , replicate1 | 167 | 181.8 |
| S0720 | Solanum pennellii | LA716 | seedlings, two-week-old , replicate2 | 183 | 174.85 |
| S0719 | Solanum pennellii | LA716 | seedlings, two-week-old , replicate1 | 49 | 141.55 |
| S0718 | Solanum lycopersicum | M82 | seedlings, two-week-old , replicate2 | 69 | 48.07 |
| S0717 | Solanum lycopersicum | M82 | seedlings, two-week-old , replicate1 | 48 | 64.05 |
| S0716 | Solanum lycopersicum | MicroTom | fruit , 7 days post breaker | 22 | 9.2 |
| S0715 | Solanum lycopersicum | MicroTom | fruit , 5 days post breaker | 10 | 10.23 |
| S0714 | Solanum lycopersicum | MicroTom | fruit , 3 days post breaker | 115 | 28.95 |
| S0713 | Solanum lycopersicum | MicroTom | fruit , breaker stage | 30 | 8.5 |
| S0712 | Solanum lycopersicum | MicroTom | fruit , mature green | 233 | 59.61 |
| S0711 | Solanum lycopersicum | MicroTom | fruit , 11mm to 14mm in diameter | 38 | 18.3 |
| S0710 | Solanum lycopersicum | MicroTom | fruit , 5mm to 7mm in diameter | 16 | 13.29 |
| S0709 | Solanum lycopersicum | MicroTom | fruit , 1mm to 3mm in diameter | 2 | 1.13 |
| S0708 | Solanum lycopersicum | MicroTom | flower, open | 67 | 20.67 |
| S0707 | Solanum lycopersicum | MicroTom | flower bud, closed bud before flower blooming | 60 | 15.75 |
| S0373 | Solanum lycopersicum | Heinz 1706 | fruit | 4329 | 1295.73 |
| S0372 | Solanum lycopersicum | Heinz 1706 | flower | 608 | 184.01 |
| S0371 | Solanum lycopersicum | Heinz 1706 | leaf | 1538 | 463.46 |
Hits on known miRNAs
| hit miRNA | alignment |
|---|---|
| aau-miR396 | TTCCACAGCTTTCTTGAACTG ||||||||||||||||||||| TTCCACAGCTTTCTTGAACTG |
| aly-miR396a-5p | TTCCACAGCTTTCTTGAACTG ||||||||||||||||||||| TTCCACAGCTTTCTTGAACTG |
| amg-miR396 | TTCCACAGCTTTCTTGAACTG ||||||||||||||||||||| TTCCACAGCTTTCTTGAACTG |
| aqc-miR396a | TTCCACAGCTTTCTTGAACTG ||||||||||||||||||||| TTCCACAGCTTTCTTGAACTG |
| ath-miR396a | TTCCACAGCTTTCTTGAACTG ||||||||||||||||||||| TTCCACAGCTTTCTTGAACTG |
| bcy-miR396a | TTCCACAGCTTTCTTGAACTG ||||||||||||||||||||| TTCCACAGCTTTCTTGAACTG |
| bdi-miR396c | TTCCACAGCTTTCTTGAACTG ||||||||||||||||||||| TTCCACAGCTTTCTTGAACTG |
| bdi-miR396d | TTCCACAGCTTTCTTGAACTG ||||||||||||||||||||| TTCCACAGCTTTCTTGAACTG |
| bgy-miR396a | TTCCACAGCTTTCTTGAACTG ||||||||||||||||||||| TTCCACAGCTTTCTTGAACTG |
| cme-miR396b | TTCCACAGCTTTCTTGAACTG ||||||||||||||||||||| TTCCACAGCTTTCTTGAACTG |
| csi-miR396a | TTCCACAGCTTTCTTGAACTG ||||||||||||||||||||| TTCCACAGCTTTCTTGAACTG |
| csi-miR396b | TTCCACAGCTTTCTTGAACTG ||||||||||||||||||||| TTCCACAGCTTTCTTGAACTG |
| dpr-miR396 | TTCCACAGCTTTCTTGAACTG ||||||||||||||||||||| TTCCACAGCTTTCTTGAACTG |
| ghr-miR396a | TTCCACAGCTTTCTTGAACTG ||||||||||||||||||||| TTCCACAGCTTTCTTGAACTG |
| ghr-miR396b | TTCCACAGCTTTCTTGAACTG ||||||||||||||||||||| TTCCACAGCTTTCTTGAACTG |
| gma-miR396a-5p | TTCCACAGCTTTCTTGAACTG ||||||||||||||||||||| TTCCACAGCTTTCTTGAACTG |
| gma-miR396e | TTCCACAGCTTTCTTGAACTG- |||||||||||||||||||||x TTCCACAGCTTTCTTGAACTGT |
| gma-miR396i-5p | TTCCACAGCTTTCTTGAACTG ||||||||||||||||||||| TTCCACAGCTTTCTTGAACTG |
| hbr-miR396b | TTCCACAGCTTTCTTGAACTG ||||||||||||||||||||| TTCCACAGCTTTCTTGAACTG |
| lja-miR396 | TTCCACAGCTTTCTTGAACTG ||||||||||||||||||||| TTCCACAGCTTTCTTGAACTG |
| mdm-miR396b | TTCCACAGCTTTCTTGAACTG ||||||||||||||||||||| TTCCACAGCTTTCTTGAACTG |
| mtr-miR396b | TTCCACAGCTTTCTTGAACTG ||||||||||||||||||||| TTCCACAGCTTTCTTGAACTG |
| nta-miR396a | TTCCACAGCTTTCTTGAACTG ||||||||||||||||||||| TTCCACAGCTTTCTTGAACTG |
| osa-miR396a-5p | TTCCACAGCTTTCTTGAACTG ||||||||||||||||||||| TTCCACAGCTTTCTTGAACTG |
| osa-miR396b-5p | TTCCACAGCTTTCTTGAACTG ||||||||||||||||||||| TTCCACAGCTTTCTTGAACTG |
| ptc-miR396a | TTCCACAGCTTTCTTGAACTG ||||||||||||||||||||| TTCCACAGCTTTCTTGAACTG |
| ptc-miR396b | TTCCACAGCTTTCTTGAACTG ||||||||||||||||||||| TTCCACAGCTTTCTTGAACTG |
| sbi-miR396a | TTCCACAGCTTTCTTGAACTG ||||||||||||||||||||| TTCCACAGCTTTCTTGAACTG |
| sbi-miR396b | TTCCACAGCTTTCTTGAACTG ||||||||||||||||||||| TTCCACAGCTTTCTTGAACTG |
| sof-miR396 | TTCCACAGCTTTCTTGAACTG ||||||||||||||||||||| TTCCACAGCTTTCTTGAACTG |
| ssl-miR396 | TTCCACAGCTTTCTTGAACTG ||||||||||||||||||||| TTCCACAGCTTTCTTGAACTG |
| ssp-miR396 | TTCCACAGCTTTCTTGAACTG ||||||||||||||||||||| TTCCACAGCTTTCTTGAACTG |
| tcc-miR396a | TTCCACAGCTTTCTTGAACTG ||||||||||||||||||||| TTCCACAGCTTTCTTGAACTG |
| tcc-miR396b | TTCCACAGCTTTCTTGAACTG ||||||||||||||||||||| TTCCACAGCTTTCTTGAACTG |
| vvi-miR396c | TTCCACAGCTTTCTTGAACTG ||||||||||||||||||||| TTCCACAGCTTTCTTGAACTG |
| vvi-miR396d | TTCCACAGCTTTCTTGAACTG ||||||||||||||||||||| TTCCACAGCTTTCTTGAACTG |
| zma-miR396a-5p | TTCCACAGCTTTCTTGAACTG ||||||||||||||||||||| TTCCACAGCTTTCTTGAACTG |
| zma-miR396b-5p | TTCCACAGCTTTCTTGAACTG ||||||||||||||||||||| TTCCACAGCTTTCTTGAACTG |
Precursor of miRNA M00063
| 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 |
