Table 3.
Target prediction of the miRNAs differentially expressed in A. thaliana callus tissues in response to LPS elicitation
| miRNA | Target Acc | miRNA Sequence | Target aligned fragment | Expectation | Target start | Target end | Target description |
|---|---|---|---|---|---|---|---|
| miR156 | AT5G43270.1 | TGACAGAAGAGAGTGAGCAC | GUGCUCUCUCUCUUCUGUCA | 1.0 | 1188 | 1207 | Squamosa promoter binding protein-like 2 |
| miR158 | AT1G64100.1 | TCCCAAATGTAGACAAAGCA | UUCUUUGUCUACAUUUGGCA | 2.5 | 477 | 496 | Pentatricopeptide (PPR) repeat-containing |
| miR159 | AT2G32460.1 | TTTGGATTGAAGGGAGCTCTA | UAGAGCUUCCUUCAAACCAAA | 2.0 | 1004 | 1024 | Myb domain protein 101, ACC synthase |
| miR160 | AT2G28350.1 | TGCCTGGCTCCCTGTATGCCA | GGAAUACAGGGAGCCAGGCA | 1.0 | 1330 | 1349 | Auxin response factor 10 |
| miR162 | AT1G01040.1 | TCGATAAACCTCTGCATCCAG | CUGGAUGCAGAGGUAUUAUCGA | 2.0 | 3422 | 3443 | DICER-LIKE1 |
| miR165 | AT2G34710.1 | TCGGACCAGGCTTCATCCCCC | UGGGAUGAAGCCUGGUCCGG | 1.5 | 871 | 890 | Homeobox-leucine zipper family protein |
| miR166 | AT2G34710.1 | TTCGGACCAGGCTTCATTCCCC | GGGAUGAAGCCUGGUCCGGA | 1.0 | 872 | 891 | Homeobox-leucine zipper family |
| miR167 | AT1G67120.1 | GATCATGTTCGCAGTTTCACC | GGUGAAACUGCGUCACAUGAUC | 3.0 | 1909 | 1930 | Transcription factor binding; ARF6 |
| mIR169 | AT1G17590.1 | TAGCCAAGGATGACTTGCCT | AGGGAAGUCAUCCUUGGCUG | 1.5 | 1233 | 1252 | CCAAT-binding TF (CBF-B/NF-YA) |
| miR2934 | AT1G49770.1 | TCTTTCTGCAAACGCCTTGGA | CCAAGGCUUAUGCAGAGAGA | 2.5 | 992 | 1011 | bHLH DNA-binding superfamily protein |
| miR319 | AT3G15030.1 | TTGGACTGAAGGGAGCTCCTTC | GAGGGGUCCCCUUCAGUCCAG | 2.5 | 1476 | 1496 | TCP family transcription factor 4 |
| miR396 | AT2G36400.1 | TTCCACAGCTTTCTTGAACTG | CCGUUCAAGAAAGCCUGUGGAA | 2.0 | 746 | 767 | Growth-regulating factor 4 |
| miR398 | AT4G27050.2 | GGGTTGATATGAGAACACACG | GUGUGUUUUUAUGUCAAUCU | 2.5 | 154 | 173 | F-box/RNI-like superfamily protein |
| miR399 | AT2G33770.1 | TGCCAAAGGAGAGTTGCCCTG | AGGGCAAAUCUUCUUUGGCA | 1.5 | 608 | 627 | Ubiquitin-protein ligase |
| miR401 | AT5G34863.1 | ACAATGGAGATTAGGAGACATTTT | AAAAUGUCUCCUUAUCUCCAUUGU | 1.0 | 329 | 352 | Transposable element gene |
| miR403 | AT1G31280.1 | GGATTAGATTCACGCACAAACTC | GAGUUUGUGCGUGAAUCUAAUUG | 1.5 | 3223 | 3245 | AGO2 | Argonaute family protein |
| miR405 | AT1G27880.1 | AAATGAGTTATGGGTTAGACCCGT | GUCUGGUCCAAGACUCAUUU | 3.0 | 2633 | 2653 | DEAD/DEAH box RNA helicase family protein |
| miR407 | AT3G20220.1 | GGGGAAAAATGTCAAAAAAATCGC | UGAUUUUUUUGAUAUCUUUCUUU | 3.0 | 197 | 219 | SAUR-like auxin-responsive protein family |
| miR408 | AT2G02850.1 | TGCACTGCCTCTTCCCTGGCT | CCAAGGGAAGAGGCAGUGCA | 2.0 | 97 | 116 | Plantacyanin |
| miR5026 | AT3G62340.1 | AAAGTTAGTAACTCAAAGGCTCGT | AGCUUUUGAGUUUUUAACUUC | 3.0 | 166 | 186 | WRKY68, AtWRKY68 | WRKY family TF |
| miR5029 | AT4G04570.1 | AAUGAGAGAGAACACUGCAAA | UUGUGGUGUUUACUUUCAUU | 3.0 | 964 | 983 | Cysteine-rich RLK |
| miR5635 | AT1G20230.1 | ATTTAATACCTGAACTTTCAAAGA | UGGAAAGUUCAGGUAUUGAGG | 3.0 | 623 | 643 | Pentatricopeptide repeat (PPR) |
| miR5638 | TCCACACTAGTGTAACGACAGTG | Unknown | |||||
| miR5641 | AT3G43571.1 | CATGGAGGAGATATTTGGTAA | UUAUCUAAUAUUUCUUCCAUG | 2.5 | 528 | 548 | Transposable element gene |
| miR5642 | AT5G04010.1 | CAAGAACATCTTCGTTACGGAT | AGUUUUAAUGAAGAUGUUCUUG | 2.5 | 754 | 775 | F-box family protein |
| miR5643 | AT1G71840.1 | AGAAGACACAGAGACAAAGACTCA | GGGUUUUUGUACUUUGUGUCUUCU | 3.0 | 71 | 94 | Transducin WD-40 repeat family protein |
| miR5651 | AT1G43260.1 | TCGTTACTATTTGAACCGCACC | UGUUGUUCAAGUAGUAACGA | 2.0 | 504 | 523 | hAT transposon superfamily protein |
| miR5655 | AT5G02480.1 | CTTTTCCTCCTCCTCCACCACC | GGUGGUGGAGGAGGAGGAGGAG | 1.0 | 992 | 1013 | HSP20-like chaperones superfamily protein |
| miR5662 | AT5G60410.1 | AGAGGAAAATATAGAGATCACCAT | UGGUUGUCUUUUUAUUUUCCUCU | 3.0 | 10 | 32 | DNA-binding protein: MIZ/SP-RING Zinc finger, PHD-finger |
| miR773 | AT5G64270.1 | TTTGCTTCCAGCTTTTGTC | AGACGGAAGAUGGAAGCAGA | 172 | 191 | Splicing factor, putative | |
| miR782 | AT3G29152.1 | TCTTTCTGCAAACGCCT | AGAACACCAAACGUGUUUGU | 260 | 279 | Protease inhibitor/seed storage/LTP family protein | |
| miR783 | AT5G43530.1 | CAAAAGATCTGGTGATGAAGTTGA | UGGACUUCAUUUUUGGAUCUUUUG | 3.0 | 3406 | 3429 | Helicase protein with RING/U-box domain |
| miR822 | AT5G02330.1 | GCGGGAAGCATTTGCACATGTT | AGCAUGUGCAAAUGCUUCUCGC | 0.5 | 1254 | 1275 | Cysteine/Histidine-rich C1 domain family protein |
| miR824 | AT3G08870.1 | CCTTCTCATCGATGGTCTAGA | UUUAGGCCAUCGAUGAGAAUG | 2.5 | 1873 | 1893 | Concanavalin A-like lectin protein kinase protein |
| miR829 | AT5G18560.1 | AGCTCTGATACCAAATGA | UUACCUUGAAGUUUUGAUUUG | 1.5 | 1284 | 1304 | AP2 domain-containing TF/ ethylene response factor |
| mIR842 | AT1G60130.1 | CATGGTCAGATCCGTCATCCC | GGGAUGAUGGAUCCGACCAUG | 1.5 | 86 | 106 | Mannose-binding lectin superfamily protein |
| miR855 | AT5G02490.1 | AAACTCGAAAGCGTCTAGGACTTT | ACUUUUUCUUAGCUUUUUCU | 3 | 47 | 66 | Heat shock cognate 70 kDa protein 2 (HSC70-2) (HSP70-2) |
Expectation: value assigned to the alignment of the mature miRNA and the target. The value ranges from 0 (perfect alignment) to 5); Target start: the base position where the annealing with the miRNA starts; Target end: the base position where the annealing with the miRNA ends.