Table 2

New miRNAs in P. trichocarpa
Counts of Found
miRNAs Sequences(5’-3’) miRNAs miRNA Locations Arm LP MEF by
(miRNAs*) (nt) (kcal/mol) others
Ptc-miRn1 CUGUUAUGAAUUGAUGGAGUG 71(10) scaffold_14:13399032:13399142:- 3’ 111 −56.3
Ptc-miRn2 UGGUAAUGCAAGUGUUGCUAA 22(15) scaffold_11:1025164:1025342:+ 3’ 179 −67.2
Ptc-miRn3 UAGAUUGUUUUUAUGCUUUGA 19(2) scaffold_16:10809578:10809788:+ 5’ 211 −106.5 D
Ptc-miRn4 CUCUUCAAAUAAAUCGUGGGA 380(12) scaffold_4:10873191:10873312:- 3’ 122 −66.8
Ptc-miRn5 AAUGUUGUUAUUAACACUGUA 127(27) scaffold_4:20884831:20884933:+ 3’ 103 −48.2
Ptc-miRn6a UUAUGCAUUUUUGUCCCUCGC 171(1) scaffold_4:2221707:2221834:+ 3’ 128 −64.5
Ptc-miRn6b UUAUGCAUUUUUGUCCCUCGC 171(52) scaffold_5:24265933:24266061:+ 3’ 129 −63.2 F
Ptc-miRn6c UUAUGCAUUUUUGUCCCUCGC 171(49) scaffold_5:24270121:24270264:+ 3’ 144 −67.7
Ptc-miRn6d UUAUGCAUUUUUGUCCCUCGC 171(1) scaffold_5:24280115:24280237:+ 3’ 123 −51.6 F
Ptc-miRn7a UCUUAUGCGUUUUUGUCUCU 238(3) scaffold_5:24266243:24266355:+ 3’ 113 −60.7 D
Ptc-miRn7b UCUUAUGCGUUUUUGUCUCU 238(26) scaffold_5:24270440:24270552:+ 3’ 113 −61.6 CD
Ptc-miRn8 UUUGGUUAUUGUCUCGAGACA 1664(23) scaffold_15:1581044:1581277:- 5’ 234 −95.6
Ptc-miRn9 UUUCUUAUCGAUCACUAGACG 41(1) scaffold_1112:3373:3393:+ 3’ 116 −54.4
Ptc-miRn10 UCUCUUCUGUUCCUGAACGGU 16(7) scaffold_1:15618173:15618365:+ 3’ 193 −63.4
Ptc-miRn11 UUGCUGAAACGAUUGAACUAU 70(2) scaffold_9:10835006:10835091:+ 3’ 86 −48.6 E
Ptc-miRn12 UCUUGAGAACAUGAUGAAUCG 11(1) scaffold_11:4410758:4410914:+ 5’ 157 −57.7
Ptc-miRn13 UGAUGAUUAAUUGACUGCAAA 754(51) scaffold_1:34025510:34025606:+ 5’ 97 −60.1 E
Ptc-miRn14 AUCAUAUAGGUUGAUCCUCGU 18(1) scaffold_6:6189111:6189190:- 5’ 80 −58.6
Ptc-miRn15 UCUGUCGCUGGAAAGAUGGUAC 57000(57) scaffold_17:10902829:10902928:+ 5’ 100 −66.7 AE
Ptc-miRn16 AGAUGGGCAUCGGCAUUGUGA 116(7) scaffold_13:797593:797704:- 3’ 112 −48.9
Ptc-miRn17 CGCUCGCCAGCGUUGCACCACC 618(247) scaffold_1:10455697:10455799:- 5’ 103 −47.3 E
Ptc-miRn18 UUUGAAAUUGAACAAAUGGUA 10(1) scaffold_5:17113917:17114027:+ 5’ 111 −64.6
Ptc-miRn19 UUGCAUGCAUGAACUUGAAAU 178(4) scaffold_4:20393549:20393757:+ 3’ 209 −81.1 B
Ptc-miRn20 UUGAGAAAAGUCAAUCGGACC 11(1) scaffold_13:7256997:7257111:- 5’ 115 −48.5
Ptc-miRn21 UGUUCAGAUCAGUAGAUAGCA 1310(29) scaffold_8:207741:207864:- 5’ 124 −46.6 BE
Ptc-miRn22 UAGAGCAGAUUGUAAGGGAAG 528793(209) scaffold_1:5198865:5198974:- 3’ 110 −49.3 CDE
Ptc-miRn23 UUGAAGAAAGGUAGACAGAUAG 207(1) scaffold_3:14589106:14589377:- 3’ 272 −74.3 D
Ptc-miRn24a CGAACGUUGACCGAAUGUGAA 15(3) scaffold_10:11417598:11417684:- 5’ 87 −31.9
Ptc-miRn24b CGAACGUUGACCGAAUGUGAA 15(3) scaffold_1646:4003:4023:+ 5’ 88 −35.4
Ptc-miRn25 UUGUACACAGAAUAGGUGAAAU 1624(7) scaffold_5:1237647:1237753:+ 3’ 107 −35.4 CE
Ptc-miRn26 UUACCAAGUUUCAAAUUCUCA 8(5) scaffold_16:2500220:2500318:- 5’ 99 −53.1
Ptc-miRn27 GCUAGGACCAAGUUUUUUGGA 367(50) scaffold_13:9970810:9970906:+ 5’ 97 −58
Ptc-miRn28 GAUGACAUGGACACCAAAAUC 9(6) scaffold_1:35822741:35822925:- 5’ 185 −64
Ptc-miRn29 ACACAGAAACUCCAAGCCCAC 48(2) scaffold_15:14059579:14059742:- 3’ 164 −88.4
Ptc-miRn30 UGAUCUAGAGAACCGUUGCU 38(3) scaffold_15:5977842:5977957:+ 5’ 116 −54.5
Ptc-miRn31 UACAUGUAGAGACCACCAAAC 75(51) scaffold_10:2022789:2023023:+ 5’ 235 −97.1
Ptc-miRn32 UGUCGCAGGAGAGAUGGCGCUA 216(21) scaffold_17:10888890:10889033:+ 5’ 144 −67.8 D
Ptc-miRn33 UAGUUCCCAACCUACACCACA 6(2) scaffold_12:5445549:5445646:+ 5’ 98 −63.8
Ptc-miRn34 UAAUUAGAACUCAUACUAGAC 44(4) scaffold_13:3364782:3364868:+ 5’ 87 −38.6
Ptc-miRn35 UUGCCGACCCCACCCAUGCCAA 1127(309) scaffold_10:12814698:12814812:- 3’ 115 −49 D
Ptc-miRn36 UGGAUGAUCAUGUUGGCAACC 1614(364) scaffold_4:6132662:6132818:+ 3’ 157 −60.3 BE
Ptc-miRn37 UGUGAUAAUGGAGGCUAUGGU 88(1) scaffold_1:5941972:5942066:+ 3’ 95 −75.8 E
Ptc-miRn38 UAAUAAAAUCUCGACUAUUAU 249(4) scaffold_11:535912:536007:- 5’ 96 −44
Ptc-miRn39 UGGACUCCUUUGGGGAGAUGG 216(2) scaffold_15:12480557:12480647:+ 3’ 91 −41.1 BE
Ptc-miRn40 UCGAAUUUGGGCUUGAGAUUG 50787(2158) scaffold_3:9383285:9383395:+ 3’ 111 −45.4 ABE
Ptc-miRn41 GGAAACCUUUUGUGGGGGUUU 491(9) scaffold_15:12329506:12329600:- 3’ 95 −44.7 DE
Ptc-miRn42 GGCAUGAGGUGUUUGGCAAGA 1721(1155) scaffold_5:11901572:11901665:- 5’ 94 −38.9 A
Ptc-miRn43 GAUGGGAUUUUUCGGGAAGUG 41(13) scaffold_10:17756662:17756763:+ 3’ 102 −52.3
Ptc-miRn44 GUUUUCCCUGAAUCACUCCCA 15(7) scaffold_5:21920822:21920920:- 5’ 99 −55.8
Ptc-miRn45a UGGGUGGGAGGUGUGGUAGCU 8(1) scaffold_5:9237322:9237483:- 5’ 162 −79.9
Ptc-miRn45b UGGGUGGGAGGUGUGGUAGCU 8(1) scaffold_724:8193:8213:+ 5’ 166 −78.7
Ptc-miRn46 ACAUGUGCUGGGUAGGAGGAA 21(4) scaffold_6:9390506:9390758:- 3’ 253 −86.8
Ptc-miRn47 AGUGGCAUUGGAGGUAUCCC 297(18) scaffold_1:22901250:22901371:- 3’ 122 −34.7 D
Ptc-miRn48 UCUCAAGCCCAAAUUCGAUC 8(2) scaffold_3:9383296:9383382:- 5’ 87 −35 B
Ptc-miRn49 CAAGGAGUAAUUAGUGACAUC 974(1) scaffold_9:7737213:7737443:+ 5’ 231 −63.3
Ptc-miRn50 UGAUAUGUGGCAUUCAAUCGA 2880(8) scaffold_3:14915775:14915873:+ 3’ 99 −77.1 E
Ptc-miRn51a GCCGAGCUCGGGGAUUGCG 84645(465) scaffold_17:2344664:2344909:+ 3’ 246 −141.5
Ptc-miRn51b GCCGAGCUCGGGGAUUGCG 84645(465) scaffold_17:2357226:2357471:+ 3’ 246 −143
Ptc-miRn51c GCCGAGCUCGGGGAUUGCG 84645(465) scaffold_17:2307047:2307292:+ 3’ 246 −137.4
Ptc-miRn51d GCCGAGCUCGGGGAUUGCG 84645(465) scaffold_17:2279166:2279411:+ 3’ 246 −137.6
Ptc-miRn51e GCCGAGCUCGGGGAUUGCG 84645(465) scaffold_17:2268545:2268790:+ 3’ 246 −139.3
Ptc-miRn52 GGGGGUUGCUGUCAAGCAUAA 61(19) scaffold_18:2804678:2804833:+ 3’ 156 −74.6 B
Ptc-miRn53 UAAAUCAAGCCCGGUACUUUU 10(2) scaffold_11:15209261:15209374:- 5’ 114 −42.6
Ptc-miRn54a UUCAUUCCUCUUCCUAAAAUGG 1827(506) scaffold_15:8556706:8556831:+ 5’ 126 −61 ABCE
Ptc-miRn54b UUCAUUCCUCUUCCUAAAAUGG 1827(500) scaffold_12:7706162:7706287:- 5’ 126 −50.9 ABCDE

‘LM’, Length of miRNAs. ‘nt’, neuleotides. ‘LP’, Length of precursors. ‘A’, refer to [26]; ‘B’, refer to [11]; ‘C’, refer to [19]; ‘D’, refer to [15]; ‘E’, refer to [10]; ‘F’, refer to [18].

Shuai et al.

Shuai et al. BMC Genomics 2013 14:233   doi:10.1186/1471-2164-14-233

Open Data