Table 10.
List of putative targets of conserved miRNAs and their mode of inhibition predicted both by psRNATarget server (http://plantgrn.noble.org/psRNATarget/) and by MIRANDA included in the LeARN pipeline
|
microRNA family |
Target gene |
UPE |
Free energy |
miRNA size |
miRNA aligned fragment |
Target aligned fragment |
Inhibition |
MiR position |
miR position binding with respect to CDS |
||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Name | Accession No | Gene name | Contig accession No | No bases | bp | ||||||
| miR156 |
acc_480780 |
HbAP2-9 |
hevea_454_rep_c24306 |
24.478 |
−24.41 |
23 |
UGACAGAAGAGAGAGAGCACAUC |
UACUCUCUUUUUUCUGCCAA |
Cleavage |
1001-1020 |
Inside CDS & after AP2 domain |
| miR159 |
acc_19665 |
HbERF-IXc2 |
hevea_454_c72747 |
13.691 |
−25.86 |
23 |
UUUUGAUUGAAGGGAGCUCUAAU |
GAGCACCCUUCAAUUAAG |
Cleavage |
297-314 |
Inside CDS & after AP2 domain |
| miR159 |
acc_19665 |
HbERF-VI-L1 |
hevea_454_rep_c17780 |
16.359 |
−27.80 |
23 |
UUUUGAUUGAAGGGAGCUCUAAU |
GUUCUAGCUUCCUUCAAGCAGAG |
Cleavage |
50-72 |
outside CDS, 5’UTR & before AP2 domain |
| miR172 |
acc_502684 |
HbAP2-18 |
hevea_454_rep_c22185 |
15.621 |
−21.57 |
21 |
UAGCAUCAUCAAGAUUUUUAU |
AAGAGAAUCCUGAUGAUGCUG |
Cleavage |
1473-1493 |
Inside CDS & after AP2 domain |
| miR172 |
acc_502684 |
HbAP2-20 |
hevea_454_rep_c45080 |
17.625 |
−24.25 |
21 |
UAGCAUCAUCAAGAUUUUUAU |
AUGAGAAUCCUGAUGAUGCUG |
Cleavage |
990-1010 |
Inside CDS & after AP2 domain |
| miR393 |
acc_112860 |
HbAP2-4 |
hevea_454_c60993 |
24.258 |
−22.79 |
25 |
UUCCAAAGGGAUCGCAUUGAUUAUC |
AGCAAUGUUAUUCCUUUGGC |
Cleavage |
198-217 |
Inside CDS & before AP2 domain |
| miR395 |
acc_262739 |
HbERF-IXc3 |
hevea_454_c37716 |
15.053 |
−24.47 |
25 |
CUGAAGUGUUUGGGGGACCUCAUC |
GAGAAAGUUCUCCAAUCACUUCAA |
Translation |
243-266 |
Inside CDS & after AP2 domain |
| miR396 |
acc_7978 |
HbRAV-2 |
hevea_454_rep_c13430 |
22.097 |
−22.40 |
24 |
CCACAGCUUUCUUGAACUGCAAUC |
GAGUUCAAGAAAGCGGUU |
Cleavage |
562-579 |
Inside CDS & after AP2 domain |
| miR408 |
acc_135004 |
HbERF-IXb1 |
hevea_454_c13287 |
14.501 |
−23.60 |
23 |
UGCACUGCCUCUUCCCUGCCAUC |
AAGAGAAGAGGCAGUACA |
Cleavage |
118-135 |
Inside CDS & cut AP2 domain |
| miR408 |
acc_184014 |
HbERF-VIIa9 |
hevea_454_rep_c64305 |
24.62 |
−28.45 |
24 |
UACACUGCCUCUUCCCUGGCUAUC |
UGCGAGCAGGAGGAGAGGCAGU |
Cleavage |
207-228 |
Inside CDS & before AP2 domain |
| miR408 |
acc_184014 |
HbERF-VIIa13 |
hevea_454_rep_c8113 |
24.62 |
−28.45 |
24 |
UACACUGCCUCUUCCCUGGCUAUC |
UGCGAGCAGGAGGAGAGGCAGU |
Cleavage |
518-539 |
Inside CDS & before AP2 domain |
| miR894 |
S_seq_24257 |
HbERF-IIa2 |
hevea_454_rep_c7563 |
15,655 |
−19,42 |
16 |
UGUUUCACGUCGGGUU |
AACCUGACUUGAACCA |
Cleavage |
760-775 |
Inside CDS & after AP2 domain |
| miR894 |
S_seq_73030 |
HbAP2-6 |
hevea_454_rep_c16078 |
18,933 |
−22,38 |
17 |
CGUUUAACGUCGGGUUC |
GAAGCCGAUGUUGAACA |
Cleavage |
694-710 |
3’ region & after CDS |
| miR894 |
S_seq_174443 |
HbERF-IIIe3 |
hevea_454_rep_c58258 |
21,025 |
−23,87 |
20 |
UCUUCGUUUCACGUCGGGUU |
AAUCUGCCGUGGUACGAGGA |
Cleavage |
653-672 |
Inside CDS & after AP2 domain |
| miR894 |
S_seq_181990 |
HbERF-IXc5 |
hevea_454_rep_c36947 |
23,707 |
−25,35 |
20 |
GUUUCACAUCGGGUUCACCA |
UGGAGAAAUCCAUGUGAAAU |
Translation |
901-920 |
5’ region & before CDS |
| miR894 |
S_seq_376904 |
HbERF-VIIa20 |
hevea_454_rep_c710 |
17,302 |
−27 |
16 |
GUGCGUUUCACGUCGG |
UUGCCGUGAAACGCAU |
Cleavage |
130-145 |
Inside CDS & before AP2 domain |
| miR894 |
S_seq_376904 |
HbERF-VIIa23 |
hevea_454_rep_c88669 |
17,295 |
−27 |
16 |
GUGCGUUUCACGUCGG |
UUGCCGUGAAACGCAU |
Cleavage |
73-88 |
Inside CDS & before AP2 domain |
| miR1511 |
S_seq_556556 |
HbERF-IXc6 |
hevea_454_rep_c18341 |
22,461 |
−27,04 |
19 |
AACCAGGCUCUGAUACCAU |
AUGGCAUCAGGGUUUGGUU |
Cleavage |
449-467 |
Inside CDS & inside AP2 domain |
| miRn11 |
S_seq_275942 |
HbERF-VIIa2 |
hevea_454_rep_c40731 |
16,586 |
−26,87 |
16 |
AGUUUGGCUGGGGCGG |
UCGCCUUAGCUAAACA |
Cleavage |
37-52 |
5’ region & before CDS |
| miRn11 |
S_seq_275942 |
HbERF-VIIIa7 |
hevea_454_rep_c16802 |
16,135 |
−24,03 |
19 |
AGUUUGGCUGGGGCGGCAC |
GCGCAGCCCAAGCCAAACC |
Translation |
355-373 |
Inside CDS & after AP2 domain |
| miRn11 |
S_seq_11884 |
HbERF-IIId3 |
hevea_454_c39573 |
13,87 |
−31,03 |
16 |
GGGAGUUUGGCUGGGG |
UCCUAGCCAAAUUCUU |
Cleavage |
405-420 |
Inside CDS & inside AP2 domain |
| miRn11 |
S_seq_11884 |
HbERF-Xa8 |
hevea_454_c51284 |
21,466 |
−28,52 |
15 |
GGGAGUUUGGCUGGG |
CCUAGCCAAACUCUA |
Cleavage |
419-433 |
Inside CDS & Inside AP2 domain |
| miRn11 |
S_seq_4512 |
HbERF-VI5 |
hevea_454_c22933 |
4,586 |
−24,23 |
17 |
GAGUUUGGCUGGGGCGG |
UCGUCCAAGCCCAACUC |
Translation |
215-231 |
5’ region & before CDS |
| miRn11 |
S_seq_422499 |
HbERF-VIIa4 |
hevea_454_rep_c1157 |
11,652 |
−23,53 |
16 |
GAGUUUGGCUGGGGCU |
AGUCCUAUCCGAACUC |
Translation |
457-472 |
Inside CDS & before AP2 domain |
| miRn11 |
S_seq_234287 |
HbSoloist3 |
hevea_454_rep_c46638 |
20,623 |
−37,87 |
19 |
UCAGGUGGG-GAGUUUGGCU |
AGCCAGACUCAUCCACCUGA |
Translation |
618-637 |
Inside CDS & after AP2 domain |
| miRn12 |
S_seq_119244 |
HbERF-IIa1 |
hevea_454_rep_c8625 |
11,7 |
−21,45 |
16 |
UUUGCAGUUCGAAAGU |
AUUUUUUAACUGUAAG |
Translation |
982-997 |
5’ region & before CDS |
| miRn12 |
S_seq_7691 |
HbAP2-10 |
hevea_454_rep_c22185 |
23,384 |
−26,47 |
17 |
UUAGCAGUUCGAAAGUG |
CACCCUUGAACUGCUAA |
Cleavage |
39-55 |
3’ region & after CDS |
| miRn12 |
S_seq_2869 |
HbERF-Xa1 |
hevea_454_c58761 |
22,067 |
−32,35 |
17 |
UUGGCAGU-UCGAAAGUG |
UACUUUCGAUACUGCCGA |
Translation |
611-628 |
Inside CDS & inside AP2 domain |
| miRn14 | S_seq_358709 | HbERF-Ib5 | hevea_454_rep_c4396 | 8,491 | −24 | 26 | UAGAACACAAUUAUAGGAAUCAAUAU | AUAUUGGU-CUUGUACUUGUGUUCUG | Translation | 1936-1960 | 3’ region & after CDS |
Target accessibility is represented as the maximum energy needed (UPE) to unpair the secondary structure around target site on target mRNA. The lower the energy the greater the possibility that small RNA is able to contact (and cleave) target mRNA. The lower the free energy the greater the possibility that small RNA is able to contact target mRNA. The predicted microRNA was based on a free energy threshold below −20 kcal/mol.