TarDB: A miRNA Target Database in Plants.


TarDB employs cross-species conservation filter, degradome and sRNA-seq data to identify high-confidence miRNA targets in plants.



miRNA ID

mtr-miR156a

Organism

Medicago truncatula

Species

Mature miRNA Sequence(5'-3')

UGACAGAAGAGAGAGAGCACA

miRBase

Precursor miRNA Sequence(5'-3')

AGCCAUGAAUCAGUCCGAGAUGACAGAAGAGAGAGAGCACACCCACCUGAUUACAAGUAACAAAAAACUACCAACUAUCAACAUUUUGUCUACUAUGAAGAAAAUCACAUGUCUAGACUAUAGUUACGAAUGGAAGAUACAUUCAAUGAUGUUUAUGAAAAUUUGAGACGGUCGAGGACUAUAGUUACUCUAUCGCAUACAUUUAAUGACAAAAAAAAUUGUGUACUCUUAUUUAUUUUCAAUACAUCUUCAUUCAAUUUCUAUGCAAGAAUCAAAAUGCAGUAUAAAAAAUUGCAUUCAAUAUCAUGGUAAAAAAAUUGUUCAAAAAAAGUAAAUAUCAUGGUAAAAAAAUCAUUAGAUUUUGCAAUAAGUAAGAGUCAAGUUUUACCUUGUGAGGAAUUCCUCCCAACAGAAUCAUGGGAGCUCUUUCUUCUUCUCUCAUUGUGCCCUGCCAGUCUCC

miRBase

Precursor miRNA Structure(5'-3') 

AGCCAUGAAU   UC  A     C      -        ACA    CC     ACAAGUAACAAAAAACUACCAACUAUCAACAUUUUGUCUACUAUGAAGAAAAUCACAUGUCUAGACUAUAGUUACGAAUGGAAGAUACAUUCAAUGAUGUUUAUGAAAAUUUGAGACGGUCGAGGACUAUAGUUACUCUAUCGCAUACAUUUAAUGACAAAAAAAAUUGUGUACUCUUA 
          CAG  CG GAUGA AGAAGA GAGAGAGC   CCCA  UGAUU                                                                                                                                                                                   U
          |||  || ||||| |||||| ||||||||   ||||  |||||                                                                                                                                                                                    
          GUC  GU UUACU UCUUCU CUUUCUCG   GGGU  ACUAA                                                                                                                                                                                   A
-CCUCUGACC   CC  G     C      U        --A    --     GACAACCCUCCUUAAGGAGUGUUCCAUUUUGAACUGAGAAUGAAUAACGUUUUAGAUUACUAAAAAAAUGGUACUAUAAAUGAAAAAAACUUGUUAAAAAAAUGGUACUAUAACUUACGUUAAAAAAUAUGACGUAAAACUAAGAACGUAUCUUUAACUUACUUCUACAUAACUUUUAU

Homologous Mature miRNAs   miRNAs are clustered by CD-HIT with sequence identity of >85% and word size of 5.

rco-miR156e         ----UGACAGAAGAGAGAGAGCACA
tcc-miR156a         ----UGACAGAAGAGAGAGAGCACA
bdi-miR156a         ----UGACAGAAGAGAGAGAGCACA
zma-miR156j-5p      ----UGACAGAAGAGAGAGAGCACA
gma-miR156b         ----UGACAGAAGAGAGAGAGCACA
mtr-miR156a         ----UGACAGAAGAGAGAGAGCACA
sbi-miR156d         ----UGACAGAAGAGAGAGAGCACA
osa-miR156k         ----UGACAGAAGAGAGAGAGCACA
bdi-miR156j         ----UGACAGAAGAGAGAGAGCAC-
ath-miR156j         ----UGACAGAAGAGAGAGAGCAC-
sit-miR156e         ----UGACAGAAGAGAGAGAGCAC-
mdm-miR156t         ---UUGACAGAAGAGAGAGAGCAC-
mdm-miR156u         ---UUGACAGAAGAGAGAGAGCAC-
mdm-miR156v         ---UUGACAGAAGAGAGAGAGCAC-
mdm-miR156w         ---UUGACAGAAGAGAGAGAGCAC-
mes-miR156k         ---UUGACAGAAGAGAGAGAGCAC-
gma-miR156f         ---UUGACAGAAGAGAGAGAGCACA
esa-miR156b         ----UGACAGAAGAGAGAGAGCAC-
esa-miR156c         ----UGACAGAAGAGAGAGAGCAC-
pvi-miR156p         ---AUGACAGAAGAGAGAGAGCAC-
pvi-miR156r         ---AUGACAGAAGAGAGAGAGCAC-
bra-miR156n         ----UGACAGAAGAGAGAGAGCAC-
bra-miR156p         ----UGACAGAAGAGAGAGAGCAC-
csi-miR3946         UUGUAGAGAAAGAGAAGAGAGCAC-
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