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

mpo-miR-b3.0r1-8350

Organism

Marchantia polymorpha

Species

Mature miRNA Sequence(5'-3')

CGGAUCAUGUGGAGACUCACC

Plant sRNA Gene (Penn State Uni)

Precursor miRNA Sequence(5'-3')

AUUUUGGCUCCAAUGGGUGGAUGGGCUCGAAAGAUCUGAGGUGAGUCUUCUCCACCUGUUCUGUACUAAAUGUUGACUGCUGUAACGCAGUACGAUUGGUACGGAUCAUGUGGAGACUCACCUCAGAUUUUGGUUCAGUGACUGAAACAUAUACGGCCGAGGCUUCUUCAAUCGCGAGUUGCGCAACAGGUGCAAGUAGAGUAAAUCUCUUUCCUUACUAAGAGAUUACAGCUGUCAUGUCGUCUUAAGAAUGUCGAGUUUGAUGCAGUGGC

Precursor miRNA Structure(5'-3') 

-------------------------------------------------------------------------------------------------------------A        -CCA   ----   G A      CGA                 UUC     C  U          A   UG     UG 
                                                                                                              UUUUGGCU    AUG    GGU G UGGGCU   AAGAUCUGAGGUGAGUC   UCCAC UG UCUGUACUAA UGU  ACUGC  U
                                                                                                              ||||||||    |||    ||| | ||||||   |||||||||||||||||   ||||| || |||||||||| |||  |||||   
                                                                                                              GGAGCCGG    UAC    UCA U ACUUGG   UUUUAGACUCCACUCAG   AGGUG AC AGGCAUGGUU GCA  UGACG  C
CGGUGACGUAGUUUGAGCUGUAAGAAUUCUGCUGUACUGUCGACAUUAGAGAAUCAUUCCUUUCUCUAAAUGAGAUGAACGUGGACAACGCGUUGAGCGCUAACUUCUUC        CAUA   AAAG   G G      ---                 ---     U  U          A   --     CA

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

mpo-miR-b3.0r1-8350      --CGGAUCAUG-UGG-AGACUCACC---
stu-miR167a-3p           ----GAUCAUG-UGGCAGCCUCACC---
csi-miR167d-3p           AUCGGAUCAUG-UGGUAGCUUCACC---
stu-miR167d-3p           ----GAUCAUG-UGGUUGCUUCACC---
mtr-miR167b-3p           ----GAUCAUG-UUGGAGCUUCACC---
ath-miR167c-3p           --UAGGUCAUGCUGGUAGUUUCACC---
stu-miR167b-3p           ----GAUCAUG-UGGCAGCAUCACC---
bol-miR167c              ------UGAAGCUGCCAGCAUGAUCUAU
mac-miR167a              ------UGAAGCUGCCAGCAUGAUCUGA
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