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

aly-miR163-3p.1

Organism

Arabidopsis lyrata

Species

Mature miRNA Sequence(5'-3')

UGAAGAGGACUUGGAACUCGAUC

miRBase

Precursor miRNA Sequence(5'-3')

GUGGGAGACAAGUACCUUCGAGAAACCGGCCAAAACCCGGUGGAUAAAAUCGAGUUCCAGCCUCCUCAGAGACUUUAGCAACAACGAUUUCAACACUCUCUUACAGGAACUUCCUCCAGGCAGAAGAUACUGUCUUGCGAAGUUCCGGGUUCCUUCUUCGUCCGUGAGUCAUGAUCAAGAUACGCUUUCUUGACCACAUGGUUGAACCAGUGCAAUGCAUGUUGCUGUUCCACAUGGGAGAGUCGCGGUUUUUGAUCCCUUUGGGGAUUUUGGAGGUGAAAUGGAACGCGUAAUUGAUGACUCCUAUGUGGAAACUCUUAUGUCGAAGAAGGAACCGCGAUUUUGCUAAUCCAAGUGCUUAAAUCGUUGAGGCUGAAGUCGUUGAAGAGGACUUGGAACUCGAUCUUAUCCACCGCGUUUUAUCCGGUUUCUCUGUGGGUUGUGAAAUAUUUUAU

miRBase

Precursor miRNA Structure(5'-3') 

-----GUGGGAG   AGU    U -          CC     C          A           - -    C    A         AA         CAA    CUCUUACAGGAACUUCCUCCAGGCAGAAGAUACUGUCUUGCGAAGUUCCGGGUUCCUUCUUCGUCCGUGAGUCAUGAUCAAGAUACGCUUUCUUGACCACAUGGUUGAACCAGUGCAAUGCAUGUUG 
            ACA   ACCU C GAGAAACCGG  AAAAC CGGUGGAUAA AUCGAGUUCCA G CCUC UCAG GACUUUAGC  CAACGAUUU   CACU                                                                                                                               C
            |||   |||| | ||||||||||  ||||| |||||||||| ||||||||||| | |||| |||| |||||||||  |||||||||   ||||                                                                                                                                
            UGU   UGGG G CUCUUUGGCC  UUUUG GCCACCUAUU UAGCUCAAGGU C GGAG AGUU CUGAAGUCG  GUUGCUAAA   GUGA                                                                                                                               U
UAUUUUAUAAAG   ---    U U          UA     C          C           U A    A    G         GA         UUC    ACCUAAUCGUUUUAGCGCCAAGGAAGAAGCUGUAUUCUCAAAGGUGUAUCCUCAGUAGUUAAUGCGCAAGGUAAAGUGGAGGUUUUAGGGGUUUCCCUAGUUUUUGGCGCUGAGAGGGUACACCUUG

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

ath-miR163           UUGAAGAGGACUUGGAACUUCGAU-
aly-miR163-3p.1      -UGAAGAGGACUUGGAACU-CGAUC
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