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

ath-miR160c-3p

Organism

Arabidopsis thaliana

Species

Mature miRNA Sequence(5'-3')

CGUACAAGGAGUCAAGCAUGA

miRBase

Precursor miRNA Sequence(5'-3')

GUUAUGCCUGGCUCCCUGUAUGCCACGAGUGGAUACCGAUUUUGGUUUUAAAAUCGGCUGCCGGUGGCGUACAAGGAGUCAAGCAUGAC

miRBase

Precursor miRNA Structure(5'-3') 

       C       C          GA    AUA         G 
GUUAUGC UGGCUCC UGUAUGCCAC  GUGG   CCGAUUUUG U
||||||| ||||||| ||||||||||  ||||   |||||||||  
CAGUACG ACUGAGG ACAUGCGGUG  CGUC   GGCUAAAAU U
       A       A          GC    ---         U

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

osa-miR160a-3p      GCGUGCA-AGGAGCCAAGCAUG-
osa-miR160b-3p      GCGUGCA-AGGAGCCAAGCAUG-
osa-miR160d-3p      GCGUGCG-AGGAGCCAAGCAUG-
aly-miR160c-3p      GCGUACA-AGGAGCCAAGCAUG-
aly-miR160b-3p      GCGUACAGAGUAGUCAAGCAUG-
ath-miR160c-3p      -CGUACA-AGGAGUCAAGCAUGA
                     *** *  ** ** ********