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

sly-miR393

Organism

Solanum lycopersicum

Species

Mature miRNA Sequence(5'-3')

AUCAUGCGAUCUCUUCGGAAU

miRBase

Precursor miRNA Sequence(5'-3')

AUUAUUCCAAAGGGAUCGCAUUGAUCCUGUGUUCCAAAUUAAUUAACCAUGGGACUAUGGGAUCAUGCGAUCUCUUCGGAAUUCUCC

miRBase

Precursor miRNA Structure(5'-3') 

--AUU     A            U        -      AAUUA 
     AUUCC AAGGGAUCGCAU GAUCCUGU GUUCCA     A
     ||||| |||||||||||| |||||||| ||||||     U
     UAAGG UUCUCUAGCGUA CUAGGGUA CAGGGU     A
CCUCU     C            -        U      ACCAA

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

stu-miR393-3p       AUCAUGCGAUCUCUUCGGAAU-
sly-miR393          AUCAUGCGAUCUCUUCGGAAU-
csi-miR393b-3p      -UCAUGCGAUCCCUUCGGAAUU
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