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

mdm-miR3627c

Organism

Malus domestica

Species

Mature miRNA Sequence(5'-3')

UCGCAGGAGAGAUGGCACUA

miRBase

Precursor miRNA Sequence(5'-3')

GGGGAUUUAUGUUCGCAGGAGAGAUGGCACUAAUUGUACUGCAAUUGCGUCAACAAUUGUUGCCAUCUCUCCUGUGACCAAAAAUCUCU

miRBase

Precursor miRNA Structure(5'-3') 

        A  U                 C       -AC   A 
GGGGAUUU UG UCGCAGGAGAGAUGGCA UAAUUGU   UGC A
|||||||| || ||||||||||||||||| |||||||   |||  
UCUCUAAA AC AGUGUCCUCUCUACCGU GUUAACA   GCG G
        A  C                 U       ACU   U

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

fve-miR3627a        UCGCAGGAGAGAUGGCACUACC
fve-miR3627b        UCGCAGGAGAGAUGGCACUACC
mdm-miR3627c        UCGCAGGAGAGAUGGCACUA--
mdm-miR3627b        UCGCAGGAGAGAUGGCACUA--
mdm-miR3627a        UCGCAGGAGAGAUGGCACUA--
stu-miR3627-5p      UCGCAGGAGAGAUGGCACUUAG
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