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

ptc-miR169w

Organism

Populus trichocarpa

Species

Mature miRNA Sequence(5'-3')

UAGCCAAGGAUGACUUGCCCA

miRBase

Precursor miRNA Sequence(5'-3')

CGUGUUUGGUAGCCAAGGAUGACUUGCCCACUCUAUGGAAAGAGUUCUCAAGCACACGGCAGAGAGGACCCUUACUUCGGCUCUGGGCAGUCACCUUGGCUAUGCUGAC

miRBase

Precursor miRNA Structure(5'-3') 

CGU   -UG          A     U     CUCUA    --   A      -AA  A 
   GUU   GUAGCCAAGG UGACU GCCCA     UGGA  AAG GUUCUC   GC C
   |||   |||||||||| ||||| |||||     ||||  ||| ||||||   || A
   CAG   UAUCGGUUCC ACUGA CGGGU     GCUU  UUC CAGGAG   CG G
---   UCG          -     -     -CUCG    CA   C      AGA  G

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

lus-miR169a       UAGCCAAGGAUGACUUGCCCA--
lus-miR169d       UAGCCAAGGAUGACUUGCCCA--
ptc-miR169w       UAGCCAAGGAUGACUUGCCCA--
ptc-miR169v       UAGCCAAGGAUGACUUGCCCA--
ptc-miR169ac      UAGCCAAGGACGACUUGCCCA--
ptc-miR169ad      UAGCCAAGGACGACUUGCCCA--
ptc-miR169ae      UAGCCAAGGACGACUUGCCCA--
ptc-miR169af      UAGCCAAGGACGACUUGCCCA--
osa-miR169q       UAGCCAAGGA-GACU-GCCCAUG
zma-miR169d       UAGCCAAGGA-GACU-GCCUAUG
zma-miR169e       UAGCCAAGGA-GACU-GCCUACG
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