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

lus-miR169a

Organism

Linum usitatissimum

Species

Mature miRNA Sequence(5'-3')

UAGCCAAGGAUGACUUGCCCA

miRBase

Precursor miRNA Sequence(5'-3')

AGGACCAGGGUGUUACAUGAAAGAUCAGAACUUGUUUGGUAGCCAAGGAUGACUUGCCCACAUUUCUCUGCUGCUAGCUGCAUCUUACUUACAGAGUUUGUCUGGGCAGUCUCCUUGGUUAUGCUGACAGGUUAUGAUCUCUCAUGUUAUGCCCUUUGUUCU

miRBase

Precursor miRNA Structure(5'-3') 

     -C       U      A      G        -UG           U    U     C  -UU     --------C   U 
AGGAC  AGGGUGU ACAUGA AGAUCA AACUUGUU   GUAGCCAAGGA GACU GCCCA AU   CUCUG         UGC A
|||||  ||||||| |||||| |||||| ||||||||   ||||||||||| |||| ||||| ||   |||||         ||| G
UCUUG  UCCCGUA UGUACU UCUAGU UUGGACAG   UAUUGGUUCCU CUGA CGGGU UG   GAGAC         ACG G
     UU       U      C      A        UCG           -    -     C  UUU     AUUCAUUCU   U

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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