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-miR169d

Organism

Linum usitatissimum

Species

Mature miRNA Sequence(5'-3')

UAGCCAAGGAUGACUUGCCCA

miRBase

Precursor miRNA Sequence(5'-3')

GGGUGUUACAUGAAAGAUCAGAACUUGUUUGGUAGCCAAGGAUGACUUGCCCACAUUUCUCUGCUGCUAGCUGCAUCUUACUUAACAGUACAGAAAUUAAGGAAUUGUUUUGGGCAGUCUCCUUGGUUAUGCUGACAGUUUACAAUCUCUCAUGCUAUGCCC

miRBase

Precursor miRNA Structure(5'-3') 

      UA     A    -CA     U   -UG           U    U    ---   U    CUGCUGCUAGCUGCAUCUU 
GGGUGU  CAUGA AGAU   GAACU GUU   GUAGCCAAGGA GACU GCCC   ACA UUCU                   A
||||||  ||||| ||||   ||||| |||   ||||||||||| |||| ||||   ||| ||||                    
CCCGUA  GUACU UCUA   UUUGA CAG   UAUUGGUUCCU CUGA CGGG   UGU AAGG                   U
      UC     C    ACA     -   UCG           -    -    UUU   U    AAUUAAAGACAUGACAAUU

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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