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

aly-miR169j-3p

Organism

Arabidopsis lyrata

Species

Mature miRNA Sequence(5'-3')

GGCAGUCUCCUUGGCUAUC

miRBase

Precursor miRNA Sequence(5'-3')

GAAUGAGGCAAAACAUAUUGAGUAAUGGAGUGUAUAAUGAGGAAGAGAGGUCUAACAUGGCGAAAAGAGUCAUGUUUAAUAGCCAAGGAUGACUUGCCUGAUCUUUUUCACCUCCAUGAUUCAAUUUGAAGUUCAUGCGUUUUGGAUUAUUAUGCAUCUAAAAGGUAUAAUAAUUCGAAAAUCAUGUUGAAUCAUGCGGGUUAGGUUUCAGGCAGUCUCCUUGGCUAUCUUGACAUGCUUUUUUCAUCCAUGUUAUACCUGUUUUUCUUUCUGUCUCUAAAGUCACUAUUAAGUCUCUUC

miRBase

Precursor miRNA Structure(5'-3') 

   U     AAAAC   U   G AA     UGU   AU        G    C        -C        U      -UA           U    U      UCUU   C    C          UUUGAAGUU    CG                AUC 
GAA GAGGC     AUA UGA U  UGGAG   AUA  GAGGAAGA AGGU UAACAUGG  GAAAAGAG CAUGUU   AUAGCCAAGGA GACU GCCUGA    UUU ACCU CAUGAUUCAA         CAUG  UUUUGGAUUAUUAUGC   U
||| |||||     ||| ||| |  |||||   |||  |||||||| |||| ||||||||  |||||||| ||||||   ||||||||||| |||| ||||||    ||| |||| ||||||||||         ||||  ||||||||||||||||   A
CUU CUCUG     UAU ACU A  AUCUC   UGU  UUCUUUUU UCCA AUUGUACC  CUUUUUUC GUACAG   UAUCGGUUCCU CUGA CGGACU    GGA UGGG GUACUAAGUU         GUAC  AAAGCUUAAUAAUAUG   A
   -     --AAU   C   G -A     ---   CU        G    U        UA        -      UUC           -    -      --UU   U    C          ---------    UA                GAA

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

aly-miR169k-3p      GGCAGUCU---CCUUGGCUAUC
aly-miR169l-3p      GGCAGUCU---CCUUGGCUAUC
aly-miR169j-3p      GGCAGUCU---CCUUGGCUAUC
aly-miR169h-3p      GGCAGUCU---CCUUGGCUAUU
stu-miR169a-3p      -GCAGUCU---CCUUGGCUACU
stu-miR169b-3p      -GCAGUCU---CCUUGGCUACU
stu-miR169c-3p      -GCAGUCU---CCUUGGCUACC
mtr-miR169d-3p      GGCAGGUCAUCCUUCGGCUAUA
mtr-miR169e-3p      GGCAGGUCAUCCUUCGGCUAUA
                     ****      * * *****