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

ath-miR164b-3p

Organism

Arabidopsis thaliana

Species

Mature miRNA Sequence(5'-3')

CAUGUGCCCAUCUUCACCAUC

miRBase

Precursor miRNA Sequence(5'-3')

GAUGGAGAAGCAGGGCACGUGCAUUACUAGCUCAUAUAUACACUCUCACCACAAAUGCGUGUAUAUAUGCGGAAUUUUGUGAUAUAGAUGUGUGUGUGUGUUGAGUGUGAUGAUAUGGAUGAGUUAGUUCUUCAUGUGCCCAUCUUCACCAUC

miRBase

Precursor miRNA Structure(5'-3') 

     A    CA         CAUU          A    ----   U    - -    A      G     AU    A 
GAUGG GAAG  GGGCACGUG    ACUAGCUCAU UAUA    CAC CUCA C CACA AUGCGU UAUAU  GCGG A
||||| ||||  |||||||||    |||||||||| ||||    ||| |||| | |||| |||||| |||||  ||||  
CUACC CUUC  CCCGUGUAC    UGAUUGAGUA GUAU    GUG GAGU G GUGU UGUGUA AUAUA  UGUU U
     A    UA         UUCU          G    AGUA   U    U U    G      G     -G    U

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

ath-miR164b-3p      CAUGUGCCCAUCUUCACCAUC
aly-miR164b-3p      CAUGUGCCCAUCUUCACCAUC
zma-miR164c-3p      CAUGUGCCCUUCUUCUCCAUC
zma-miR164h-3p      CAUGUGCCCUUCUUCUCCAUC
csi-miR164a-3p      CAUGUGCCCUUCUUCCCCAUC
zma-miR164b-3p      -AUGUGCCCAUCUUCUCCACC
bdi-miR164a-3p      CAUGUGCCCUUCUUCUCCACC
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