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-miR164b-3p

Organism

Arabidopsis lyrata

Species

Mature miRNA Sequence(5'-3')

CAUGUGCCCAUCUUCACCAUC

miRBase

Precursor miRNA Sequence(5'-3')

GAUGGAGAAGCAGGGCACGUGCAUUACUAGCUCAUCUCGUAUGCAUAUAUAUAUACAUCCUCACCACAAAUGCGUGUAUAUGUGCGGAGAUAUAGAUAUAUAUGUGUGUGGAGUGUGAUGAUAUAAAUGAGUUAGUUCUUCAUGUGCCCAUCUUCACCAUC

miRBase

Precursor miRNA Structure(5'-3') 

     A    CA         CAUU          -------------   G               -ACAUC   AC    A   C 
GAUGG GAAG  GGGCACGUG    ACUAGCUCAU             CUC UAUGCAUAUAUAUAU      CUC  CACA AUG G
||||| ||||  |||||||||    ||||||||||             ||| |||||||||||||||      |||  |||| |||  
CUACC CUUC  CCCGUGUAC    UGAUUGAGUA             GAG GUGUGUGUAUAUAUA      GAG  GUGU UAU U
     A    UA         UUCU          AAUAUAGUAGUGU   -               GAUAUA   GC    A   G

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
                     ******** ***** *** *