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

bdi-miR408-5p

Organism

Brachypodium distachyon

Species

Mature miRNA Sequence(5'-3')

CAGGGAUGGAGCAGAGCAUGG

miRBase

Precursor miRNA Sequence(5'-3')

GGGGAGGAGACAGGGAUGGAGCAGAGCAUGGGAUGGGGCUAACAGCAAAAUUACGUUCGUUAUUACUUCCACUAUAUGCUGUGAGAGCUGCUGCUGCUGUGUUGUUGCUCCCUCCCCUGCACUGCCUCUUCCCUGGCUCCCCUGC

miRBase

Precursor miRNA Structure(5'-3') 

-G   A    A      U    -   A   U    U     U       AAAUUACGUUCGUUAUUACUUCCAC 
  GGG GGAG CAGGGA GGAG CAG GCA GGGA GGGGC AACAGCA                         U
  ||| |||| |||||| |||| ||| ||| |||| ||||| |||||||                          
  UCC CCUC GUCCCU UCUC GUC CGU CCCU CCUCG UUGUUGU                         A
CG   -    G      -    C   A   C    C     -       GUCGUCGUCGUCGAGAGUGUCGUAU

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

zma-miR408b-5p      -CAGGGACGAGGCAGAGCAUGG
stu-miR408a-5p      ACAGGGACGAGGCAGCGCAUG-
osa-miR408-5p       -CAGGGAUGAGGCAGAGCAUGG
bdi-miR408-5p       -CAGGGAUGGAGCAGAGCAUGG
                     ****** *  **** *****