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

bra-miR5654a

Organism

Brassica rapa

Species

Mature miRNA Sequence(5'-3')

AUAAAUCCCAAGCAUCAUCCA

miRBase

Precursor miRNA Sequence(5'-3')

UAAUGAUGUAUUGUAGCUCUGCGUUUCUUGUUCGUUCACUCUUUUGUCAGGUAUUAACAAGAUAAAUCCCAAGCAUCAUCCACCUUAUUAGCCCUUGAACAUGAAGGCUUGUAAAAUGGAUGAUGCUUGGGAUUUAUUUUGUACUCUCCUCUUCUAAAAGAGUGUUGCCUCCAUAGGACUACCAAUGAUUUCAGA

miRBase

Precursor miRNA Structure(5'-3') 

UAA   U  -    -   CUCUGCGUU      --UC  -U          --UC   UAUUA                          CC    U    C  GA 
   UGA GU AUUG UAG         UCUUGU    GU  CACUCUUUUG    AGG     ACAAGAUAAAUCCCAAGCAUCAUCCA  UUAU AGCC UU  A
   ||| || |||| |||         ||||||    ||  ||||||||||    |||     ||||||||||||||||||||||||||  |||| |||| ||   
   ACU UA UAAC AUC         AGGAUA    CG  GUGAGAAAAU    UCC     UGUUUUAUUUAGGGUUCGUAGUAGGU  AAUG UCGG AG  U
-AG   U  G    C   ---------      CCUC  UU          CUUC   UCUCA                          AA    U    A  UA

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

bra-miR5654a        ---AUAAAUCCCAAGCAUCAUCCA
bra-miR5654b        ---AUAAAUCCCAAGCAUCAUCCA
ath-miR5654-5p      ---AUAAAUCCCAA-CAUCUUCCA
esa-miR5654         ---AUAAAUCCCAUGCAUCUUCCA
ath-miR5654-3p      UGGAAGAUGCUUUGGGAUUUAUU-
                       *  *  *      **