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-miR2111d

Organism

Brassica rapa

Species

Mature miRNA Sequence(5'-3')

AUCCUCGGGACACAGAUUACC

PmiREN

Precursor miRNA Sequence(5'-3')

GATACTTGGTGAGGAACTGGTAATCTGCATCCTGAGGTTTAAAAACTCATAGACATGTAAAGCAAATTGTATACATGATTTTTAATCCTCGGGACACAGATTACCTCTTCCTTACTCGAGGTACA

PmiREN

Precursor miRNA Structure(5'-3') 

-GAUA    -        CU         CA        U       C    --AG   UGUAA 
     CUUG GUGAGGAA  GGUAAUCUG  UCCUGAGG UUAAAAA UCAU    ACA     A
     |||| ||||||||  |||||||||  |||||||| ||||||| ||||    |||      
     GAGC CAUUCCUU  CCAUUAGAC  AGGGCUCC AAUUUUU AGUA    UGU     A
ACAUG    U        CU         AC        U       -    CAUA   UAAAC

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

aly-miR2111a-3p      GUCCUCGGGAUGCGGAUUACC
aly-miR2111c-3p      GUCCUCGGGAUGCGGAUUACC
ath-miR2111a-3p      GUCCUCGGGAUGCGGAUUACC
bra-miR2111f         GACCUCAGGAUGCGGAUUACC
fve-miR2111b-3p      GCCCUUGGGAUGCGGAUUACC
bra-miR2111c         AUCCUCGGGAUGCGGAUUACC
aly-miR2111b-3p      AUCCUCGGGAUACAGAUUACC
bra-miR2111d         AUCCUCGGGACACAGAUUACC
ath-miR2111b-3p      AUCCUCGGGAUACAGUUUACC
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