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-miR169h-3p

Organism

Brachypodium distachyon

Species

Mature miRNA Sequence(5'-3')

GGCAGUCACCUUGGCUAGC

miRBase

Precursor miRNA Sequence(5'-3')

CUUGCAUGAGGGCCAGAGCCUGCUUCCUCCGGUAGCCAAGGAUGACUUGCCUAUAUUUGCUCCUUCAGAAGUCCUGGUUAAUUACAUGCCAGGUUUCAGAUGAGUUUGGCGAUAGGCAGUCACCUUGGCUAGCCUGAGUGGCUCUUGCCUCUUAUGGAAGGCCU

miRBase

Precursor miRNA Structure(5'-3') 

----   G      -   C      UGCUUC   C   -        A     U      --AUUU    CU  A    U      UAA 
    CUU CAUGAG GGC AGAGCC      CUC GGU AGCCAAGG UGACU GCCUAU      GCUC  UC GAAG CCUGGU   U
    ||| |||||| ||| ||||||      ||| ||| |||||||| ||||| ||||||      ||||  || |||| ||||||   U
    GAA GUAUUC CCG UCUCGG      GAG CCG UCGGUUCC ACUGA CGGAUA      UGAG  AG CUUU GGACCG   A
UCCG   G      U   U      -----U   U   A        -     -      GCGGUU    -U  A    -      UAC

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

tae-miR169          GGGCAAGUCACCCUGGGCUACC
sit-miRN3032        GGGCAAAUCAUCC-GGGCUAAC
bdi-miR169k-3p      GGGCAAGUCAGCC-UGGCUACC
osa-miR169r-3p      UGGCAAGUC-UCCUCGGCUACC
bdi-miR169h-3p      --GGCAGUCACCU-UGGCUAGC
sbi-miR169d-3p      -GGGCGGUCACCU-UGGCUAGC
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