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

dca-miR164-b2.0r1-13907

Organism

Daucus carota

Species

Mature miRNA Sequence(5'-3')

CGUGUGCUCUUGCUCUCCAGC

Plant sRNA Gene (Penn State Uni)

Precursor miRNA Sequence(5'-3')

CUGCUCAAGUUUAUGAGACAAUGCCACGGAACAAUGGGAUUGGUGAUUCAUGCUGGAGAAGCAGGGCACAUGCUAGAUGCUUCAGUUGAUGAUUGGAGAAUGUCGCGUGUGCUCUUGCUCUCCAGCUUGGGACCUAUCCCAGUUCAG

Precursor miRNA Structure(5'-3') 

CUGCUCAAGUUUAUGAGACAAUGCCACG    AA      U   GA    U        A     -        U G  G          
                            GAAC  UGGGAU GGU  UUCA GCUGGAGA GCAGG GCACAUGC A AU CUUCAGUUG 
                            ||||  |||||| |||  |||| |||||||| ||||| |||||||| | || |||||||| A
                            CUUG  ACCCUA CCA  GGGU CGACCUCU CGUUC CGUGUGCG U UA GAGGUUAGA 
--------------------------GA    --      U   --    U        -     U        C G  A

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

dca-miR164-b2.0r1-13907      CGUGUGCUCUUGCUCUCCAGC
stu-miR164-3p                CAUGUGCUCUAGCUCUCCAGC
dca-miR164-b2.0r1-17943      CAUGUGCUCUUGCUCUCCUGC
                             * ******** ******* **