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

ptc-miR167f-3p

Organism

Populus trichocarpa

Species

Mature miRNA Sequence(5'-3')

AGAUCAUGUGGCAGUUUCACC

miRBase

Precursor miRNA Sequence(5'-3')

CUCUAUCAGUUGAAGCUGCCAGCAUGAUCUUAGCCUUCCUCCUUUGUUGAGGAAAGAAACAGAUCAUGUGGCAGUUUCACCUGUUGU

miRBase

Precursor miRNA Structure(5'-3') 

CUCUAU   U           G        -UAG C      CU 
      CAG UGAAGCUGCCA CAUGAUCU    C UUCCUC  U
      ||| ||||||||||| ||||||||    | ||||||  U
      GUC ACUUUGACGGU GUACUAGA    G AAGGAG  U
--UGUU   C           -        CAAA A      UU

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

csi-miR167a-3p      AGAUCAUCUG-GCAGUUUCACC
mdm-miR167a         AGAUCAUCUG-GCAGUUUCACC
ptc-miR167h-3p      AGAUCAUGUG-GCAGUUUCACC
ptc-miR167g-3p      AGAUCAUGUG-GCAGUUUCACC
ptc-miR167f-3p      AGAUCAUGUG-GCAGUUUCACC
ath-miR167a-3p      -GAUCAUGUUCGCAGUUUCACC
aly-miR167a-3p      -GAUCAUGUUCGCAGUUUCACC
zma-miR167h-3p      -GAUCAUGUU-GCAGCUUCAC-
bdi-miR167d-3p      AGAUCAUGUU-GCAGCUUCAC-
zma-miR167i-3p      -GAUCAUGUU-GCAGCUUCAC-
                     ****** *  **** *****