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-miR171j

Organism

Populus trichocarpa

Species

Mature miRNA Sequence(5'-3')

CGAGCCGAAUCAAUAUCACU

miRBase

Precursor miRNA Sequence(5'-3')

GAAGCAGACAUGGCGUGGUAUUGAUCCGGCUCUUCUUCUGUAUUUGCAUCAGAAGUUUUUCGCUGAAGACGAGCCGAAUCAAUAUCACUCUUGUACGCUUC

miRBase

Precursor miRNA Structure(5'-3') 

     AG   U  C           C      U     U  -AUUU  AU 
GAAGC  ACA GG GUGGUAUUGAU CGGCUC UCUUC GU     GC  C
|||||  ||| || ||||||||||| |||||| ||||| ||     ||  A
CUUCG  UGU CU CACUAUAACUA GCCGAG AGAAG CG     UG  A
     CA   U  -           A      C     U  CUUUU  AA

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

ptc-miR171m         CGAGCCGAAUCAAUAUCACU-
ptc-miR171j         CGAGCCGAAUCAAUAUCACU-
ptc-miR171l-3p      CGAGCCGAAUCAAUAUCACU-
ppe-miR171d-3p      CGAGCCGAAUCAAUAUCACUC
gma-miR171r         CGAGCCGAAUCAAUACCACUC
gma-miR171s         CGAGCCGAAUCAAUACCACUC
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