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-miR3627b

Organism

Populus trichocarpa

Species

Mature miRNA Sequence(5'-3')

UGUCGCAGGAGAGAUGGCGCUA

miRBase

Precursor miRNA Sequence(5'-3')

GGGGGUUUCUUGUCGCAGGAGAGAUGGCGCUAGCUAACCAUGGUCAUAUCAUAUAUAUCAUAUGGCAAGUAUUACUUGCUCUUUGUAUGUAUCAGCUGUAAAGAUAGCUCAGCUAAAGCCAUCCUCCUGCGACUGGACACCCUG

miRBase

Precursor miRNA Structure(5'-3') 

G     U   U          A      GC     AACCAUGGUCAUAUCAUAUAUAUCAUAUGGCAAGUA 
 GGGGU UCU GUCGCAGGAG GAUGGC  UAGCU                                    U
 ||||| ||| |||||||||| ||||||  |||||                                    U
 UCCCA AGG CAGCGUCCUC CUACCG  AUCGA                                    U
G     C   U          -      AA     CUCGAUAGAAAUGUCGACUAUGUAUGUUUCUCGUUC

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

vvi-miR3627-5p      UUGUCGCAGGAGAGACGGCACU-
gma-miR5786         -UGUCGCAGGAUAGAGGGCACU-
ptc-miR3627b        -UGUCGCAGGAGAGAUGGCGCUA
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