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-miR160c-3p

Organism

Populus trichocarpa

Species

Mature miRNA Sequence(5'-3')

GCGUAUGAGGAGCCAUGCAUA

miRBase

Precursor miRNA Sequence(5'-3')

AUAUUAUAUGUGCCUGGCUCCCUGUAUGCCAUUUGCAGAGCCCACCGGUUCUUCGAUGGCCUCCGUGGAUGGCGUAUGAGGAGCCAUGCAUAUUCACA

miRBase

Precursor miRNA Structure(5'-3') 

AUAUUAU      C       C              A   C   C   U 
       AUGUGC UGGCUCC UGUAUGCCAUUUGC GAG CCA CGG U
       |||||| ||||||| |||||||||||||| ||| ||| |||  
       UAUACG ACCGAGG GUAUGCGGUAGGUG CUC GGU GCU U
--ACACU      U       A              C   C   A   U

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

ath-miR160a-3p      GCGUAUGAGGAGCCAUGCAUA
ptc-miR160b-3p      GCGUAUGAGGAGCCAUGCAUA
ptc-miR160c-3p      GCGUAUGAGGAGCCAUGCAUA
csi-miR160a-3p      GCGUAUGAGGAGCCAUGCAUA
aly-miR160a-3p      GCGUAUGAGGAGCCAUGCAUA
cpa-miR160c-3p      GCGUAUGAGGAGCCAUGCAUA
cpa-miR160f-3p      GCGUAUGAGGAGCCAUGCAUA
stu-miR160a-3p      GCGUAUGAGGAGCCAAGCAUA
gma-miR160a-3p      GCGUAUGAGGAGCCAAGCAUA
csi-miR160b-3p      GCGUACGAGGAGCCAAGCAUA
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