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-miR472b

Organism

Populus trichocarpa

Species

Mature miRNA Sequence(5'-3')

UUUUCCCAACUCCACCCAUCCC

miRBase

Precursor miRNA Sequence(5'-3')

UUACUGGAUGGGUGAGUGGGGAAGAUAACUAAGCUCUGUUUGUUAUUUUCCCAACUCCACCCAUCCCAUAG

miRBase

Precursor miRNA Structure(5'-3') 

UUACU         -   G           U      
     GGAUGGGUG AGU GGGAAGAUAAC AAGCU 
     ||||||||| ||| ||||||||||| |||| C
     CCUACCCAC UCA CCCUUUUAUUG UUUGU 
GAUAC         C   A           -

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

ptc-miR472b         --UUUUCCCAACUCCACCCAUCCC
csi-miR482f-3p      ---UUUUCCCACACCUCCCAUCCC
ptc-miR472a         --UUUUCCCUACUCCACCCAUCCC
mes-miR482          --UCUUCCCUACUCCACCCAUUCC
ath-miR472-3p       --UUUUUCCUACUCCGCCCAUACC
aly-miR472-3p       --UUUUUCCUACUCCGCCCAUACC
csi-miR482f-5p      ---GAUGGGUGAGUUGGGAAAAUA
csi-miR482d-5p      UGGUAUGGGUGAGUAGGGAAG---
                         *             *