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

csi-miR482f-3p

Organism

Citrus sinensis

Species

Mature miRNA Sequence(5'-3')

UUUUCCCACACCUCCCAUCCC

miRBase

Precursor miRNA Sequence(5'-3')

GGGAAGUCUUGGAGAUGGGUGAGUUGGGAAAAUAAUAACUUUCUUCACGAAAGAAAGCAAUUUUUUUCCCACACCUCCCAUCCCUAAGAUUUUC

miRBase

Precursor miRNA Structure(5'-3') 

G           A      U A  -        U   AA       C 
 GGAAGUCUUGG GAUGGG G GU UGGGAAAA AAU  CUUUCUU A
 ||||||||||| |||||| | || |||||||| |||  ||||||| C
 CUUUUAGAAUC CUACCC C CA ACCCUUUU UUA  GAAAGAA A
-           C      U -  C        U   AC       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---
                         *             *