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-miR482d-5p

Organism

Citrus sinensis

Species

Mature miRNA Sequence(5'-3')

UGGUAUGGGUGAGUAGGGAAG

miRBase

Precursor miRNA Sequence(5'-3')

AGAGGGAGUUGAAGGAUAUUGGGAAGGUUUUGGUAUGGGUGAGUAGGGAAGAUAAUUUAACUAAGUAAUAAUAAUAUCACUUUUUUCAUUAUUACUAUUUACUUAAGGAAUUUGUAUAUCUUCCCUACUCCACCCAUGCCAUAGGUUUCCCAUUAUUCCUCCCUCUCCUUAUC

miRBase

Precursor miRNA Structure(5'-3') 

-------        UUGAA     U       G  U           -             -----    AAC       -  A     UCACU 
       AGAGGGAG     GGAUA UGGGAAG UU UGGUAUGGGUG AGUAGGGAAGAUA     AUUU   UAAGUAA UA UAAUA     U
       ||||||||     ||||| ||||||| || ||||||||||| |||||||||||||     ||||   ||||||| || |||||     U
       UCUCCCUC     CUUAU ACCCUUU GA ACCGUACCCAC UCAUCCCUUCUAU     UAAG   AUUCAUU AU AUUAU     U
CUAUUCC        -----     U       G  U           C             AUGUU    -GA       U  C     UACUU

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---
                         *             *