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

ath-miR858a

Organism

Arabidopsis thaliana

Species

Mature miRNA Sequence(5'-3')

UUUCGUUGUCUGUUCGACCUU

miRBase

Precursor miRNA Sequence(5'-3')

CUCAUCUUUGUUUCGUUGUCUGUUCGACCUUGGUCUCGAUCUCUCCUCAAAACCCUAAUACGCGCUUUAUCGUUUAUUUCAUUCAUCCAUCCUUCUUAUGAUCAUCAUAAACUAACGUACAUGGUUUAUCGGUUUGUUAUUGAUGGGGAUUGGGGUAGAUAGACGAUCGAAACUUUUGAUUUCUGAG

miRBase

Precursor miRNA Structure(5'-3') 

    ----  -UUU      -         CG           G   UCUCCUCA     CUAAUACGCGCUUUAUCGUUUAUUUCAUUCAUCCAUC 
CUCA    UC    GUUUCG UUGUCUGUU  ACCUUGGUCUC AUC        AAACC                                     C
||||    ||    |||||| |||||||||  ||||||||||| |||        |||||                                      
GAGU    AG    CAAAGC AGCAGAUAG  UGGGGUUAGGG UAG        UUUGG                                     C
    CUUU  UUUU      U         -A           G   --UUAUUG     CUAUUUGGUACAUGCAAUCAAAUACUACUAGUAUUCU

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

bra-miR858b        UUUCGUUGUCUGUUCGACCUU-
ath-miR858a        UUUCGUUGUCUGUUCGACCUU-
aly-miR858-5p      UUUCGUUGUCUGUUCGACCUU-
ppe-miR858         -CUCGUUGUCUGUUCGACCUUG
csi-miR858-3p      -CUCGUUGUCUGUUCGACCUUG
ath-miR858b        -UUCGUUGUCUGUUCGACCUUG
zos-miR858         -UUCGUUGUCUGUUCGACCUUG
bra-miR858a        -UUCGUUGUCUGUUCGACCUUG
mdm-miR858         -UUCGUUGUCUGUUCGACCUGA
                     ******************