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-miR858b

Organism

Arabidopsis thaliana

Species

Mature miRNA Sequence(5'-3')

UUCGUUGUCUGUUCGACCUUG

miRBase

Precursor miRNA Sequence(5'-3')

CCUACCCGAAGGGUUUUGGAGAGUAGACAAAGAGACAAACAUAGAGGUGUGAGUUUGGUUUGGUUUUGGGUUUUGGGGGGUUGGUAGUGUUUGAGGUCCAUAUGCCUCGAUCUUCCGCUUCUAUUAAUUAAUUUUCUCUAUUAGAAAUAUUAUCUAAUUAUUCCACUCCAUCGAACCAUGCACAUAUAUAAUGAUAUGUAUAAGCCCAUCAAAGUUUUUGAAUUCAGUGCAAACACUUGUCAAAGGAGCAGUCCCGAUCUGGUUCCAUCUUAUCUUCGUUGUCUGUUCGACCUUGGCUUUGGC

miRBase

Precursor miRNA Structure(5'-3') 

CCUAC      GGUUUU  -A          A  GACAAACAUAGAGGUGUGAGUUUGGUUUGGUUUUGGGUUUUGGGGGGUUGGUAGUGUUUGAGGUCCAUAUGCCUCGAUCUUCCGCUUCUAUUAAUUAAUUUUCUCUAUUAGAAAUAUUAU 
     CCGAAG      GG  GAGUAGACAA GA                                                                                                                        C
     ||||||      ||  |||||||||| ||                                                                                                                         
     GGUUUC      CC  CUUGUCUGUU CU                                                                                                                        A
----C      --GGUU  AG          G  UCUAUUCUACCUUGGUCUAGCCCUGACGAGGAAACUGUUCACAAACGUGACUUAAGUUUUUGAAACUACCCGAAUAUGUAUAGUAAUAUAUACACGUACCAAGCUACCUCACCUUAUUAA

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
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