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-miR396e-3p

Organism

Citrus sinensis

Species

Mature miRNA Sequence(5'-3')

GCUCAAGAAUGCCGUGGGAAA

miRBase

Precursor miRNA Sequence(5'-3')

GGAAAUUAAUUAAAGGUCUUUUGCAUGCUUUUCCACGGCUUUCUUGAACUUAAUUAGUACGGUUAAUUUUUUUGUGCUAUUAACAAGCAAUUAAUAUGCAAAUCUUUAAUCAGUGCAAAGCUCAAGAAUGCCGUGGGAAAACAUGAAAGGUUUUUGUCGUGCCACCACCC

miRBase

Precursor miRNA Structure(5'-3') 

----  AAAUUAAU      U     G    C           U       A   AAUUA    -      UUUU      C      CA 
    GG        UAAAGG CUUUU CAUG UUUUCCACGGC UUCUUGA CUU     GUAC GGUUAA    UUUGUG UAUUAA  A
    ||        |||||| ||||| |||| ||||||||||| ||||||| |||     |||| ||||||    |||||| ||||||  G
    CC        GUUUUU GGAAA GUAC AAAGGGUGCCG AAGAACU GAA     CGUG CUAAUU    AAACGU AUAAUU  A
CCCA  ACCGUGCU      -     -    A           U       C   ----A    A      -UCU      -      AA

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

csi-miR396e-3p      GCUCAAGAAUGCCGUGGGAAA-
zma-miR396e-3p      GGUCAAGAAAGCCGUGGGAAG-
ptc-miR396g-3p      -CUCAAGAAAGCCGUGGGAAAA
ptc-miR396e-3p      -CUCAAGAAAGCUGUGGGAGA-
                      ******* ** ******