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

bdi-miR396b-3p

Organism

Brachypodium distachyon

Species

Mature miRNA Sequence(5'-3')

GUUCAAGAAAGCCCAUGGAAA

miRBase

Precursor miRNA Sequence(5'-3')

GGAGUAGUAAAAGAGAUGCGCGGGCAUGCUUUCCACAGGCUUUCUUGAACUGUGAACUCGUGGGGGUGUUCUCCUCUGAAUUGUGUCGUGGAAUUGCGGGCUUGUUCUUUAUCCGUCGAUCUCUCCGCCUGUUGAUGGUUCAAGAAAGCCCAUGGAAACCAUGCCGCCAUCUUGGUCUCGCGUCCCCGU

miRBase

Precursor miRNA Structure(5'-3') 

----   GUA UA AA      C    G    C      CA                G   UC       UGUUCUCCUCUGAAUUGUGUCGUGGA 
    GGA   G  A  GAGAUG GCGG CAUG UUUCCA  GGCUUUCUUGAACUGU AAC  GUGGGGG                          A
    |||   |  |  |||||| |||| |||| ||||||  |||||||||||||||| |||  |||||||                          U
    CCU   C  U  UUCUAC CGCC GUAC AAAGGU  CCGAAAGAACUUGGUA UUG  CGCCUCU                          C
UGCC   GCG UC GG      -    -    C      AC                G   UC       CUAGCUGCCUAUUUCUUGUUCGGGCG

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

osa-miR396e-3p      AUGGUUCAAGAAAGCCCAUGGAAA
bdi-miR396b-3p      ---GUUCAAGAAAGCCCAUGGAAA
bdi-miR396a-3p      ---GUUCAAGAAAGUCCUUGGAAA
osa-miR396f-3p      AUAGUUCAAGAAAGUCCUUGGAAA
smo-miR396          ----UUCCACGGCUUUCUUGAACC
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