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

aly-miR156f-3p

Organism

Arabidopsis lyrata

Species

Mature miRNA Sequence(5'-3')

GCUCACUCUCUAUCUGUCACC

miRBase

Precursor miRNA Sequence(5'-3')

GUAUGUGAUAUUAAGAGGUAUAUAUGAAUCAUAAAUAUGGAUGGUUUGAUUGAUGAGUAAUUGAUGGUGACAGAAGAGAGUGAGCACACAUGGUGGCUUUCUUGCAUAUUUGAUGGUUUCAUGCUUGAAGCUAUGUGUGCUCACUCUCUAUCUGUCACCCCCUUCUCUCUCUCUAUAUACACCAUUUAAAUUUAUUUUAUAGAGUUAUAUACAAUUUGAUUUUGAUAC

miRBase

Precursor miRNA Structure(5'-3') 

----------------         AUUAAGAGGUAUA      UC      A        -UUG  U  U   -UAAUU AU         -                    GGCU   UU   UAUU   U 
                GUAUGUGAU             UAUGAA  AUAAAU UGGAUGGU    AU GA GAG      G  GGUGACAGA AGAGAGUGAGCACACAUGGU    UUC  GCA    UGA G
                |||||||||             ||||||  |||||| ||||||||    || || |||      |  ||||||||| ||||||||||||||||||||    |||  |||    ||| G
                CAUAUAUUG             AUAUUU  UAUUUA AUUUACCA    UA CU CUC      C  CCACUGUCU UCUCUCACUCGUGUGUAUCG    AAG  CGU    ACU U
CAUAGUUUUAGUUUAA         -----------AG      --      A        CAUA  U  -   UCUCUU CC         A                    ----   UU   ----   U

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

mtr-miR156c-3p      UGCUUACUCUCUAUCUGUCACC
aly-miR156e-3p      -GCUUACUCUCUCUCUGUCACC
stu-miR156g-3p      -GCUUACUCUCUAUCUGUCACC
sly-miR156e-3p      -GCUUACUCUCUAUCUGUCACC
aly-miR156f-3p      -GCUCACUCUCUAUCUGUCACC
ath-miR156f-3p      -GCUCACUCUCUAUCCGUCACC
csi-miR156c-3p      -GCUCACUCUCUAUCUGUCACC
                     *** ******* ** ******