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-miR159b-5p

Organism

Arabidopsis lyrata

Species

Mature miRNA Sequence(5'-3')

GAGCUCCUUGAAGUUCAAUGG

miRBase

Precursor miRNA Sequence(5'-3')

GGAAGAAGAAGAGGAAGAGCUCCUUGAAGUUCAAUGGAGGGUUUAGCAGGGUAAAGUAAAGCUGCUAAGCUAUGGAUCCCAUAAACCUUAUCAAAUUCAAAAUAAGGAUUUUUUAUGGAUUCCAUAUCUCAGGAGCUUUCACUUACCCCUUUAAUGGCUUCACUCUUCUUUGGAUUGAAGGGAGCUCUUCAUCUCUACCUCC

miRBase

Precursor miRNA Structure(5'-3') 

   A A   A  G            GA       U       UU   ------    UA    -      G  A  C      UC       ----      CAAA 
GGA G AGA GA GAAGAGCUCCUU  AGUUCAA GGAGGGU  AGC      AGGG  AAGU AAAGCU CU AG UAUGGA  CCAUAAA    CCUUAU    U
||| | ||| || ||||||||||||  ||||||| |||||||  |||      ||||  |||| |||||| || || ||||||  |||||||    ||||||     
CCU C UCU CU CUUCUCGAGGGA  UUAGGUU CUUCUCA  UCG      UCCC  UUCA UUUCGA GA UC AUACCU  GGUAUUU    GGAAUA    A
   C A   -  A            AG       U       CU   GUAAUU    CA    C      G  C  U      UA       UUUA      AAAC

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

ath-miR159b-5p      GAGCUCCUUGAAGUUCAAUGG
aly-miR159b-5p      GAGCUCCUUGAAGUUCAAUGG
gma-miR159a-5p      GAGCUCCUUGAAGUCCAAUUG
gma-miR159e-5p      GAGCUCCUUGAAGUCCAAUU-
fve-miR159a-5p      GAGCUCCUUGAAGUCCAAUAG
aly-miR159a-5p      GAGCUCCUUGAAGUUCAAACG
csi-miR159a-5p      GAGCUCCUUGAAGUCCAAAAG
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