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-miR159a-5p

Organism

Arabidopsis lyrata

Species

Mature miRNA Sequence(5'-3')

GAGCUCCUUGAAGUUCAAACG

miRBase

Precursor miRNA Sequence(5'-3')

GAGAAAAAAAAAGAUGGAAGUAGAGCUCCUUGAAGUUCAAACGAGAGUUGAGCAGGGUAAAGAAAAGCUGCUAAGCUAUGGAUCCCAUAAGCCCUAAUCCUUAUAAAGAAAAAAAAGGAUUUGGUUAUAUGGCUUGCAUAUCUCAGGAGCUUUAACUUGCCCUUUAAUGGCUUUUACUCUUCUUUGGAUUGAAGGGAGCUCUACAUCUUCUUUCACCUUCUC

miRBase

Precursor miRNA Structure(5'-3') 

     AAAA     U   A            GA        C      -U    ------       AGA      G  A  C    G UC     -    CU       AUAAA 
GAGAA    AAAGA GGA GUAGAGCUCCUU  AGUUCAAA GAGAGU  GAGC      AGGGUAA   AAAGCU CU AG UAUG A  CCAUA AGCC  AAUCCUU     G
|||||    ||||| ||| ||||||||||||  |||||||| ||||||  ||||      |||||||   |||||| || || |||| |  ||||| ||||  |||||||      
CUCUU    UUUCU UCU CAUCUCGAGGGA  UUAGGUUU UUCUCA  UUCG      UCCCGUU   UUUCGA GA UC AUAC U  GGUAU UUGG  UUAGGAA     A
     CCAC     -   A            AG        C      UU    GUAAUU       CAA      G  C  U    G UC     A    -U       AAAAA

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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