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-miR319b-5p

Organism

Arabidopsis lyrata

Species

Mature miRNA Sequence(5'-3')

AGAGCUUUCUUCGGUCCACUC

miRBase

Precursor miRNA Sequence(5'-3')

AAAUGUUAAUAUGGUUAUAGAUGUUGAGUUGGUGAAGGAAGAGAGCUUUCUUCGGUCCACUCAUGGAGUAAUAUGUGAGAUUUAAUUGACUCUCGACUCAUUCAUCCAAAUACCAAAUGAAAGAACAUGUUCUCAUAUGGUAAAUGAAUGAAUGAUGCGAGAGACAAAUUGAGUCUUCACUUCUCUAUGCUUGGACUGAAGGGAGCUCCCUAUUUUUAUUUUUUCUCGGUCGUACACAUUUCAUUU

miRBase

Precursor miRNA Structure(5'-3') 

     UUAAU   GU   A   GU    --UU        A  A                 CU       UAAUAU    -         -GA      AC        C  AA     A    AA   C 
AAAUG     AUG  UAU GAU  UGAG    GGUGAAGG AG GAGCUUUCUUCGGUCCA  CAUGGAG      GUGA GAUUUAAUU   CUCUCG  UCAUUCAU CA  UACCA AUGA  GAA A
|||||     |||  ||| |||  ||||    |||||||| || |||||||||||||||||  |||||||      |||| |||||||||   ||||||  |||||||| ||  ||||| ||||  |||  
UUUAC     UAC  AUG CUG  GCUC    UUAUUUUU UC CUCGAGGGAAGUCAGGU  GUAUCUC      CACU CUGAGUUAA   GAGAGC  AGUAAGUA GU  AUGGU UACU  CUU U
     ---UU   AC   -   --    UUUU        A  C                 UC       ----UU    U         ACA      GU        A  AA     A    --   G

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

mdm-miR319b-5p        -GAGCUUU-CUUCAGUCCACUC-
mtr-miR319b-5p        -GAGCUUU-CUUUAGUCCACUCA
mdm-miR319e           -GAGCUUU-CUUCAGUCCACUC-
mdm-miR319c-5p        -GAGCUCUUCUUCAGUCCAGUCC
mdm-miR319h           -GAGCUCUUCUUCAGUCCAGUCC
bdi-miR319b-5p        AGAGCUCU-CUUCAGUCCACUC-
mtr-miR319d-5p        AGAGCUCU-CUUCAGUCCACUC-
zma-miR319a-5p        -GAGCUCU-CUUCAGUCCACUC-
zma-miR319c-5p        -GAGCUCU-CUUCAGUCCACUC-
mdm-miR319g           -GAGCUUU-CUUCAGUCCACUC-
mdm-miR319f           -GAGCUUU-CUUCAGUCCACUC-
mtr-miR319a-5p        AGAGCUUC-CUUCAGUCCACUC-
aly-miR319b-5p        AGAGCUUU-CUUCGGUCCACUC-
ppt-miR319d-5p.1      -GAGCUUU-CUUCGGUCCAAUA-
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