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

mdm-miR319f

Organism

Malus domestica

Species

Mature miRNA Sequence(5'-3')

GAGCUUUCUUCAGUCCACUC

miRBase

Precursor miRNA Sequence(5'-3')

GAUCUUAGAGAUAGUUURAGUGAGCUUUCUUCAGUCCACUCAUGGAAGGGCAAAGGGUUUGAAUUAGCUGCCGACUCAUUCAUUCAAACUCAGUAGAAAUGGAGUGGAUAUUUCWACUGUGAAUGUGUGAAUGAUGCGGGAGAUAACUUCAUUCUUUUCUUCUCUGUGCUUGGACUGAAGGGAGCUCCCUUUUACUGUCUUCUUUGU

miRBase

Precursor miRNA Structure(5'-3') 

GAUCUUA        UUR  U                 CU      A   C      UU    -   G  G   AC        U  AA U    A      GA 
       GAGAUAGU   AG GAGCUUUCUUCAGUCCA  CAUGGA GGG AAAGGG  UGAA UUA CU CCG  UCAUUCAU CA  C CAGU GAAAUG  G
       ||||||||   || |||||||||||||||||  |||||| ||| ||||||  |||| ||| || |||  |||||||| ||  | |||| ||||||  U
       UUCUGUCA   UC CUCGAGGGAAGUCAGGU  GUGUCU UUC UUUUCU  ACUU AAU GA GGC  AGUAAGUG GU  G GUCA CUUUAU  A
-UGUUUC        UUU  C                 UC      C   -      -U    C   A  G   GU        U  AA U    W      AG

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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