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

stu-miR5303h

Organism

Solanum tuberosum

Species

Mature miRNA Sequence(5'-3')

AACAUUUUUGAAGAGUCUGAGCAA

miRBase

Precursor miRNA Sequence(5'-3')

GCUCAAACUCUCCAAAAUUGUUGCCGCACUCGUGUCGGAUCCUCCAAAAAAGAGCACUACUUUUGGUGGAUCCAACACACUCUUCAACAUUUUUGAAGAGUCUGAGCAA

miRBase

Precursor miRNA Structure(5'-3') 

--     A     C     U     CCGCACUC    C      U      AAGA 
  GCUCA ACUCU CAAAA UGUUG        GUGU GGAUCC CCAAAA    G
  ||||| ||||| ||||| |||||        |||| |||||| ||||||    C
  CGAGU UGAGA GUUUU ACAAC        CACA CCUAGG GGUUUU    U
AA     C     A     U     --UUCUCA    A      U      CAUC

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

stu-miR5303g      -AUAUUUUUGAAGAGUCUGAGCAAC
stu-miR5303i      -AUAUUUUUGAAGAGUCUGAGCAAC
stu-miR5303j      AAUAUUUUUGAAGAGUCUGAGCAA-
stu-miR5303h      AACAUUUUUGAAGAGUCUGAGCAA-
sly-miR5303       ----UUUUUGAAGAGUUCGAGCAAC
stu-miR7997a      -AUGCUGCUCGGACUCUUCAAA---
stu-miR7997b      -AUGCUGCUCGGACUCUUCAAA---
stu-miR7997c      -AUAUUGCUCGGACUCUUCAAAAAU
                       *  *          *