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-miR5303j

Organism

Solanum tuberosum

Species

Mature miRNA Sequence(5'-3')

AAUAUUUUUGAAGAGUCUGAGCAA

miRBase

Precursor miRNA Sequence(5'-3')

GCUCGGACUAUUCAAAUUGCUGCCCCACCCUGUGUAAGAUCCUCCAAAAAUGACUACUUUUGAAGGAUUAAACACGCAUCCGGCAAUAUUUUUGAAGAGUCUGAGCAA

miRBase

Precursor miRNA Structure(5'-3') 

--         A      -UUGC    CCACCC     AA      C     AUG 
  GCUCGGACU UUCAAA     UGCC      UGUGU  GAUCCU CAAAA   A
  ||||||||| ||||||     ||||      |||||  |||||| |||||    
  CGAGUCUGA AAGUUU     ACGG      GCACA  UUAGGA GUUUU   A
AA         G      UUAUA    -CCUAC     AA      A     CAU

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
                       *  *          *