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-miR171b-5p

Organism

Arabidopsis lyrata

Species

Mature miRNA Sequence(5'-3')

AGAUAUUAGUGCGGUUCAAUC

miRBase

Precursor miRNA Sequence(5'-3')

GAGUGAUUUUAUGUAAGGUAACGCGAGAUAUUAGUGCGGUUCAAUCAAAUAGUCGUCCUCUUAACUCAUGGAGAUCGGUGUUGUUCGAUUGAGCCGUGCCAAUAUCACGCGGUAAACCAAAAUGGCAAAGAUCGAUC

miRBase

Precursor miRNA Structure(5'-3') 

  G       A   ----AA   --AA    A      A             A     --   UC    UAA 
GA UGAUUUU UGU      GGU    CGCG GAUAUU GUGCGGUUCAAUC AAUAG  UCG  CUCU   C
|| ||||||| |||      |||    |||| |||||| ||||||||||||| |||||  |||  ||||    
CU GCUAGAA ACG      CCA    GCGC CUAUAA CGUGCCGAGUUAG UUGUU  GGC  GAGG   A
  A       -   GUAAAA   AAUG    A      C             C     GU   UA    UAC

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

ath-miR171b-5p      AGAUAUUAGUGCGGUUCAAUC
aly-miR171b-5p      AGAUAUUAGUGCGGUUCAAUC
ath-miR171c-5p      AGAUAUUGGUGCGGUUCAAUC
gma-miR171c-5p      AGAUAUUGGUGCGGUUCAAUC
stu-miR171d-5p      AGAUAUUGGUGCGGUUCAAUU
fve-miR171c-5p      AGAUAUUGGUGCGGUUCAAUC
aly-miR171c-5p      AGAUAUUGGUGCGGUUCAAUC
gma-miR171o-5p      AGAUAUUGGUACGGUUCAAUC
lus-miR171d         AGAUAUUGGUGCGGUUCAAUC
osa-miR171c-5p      GGAUAUUGGUGCGGUUCAAUC
bdi-miR171c-5p      CGGUAUUGGUGCGGUUCAAUC
                     * **** ** *********