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-miR169e-3p

Organism

Arabidopsis lyrata

Species

Mature miRNA Sequence(5'-3')

GCAAGUUGACCUUGGCUCUGU

miRBase

Precursor miRNA Sequence(5'-3')

GUCACUAAUUGUAUCAUAGAGUCUUGCAUGGAAAAAAUAGAGAAUGAGAUUGAGCCAAGGAUGACUUGCCGAAUUUAUUAACAAAUCUCAAAUGAUUAUGGUGCCCGGCAAGUUGACCUUGGCUCUGUUUCCUUCUCUUCUUUUCGAUGUCAAACUCUAGAUAUAUCAAUCGAU

miRBase

Precursor miRNA Structure(5'-3') 

   ACUAAU      A      C   -   G     AAU      U     U         AU         AAUU     ACA    UC 
GUC      UGUAUC UAGAGU UUG CAU GAAAA   AGAGAA GAGAU GAGCCAAGG  GACUUGCCG    UAUUA   AAUC  A
|||      |||||| |||||| ||| ||| |||||   |||||| ||||| |||||||||  |||||||||    |||||   ||||   
UAG      AUAUAG AUCUCA AAC GUA CUUUU   UCUCUU CUUUG CUCGGUUCC  UUGAACGGC    GUGGU   UUAG  U
   CUAACU      -      -   U   G     -CU      C     U         AG         --CC     --A    UA

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

aly-miR169e-3p      GCAAGUUGACCUUGGCUCUGU
aly-miR169g-3p      GCAAGUUGACCUUGGCUCUGU
aly-miR169d-3p      GCAAGUUGACCUUGGCUCUGU
ath-miR169f-3p      GCAAGUUGACCUUGGCUCUGC
aly-miR169f-3p      GCAAGUUGACCUUGGCUCUGC
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