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-miR156a-3p

Organism

Arabidopsis lyrata

Species

Mature miRNA Sequence(5'-3')

GCUCACUGCUCUUUCUGUCAGA

miRBase

Precursor miRNA Sequence(5'-3')

GGGUUGGUUGUGAGUGAAAGAGUUGGGACAAGAGAAACGCAAAGAAACUGACAGAAGAGAGUGAGCACACAAAGGCAAUUUGCAUAUCAUUGCAUUUGCUUCUCUUGCGUGCUCACUGCUCUUUCUGUCAGAUUCCGGUGCUGAUCUCUUUGGCCUGUCCUCGAUCUCUUUGUCUCAAUCUCUC

miRBase

Precursor miRNA Structure(5'-3') 

   UU   UG    UG      -   -     ------     AAC   -AA   A         -   -         A   ---      UU    UA 
GGG  GGU  UGAG  AAAGAG UUG GGACA      AGAGA   GCA   GAA CUGACAGAA GAG AGUGAGCAC CAA   AGGCAA  UGCA  U
|||  |||  ||||  |||||| ||| |||||      |||||   |||   ||| ||||||||| ||| ||||||||| |||   ||||||  ||||   
CUC  CUA  ACUC  UUUCUC AGC CCUGU      UCUCU   CGU   CUU GACUGUCUU CUC UCACUCGUG GUU   UUCGUU  ACGU  U
   -U   --    UG      U   U     CCGGUU     AGU   GGC   A         U   G         C   CUC      -U    UA

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

stu-miR156k-3p      GCUCACUGCUCUAUCUGUCACC
sly-miR156d-3p      GCUCACUGCUCUAUCUGUCACC
stu-miR156j-3p      GCUCACUGCUCUAUCUGUCACC
stu-miR156i-3p      GCUCACUGCUCUAUCUGUCACC
stu-miR156h-3p      GCUCACUGCUCUAUCUGUCACC
zma-miR156l-3p      GCUCACUGCUCUAUCUGUCACC
zma-miR156i-3p      GCUCACUGCUCUAUCUGUCAUC
bdi-miR156f-3p      GCUCACUGCUCUAUCUGUCAGC
osa-miR156b-3p      GCUCACU-CUCUAUCUGUCAGC
ath-miR156c-3p      GCUCACUGCUCUAUCUGUCAGA
aly-miR156a-3p      GCUCACUGCUCUUUCUGUCAGA
aly-miR156c-3p      GCUCACUGCUCUAUCUGUCAGA
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