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-miR399b-5p

Organism

Arabidopsis lyrata

Species

Mature miRNA Sequence(5'-3')

GGGCGCCUCUCCAUUGGCAGG

miRBase

Precursor miRNA Sequence(5'-3')

CAUGUAAGCUCACAAGUUUUAGGGCGCCUCUCCAUUGGCAGGUCCUUUAUUUCCAAAUAUACACAUACAUAUAUGAAUAUAGAAAAUUUCGAUUUAUAUAUGACCUGCCAAAGGAGAGUUGCCCUGAAACUGGUUCAGCUUAAUUAAACACAUG

miRBase

Precursor miRNA Structure(5'-3') 

     --------     -C  A            C      A          CUUUAUUUCCAAAUAUACACAUAC          AUA     
CAUGU        AAGCU  AC AGUUUUAGGGCG CUCUCC UUGGCAGGUC                        AUAUAUGAAU   GAAA 
|||||        |||||  || |||||||||||| |||||| ||||||||||                        ||||||||||   ||| A
GUACA        UUCGA  UG UCAAAGUCCCGU GAGAGG AACCGUCCAG                        UAUAUAUUUA   CUUU 
     CAAAUUAA     CU  G            U      A          ------------------------          --G

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

aly-miR399e-5p      GGGCGAAUCCUCUAUUGGCAGG
csi-miR399e-5p      GGGC-AAUUCUCUAUUGGCAGU
stu-miR399g-5p      GGGC-UACUCUCUAUUGGCAUG
stu-miR399h         GGGC-UACUCUCUAUUGGCAUG
stu-miR399f-5p      GGGC-UACUCUCUAUUGGCAUG
stu-miR399e-5p      GGGC-UACUCUCUAUUGGCAUG
stu-miR399d-5p      GGGC-UACUCUCUAUUGGCAUG
stu-miR399c-5p      GGGC-UACUCUCUAUUGGCAUG
stu-miR399b-5p      GGGC-UACUCUCUAUUGGCAUG
stu-miR399a-5p      GGGC-UACUCUCUAUUGGCAUG
aly-miR399b-5p      GGGC-GCCUCUCCAUUGGCAGG
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