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

csi-miR393b-3p

Organism

Citrus sinensis

Species

Mature miRNA Sequence(5'-3')

UCAUGCGAUCCCUUCGGAAUU

miRBase

Precursor miRNA Sequence(5'-3')

UGAGAGUUCUUGAUUAGUGCAGGUGGAGAGUUCCAAAGGGAUCGCAUUGAUCUGAUGAUAACAUUAAAUUAAUCACUCAAACGGGUUGAUUUUAUUAUAUAUAUGAUUUCUUUCAUUUUUAGAUCAUGCGAUCCCUUCGGAAUUCCCCAUCUAUGGCUCUAAAUUUUUAUAUAU

miRBase

Precursor miRNA Structure(5'-3') 

-----        CUUGAU   U  ---      A       A            U      AUGAUAACAUUAAAUUAAUCACUCAAACGGG 
     UGAGAGUU      UAG GC   AGGUGG GAGUUCC AAGGGAUCGCAU GAUCUG                               U
     ||||||||      ||| ||   |||||| ||||||| |||||||||||| ||||||                               U
     AUUUUUAA      AUC CG   UCUACC CUUAAGG UUCCCUAGCGUA CUAGAU                               U
UAUAU        ------   U  GUA      C       C            -      UUUUACUUUCUUUAGUAUAUAUAUUAUUUUA

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

stu-miR393-3p       AUCAUGCGAUCUCUUCGGAAU-
sly-miR393          AUCAUGCGAUCUCUUCGGAAU-
csi-miR393b-3p      -UCAUGCGAUCCCUUCGGAAUU
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