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

ppe-miR399b

Organism

Prunus persica

Species

Mature miRNA Sequence(5'-3')

UCUGCCAAAGGAGAAUUGCCC

miRBase

Precursor miRNA Sequence(5'-3')

UGAAUAACAGGGCAAUUUUCCUUUGGCAGAAAUAAUUAUAUAUAUUUGGUGCAUUUACUCUCAAUCUCAAGUACCGGCACCGAAUGCUUUCUGCCAAAGGAGAAUUGCCCUGCCAUUCA

miRBase

Precursor miRNA Structure(5'-3') 

     AA                         UAAUUAUAUA          AUU    CUCA 
UGAAU  CAGGGCAAUUUUCCUUUGGCAGAAA          UAUUUGGUGC   UACU    A
|||||  |||||||||||||||||||||||||          ||||||||||   ||||     
ACUUA  GUCCCGUUAAGAGGAAACCGUCUUU          GUAAGCCACG   AUGA    U
     CC                         ---------C          GCC    ACUC

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

dca-miR399-b2.0r1-4355      ---------GGGCAA-UACUCCACUGGCAGU
dca-miR399-b2.0r1-4356      ---------GGGCAA-UACUCCACUGGCAGU
aly-miR399g-5p              ---------GGGCAAAUACUCCAUUGGCAGA
aly-miR399i-5p              ---------GGGCAAAUACUCCAUUGGCAGA
aly-miR399d-5p              ---------GGGCGAAUACUCCUAUGGCAGA
csi-miR399f-5p              ---------GGGCAA-UUCUCCUUUGGCAGA
ppe-miR399b                 UCUGCCAAAGGAGAAUUGCCC----------
                                     **   * * * *