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-miR399d-5p

Organism

Arabidopsis lyrata

Species

Mature miRNA Sequence(5'-3')

GGGCGAAUACUCCUAUGGCAGA

miRBase

Precursor miRNA Sequence(5'-3')

GAGAGAUAAUGUAUGGUUGGAUUACUGGGCGAAUACUCCUAUGGCAGAUAGCUUUGCCUAGAUAUGCAAGCAAAAUGCUUCUCUGCCAAAGGAGAUUUGCCCCGCAAUUCAUCCAUGCAAAACAAUACAUCUUUC

miRBase

Precursor miRNA Structure(5'-3') 

       -------AA       U      A U        A     A       -U   --     CUAGA 
GAGAGAU         UGUAUGG UGGAUU C GGGCGAAU CUCCU UGGCAGA  AGC  UUUGC     U
|||||||         ||||||| |||||| | |||||||| ||||| |||||||  |||  |||||      
CUUUCUA         ACGUACC ACUUAA G CCCGUUUA GAGGA ACCGUCU  UCG  AAACG     G
       CAUAACAAA       U      C C        -     A       CU   UA     AACGU

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----------
                                     **   * * * *