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-miR399g-5p

Organism

Arabidopsis lyrata

Species

Mature miRNA Sequence(5'-3')

GGGCAAAUACUCCAUUGGCAGA

miRBase

Precursor miRNA Sequence(5'-3')

GAUGAUGCAUGGUUGGAUUACAGGGCAAAUACUCCAUUGGCAGAUAGUUUUCGCUACAUCUAUAUUAUUUGUUAUUAUAUGGGUGAAUCAAUGUAUGAAAAAUACUUUACUGCCAAAGGAGAUUUGCCCCGCAAUUUGUUCCAUGCAAAAGAACAUC

miRBase

Precursor miRNA Structure(5'-3') 

-----GAUGA       -U      A A        A    A       AUAGUUUUCGCUACAUCUAUAUUAUUUGUUAU 
          UGCAUGG  UGGAUU C GGGCAAAU CUCC UUGGCAG                                U
          |||||||  |||||| | |||||||| |||| |||||||                                 
          ACGUACC  GUUUAA G CCCGUUUA GAGG AACCGUC                                A
CUACAAGAAA       UU      C C        -    A       AUUUCAUAAAAAGUAUGUAACUAAGUGGGUAU

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