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-miR399i-5p

Organism

Arabidopsis lyrata

Species

Mature miRNA Sequence(5'-3')

GGGCAAAUACUCCAUUGGCAGA

miRBase

Precursor miRNA Sequence(5'-3')

GCAUGGUUGGAUUACAGGGCAAAUACUCCAUUGGCAGAUAGUUUUCGUUGCAUCUAUAUUAUUGAUUAUCGAUGUAUGAAAAAUUCUUUACUGCCAAAGGAGAUUUGCCCCGCAAUUCAUCCCGUGC

miRBase

Precursor miRNA Structure(5'-3') 

      -U      A A        A    A       - U  ---       U     U   UUA 
GCAUGG  UGGAUU C GGGCAAAU CUCC UUGGCAG A AG   UUUUCGU GCAUC AUA   U
||||||  |||||| | |||||||| |||| ||||||| | ||   ||||||| ||||| |||    
CGUGCC  ACUUAA G CCCGUUUA GAGG AACCGUC U UC   AAAAGUA UGUAG UAU   A
      CU      C C        -    A       A U  UUA       -     C   UAG

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