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

dca-miR399-b2.0r1-4355

Organism

Daucus carota

Species

Mature miRNA Sequence(5'-3')

GGGCAAUACUCCACUGGCAGU

Plant sRNA Gene (Penn State Uni)

Precursor miRNA Sequence(5'-3')

AAAAUCCUGGUGAGUUGUUCAUUGUCAAGCAAAUGUACUACUGUAUUACGGGGCAAUACUCCACUGGCAGUAGCCACUACAACUGCGGAUUGUGAACAUUUAUUUCACAUGGCAGAUUAGUCACGAGCUCACUGCCAAGGGAGAUUUGCCCCGCAAUUCAGCUCUACUUAUCAUCGUAAACAGUAUUU

Precursor miRNA Structure(5'-3') 

AAAAUCCUGGUGAGUUGUUCAUUGUCAAGCAAAUGUACUA   U   A        UA    AC       -   - ---    CAA    GGAU      CA 
                                        CUG AUU CGGGGCAA  CUCC  UGGCAGU AGC C   ACUA   CUGC    UGUGAA  U
                                        ||| ||| ||||||||  ||||  ||||||| ||| |   ||||   ||||    ||||||  U
                                        GAC UAA GCCCCGUU  GAGG  ACCGUCA UCG G   UGAU   GACG    ACACUU  U
-------------UUUAUGACAAAUGCUACUAUUCAUCUC   U   C        UA    GA       C   A CAC    -UA    --GU      UA

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