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-b2.0r1-4356

Organism

Daucus carota

Species

Mature miRNA Sequence(5'-3')

GGGCAAUACUCCACUGGCAGU

Plant sRNA Gene (Penn State Uni)

Precursor miRNA Sequence(5'-3')

AAAUGUACUGAUGUAUUACUGGGCAAUACUCCACUGGCAGUAGCUACGUCAUUUUGAUUGCAGAUUGUGAACAUUUAAUGUCACAUGGCAUAUCAGUGAUAAGAGCUCACCGCCAAGGGAGAUUUGCCCUGCAAUUCAGCUGUACAAAUGA

Precursor miRNA Structure(5'-3') 

--AAA     UGA  U   A U      UA    AC    A  -    -AC     UU    -   AGAU     A     
     UGUAC   UG AUU C GGGCAA  CUCC  UGGC GU AGCU   GUCAU  UGAU UGC    UGUGA CAUU 
     |||||   || ||| | ||||||  ||||  |||| || ||||   |||||  |||| |||    ||||| ||| U
     ACAUG   AC UAA G CCCGUU  GAGG  ACCG CA UCGA   UAGUG  ACUA ACG    ACACU GUAU 
AGUAA     UCG  U   C U      UA    GA    C  C    GAA     --    U   --GU     -

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