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

bra-miR9560a

Organism

Brassica rapa

Species

Mature miRNA Sequence(5'-3')

ACAGGUGGUGGAACAAAUAUGAGU

PmiREN

Precursor miRNA Sequence(5'-3')

TGAAGATTAAGTGTGTATTGACAGGTGGTGGAACAAATATGAGTTTGTATAGTAGTCGAACAAAATGAAACTCATATTAGTTCTACCTCCTGTTGAAGCCCACATTAATCTGAAT

PmiREN

Precursor miRNA Structure(5'-3') 

-UGA       -   U  A        U        A           -GUAUA  AG 
    AGAUUAA GUG GU UUGACAGG GGUGGAAC AAUAUGAGUUU      GU  U
    ||||||| ||| || |||||||| |||||||| |||||||||||      ||   
    UCUAAUU CAC CG AGUUGUCC CCAUCUUG UUAUACUCAAA      CA  A
UAAG       A   C  A        U        A           GUAAAA  AG

Homologous Mature miRNAs   miRNAs are clustered by CD-HIT with sequence identity of >85% and word size of 5.

bra-miR9560a        --ACAGGUGGUGGAACAAAUAUGAGU
bra-miR9560b        --ACAGGUGGUGGAACAAAUAUGAGU
csi-miR9560-5p      --ACAGGAGGUGGAACAAAUAUGAAA
csi-miR9560-3p      UCAUAUUUGCUCCACCACCUGUGG--
                      * *   * *  * **  * **