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-miR9560b

Organism

Brassica rapa

Species

Mature miRNA Sequence(5'-3')

ACAGGUGGUGGAACAAAUAUGAGU

PmiREN

Precursor miRNA Sequence(5'-3')

TTAAGCTTAAGTGTGTATTGACAGGTGGTGGAACAAATATGAGTTTTTGAACATTAGTCAAACAAAATTAAACTCATATTAGTTCTACCTCCTGCTGAAGCCCACATTAATCTGAAT

PmiREN

Precursor miRNA Structure(5'-3') 

-UUA  C    -   U  A   A    U        A           --------    AC 
    AG UUAA GUG GU UUG CAGG GGUGGAAC AAUAUGAGUUU        UUGA  A
    || |||| ||| || ||| |||| |||||||| |||||||||||        ||||  U
    UC AAUU CAC CG AGU GUCC CCAUCUUG UUAUACUCAAA        AACU  G
UAAG  U    A   C  A   C    U        A           UUAAAACA    GA

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