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-miR845

Organism

Brassica rapa

Species

Mature miRNA Sequence(5'-3')

CGGCUCUGAUACCAAUUGAUG

PmiREN

Precursor miRNA Sequence(5'-3')

ATCGCCTCGTTTTCATCACGTCGATTGGTGCCAAAGCCATGCTAATTACGTCTCTGTCAAGAGGAATTTTGCACGGCTCTGATACCAATTGATGCAATGAAAACATCGATTTCG

PmiREN

Precursor miRNA Structure(5'-3') 

----    CCUC        CA            C  A    A   UAAUUACG     G 
    AUCG    GUUUUCAU  CGUCGAUUGGUG CA AGCC UGC        UCUCU U
    ||||    ||||||||  |||||||||||| || |||| |||        |||||  
    UAGC    CAAAAGUA  GUAGUUAACCAU GU UCGG ACG        GGAGA A
GCUU    --UA        AC            A  C    C   --UUUUAA     A

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

vvi-miR845a          UAGCUCUGAUACCAAUU-GAUA----
vvi-miR845b          UAGCUCUGAUACCAAUU-GAUA----
bra-miR845           CGGCUCUGAUACCAAUU-GAUG----
esa-miR845           CGGCUCUGAUACCAAUU-GAUG----
ath-miR845a          CGGCUCUGAUACCAAUU-GAUG----
vvi-miR845c          AGGCUCUGAUACCAAUU-GAUG----
vvi-miR845d          UGGCUCUGAUACCAAUU-GAUG----
vvi-miR845e          UGGCUCUGAUACCAAUU-GAUG----
aly-miR845b-3p       UCGCUCUGAUACCAAAU-GAUG----
ath-miR845b          UCGCUCUGAUACCAAAUUGAUG----
ath-miR829-3p.1      -AGCUCUGAUACCAAAU-GAUGGAAU
bdi-miR845           -UGCUCUGAUACCAAUU-GUUGG---
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