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

pvu-miR1514a

Organism

Phaseolus vulgaris

Species

Mature miRNA Sequence(5'-3')

UUCAUUUUGAAAAUAGGCAUUG

miRBase

Precursor miRNA Sequence(5'-3')

AUUGAAGAACACCUUGCCUACCUUCUCACUGCAUUCUUUUGAAUGGAAACAGGGCUUUCCUGUUUUCAUUUUGAAAAUAGGCAUUGCAUUACAUUUCGAUGCGUCUUCCAAUUCCAAUGCCUAUUUUAAGAUGAAAACAAGGAUACACUGUUUUUGUUUGAAACUGUUGUGAAGGAAGAUAAGACUCCCGAGUUCUUCAAUU

miRBase

Precursor miRNA Structure(5'-3') 

-          A ------    C  A   UC    U   UUC                GGCUU    -               A        -------------     AC 
 AUUGAAGAAC C      CUUG CU CCU  UCAC GCA   UUUUGAAUGGAAACAG     UCCU GUUUUCAUUUUGAAA UAGGCAUU             GCAUU  A
 |||||||||| |      |||| || |||  |||| |||   ||||||||||||||||     |||| ||||||||||||||| ||||||||             |||||  U
 UAACUUCUUG G      GAAU GA GGA  AGUG UGU   AAAGUUUGUUUUUGUC     AGGA CAAAAGUAGAAUUUU AUCCGUAA             CGUAG  C
U          A CCCUCA    A  A   --    U   --C                -ACAU    A               -        CCUUAACCUUCUG     CU

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

pvu-miR1514a         --UUCAUUUUGAAAAUAGGCAUUG
gma-miR1514a-5p      --UUCAUUUUUAAAAUAGGCAUU-
gma-miR1514b-5p      --UUCAUUUUUAAAAUAGACAUU-
gma-miR1514a-3p      AUGCCUAUUUUAAAAUGAAAA---
gma-miR1514b-3p      AUGCCUAUUUUAAAAUGAAAA---
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