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

ppt-miR536b

Organism

Physcomitrella patens

Species

Mature miRNA Sequence(5'-3')

UUCGUGCCAAGCUGUGUGCAAC

miRBase

Precursor miRNA Sequence(5'-3')

GUCGGCAGUUUUCGUAUUUCGCCGACUUCGGUGACUGCAGAAAGUCGAAACAGUAGAGAGCCUGUUGAAUUGCAGCGGUAGACUUGUCUGGCAUCAUUUGGUAGUCGUCAAACUUAUUCUCCCCGAGUUGUAGCGGAAUGAUACCAGAAAUUCGUGCCAAGCUGUGUGCAACCAAGGGGUUUGUUACUUAAGAUCCACAUGGGAGGAGCGUCCCUACCAGCA

miRBase

Precursor miRNA Structure(5'-3') 

GUCGGCAGUUUUCGUAUUUCGCCGACUUCGGUGACUGCAGAAAGUCGAAAC     A      G   ---AAU      --    GACUUG     C       G  ---- G   UCAAACU 
                                                   AGUAG GAGCCU UUG      UGCAGC  GGUA      UCUGG AUCAUUU GU    A UCG       U
                                                   ||||| |||||| |||      ||||||  ||||      ||||| ||||||| ||    | |||        
                                                   UCAUU UUUGGG AAC      GUGUCG  CCGU      AGACC UAGUAAG CG    U AGC       U
-----------------ACGACCAUCCCUGCGAGGAGGGUACACCUAGAAU     G      G   CAACGU      AA    GCUUAA     A       G  AUGU G   CCCUCUU

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

ppt-miR536a              UUCGUGCCAAGCUGUGUGCAAC
ppt-miR536f              UUCGUGCCAAGCUGUGUGCA--
ppt-miR536b              UUCGUGCCAAGCUGUGUGCAAC
ppt-miR536d              UUCGUGCCAAGCUGUGUGCAAC
ppt-miR536e              UUCGUGCCAAGCUGUGUGCAAC
mpo-miR-b3.0r1-4273      -CCGUGCCAAGCUGUGUGCAUC
smo-miR536               -UCGUGUCAAGCUGUGUGCAUC
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