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

zma-miR319d-5p

Organism

Zea mays

Species

Mature miRNA Sequence(5'-3')

AGAGCGUCCUUCAGUCCACUC

miRBase

Precursor miRNA Sequence(5'-3')

UGGUCGCCGGCCGGAUGGAAGAGAGCGUCCUUCAGUCCACUCAGGGGCGGUGCUAGGGUCGGAUUAGCUGCCGACUCAUUCACCCACAUGCCAAGCAAACGGCCAUGGAAACGAGCUUCGCAGAUGAGUGAAUGAAGCGGGAGGUAAAAGCUUCGAUCUCGCACCGUCUUUGCUUGGACUGAAGGGUGCUCCCUCCGAUCCUUUCCUUGUUU

miRBase

Precursor miRNA Structure(5'-3') 

UGGUCGCCGGCC    -   A A                 CU            UA        ----   G  G   AC        C  CA   C    AAA  GCCA 
            GGAU GGA G GAGCGUCCUUCAGUCCA  CAGGGGCGGUGC  GGGUCGGA    UUA CU CCG  UCAUUCAC CA  UGC AAGC   CG    U
            |||| ||| | |||||||||||||||||  ||||||||||||  ||||||||    ||| || |||  |||||||| ||  ||| ||||   ||     
            CCUA CCU C CUCGUGGGAAGUCAGGU  GUUUCUGCCACG  UCUAGCUU    AAU GA GGC  AGUAAGUG GU  ACG UUCG   GC    A
-UUUGUUCCUUU    G   C -                 UC            -C        CGAA   G  G   GA        A  AG   C    --A  AAAG

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

zma-miR319b-5p      AGAGCGUCCUUCAGUCCACUC
zma-miR319d-5p      AGAGCGUCCUUCAGUCCACUC
sly-miR319c-5p      AGAGCUUCCUUCAGCCCACUC
aly-miR319a-5p      AGAGCUUCCUUGAGUCCAUUC
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