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

osa-miR2118o

Organism

Oryza sativa

Species

Mature miRNA Sequence(5'-3')

CUCCUGAUGCCUCCCAAGCCUA

miRBase

Precursor miRNA Sequence(5'-3')

GGAAGAGGAAGAAAAGAGGGCCAAGGAGCAGUGGGCAUGGGGACAUGAAGGAAUGCUUAAGCCCCUCUCCAAUCCUCGCAUGAGAUUGGAGAUGGAGUUAUGAGUUCUCCUGAUGCCUCCCAAGCCUAUUGUUCCUUGGUGCUCCUUCCUCUUCC

miRBase

Precursor miRNA Structure(5'-3') 

           AAAA   G                 A    - A   GA    AU     -   -  C         C  G 
GGAAGAGGAAG    GAG GCCAAGGAGCAGUGGGC UGGG G CAU  AGGA  GCUUA AGC CC UCUCCAAUC UC C
|||||||||||    ||| ||||||||||||||||| |||| | |||  ||||  ||||| ||| || ||||||||| ||  
CCUUCUCCUUC    CUC UGGUUCCUUGUUAUCCG ACCC C GUA  UCCU  UGAGU UUG GG AGAGGUUAG AG G
           ----   G                 A    U C   -G    CU     A   A  U         -  U

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

zma-miR2118d        UUCCUGAUGCCUCCCAUGCCUA
sbi-miR2118-3p      UUCCUGAUGCCUCCCAUGCCUA
osa-miR2118o        CUCCUGAUGCCUCCCAAGCCUA
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