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

sly-miR391

Organism

Solanum lycopersicum

Species

Mature miRNA Sequence(5'-3')

ACGCAGGAGAGAUGAUGCUGGA

miRBase

Precursor miRNA Sequence(5'-3')

AAGGCUUGCUACGCAGGAGAGAUGAUGCUGGACGAUAGAGAAAAUGGGAUUUAAUUUAUUGGCCAGCAUCAUACUCCUGCAUAUUAAGCCU

miRBase

Precursor miRNA Structure(5'-3') 

A       C  C       AG          A       GA      
 AGGCUUG UA GCAGGAG  AUGAUGCUGG CGAUAGA  AAAUG 
 ||||||| || |||||||  |||||||||| |||||||  |||| G
 UCCGAAU AU CGUCCUC  UACUACGACC GUUAUUU  UUUAU 
-       U  A       -A          G       AA

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

stu-miR391-5p      UACGCAGGAGAGAUGAUGCUG--
sly-miR391         -ACGCAGGAGAGAUGAUGCUGGA
gma-miR391-5p      UACGCAGGAGAGAUGACGCUGU-
mdm-miR391         UACGCAGGAGAGAUGACGCCG--
                    *************** ** *