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-miR5303

Organism

Solanum lycopersicum

Species

Mature miRNA Sequence(5'-3')

UUUUUGAAGAGUUCGAGCAAC

miRBase

Precursor miRNA Sequence(5'-3')

GUUGCUCGGACUCUCCAAAAAUGUUGCCAAACCCGUGUCUGAUCCUUCAAAAAUACAUUAUUUUUGUAGGACACCUAUGGACCUUUUUGAAGAGUUCGAGCAAC

miRBase

Precursor miRNA Structure(5'-3') 

              C      U  UGCCAAAC     UC  A    U          
GUUGCUCGGACUCU CAAAAA GU        CCGUG  UG UCCU CAAAAAUAC 
|||||||||||||| |||||| ||        |||||  || |||| |||||||| A
CAACGAGCUUGAGA GUUUUU CA        GGUAU  AC AGGA GUUUUUAUA 
              A      C  --------     CC  -    U

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

stu-miR5303g      -AUAUUUUUGAAGAGUCUGAGCAAC
stu-miR5303i      -AUAUUUUUGAAGAGUCUGAGCAAC
stu-miR5303j      AAUAUUUUUGAAGAGUCUGAGCAA-
stu-miR5303h      AACAUUUUUGAAGAGUCUGAGCAA-
sly-miR5303       ----UUUUUGAAGAGUUCGAGCAAC
stu-miR7997a      -AUGCUGCUCGGACUCUUCAAA---
stu-miR7997b      -AUGCUGCUCGGACUCUUCAAA---
stu-miR7997c      -AUAUUGCUCGGACUCUUCAAAAAU
                       *  *          *