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

ath-miR472-3p

Organism

Arabidopsis thaliana

Species

Mature miRNA Sequence(5'-3')

UUUUUCCUACUCCGCCCAUACC

miRBase

Precursor miRNA Sequence(5'-3')

UCUGUAUGUAUGUAUGGUCGAAGUAGGCAAAAUCUCACCUUUCUAGCAGAUCAACAAUGAAUUUUGUGGAAUAGAUGUUGGAUUUGUAAGGUUUUGGUGUUUGCAAGUGUUGAGAUGCGCAAGAUUUGAGUAAGAUUUUUCCUACUCCGCCCAUACCAUACAUACACC

miRBase

Precursor miRNA Structure(5'-3') 

UC          -     U  A      C       CACCUUUCUAGCAGAUCAACAAUGAAUUUUGUGGAAUAGAUGUUGGA 
  UGUAUGUAUG UAUGG CG AGUAGG AAAAUCU                                               U
  |||||||||| ||||| || |||||| |||||||                                               U
  ACAUACAUAC AUACC GC UCAUCC UUUUAGA                                               U
CC          C     C  C      U       AUGAGUUUAGAACGCGUAGAGUUGUGAACGUUUGUGGUUUUGGAAUG

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

ptc-miR472b         --UUUUCCCAACUCCACCCAUCCC
csi-miR482f-3p      ---UUUUCCCACACCUCCCAUCCC
ptc-miR472a         --UUUUCCCUACUCCACCCAUCCC
mes-miR482          --UCUUCCCUACUCCACCCAUUCC
ath-miR472-3p       --UUUUUCCUACUCCGCCCAUACC
aly-miR472-3p       --UUUUUCCUACUCCGCCCAUACC
csi-miR482f-5p      ---GAUGGGUGAGUUGGGAAAAUA
csi-miR482d-5p      UGGUAUGGGUGAGUAGGGAAG---
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