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-miR833a-3p

Organism

Arabidopsis thaliana

Species

Mature miRNA Sequence(5'-3')

UAGACCGAUGUCAACAAACAAG

miRBase

Precursor miRNA Sequence(5'-3')

GGACGUAGAUGGUACUCUUACAGAUGGUGAUCGUGAAAACAAACGGAGGAGUUUGUUUGUUGUACUCGGUCUAGUUCAAACCAAAACAUCUUUGCAAAUAUGUAUGGUUUGAGCUAGACCGAUGUCAACAAACAAGCUGCUUCGUUUGUAUUCACCAUCAACAUCUUUAAGAAACGCUGCACCACUC

miRBase

Precursor miRNA Structure(5'-3') 

----  AC    A  GUAC     C     G    C     A          G             U  -                  AA    C  U 
    GG  GUAG UG    UCUUA AGAUG UGAU GUGAA ACAAACGGAG AGUUUGUUUGUUG AC UCGGUCUAGUUCAAACCA  ACAU UU G
    ||  |||| ||    ||||| ||||| |||| ||||| |||||||||| ||||||||||||| || ||||||||||||||||||  |||| ||  
    CC  CGUC GC    AGAAU UCUAC ACUA CACUU UGUUUGCUUC UCGAACAAACAAC UG AGCCAGAUCGAGUUUGGU  UGUA AA A
CUCA  -A    -  --AA     U     A    C     A          G             -  U                  -A    U  A

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

ath-miR833a-3p      UAGACCGAUGUCAACAAACAAG
aly-miR833-3p       UAGACCGAUGUCAACAAACAAG
ath-miR833b         -UGUUUGUUGACAUCGGUCUAG
                      *   * ** ** *   * **