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-miR5485

Organism

Oryza sativa

Species

Mature miRNA Sequence(5'-3')

UGACAACUGGUAGCAGAGCAA

miRBase

Precursor miRNA Sequence(5'-3')

CUUGGAGUGGUGACAACUGGUAGCAGAGCAAUGUCAUCUCCACUUGCCGGUUGUUCCUGGUAUGUCGAGGGAUACUGGUGCUGACAUUGCUCUGAUACCAAUUGUCGGCACUCUAGGC

miRBase

Precursor miRNA Structure(5'-3') 

-         G      C     G             U UCCACUU      U      G U 
 CUUGGAGUG UGACAA UGGUA CAGAGCAAUGUCA C       GCCGGU GUUCCU G A
 ||||||||| |||||| ||||| ||||||||||||| |       |||||| |||||| | U
 GGAUCUCAC GCUGUU ACCAU GUCUCGUUACAGU G       UGGUCA UAGGGA C C
C         G      A     A             C -------      -      G U

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

csi-miR535c-3p      GUGCUCUCUACCAUUGUCAUA----
csi-miR535d-3p      GUGCUCUCUACCAUUGUCAUA----
csi-miR535b-3p      GUGCUCUCUACCAUUGUCAUA----
osa-miR5485         ----UGACAACUGGUAGCAGAGCAA
                        *  * **   *  ** *