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

sit-miR1432

Organism

Setaria italica

Species

Mature miRNA Sequence(5'-3')

UCAGGAGAGAUGACACCGAC

PmiREN

Precursor miRNA Sequence(5'-3')

TGTGGGTGTGCGTCCTACGCTCAGGAGAGATGACACCGACGTCGGACGGGTCGATCGAGATGTGCATCTGCTGTGTCGATCCGTCTGAAGCCGGTGTCATTTCCCCTGAACTTAGGACCCATTAGCCCTGA

PmiREN

Precursor miRNA Structure(5'-3') 

UGU    --   C      C C     A            A G              ---CG    G 
   GGGU  GUG GUCCUA G UCAGG GAGAUGACACCG C UCGGACGGGUCGAU     AGAU U
   ||||  ||| |||||| | ||||| |||||||||||| | ||||||||||||||     ||||  
   CCCG  UAC CAGGAU C AGUCC CUUUACUGUGGC G AGUCUGCCUAGCUG     UCUA A
AGU    AU   C      U A     C            C A              UGUCG    C

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

pvi-miR1432b        -UCAGGAGAGAUGACACCGAC-
bdi-miR1432         UUCAGGAGAGAUGACACCGACA
osa-miR1432-5p      AUCAGGAGAGAUGACACCGAC-
sit-miR1432         -UCAGGAGAGAUGACACCGAC-
zma-miR1432-5p      CUCAGGAGAGAUGACACCGAC-
sbi-miR1432         CUCAGGAGAGAUGACACCGAC-
pvi-miR1432a        CUCAGGAGAGAUGACACCGAUG
                     *******************