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

bdi-miR169i

Organism

Brachypodium distachyon

Species

Mature miRNA Sequence(5'-3')

CCAGCCAAGAAUGGCUUGCCUA

miRBase

Precursor miRNA Sequence(5'-3')

UGGAGACGAGGAGCCCCUUUGCAGGCUCUACCAGCCAAGAAUGGCUUGCCUAUGCCCACGUUCUGUUUCAUCACCACUGGGCUUAAUCUUGGAGCCCUGGUGAUGGAUGAGAUGUGAUUGUAUGGUCAAGCCAUCUUGGCUAGAAGAGAGAUCCUCGUCCCCCAUGCUAGGCUGC

miRBase

Precursor miRNA Structure(5'-3') 

--UGGAGACGAGGAGCCCCUUUGCAGG    A C        A       C      --C     U  GU          CU      AA 
                           CUCU C AGCCAAGA UGGCUUG CUAUGC   CACGU CU  UUCAUCACCA  GGGCUU  U
                           |||| | |||||||| ||||||| ||||||   ||||| ||  ||||||||||  ||||||  C
                           GAGA G UCGGUUCU ACCGAAC GGUAUG   GUGUA GA  AGGUAGUGGU  CCCGAG  G
CGUCGGAUCGUACCCCCUGCUCCUAGA    A A        -       U      UUA     -  GU          --      GU

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

sbi-miR169q         -UAGCCAAGAAUGGCUUGCCUA
bdi-miR169j-5p      -UAGCCAGGAAUGGCUUGCCUA
sbi-miR169p         -UAGCCAAGAAUGGCUUGCCUA
zma-miR169q-5p      -UAGCCAAGAAUGGCUUGCCUA
zma-miR169n-5p      -UAGCCAAGAAUGGCUUGCCUA
zma-miR169m-5p      -UAGCCAAGAAUGGCUUGCCUA
bdi-miR169i         CCAGCCAAGAAUGGCUUGCCUA
zos-miR169a         -CAGCCAAGGAUGACUUGCCUA
zos-miR169b         -CAGCCAAGGAUGACUUGCCUA
                      ***** * *** ********