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-miR167d-3p

Organism

Brachypodium distachyon

Species

Mature miRNA Sequence(5'-3')

AGAUCAUGUUGCAGCUUCAC

miRBase

Precursor miRNA Sequence(5'-3')

UGGACGGCUCAAUUUGAUGGUGUGAGAGGUUGAAGCUGCCAGCAUGAUCUGAUCACCGUCCAACGUAACCGAACACAUGUCGAUCGACUUCCGAUUGCGCCGGUUAUCUUGGUAGGAAUAUAUAUAUAUGAGCUUCCAUUGCAAGGGUUCUUCAGAUCAUGUUGCAGCUUCACUCUCUCAUCACCACCGAAAGAUCCAAAUUAA

miRBase

Precursor miRNA Structure(5'-3') 

--UGGAC  C  AA    A     -       U         C            UCACCGUCCAACGUAACCGAACACAUGUCGAUCGACUUCCGAUUGCGC 
       GG UC  UUUG UGGUG UGAGAGG UGAAGCUGC AGCAUGAUCUGA                                                C
       || ||  |||| ||||| ||||||| ||||||||| ||||||||||||                                                G
       CC AG  AAGC ACCAC ACUCUCU ACUUCGACG UUGUACUAGACU                                                U
AAUUAAA  U  -A    C     U       C         -            UCUUGGGAACGUUACCUUCGAGUAUAUAUAUAUAAGGAUGGUUCUAUU

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

csi-miR167a-3p      AGAUCAUCUG-GCAGUUUCACC
mdm-miR167a         AGAUCAUCUG-GCAGUUUCACC
ptc-miR167h-3p      AGAUCAUGUG-GCAGUUUCACC
ptc-miR167g-3p      AGAUCAUGUG-GCAGUUUCACC
ptc-miR167f-3p      AGAUCAUGUG-GCAGUUUCACC
ath-miR167a-3p      -GAUCAUGUUCGCAGUUUCACC
aly-miR167a-3p      -GAUCAUGUUCGCAGUUUCACC
zma-miR167h-3p      -GAUCAUGUU-GCAGCUUCAC-
bdi-miR167d-3p      AGAUCAUGUU-GCAGCUUCAC-
zma-miR167i-3p      -GAUCAUGUU-GCAGCUUCAC-
                     ****** *  **** *****