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-miR169c-3p

Organism

Brachypodium distachyon

Species

Mature miRNA Sequence(5'-3')

GGCAGGUUGUCCUUGGCUAC

miRBase

Precursor miRNA Sequence(5'-3')

UUGCCAUACGCUAAGAGGCAGAGAAGGGGAUGCAGCCAAGGAUGACUUGCCGGCUCCUGGUGUUGGGGGAAUUGCAGCUUUGUUGAGCCUUGAGUUAGCCGGCAGGUUGUCCUUGGCUACACCUAGUUCUCUUCUUCUGGUGUUUGGCCCU

miRBase

Precursor miRNA Structure(5'-3') 

-UU    U      A    C      -G   A  C                     UCCUGGUGUUGGGGGAAUUG 
   GCCA ACGCUA GAGG AGAGAA  GGG UG AGCCAAGGAUGACUUGCCGGC                    C
   |||| |||||| |||| ||||||  ||| || |||||||||||||||||||||                    A
   CGGU UGUGGU CUUC UCUCUU  UCC AC UCGGUUCCUGUUGGACGGCCG                    U
UCC    U      -    U      GA   -  A                     AUUGAGUUCCGAGUUGUUUC

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

zma-miR169a-3p      --GGCAAGU-UGUUCUU-GGCUACA
zma-miR169b-3p      --GGCAAGU-UGUUCUU-GGCUACA
bdi-miR169a-3p      --GGCGAGU-UGUUCUU-GGCUACA
bdi-miR169c-3p      --GGCAGGU-UGUCCUU-GGCUAC-
ptc-miR169b-3p      --GGCAGGU-UGUUCUU-GGCUAC-
ath-miR169b-3p      --GGCAAGU-UGUCCUUCGGCUACA
aly-miR169b-3p      --GGCAAGU-UGUCCUUCGGCUACA
zma-miR169r-3p      --GGCAAGU-UGUCCUU-GGCUACA
zma-miR169c-3p      --GGCAAGUCUGUCCUU-GGCUACA
aly-miR169a-3p      --GGCAAGU-UGUCCUU-GGCUACA
ath-miR169a-3p      --GGCAAGU-UGUCCUU-GGCUAC-
csi-miR169n-3p      --GGCAAGU-UGCCCUU-GGCUACA
osa-miR169p         UAGCCAAGGACAAACUU--GCCGG-
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