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

zma-miR169c-3p

Organism

Zea mays

Species

Mature miRNA Sequence(5'-3')

GGCAAGUCUGUCCUUGGCUACA

miRBase

Precursor miRNA Sequence(5'-3')

AUGAGGUAGAGAACGGGAUGCAGCCAAGGAUGACUUGCCGGCUCCUGGAACCUGGAGGCGUCUCAGCUUGCUGUGCUGUGGCUUAGAACUUAGUCGGCAAGUCUGUCCUUGGCUACACCUAGUUCUCUUCCUCU

miRBase

Precursor miRNA Structure(5'-3') 

AU    U       -   A  C          -           UCCUGGAACCUGGAGGCGUCUCAG 
  GAGG AGAGAAC GGG UG AGCCAAGGAU GACUUGCCGGC                        C
  |||| ||||||| ||| || |||||||||| |||||||||||                         
  CUCC UCUCUUG UCC AC UCGGUUCCUG CUGAACGGCUG                        G
-U    U       A   -  A          U           AUUCAAGAUUCGGUGUCGUGUCGU

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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