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-miR169r-3p

Organism

Zea mays

Species

Mature miRNA Sequence(5'-3')

GGCAAGUUGUCCUUGGCUACA

miRBase

Precursor miRNA Sequence(5'-3')

GCAGCCAAGGAUGACUUGCCGGGUAUUUUGAGCAUGCAUGUUACAGGGGAGCAUAUGCAAUCUGUUUGGAAUUUUGAGCCCAUACCGUGCGGUGCCUGUCUUCCGGCAAGUUGUCCUUGGCUACAU

miRBase

Precursor miRNA Structure(5'-3') 

-- C                     UAUUUU A    -     U  CAG   AG  --UA G   U 
  G AGCCAAGGAUGACUUGCCGGG      G GCAU GCAUG UA   GGG  CA    U CAA C
  | |||||||||||||||||||||      | |||| ||||| ||   |||  ||    | ||| U
  C UCGGUUCCUGUUGAACGGCCU      C CGUG CGUGC AU   CCC  GU    A GUU U
UA A                     -UCUGU -    G     C  --A   GA  UUUA G   U

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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