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-miR396a-3p

Organism

Brachypodium distachyon

Species

Mature miRNA Sequence(5'-3')

GUUCAAGAAAGUCCUUGGAAA

miRBase

Precursor miRNA Sequence(5'-3')

GCGCGGCUCAAUUACAGGUUGCGGCCAUGCUCUCCACAGGCUUUCUUGAACUGUGAACUCGUGCGCCUAGCCUGCUAGCUGCUCAAUUCGAUCUGUCAUCCUCGGUUCGAUUCGAUCUGAAUUGCUUGUAUAUGAUAUGAUGUGCCUUGUUGAUGGUUCAAGAAAGUCCUUGGAAAACAUGGCCGCCGCCUCUUUCCCCUGCUGGCUUA

miRBase

Precursor miRNA Structure(5'-3') 

---  G    -UCAAUUAC    U         CUC    CA                G   UCGUGCGCCUAGCCUGCUAGCUGCUCAAUUCGAUCUGUCAUCCU 
   GC CGGC         AGGU GCGGCCAUG   UCCA  GGCUUUCUUGAACUGU AAC                                            C
   || ||||         |||| |||||||||   ||||  |||||||||||||||| |||                                             
   CG GUCG         UCCG CGCCGGUAC   AGGU  CUGAAAGAACUUGGUA UUG                                            U
AUU  -    UCCCCUUUC    C         AAA    UC                G   UUCCGUGUAGUAUAGUAUAUGUUCGUUAAGUCUAGCUUAGCUUG

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

osa-miR396e-3p      AUGGUUCAAGAAAGCCCAUGGAAA
bdi-miR396b-3p      ---GUUCAAGAAAGCCCAUGGAAA
bdi-miR396a-3p      ---GUUCAAGAAAGUCCUUGGAAA
osa-miR396f-3p      AUAGUUCAAGAAAGUCCUUGGAAA
smo-miR396          ----UUCCACGGCUUUCUUGAACC
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