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

atr-miR477

Organism

Amborella trichopoda

Species

Mature miRNA Sequence(5'-3')

AGAGGCCUUAGGGGAGAGUGG

miRBase

Precursor miRNA Sequence(5'-3')

CUAGAUCUAUGCAGAUGGGAGUAGAGGACCAAGAAAAAUUUCAGGGCACCUAAUCUUCACUCUCCCUCAAGGGCUUCUGGUCCUUACCAUUCAUGGUAAGAGGAAUAGAGGCCUUAGGGGAGAGUGGAUGCUAGGUGUUUUGGUUUCUAUCAAUCGGUUAUACUUCCUAGCCUUGGCCUUAG

miRBase

Precursor miRNA Structure(5'-3') 

---CUAGAUCUAUGCAGAUGGGAGUAGAGGACCA     AAUU            AUC            CA          G     --    U 
                                  AGAAA    UCAGGGCACCUA   UUCACUCUCCCU  AGGGCUUCUG UCCUU  ACCA U
                                  |||||    ||||||||||||   ||||||||||||  |||||||||| |||||  ||||  
                                  UCUUU    GGUUUUGUGGAU   AGGUGAGAGGGG  UUCCGGAGAU AGGAG  UGGU U
GAUUCCGGUUCCGAUCCUUCAUAUUGGCUAACUA     ----            CGU            -A          A     AA    A

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

ptc-miR477e-3p      UGAGGCCUUUGGGGGAGAGUGG
csi-miR477d-3p      UGAGGCCGUUGGGG-AGAGUGG
atr-miR477          AGAGGCCUUAGGGG-AGAGUGG
vvi-miR477b-3p      CGAAGUCUUUGGGG-AGAGUGG
ptc-miR477a-3p      GGAUGCCUUUGGGGGAGAUUG-
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