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

ptc-miR393a-3p

Organism

Populus trichocarpa

Species

Mature miRNA Sequence(5'-3')

AUCAUGCUAUCCCUUUGGAUU

miRBase

Precursor miRNA Sequence(5'-3')

AGAGGAGGCAUCCAAAGGGAUCGCAUUGAUCCCAAGUGUCUGUCCCCCAUAAUUUUGGAUCAUGCUAUCCCUUUGGAUUCCUCCU

miRBase

Precursor miRNA Structure(5'-3') 

AG      C            C    U     C    GUCUGU 
  AGGAGG AUCCAAAGGGAU GCAU GAUCC AAGU      C
  |||||| |||||||||||| |||| ||||| ||||       
  UCCUCC UAGGUUUCCCUA CGUA CUAGG UUUA      C
--      U            U    -     U    AUACCC

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

ath-miR393a-3p      AUCA-UGCUAUCUCUUUGGAUU
aly-miR393a-3p      AUCA-UGCUAUCUCUUUGGAUU
csi-miR393c-3p      AUCA-UGCUAUCCCUUUGGAUU
mdm-miR393h         AUCA-UGCUAUCCCUUUGGAUU
mdm-miR393g         AUCA-UGCUAUCCCUUUGGAUU
gma-miR393c-3p      AUCA-UGCUAUCCCUUUGGAUU
ptc-miR393b-3p      AUCA-UGCUAUCCCUUUGGAUU
ptc-miR393a-3p      AUCA-UGCUAUCCCUUUGGAUU
osa-miR393b-3p      -UCAGUGCAAUCCCUUUGGAAU
zma-miR393c-3p      GUCAGUGCAAUCCCUUUGGAAU
bdi-miR393b-3p      -UCAGUGCAAUCCCUUUGGAAU
zma-miR393a-3p      AUCAGUGCAAUCCCUUUGGAAU
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