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

mdm-miR393g

Organism

Malus domestica

Species

Mature miRNA Sequence(5'-3')

AUCAUGCUAUCCCUUUGGAUU

miRBase

Precursor miRNA Sequence(5'-3')

UAUAUUGCAACUAGAGGAGGCAUCCAAAGGGAUCGCAUUGAUCCCAGCUAGCUAUUUCUUUCCAUCGUUUGGUUUGGAUCAUGCUAUCCCUUUGGAUUUCUCCUUUGGAAGCUUCAA

miRBase

Precursor miRNA Structure(5'-3') 

UAUAUU  AA          C            C    U     C      - UAUUUC 
      GC  CUAGAGGAGG AUCCAAAGGGAU GCAU GAUCC AGCUAG C      U
      ||  |||||||||| |||||||||||| |||| ||||| |||||| |       
      CG  GGUUUCCUCU UAGGUUUCCCUA CGUA CUAGG UUGGUU G      C
-AACUU  AA          U            U    -     U      U CUACCU

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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