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

aly-miR393a-3p

Organism

Arabidopsis lyrata

Species

Mature miRNA Sequence(5'-3')

AUCAUGCUAUCUCUUUGGAUU

miRBase

Precursor miRNA Sequence(5'-3')

AGCAACUAGAGGAAGGAUCCAAAGGGAUCGCAUUGAUCCUAAUAAAGGUGAAUUACCCCAAUCUUUUCUUAAUAAUUAGCAAACAAAUCAAAAAAAUUUGCUUGGUUUUGGAUCAUGCUAUCUCUUUGGAUUCAUCCUUCGGUAGCU

miRBase

Precursor miRNA Structure(5'-3') 

   A   A     A              C    U     UAAUAA         -ACCCCAAUCU   -  UAA 
AGC ACU GAGGA GGAUCCAAAGGGAU GCAU GAUCC      AGGUGAAUU           UUU CU   U
||| ||| ||||| |||||||||||||| |||| |||||      |||||||||           ||| ||    
UCG UGG UUCCU CUUAGGUUUCUCUA CGUA CUAGG      UUCGUUUAA           AAA GA   U
   A   C     A              U    -     UUUUGG         AAAAACUAAAC   C  UUA

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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