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-miR393b-3p

Organism

Brachypodium distachyon

Species

Mature miRNA Sequence(5'-3')

UCAGUGCAAUCCCUUUGGAAU

miRBase

Precursor miRNA Sequence(5'-3')

GCUGGCAAAUUAGUGUAAGCUUCAGGAAGCUAGUGGAGGACUCCAAAGGGAUCGCAUUGAUCUCAUCAGCUGCAUCCAAGCAUGAAUCAACGGAUGGAUGGAUCGAUGCAUAUGCAAGAUCAGUGCAAUCCCUUUGGAAUUCUCGACUCGCCUCUGCCUCGGUCGGUCACGCGC

miRBase

Precursor miRNA Structure(5'-3') 

--  -    AA   -  U  AAGCUUCA   A  U   G     C           C          CAU  GC      CAAG   GA   A 
  GC UGGC  AUU AG GU        GGA GC AGU GAGGA UCCAAAGGGAU GCAUUGAUCU   CA  UGCAUC    CAU  AUC A
  || ||||  ||| || ||        ||| || ||| ||||| ||||||||||| ||||||||||   ||  ||||||    |||  |||  
  CG ACUG  UGG UC CG        UCU CG UCA CUCUU AGGUUUCCCUA CGUGACUAGA   GU  ACGUAG    GUA  UAG G
CG  C    GC   C  -  --------   C  C   G     A           A          -AC  AU      CUAG   GG   G

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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