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-miR319b-5p

Organism

Malus domestica

Species

Mature miRNA Sequence(5'-3')

GAGCUUUCUUCAGUCCACUC

miRBase

Precursor miRNA Sequence(5'-3')

GCAGUGGUGAAGAGAGCUUUCUUCAGUCCACUCAUGGGUGGCGGUAGGAUUUAAUUAGCUGCCGAGUCAUUCAUCCAAAUACUGGGUUAUUAGUAGGAUGACAUCCAGUAAAUGUGUGAAUGAAGCGGGAGACAAAUUGGAUCUUAAGCUUCCUGUACUUGGACUGAAGGGAGCUCCCUUAAUUAAUUACUUC

miRBase

Precursor miRNA Structure(5'-3') 

GC      ----G   A                 CUC     U   GG            A -  G   AG        C  AA      --      A 
  AGUGGU     AAG GAGCUUUCUUCAGUCCA   AUGGG GGC  UAGGAUUUAAUU G CU CCG  UCAUUCAU CA  UACUGG  GUUAUU G
  ||||||     ||| |||||||||||||||||   ||||| |||  |||||||||||| | || |||  |||||||| ||  ||||||  |||||| U
  UCAUUA     UUC CUCGAGGGAAGUCAGGU   UGUCC UCG  AUUCUAGGUUAA C GA GGC  AGUAAGUG GU  AUGACC  CAGUAG G
CU      AUUAA   C                 UCA     U   -A            A A  G   GA        U  AA      UA      G

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

mdm-miR319b-5p        -GAGCUUU-CUUCAGUCCACUC-
mtr-miR319b-5p        -GAGCUUU-CUUUAGUCCACUCA
mdm-miR319e           -GAGCUUU-CUUCAGUCCACUC-
mdm-miR319c-5p        -GAGCUCUUCUUCAGUCCAGUCC
mdm-miR319h           -GAGCUCUUCUUCAGUCCAGUCC
bdi-miR319b-5p        AGAGCUCU-CUUCAGUCCACUC-
mtr-miR319d-5p        AGAGCUCU-CUUCAGUCCACUC-
zma-miR319a-5p        -GAGCUCU-CUUCAGUCCACUC-
zma-miR319c-5p        -GAGCUCU-CUUCAGUCCACUC-
mdm-miR319g           -GAGCUUU-CUUCAGUCCACUC-
mdm-miR319f           -GAGCUUU-CUUCAGUCCACUC-
mtr-miR319a-5p        AGAGCUUC-CUUCAGUCCACUC-
aly-miR319b-5p        AGAGCUUU-CUUCGGUCCACUC-
ppt-miR319d-5p.1      -GAGCUUU-CUUCGGUCCAAUA-
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