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

zma-miR393a-3p

Organism

Zea mays

Species

Mature miRNA Sequence(5'-3')

AUCAGUGCAAUCCCUUUGGAAU

miRBase

Precursor miRNA Sequence(5'-3')

CCAGGAAGCUGGUGGAGGACUCCAAAGGGAUCGCAUUGAUCUAUUCUCACCUGCCGCCUGCUGCAUGCGAUGCGAGUCGACGACAAGAUCAGUGCAAUCCCUUUGGAAUUUUCCACUCGCGCCUUC

miRBase

Precursor miRNA Structure(5'-3') 

CC   AA  U         C           C          AU  -  -  C   --   C    
  AGG  GC GGUGGAGGA UCCAAAGGGAU GCAUUGAUCU  UC UC AC UGC  CGC UGC 
  |||  || ||||||||| ||||||||||| ||||||||||  || || || |||  ||| || U
  UCC  CG UCACCUUUU AGGUUUCCCUA CGUGACUAGA  AG AG UG GCG  GCG ACA 
CU   -G  C         A           A          AC  C  C  A   UA   U

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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