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-miR161-3p.1

Organism

Arabidopsis lyrata

Species

Mature miRNA Sequence(5'-3')

CCGGUUUAGUCACUUUCAC

miRBase

Precursor miRNA Sequence(5'-3')

GAUCAAUGCAUUGAAAGUGACUACAUCGGGGUUUUGUUUUUUUGUUGCUCCCACGAUCGAAUCGAUAUGAGGAAGAUGAAAAAUUAAUCAACCCCGGUUUAGUCACUUUCACUGCAUUAAUC

miRBase

Precursor miRNA Structure(5'-3') 

   C      U            C         --   U         GC   -  CG      
GAU AAUGCA UGAAAGUGACUA AUCGGGGUU  UUG UUUUUUGUU  UCC CA  AUCGA 
||| |||||| |||||||||||| |||||||||  ||| |||||||||  ||| ||  |||| A
CUA UUACGU ACUUUCACUGAU UGGCCCCAA  AAU AAAAAGUAG  AGG GU  UAGCG 
   A      C            U         CU   U         -A   A  -A

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

cru-miR161           UUGAAAGUGACUACAUCGGGG-
aly-miR161-5p.1      UUGAAAGUGACUACAUCGGGG-
ath-miR161.1         -UGAAAGUGACUACAUCGGGGU
aly-miR161-3p.1      -CCGGUUUAGUCACUUUCAC--
                            *    ** *