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-miR394a-3p

Organism

Arabidopsis lyrata

Species

Mature miRNA Sequence(5'-3')

AGGUGGGUAUACUGCCAAUA

miRBase

Precursor miRNA Sequence(5'-3')

UAGAUUGGAUCUUUAAACUUUUGUUCCUUUUCAUGAGGGUUUGACAAAGAGUUUCUUACAGACAUCUUUGGCAUUCUGUCCACCUCCUCCUGUACAUGUGUGUAUAUAUAUGUGUUUUGUGUGGAAGAAGGAGGUGGGUAUACUGCCAAUAGAGAUCUGUUAGGGUUUCUUCGUAAAACCCUCUUGAUCUAUAUACAACUUUAUCAAUGUCUUGAAUCUG

miRBase

Precursor miRNA Structure(5'-3') 

      --    CUUUAAACUU    -UCCUUU   U        G  A     U    U     CA   -      UUC            C  --------GU         U 
UAGAUU  GGAU          UUGU       UCA GAGGGUUU AC AAGAG UUCU ACAGA  UCU UUGGCA   UGUCCACCUCCU CU          ACAUGUGUG A
||||||  ||||          ||||       ||| |||||||| || ||||| |||| |||||  ||| ||||||   |||||||||||| ||          |||||||||  
GUCUAA  UCUG          AACA       AGU CUCCCAAA UG UUCUU GGGA UGUCU  AGA AACCGU   AUGGGUGGAGGA GA          UGUGUAUAU U
      GU    UAACUAUUUC    UAUAUCU   U        A  C     U    U     AG   U      CAU            A  AGGUGUGUUU         A

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

sly-miR394-3p       AGGUGGGCAUACUGUCAACA-
gma-miR394b-3p      AGGUGGGCAUACUGUCAACU-
ath-miR394b-3p      AGGUGGGCAUACUGCCAAUAG
aly-miR394a-3p      AGGUGGGUAUACUGCCAAUA-
zma-miR394a-3p      AGGUGGGCAUACUGCCAAUG-
zma-miR394b-3p      AGGUGGGCAUACUGCCAAUG-
aly-miR394b-3p      AGGUGGACAUAUUGCCAACA-
                    ******  *** ** ***