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-miR162b-5p

Organism

Arabidopsis lyrata

Species

Mature miRNA Sequence(5'-3')

GGAGGCAGCGGUUCAUCGAUC

miRBase

Precursor miRNA Sequence(5'-3')

UUUUUUUAGUUCUCUCCUCAUUUUUAUGUUUGGAUUUAGAGUGAAGUCGCUGGAGGCAGCGGUUCAUCGAUCAAUUCCUGUGAAUAUUUUUGUUUUCAAAAGCAUGAAUCGAUCGAUAAACCUCUGCAUCCAGCGCUUACUCUUCCUCAUCUGUUUAAUAAUCUAUUUGAGAAUGCUCAAAAGA

miRBase

Precursor miRNA Structure(5'-3') 

      U   UC    CUCAUUU    -GUU     ---UU       A U       G    C    C       A    C   GAAUAU     U 
UUUUUU AGU  UCUC       UUAU    UGGAU     AGAGUGA G CGCUGGA GCAG GGUU AUCGAUC AUUC UGU      UUUUG U
|||||| |||  ||||       ||||    |||||     ||||||| | ||||||| |||| |||| ||||||| |||| |||      |||||  
AGAAAA UCG  AGAG       AAUA    GUCUA     UCUCAUU C GCGACCU CGUC CCAA UAGCUAG UAAG ACG      AAAAC C
      C   UA    UUUAUCU    AUUU     CUCCU       - -       A    U    A       C    U   ------     U

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

ath-miR162a-5p      UGGAGGCAGCGGUUCAUCGAUC
ath-miR162b-5p      UGGAGGCAGCGGUUCAUCGAUC
csi-miR162-5p       UGGAGGCAGCGGUUCAUCGAUC
aly-miR162a-5p      -GGAGGCAGCGGUUCAUCGAUC
aly-miR162b-5p      -GGAGGCAGCGGUUCAUCGAUC
stu-miR162a-5p      -GGAGGCAGCGGUUCAUCGAUC
fve-miR162-5p       -GGAGGCAGCGGUUCAUCGAUC
stu-miR162b-5p      -GGAGGCAGCGGUUCAUCGAUC
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