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-miR169h-3p

Organism

Arabidopsis lyrata

Species

Mature miRNA Sequence(5'-3')

GGCAGUCUCCUUGGCUAUU

miRBase

Precursor miRNA Sequence(5'-3')

UAGAAAAUCAUAUAAGAGAAAAUGGUGACAUGAAGAAUGAGAACUUGUGUGGUAGCCAAGGAUGACUUGCCUGCGUUUUAACAAUACAAUAUCAAAGACUACUCGAUCGAUCGAUAGUCUUAGAGUUGGUUAGUCGUCAGGCAGUCUCCUUGGCUAUUCAAACAAUUCUUGUUCUCCUCAUUUCACAUCUCUCUUUCGUUUUUUG

miRBase

Precursor miRNA Structure(5'-3') 

        CAUAU      AAAUG    C    --          C    G   -          U    U     -  UU     AAUA    A  A       C    U 
UAGAAAAU     AAGAGA     GUGA AUGA  AGAAUGAGAA UUGU UGG UAGCCAAGGA GACU GCCUG CG  UUAAC    CAAU UC AAGACUA UCGA C
||||||||     ||||||     |||| ||||  |||||||||| |||| ||| |||||||||| |||| ||||| ||  |||||    |||| || ||||||| ||||  
GUUUUUUG     UUCUCU     CACU UACU  UCUUGUUCUU AACA ACU AUCGGUUCCU CUGA CGGAC GC  GAUUG    GUUG AG UUCUGAU AGCU U
        ---CU      --CUA    U    CC          -    A   U          -    -     U  -U     ----    -  A       -    A

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

aly-miR169k-3p      GGCAGUCU---CCUUGGCUAUC
aly-miR169l-3p      GGCAGUCU---CCUUGGCUAUC
aly-miR169j-3p      GGCAGUCU---CCUUGGCUAUC
aly-miR169h-3p      GGCAGUCU---CCUUGGCUAUU
stu-miR169a-3p      -GCAGUCU---CCUUGGCUACU
stu-miR169b-3p      -GCAGUCU---CCUUGGCUACU
stu-miR169c-3p      -GCAGUCU---CCUUGGCUACC
mtr-miR169d-3p      GGCAGGUCAUCCUUCGGCUAUA
mtr-miR169e-3p      GGCAGGUCAUCCUUCGGCUAUA
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