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-miR169k-3p

Organism

Arabidopsis lyrata

Species

Mature miRNA Sequence(5'-3')

GGCAGUCUCCUUGGCUAUC

miRBase

Precursor miRNA Sequence(5'-3')

GAAGGAGAUGUCAAAGAUGAAUAAGAGAACCACAUUUGGUAGCCAAGGAUGACUUGCCUGUUUCUUUGAACAAAAUGGUUGGUGUCAUGUUUGAUGUGACUACAAGUUAUAUCAAGAAUGACAUUUUGCUUAUAAAAAGACAUCAGGCAGUCUCCUUGGCUAUCCUUAUAUGUUCUUCUUUCUCAUCUCAGACAUUUACCUUC

miRBase

Precursor miRNA Structure(5'-3') 

     -       AA      AU    -    CACAUUU            U    U     -UU     GAACAAAAU   -U        G              
GAAGG AGAUGUC  AGAUGA  AAGA GAAC       GGUAGCCAAGGA GACU GCCUG   UCUUU         GGU  GGUGUCAU UUUGAUGUGACUA 
||||| |||||||  ||||||  |||| ||||       |||||||||||| |||| |||||   |||||         |||  |||||||| |||||||||||| C
CUUCC UUUACAG  UCUACU  UUCU CUUG       CUAUCGGUUCCU CUGA CGGAC   AGAAA         UCG  UUACAGUA GAACUAUAUUGAG 
     A       AC      CU    U    UAUAUUC            -    -     UAC     ----AAUAU   UU        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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