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

sly-miR156d-3p

Organism

Solanum lycopersicum

Species

Mature miRNA Sequence(5'-3')

GCUCACUGCUCUAUCUGUCACC

miRBase

Precursor miRNA Sequence(5'-3')

CAGAUGCCUAAAAAGGGUAAAAACAAAGGGGCGGUGACAGAAGAGAGUGAGCACACAUGGCGUUUUCUGGCAUGAUGUUUAUAUAUAUAUAUGCUUGAAACUAUGUGUGCUCACUGCUCUAUCUGUCACCUCCCACCAAUUCCUCUAUCUUUCUUUAUAUGUAUCUG

miRBase

Precursor miRNA Structure(5'-3') 

       --C    -       --AAAACAAAG   C         -    -               CGU    U      -    UU 
CAGAUGC   UAAA AAGGGUA           GGG GGUGACAGA AGAG AGUGAGCACACAUGG   UUUC GGCAUG AUGU  A
|||||||   |||| |||||||           ||| ||||||||| |||| |||||||||||||||   |||| |||||| ||||   
GUCUAUG   AUUU UUUCUAU           CCC CCACUGUCU UCUC UCACUCGUGUGUAUC   AAAG UCGUAU UAUA  U
       UAU    C       CUCCUUAACCA   U         A    G               ---    U      A    UA

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

stu-miR156k-3p      GCUCACUGCUCUAUCUGUCACC
sly-miR156d-3p      GCUCACUGCUCUAUCUGUCACC
stu-miR156j-3p      GCUCACUGCUCUAUCUGUCACC
stu-miR156i-3p      GCUCACUGCUCUAUCUGUCACC
stu-miR156h-3p      GCUCACUGCUCUAUCUGUCACC
zma-miR156l-3p      GCUCACUGCUCUAUCUGUCACC
zma-miR156i-3p      GCUCACUGCUCUAUCUGUCAUC
bdi-miR156f-3p      GCUCACUGCUCUAUCUGUCAGC
osa-miR156b-3p      GCUCACU-CUCUAUCUGUCAGC
ath-miR156c-3p      GCUCACUGCUCUAUCUGUCAGA
aly-miR156a-3p      GCUCACUGCUCUUUCUGUCAGA
aly-miR156c-3p      GCUCACUGCUCUAUCUGUCAGA
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