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-miR394-3p

Organism

Solanum lycopersicum

Species

Mature miRNA Sequence(5'-3')

AGGUGGGCAUACUGUCAACA

miRBase

Precursor miRNA Sequence(5'-3')

CAAUCUUGAUUUUCAUGAAGAUUUCUCAAAGGGUUCCUUACAUAGUUCUUUGGCAUUCUGUCCACCUCCUUUACCUUCAUAAUCUUCUAUUUUUUUAGAAAAAUAAUUUUUGUUAUUAUUUUUUUUAAAAAAUGGAGGUGGGCAUACUGUCAACAGAUUUGUGUUAGUUUCUCUUUGUGAAAUCUUCUUGAUGUUAAUUG

miRBase

Precursor miRNA Structure(5'-3') 

CAAUC     UU   U         U       UUC  U      U   -      UUC           UUUACCUUCAUAAUCUUCU       U           UU 
     UUGAU  UCA GAAGAUUUC CAAAGGG   CU ACAUAG UCU UUGGCA   UGUCCACCUCC                   AUUUUUU AGAAAAAUAAU  U
     |||||  ||| ||||||||| |||||||   || |||||| ||| ||||||   |||||||||||                   ||||||| |||||||||||  U
     AAUUG  AGU CUUCUAAAG GUUUCUC   GA UGUGUU AGA AACUGU   ACGGGUGGAGG                   UAAAAAA UUUUUUUAUUA  U
--GUU     -U   U         U       UUU  U      U   C      CAU           -------------------       U           UU

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-
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