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

osa-miR156b-3p

Organism

Oryza sativa

Species

Mature miRNA Sequence(5'-3')

GCUCACUCUCUAUCUGUCAGC

miRBase

Precursor miRNA Sequence(5'-3')

UUGUCUUGAGAGGGGAAGAGAUCUCUAUGGGUUUUGGAGGUCUGACAGAAGAGAGUGAGCACACACGGUGCUUUCUUAGCAUGCAAGAGCCAUGCUGGGAGCUGUGCGUGCUCACUCUCUAUCUGUCAGCCGUUCACCAUGCCCAAUAUGAUUAAUCUCCUUCUCUCAGUUGACAG

miRBase

Precursor miRNA Structure(5'-3') 

U    --          A   --    UCUA     --UU    -  U        -             A      GCUU          - A 
 UGUC  UUGAGAGGGG AGA  GAUC    UGGGU    UGGA GG CUGACAGA AGAGAGUGAGCAC CACGGU    UCUUAGCAUG C A
 ||||  |||||||||| |||  ||||    |||||    |||| || |||||||| ||||||||||||| ||||||    |||||||||| |  
 ACAG  GACUCUCUUC UCU  UUAG    ACCCG    ACUU CC GACUGUCU UCUCUCACUCGUG GUGUCG    AGGGUCGUAC G G
G    UU          C   AA    UAUA     UACC    G  -        A             C      ----          C A

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
                    ******* **** *******