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

bdi-miR444d

Organism

Brachypodium distachyon

Species

Mature miRNA Sequence(5'-3')

UGCAGUUGUUGUCUCAAGCUU

miRBase

Precursor miRNA Sequence(5'-3')

GCAAGUGGAGGCGGCAAGCUAGAGGCAGCAACUGCAUAACGUGCAAGAAAAUCGUUUCGGGCCAUACCGAUGAUUUUCUUGCAAGUUGUGCAGUUGUUGUCUCAAGCUUGCUGCCUCCCUUUGC

miRBase

Precursor miRNA Structure(5'-3') 

     U              A                   G             UU    GC 
GCAAG GGAGGCGGCAAGCU GAGGCAGCAACUGCAUAAC UGCAAGAAAAUCG  UCGG  C
||||| |||||||||||||| ||||||||||||||||||| |||||||||||||  ||||   
CGUUU CCUCCGUCGUUCGA CUCUGUUGUUGACGUGUUG ACGUUCUUUUAGU  AGCC  A
     C              A                   A             --    AU

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

bdi-miR444c           UGCAGUUGUUGUCUCAAGCUU
bdi-miR444d           UGCAGUUGUUGUCUCAAGCUU
zma-miR444b           UGCAGUUGUUGUCUCAAGCUU
zma-miR444a           UGCAGUUGUUGUCUCAAGCUU
osa-miR444c.2         UGCAGUUGUUGUCUCAAGCUU
osa-miR444b.2         UGCAGUUGUUGUCUCAAGCUU
osa-miR444f           UGCAGUUGUUGCCUCAAGCUU
osa-miR444a-3p.2      UGCAGUUGCUGCCUCAAGCUU
osa-miR444d.2         UGCAGUUGCUGCCUCAAGCUU
osa-miR444e           UGCAGUUGCUGCCUCAAGCUU
bdi-miR444b           UGCAGUUGCUGCCUCAAGCUU
hvu-miR444b           UGCAGUUGCUGUCUCAAGCUU
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