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

ptc-miR6445b

Organism

Populus trichocarpa

Species

Mature miRNA Sequence(5'-3')

UUCAUUCCUCUUCCUAAAAUGG

miRBase

Precursor miRNA Sequence(5'-3')

GGCUGCUUCUUUUUCUCUCUGGGCACGUUGUUCAUUCCUCUUCCUAAAAUGGCUUCUUCUCCUUUAGUUGUUGCAAUUAUAGGAGAGGAGAAUCCAUUUUAGGAAGGGAAUGAAUACUGUGUCGGUUUUACGAGGGAGACAAUC

miRBase

Precursor miRNA Structure(5'-3') 

GGCUGCUUCUU        ------ G      U          U             --C          U        
           UUUCUCUC      U GGCACG UGUUCAUUCC CUUCCUAAAAUGG   UUCUUCUCCU UAGUUGU 
           ||||||||      | |||||| |||||||||| |||||||||||||   |||||||||| |||||| U
           AGAGGGAG      G CUGUGU AUAAGUAAGG GAAGGAUUUUACC   GAGGAGAGGA AUUAACA 
------CUAAC        CAUUUU G      C          -             UAA          U

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

ptc-miR6445a      UUCAUUCCUCUUCCUAAAAUGG
mes-miR6445       UUCAUUCCUCUUCCUAAAAUGG
ptc-miR6445b      UUCAUUCCUCUUCCUAAAAUGG
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