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-miR482b-3p

Organism

Populus trichocarpa

Species

Mature miRNA Sequence(5'-3')

UUACCAAUACCUCUCAUGCCAA

miRBase

Precursor miRNA Sequence(5'-3')

GAGAAGAGCCGGAGGGGGAGACUGAGACCUACUGGAAGUUGUGGGCAUGAGGUGUUUGGCAAGAAAAUGGAUCUUUUCCUUAUGAUGAUUUCUUACCAAUACCUCUCAUGCCAAUGAUUUCCAGCAGUUCCUCCCUUUCCCUUCUUUCUC

miRBase

Precursor miRNA Structure(5'-3') 

     -   CC          --    AGACCUA           G         U  -    C      -------AU   U 
GAGAA GAG  GGAGGGGGAG  ACUG       CUGGAAGUUGU GGCAUGAGG GU UUGG AAGAAA         GGA C
||||| |||  ||||||||||  ||||       ||||||||||| ||||||||| || |||| ||||||         ||| U
CUCUU CUU  CCUUUCCCUC  UGAC       GACCUUUAGUA CCGUACUCU CA AACC UUCUUU         CCU U
     U   -C          CU    -------           A         C  U    A      AGUAGUAUU   U

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

osa-miR2118e        -UUCCCAAUGCCUCCCAUGCCUA
zma-miR2118f        -UUCCCAAUGCCUUCCAUGCCUA
osa-miR2118r        -UUCCCAAUGCCUCCCAUGCCUA
mac-miR482b         -UUUCCAAUACCUCCCAUGCCAA
ptc-miR482b-3p      -UUACCAAUACCUCUCAUGCCAA
stu-miR482c         -UUUCCUAUUCCACCCAUGCCAA
sly-miR482d-3p      -UUUCCUAUUCCACCCAUGCCAA
ppe-miR482e         -UUGCCUAUUCCUCCCAUGCCAA
mac-miR482a         -UUUCCAAUGCCUCCCAUGCCAA
ptc-miR1448         CUUUCCAACGCCUCCCAUAC---
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