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-miR482d-3p

Organism

Solanum lycopersicum

Species

Mature miRNA Sequence(5'-3')

UUUCCUAUUCCACCCAUGCCAA

miRBase

Precursor miRNA Sequence(5'-3')

GGAAAGGGAGGAGGGAUUUGGGAAUCUUUUGGAGUGGGUGGGAUGGAAAAAUAUUGUAUUUUUUUUUCUAACGGAAAAAAAGAUGAGAAUUGAGAUUUUUCCUAUUCCACCCAUGCCAAUGGCUUCCAGUCAUUUACUCCUUUUCC

miRBase

Precursor miRNA Structure(5'-3') 

          -GAGG    UG    U  U    A           -        ----   -G               
GGAAAGGGAG     GAUU  GGAA CU UUGG GUGGGUGGGAU GGAAAAAU    AUU  UAUUUUUUUUUCUA 
||||||||||     ||||  |||| || |||| ||||||||||| ||||||||    |||  ||||||||||||| A
CCUUUUCCUC     CUGA  CCUU GG AACC UACCCACCUUA CCUUUUUA    UAA  GUAGAAAAAAAGGG 
          AUUUA    --    C  U    G           U        GAGU   GA

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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