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

zma-miR2118f

Organism

Zea mays

Species

Mature miRNA Sequence(5'-3')

UUCCCAAUGCCUUCCAUGCCUA

miRBase

Precursor miRNA Sequence(5'-3')

UAAGAGCAGUGGGCAUGGGAACAUAGGGGAAAGCCAAACUUUCUUUACCUGUACAACUAAGGGUGGAGAACUGGAGAUUAGUUUAGUGUUUCCCAAUGCCUUCCAUGCCUAUUGUUCUUA

miRBase

Precursor miRNA Structure(5'-3') 

                    -A   A      A  C     ---------          GUAC 
UAAGAGCAGUGGGCAUGGGA  CAU GGGGAA GC AAACU         UUCUUUACCU    A
||||||||||||||||||||  ||| |||||| || |||||         ||||||||||     
AUUCUUGUUAUCCGUACCUU  GUA CCCUUU UG UUUGA         AAGAGGUGGG    U
                    CC   A      G  A     UUAGAGGUC          AAUC

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---
                     ** ** *  **   *** *