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

mes-miR482

Organism

Manihot esculenta

Species

Mature miRNA Sequence(5'-3')

UCUUCCCUACUCCACCCAUUCC

miRBase

Precursor miRNA Sequence(5'-3')

GGAGAAAAAGCAAGGAUUUUCGGAAGGUUAUGAGAUGGGUAAGUGGGGAAGAUAACUGUGGGGCUUUCGUUUUGUUUGUUAUCUUCCCUACUCCACCCAUUCCAUAGCUUUCCGAUCGUUCCUCUCUCUCC

miRBase

Precursor miRNA Structure(5'-3') 

     AAA  CA    -UUU             A       -A               -UGU     U 
GGAGA   AG  AGGA    UCGGAAGGUUAUG GAUGGGU  AGUGGGGAAGAUAAC    GGGGC U
|||||   ||  ||||    ||||||||||||| |||||||  |||||||||||||||    |||||  
CCUCU   UC  UCCU    AGCCUUUCGAUAC UUACCCA  UCAUCCCUUCUAUUG    UUUUG G
     --C  --    UGCU             C       CC               UUUG     C

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

ptc-miR472b         --UUUUCCCAACUCCACCCAUCCC
csi-miR482f-3p      ---UUUUCCCACACCUCCCAUCCC
ptc-miR472a         --UUUUCCCUACUCCACCCAUCCC
mes-miR482          --UCUUCCCUACUCCACCCAUUCC
ath-miR472-3p       --UUUUUCCUACUCCGCCCAUACC
aly-miR472-3p       --UUUUUCCUACUCCGCCCAUACC
csi-miR482f-5p      ---GAUGGGUGAGUUGGGAAAAUA
csi-miR482d-5p      UGGUAUGGGUGAGUAGGGAAG---
                         *             *