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

mdm-miR171a

Organism

Malus domestica

Species

Mature miRNA Sequence(5'-3')

UUGAGCCGCGUCAAUAUCUCC

miRBase

Precursor miRNA Sequence(5'-3')

GAAGGUAUUGACGCGCCUCAAUUUGAACGRGUGGCUYAUAUUGGAGACUUAACCAUGCGAUUCUGAUUGAGCCGCGUCAAUAUCUCC

miRBase

Precursor miRNA Structure(5'-3') 

GA             C       U   -  R    CUYAUAUU 
  AGGUAUUGACGCG CUCAAUU GAA CG GUGG        G
  ||||||||||||| ||||||| ||| || ||||         
  UCUAUAACUGCGC GAGUUAG CUU GC UACC        G
CC             C       U   A  G    AAUUCAGA

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

csi-miR171e-3p      UUGAGCCGCGUCAAUAUCUCC
csi-miR171g-3p      UUGAGCCGCGUCAAUAUCUCC
fve-miR171h         UUGAGCCGCGUCAAUAUCUCC
mdm-miR171p         UUGAGCCGCGUCAAUAUCUCC
mdm-miR171b         UUGAGCCGCGUCAAUAUCUCC
mdm-miR171a         UUGAGCCGCGUCAAUAUCUCC
ppe-miR171h         UUGAGCCGCGUCAAUAUCUCC
mes-miR171a         UUGAGCCGCGUCAAUAUCUCC
gma-miR171t         UUGAGCCGCGUCAAUAUCUCA
gma-miR171n         UUGAGCCGCGUCAAUAUCUUA
gma-miR171p         UUGAGCCGCGUCAAUAUCUUA
                    *******************