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-miR396g-3p

Organism

Populus trichocarpa

Species

Mature miRNA Sequence(5'-3')

CUCAAGAAAGCCGUGGGAAAA

miRBase

Precursor miRNA Sequence(5'-3')

UUGCAUGCUUUUCCACGGCUUUCUUGAACUUGGCACUCAAGAGACAUGAGAGUAAAGGGCUAGGCUUUCUUUUCUAUUCCUUUCGUUCUUUGAAAUUUUCCUGUUCAAAGAAUCCAUACAUAUCAGUCUCUUUAGUACAAAGCUCAAGAAAGCCGUGGGAAAAUAUGA

miRBase

Precursor miRNA Structure(5'-3') 

UUG    C                   A   G C   C       A   -GA   AAGGGCUAGGCUUUCUUUUCUAUUCCUUUC 
   CAUG UUUUCCACGGCUUUCUUGA CUU G ACU AAGAGAC UGA   GUA                              G
   |||| ||||||||||||||||||| ||| | ||| ||||||| |||   |||                               
   GUAU AAAGGGUGCCGAAAGAACU GAA C UGA UUCUCUG ACU   CAU                              C
--A    A                   C   A A   U       -   AUA   ACCUAAGAAACUUGUCCUUUUAAAGUUUCU

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

csi-miR396e-3p      GCUCAAGAAUGCCGUGGGAAA-
zma-miR396e-3p      GGUCAAGAAAGCCGUGGGAAG-
ptc-miR396g-3p      -CUCAAGAAAGCCGUGGGAAAA
ptc-miR396e-3p      -CUCAAGAAAGCUGUGGGAGA-
                      ******* ** ******