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-miR396e-3p

Organism

Zea mays

Species

Mature miRNA Sequence(5'-3')

GGUCAAGAAAGCCGUGGGAAG

miRBase

Precursor miRNA Sequence(5'-3')

UUUCCACAGCUUUCUUGAACUUCUUCUUCUUCUCUCUCUUAGAAGGGCCGUAUAGCUUCUUUGAACCUCUCUCUCUCUCUCUCUCAAAAGUGUACACGAACACUUUCUUCAUUCUCUGCCUCUCGCUCUCUGAUCUCCGAAGAAGGUCAAGAAAGCCGUGGGAAGA

miRBase

Precursor miRNA Structure(5'-3') 

--       A          A       UUCUUCUCUCUCUUAGAAGGGCCGUAUAGCUUCUUUGAACCUCUCUCUCUCUCUC 
  UUUCCAC GCUUUCUUGA CUUCUUC                                                       U
  ||||||| |||||||||| |||||||                                                        
  AAGGGUG CGAAAGAACU GAAGAAG                                                       C
AG       C          G       CCUCUAGUCUCUCGCUCUCCGUCUCUUACUUCUUUCACAAGCACAUGUGAAAACU

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