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

bra-miR158b

Organism

Brassica rapa

Species

Mature miRNA Sequence(5'-3')

UCCCAAAUGUAGACAAAGCA

PmiREN

Precursor miRNA Sequence(5'-3')

AACACGTCTTCTCGGTATTTCTTTGTCTATATTCTTGGAAAAAGCGATGAGGTCTCGTTGCACTTTCCCAAATGTAGACAAAGCAAAACCGCGATGACGTCAAAG

PmiREN

Precursor miRNA Structure(5'-3') 

--AAC     U  U    A  U             CUU     AA       G 
     ACGUC UC CGGU UU CUUUGUCUAUAUU   GGAAA  GCGAUGA G
     ||||| || |||| || |||||||||||||   |||||  |||||||  
     UGCAG AG GCCA AA GAAACAGAUGUAA   CCUUU  CGUUGCU U
GAAAC     U  C    A  C             -AC     CA       C

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

bra-miR158b         --UCCCAAAUGUAGACAAAGCA
aly-miR158b-3p      --UCCCAAAUGUAGACAAAGC-
ath-miR158a-3p      --UCCCAAAUGUAGACAAAGCA
aly-miR158a-3p      --UCCCAAAUGUAGACAAAGCA
ath-miR158b         --CCCCAAAUGUAGACAAAGCA
esa-miR158b         UUUUCCAAAUGUUGACAAAGCA
bol-miR158          -UUUCCAAAUGUAGACAAAGCA
bra-miR158a         -UUUCCAAAUGUAGACAAAGCA
esa-miR158a         -UUUCCAAAUGUAGACAAAGCA
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