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

pvi-miR159a

Organism

Panicum virgatum

Species

Mature miRNA Sequence(5'-3')

UUGCAUGACCGAGGAGCUGC

PmiREN

Precursor miRNA Sequence(5'-3')

GGTCGTTCGAAGGGTGGTACAGCTGCTCGTTCATGGTTCCCACTGTCCTATCTCATCGGCTTTGAGAGAGAGATTGTGAGATCGAGCTAGCGAGATGATTGGTTTGAGATAGGCTTGTGGTTTGCATGACCGAGGAGCTGCATCGTCCTCTTGCTGACCGC

PmiREN

Precursor miRNA Structure(5'-3') 

--     UU   -        A     G    U     GUUC    UGU         ------   GC    AG  AGA    G 
  GGUCG  CGA AGGGUGGU CAGCU CUCG UCAUG    CCAC   CCUAUCUCA      UCG  UUUG  AG   GAUU U
  |||||  ||| |||||||| ||||| |||| |||||    ||||   |||||||||      |||  ||||  ||   ||||  
  CCAGU  GUU UCCUGCUA GUCGA GAGC AGUAC    GGUG   GGAUAGAGU      AGU  GAGC  UC   CUAG G
CG     -C   C        C     G    C     GUUU    UUC         UUGGUU   -A    GA  GAG    A

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

pvi-miR159a           -UUGCAUGACCGAGGAGCUGC
pvi-miR159c           -UUGCAUGACCGAGGAGCUGC
bdi-miR159b-3p.3      UUUGCAUGACCGAGGAGCCGC
                       ***************** **