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

bdi-miR168-3p

Organism

Brachypodium distachyon

Species

Mature miRNA Sequence(5'-3')

CCCGCCUUGCACCAAGUGAAU

miRBase

Precursor miRNA Sequence(5'-3')

UGCUCCUCCCCUGCCGCCGCCGCCUCGGGCUCGCUUGGUGCAGAUCGGGACCCUCCGCCCGCCCCCGCCGGGCCGGAUCCCGCCUUGCACCAAGUGAAUCGGAGCCGGCGCAGCGACUUUUUUUUACUUAAUUCCU

miRBase

Precursor miRNA Structure(5'-3') 

-------UGCUCCUCCCCUGC   --     C   G  C             AU     CCC    -    - C 
                     CGC  CGCCG CUC GG UCGCUUGGUGCAG  CGGGA   UCCG CCCG C C
                     |||  ||||| ||| || |||||||||||||  |||||   |||| |||| |  
                     GCG  GCGGC GAG CU AGUGAACCACGUU  GCCCU   AGGC GGGC G G
UCCUUAAUUCAUUUUUUUUCA   AC     C   G  A             CC     ---    C    C C

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

zma-miR168a-3p      ---CCCGCCUUGCACCAAGUGAA-
bdi-miR168-3p       ---CCCGCCUUGCACCAAGUGAAU
hvu-miR168-3p       GAUCCCGCCUUGCACCAAGUGAAU
osa-miR168a-3p      GAUCCCGCCUUGCACCAAGUGAAU
zma-miR168b-3p      ---CCCGCCUUGCAUCAAGUGAA-
csi-miR168-3p       ---CCCGCCUUGCAUCAACUGAAU
sly-miR168a-3p      ---CCUGCCUUGCAUCAACUGAAU
fve-miR168-3p       ---CCCGCCUUGCAUCAACUGAAU
sly-miR168b-3p      ---CCCGCCUUGCAUCAACUGAAU
mtr-miR168c-3p      ---CCCGCCUUGCAUCAACUGAAU
aly-miR168a-3p      ---CCCGCCUUGCAUCAACUGAAU
ptc-miR168b-3p      ---CCCGCCUUGCAUCAACUGAAU
ptc-miR168a-3p      ---CCCGCCUUGCAUCAACUGAAU
ath-miR168a-3p      ---CCCGCCUUGCAUCAACUGAAU
esa-miRN1029        --UCCCGACU-GCAUCAACUGAAU
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