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-miR408-5p

Organism

Populus trichocarpa

Species

Mature miRNA Sequence(5'-3')

CGGGGAACAGGCAGAGCAUGG

miRBase

Precursor miRNA Sequence(5'-3')

AGAGACAGAUGAAGACGGGGAACAGGCAGAGCAUGGAUGGAGCUACUAACAGAAGUACUUGUUUUGGCUCUACCCAUGCACUGCCUCUUCCCUGGCUUGUGGCUC

miRBase

Precursor miRNA Structure(5'-3') 

A   A AGAUG   A       C      A      A        CU     AA 
 GAG C     AAG CGGGGAA AGGCAG GCAUGG UGGAGCUA  AACAG  G
 ||| |     ||| ||||||| |||||| |||||| ||||||||  |||||   
 CUC G     UUC GUCCCUU UCCGUC CGUACC AUCUCGGU  UUGUU  C
-   - --GUG   G       C      A      C        -U     CA

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

ath-miR408-5p       ACAGGGAACAAGCAGAGCAUG-
aly-miR408-5p       -CAGGGAACAAGCAGAGCAUGG
mtr-miR408-5p       ACAGGGAACAUGCAGAGCAUG-
mdm-miR408b         ACAGGGAAGAGGUAGAGCAUG-
mdm-miR408c         ACAGGGAAGAGGUAGAGCAUG-
mdm-miR408d         ACAGGGAAGAGGUAGAGCAUG-
gma-miR408a-5p      CAGGGGAACAGGCAGAGCAUG-
gma-miR408c-5p      CAGGGGAACAGGCAGAGCAUG-
ptc-miR408-5p       -CGGGGAACAGGCAGAGCAUGG
csi-miR408-5p       ACGGGGAACAGGCAGAGCAUG-
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