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

csi-miR408-5p

Organism

Citrus sinensis

Species

Mature miRNA Sequence(5'-3')

ACGGGGAACAGGCAGAGCAUG

miRBase

Precursor miRNA Sequence(5'-3')

AGGUAAUAAUAACUCUUUGGUGUGUGCGUGAGAGAGAGGCAAGAAGCAAGAGACAAAAGACGGGGAACAGGCAGAGCAUGGAUGGAACCAUUAACAGGUUCUCUGUUUUGGCUCCUCCCAUGCACUGCCUCUUCCCUGGCUCUCUGCCUUCCU

miRBase

Precursor miRNA Structure(5'-3') 

AGGUAAUAAUAACUCUUUGGUGUGUGCGUGAGAGAG   C   AA   A    CAAAA A       C      A      AU   A   UU     G 
                                    AGG AAG  GCA GAGA     G CGGGGAA AGGCAG GCAUGG  GGA CCA  AACAG U
                                    ||| |||  ||| ||||     | ||||||| |||||| ||||||  ||| |||  ||||| U
                                    UCC UUC  CGU CUCU     C GUCCCUU UCCGUC CGUACC  CCU GGU  UUGUC C
------------------------------------   -   --   -    ----- G       C      A      CU   C   -U     U

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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