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-miR1511

Organism

Brassica rapa

Species

Mature miRNA Sequence(5'-3')

AACCUGGCUCUGAUACCAUGAAGU

PmiREN

Precursor miRNA Sequence(5'-3')

ATCTTGGTTTTGAGATCTTCTACATGGTATCAAAGCCATGTTATCATTGATAACCTGGCTCTGATACCATGAAGTAAATCTTAAAACAAGACTTG

PmiREN

Precursor miRNA Structure(5'-3') 

---A     G         CUU  A          A     U        
    UCUUG UUUUGAGAU   CU CAUGGUAUCA AGCCA GUUAUCA 
    ||||| |||||||||   || |||||||||| ||||| |||||| U
    AGAAC AAAAUUCUA   GA GUACCAUAGU UCGGU CAAUAGA 
GUUC     -         AAU  A          C     C

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

bra-miR1511         -AACCUGGCUCUGAUACCAUGAAGU--
gma-miR1511         -AACCAGGCUCUGAUACCAUG------
cpa-miR8155         UAACCUGGCUCUGAUACCA--------
ppe-miR1511-3p      --ACCUGGCUCUGAUACCAUAAC----
mdm-miR1511         --ACCUAGCUCUGAUACCAUGAA----
fve-miR1511         --ACCUAGCUCUGAUACCAUGUG----
bdi-miR7782-3p      --ACCU-GCUCUGAUACCAUGUUGUGA
                      ***  ************