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

aly-miR828-5p

Organism

Arabidopsis lyrata

Species

Mature miRNA Sequence(5'-3')

UCUUGCUUAAAUGAGUAUUCCA

miRBase

Precursor miRNA Sequence(5'-3')

CAUGGACAAAGUCACAAAAGUGAUAAAAUCUCCUUCCACUUUCUAAUGUUUCUUGCUUAAAUGAGUAUUCCAUGUAAAAAAUGAGUCACUCACUCAUAUGGGUGGGUUGGGUUGGUUUUCUCUUCAUGAGAUGCUCAUUUGAGCAAGCAAUGUCUGUGAGUGGAACUAUUUAGUAUCAUGUUAUGAAUUUUGUCUUUUG

miRBase

Precursor miRNA Structure(5'-3') 

-CAU         -  CAAAA      AAAUCUCC        U UA     U                  C    --UAA     G    --        A 
    GGACAAAGU CA     GUGAUA        UUCCACUU C  AUGUU CUUGCUUAAAUGAGUAUU CAUG     AAAAU AGUC  ACUCACUC U
    ||||||||| ||     ||||||        |||||||| |  ||||| |||||||||||||||||| ||||     ||||| ||||  ||||||||  
    UCUGUUUUA GU     UACUAU        AAGGUGAG G  UGUAA GAACGAGUUUACUCGUAG GUAC     UUUUG UUGG  UGGGUGGG G
GUUU         A  -AUUG      GAUUUAUC        U UC     C                  A    UUCUC     G    GU        U

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

ath-miR828          UCUUGCUUAAAUGAGUAUUCCA
aly-miR828-5p       UCUUGCUUAAAUGAGUAUUCCA
lus-miR828a         UCUUGCUCAAAUGAGUGUUCCA
mes-miR828b         UCUUGCUCAAAUGAGUAUUCCA
mes-miR828a         UCUUGCUCAAAUGAGUAUUCCA
mdm-miR828b         UCUUGCUCAAAUGAGUAUUCCA
mdm-miR828a         UCUUGCUCAAAUGAGUAUUCCA
ptc-miR828b-5p      UCUUGCUCAAAUGAGUAUUCCA
ptc-miR828a         UCUUGCUCAAAUGAGUAUUCCA
ppe-miR828-5p       UCUUGCUCAAAUGAGUAUUCCA
gma-miR828b         UCUUGCUCAAAUGAGUAUUCCA
gma-miR828a         UCUUGCUCAAAUGAGUAUUCCA
vvi-miR828a         UCUUGCUCAAAUGAGUAUUCCA
mac-miR828          UCUUGCUCAAGUGAGUAUUCCA
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