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-miR162a-5p

Organism

Arabidopsis lyrata

Species

Mature miRNA Sequence(5'-3')

GGAGGCAGCGGUUCAUCGAUC

miRBase

Precursor miRNA Sequence(5'-3')

GAUUCGGGAAAUUUUAUGUUUCUUUGCCAUUUUUUUUGGAGUUUAGUUGGAAAAAGAGUGAGAGUCGCUGGAGGCAGCGGUUCAUCGAUCUCUUCCUGGGAACGAAUAUAUAAAUAUUGAAAAAGCAUGAAUAGAUCGAUAAACCUCUGCAUCCAGCGUUUGCCUCUUUAUCUUUGUUAUUGGCUUCAAUUUUUUUGGUUUUUGAAAAAAGUGAGGGAAAACAGAGUC

miRBase

Precursor miRNA Structure(5'-3') 

     -GGGAAA      --G    -UUU    UUUUUU        ---UAGUU   A      U A   U       G    C    C        C   C  -GGAACG     A 
GAUUC       UUUUAU   UUUC    GCCA      UUGGAGUU        GGA AAAGAG G GAG CGCUGGA GCAG GGUU AUCGAUCU UUC UG       AAUAU U
|||||       ||||||   ||||    ||||      ||||||||        ||| |||||| | ||| ||||||| |||| |||| |||||||| ||| ||       |||||  
CUGAG       GGAGUG   AAAG    UGGU      AACUUCGG        UCU UUUCUC C UUU GCGACCU CGUC CCAA UAGCUAGA AAG AC       UUAUA A
     ACAAAAG      AAA    UUUU    UUUUUU        UUAUUGUU   A      - G   -       A    U    A        U   U  GAAAAAG     A

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

ath-miR162a-5p      UGGAGGCAGCGGUUCAUCGAUC
ath-miR162b-5p      UGGAGGCAGCGGUUCAUCGAUC
csi-miR162-5p       UGGAGGCAGCGGUUCAUCGAUC
aly-miR162a-5p      -GGAGGCAGCGGUUCAUCGAUC
aly-miR162b-5p      -GGAGGCAGCGGUUCAUCGAUC
stu-miR162a-5p      -GGAGGCAGCGGUUCAUCGAUC
fve-miR162-5p       -GGAGGCAGCGGUUCAUCGAUC
stu-miR162b-5p      -GGAGGCAGCGGUUCAUCGAUC
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