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-miR395c-3p

Organism

Arabidopsis lyrata

Species

Mature miRNA Sequence(5'-3')

CUGAAGUGUUUGGGGGGACUU

miRBase

Precursor miRNA Sequence(5'-3')

AUGACAGAGCUACAAGAAGAAAGUCAAAUGUCUUCAUGAGUUCCCUUUAACGCUUCAUUGUUAAUAUUCAAACUACAUUUAUUUCCAUAAAUGUUUGAUCGAUUUGUAUAUAACACUGAAGUGUUUGGGGGGACUUUUGGUGUCAUUCUGGCGUAGUUACGAUUAU

miRBase

Precursor miRNA Structure(5'-3') 

    CA -      AAGAAGAAA    -    U U   U          U         U     -    -------    ACU        U 
AUGA  G AGCUAC         GUCA AAUG C UCA GAGUUCCCUU AACGCUUCA UGUUA AUAU       UCAA   ACAUUUAU U
||||  | ||||||         |||| |||| | ||| |||||||||| ||||||||| ||||| ||||       ||||   ||||||||  
UAUU  C UUGAUG         CGGU UUAC G GGU UUCAGGGGGG UUGUGAAGU ACAAU UAUG       AGUU   UGUAAAUA A
    AG A      ---------    C    U U   U          U         C     A    UUUAGCU    ---        C

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

cru-miR395a         -UGAAGUGUUUGAGGGUGACUC
esa-miR395h         -UGAAGUGUUUGGGGGGGACUC
cru-miR395b         CUGAAGUGUUUGGGGG-GACUC
cru-miR395f         CUGAAGUGUUUGGGGG-GACUC
esa-miR395i         CUGACGUGUUUGGGGG-GACUC
cru-miR395g         CUGAAGUGUUUGGGGG-GACUC
cru-miR395i         CUGAAGUGUUUGGGGG-GACUC
esa-miR395a         CUGAAGUGUUUGGGGG-GACUC
esa-miR395b         CUGAAGUGUUUGGGGG-GACUC
esa-miR395c         CUGAAGUGUUUGGGGG-GACUC
ath-miR395b         CUGAAGUGUUUGGGGG-GACUC
ath-miR395c         CUGAAGUGUUUGGGGG-GACUC
ath-miR395f         CUGAAGUGUUUGGGGG-GACUC
aly-miR395b-3p      CUGAAGUGUUUGGGGG-GACUC
aly-miR395f-3p      CUGAAGUGUUUGGGGG-GACUC
aly-miR395h-3p      CUGAAGUGUUUGGGGG-GACUC
aly-miR395c-3p      CUGAAGUGUUUGGGGG-GACUU
zma-miR395o-3p      GUGAAGUGUUUGGGUG-AACUC
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