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

esa-miR395b

Organism

Eutrema salsugineum

Species

Mature miRNA Sequence(5'-3')

CUGAAGUGUUUGGGGGGACUC

PmiREN

Precursor miRNA Sequence(5'-3')

AGAGTCAAATGTCCCCATGAGTTCCCTTTAACGCTTCATTGTCAATACACAAAAATCATTTATTTGATCGATTTATGTATTAACACTGAAGTGTTTGGGGGGACTCTTGGTGCCATACTGGCGTTG

PmiREN

Precursor miRNA Structure(5'-3') 

-AGA    -A   U C   U          U         U   C      C   --A    UU 
    GUCA  AUG C CCA GAGUUCCCUU AACGCUUCA UGU AAUACA AAA   AUCA  U
    ||||  ||| | ||| |||||||||| ||||||||| ||| |||||| |||   ||||   
    CGGU  UAC G GGU CUCAGGGGGG UUGUGAAGU ACA UUAUGU UUU   UAGU  U
GUUG    CA   C U   U          U         C   A      A   AGC    UU

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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