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

cru-miR395g

Organism

Capsella rubella

Species

Mature miRNA Sequence(5'-3')

CUGAAGUGUUUGGGGGGACUC

PmiREN

Precursor miRNA Sequence(5'-3')

AAAGTCAAATGTCCCCTTGAGTTCCCTTAAACGCTTCATTGTTCATACTTTGTTTTCTATCGGACCGATGATGAATCAATCTGATGAACACTGAAGTGTTTGGGGGGACTCTAGGTGCCATCTGGCACCCC

PmiREN

Precursor miRNA Structure(5'-3') 

--AAAGUCAAAUGUCCCCUU                    U       -ACU   UU   U    GA 
                    GAGUUCCCUUAAACGCUUCA UGUUCAU    UUG  UUC AUCG  C
                    |||||||||||||||||||| |||||||    |||  ||| ||||   
                    CUCAGGGGGGUUUGUGAAGU ACAAGUA    AAC  AAG UAGU  A
CCCCACGGUCUACCGUGGAU                    C       GUCU   -U   -    AG

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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