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-miR157d-3p

Organism

Arabidopsis lyrata

Species

Mature miRNA Sequence(5'-3')

GCUCUCUAUGCUUCUGUCAUC

miRBase

Precursor miRNA Sequence(5'-3')

AUGUUGUAUGUAUAGUGGAGGGUGAUAGUGUGGUUGCUGACAGAAGAUAGAGAGCACUAAGGAUGAUAUGCAAAACACACACAUAUAUGUGCUUCUAAUUGUAUUUCAUACUUAACAUCAAUGUUGAUGUGAAUCGUGAAAAAAAAAAAAGAGAGAAGAGCUAGAGGAGCAUCUGCAUCUCUAUUCCUAUGUGCUCUCUAUGCUUCUGUCAUCACCUUUUUUUCUCUAUUUCUCUCUACACAUUACAUAUUCACAU

miRBase

Precursor miRNA Structure(5'-3') 

    -U       --UA        U     ------UGU   U C         -           UA    UGAUAUGCAAAACACACACAUAUAUGUGCUUCUAAUUGUAUUUCAUACUUAACAUCAAU 
AUGU  GUAUGUA    GUGGAGGG GAUAG         GGU G UGACAGAAG AUAGAGAGCAC  AGGA                                                           G
||||  |||||||    |||||||| |||||         ||| | ||||||||| |||||||||||  ||||                                                           U
UACA  UAUACAU    CAUCUCUC UUAUC         CCA C ACUGUCUUC UAUCUCUCGUG  UCCU                                                           A
    CU       UACA        U     UCUUUUUUU   - U         G           UA    UAUCUCUACGUCUACGAGGAGAUCGAGAAGAGAGAAAAAAAAAAAAGUGCUAAGUGUAG

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

ath-miR157a-3p               GCUCUCUAGCCUUCUGUCAUC-
ath-miR157b-3p               GCUCUCUAGCCUUCUGUCAUC-
aly-miR157a-3p               GCUCUCUAGCCUUCUGUCAUCA
mtr-miR156g-3p               GCUCUCUAGACUUCUGUCAUC-
aly-miR157d-3p               GCUCUCUAUGCUUCUGUCAUC-
fve-miR156g-3p               GCUCUCUAUGCUUCUGUCAUC-
dca-miR156-b2.0r1-17334      GCUCUCUAUGCUUCUGUCAUC-
stu-miR156d-3p               GCUCUCUAUGCUUCUGUCAUCA
csi-miR156e-3p               GCUCUCUGUGCUUCUGUCAUCA
aly-miR157b-3p               GCUCUCUAAGCUUCUGUCAUCA
csi-miR156g-3p               GCUCUCUAUUCUUCUGUCAUC-
mtr-miR156h-3p               GCUCUUUAUUCUUCUGUCAUC-
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