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-miR169a-3p

Organism

Arabidopsis lyrata

Species

Mature miRNA Sequence(5'-3')

GGCAAGUUGUCCUUGGCUACA

miRBase

Precursor miRNA Sequence(5'-3')

AACGCGUAUGUGACGAAAGUAGUGUGCAGCCAAGGAUGACUUGCCGAUUUAAAUGAUCUUUCUUUAUACUCUAUUAAGACAUUUUAAGUUUCAAAUUUCUUUGGUUCUUCAAGGAUUAAGGAAGAAAGUAGGCUAUAUAUGUAGAUAUAUAUAUUAUGCUGUAUUAAAUAUAUGUACAAGAUAAGACCAAAAAAGAAAAAGUAACAAUCAUGAUCGGCAAGUUGUCCUUGGCUACACGUUACUUUGUGUCGCGCAUAGGUGUU

miRBase

Precursor miRNA Structure(5'-3') 

     G      A   ----          C                      UAA     -------C       AUACUCUAUUAAGACAUUUUAAGUUUCAAAUUUCUUUGGUUCUUCAAGGAUUAAGGAAGAAA 
AACGC UAUGUG CGA    AAGUAGUGUG AGCCAAGGAUGACUUGCCGAUU   AUGAU        UUUCUUU                                                              G
||||| |||||| |||    |||||||||| ||||||||||||||||||||||   |||||        |||||||                                                               
UUGUG AUACGC GCU    UUCAUUGCAC UCGGUUCCUGUUGAACGGCUAG   UACUA        AAAGAAA                                                              G
     G      -   GUGU          A                      ---     ACAAUGAA       AAACCAGAAUAGAACAUGUAUAUAAAUUAUGUCGUAUUAUAUAUAUAGAUGUAUAUAUCGGA

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

zma-miR169a-3p      --GGCAAGU-UGUUCUU-GGCUACA
zma-miR169b-3p      --GGCAAGU-UGUUCUU-GGCUACA
bdi-miR169a-3p      --GGCGAGU-UGUUCUU-GGCUACA
bdi-miR169c-3p      --GGCAGGU-UGUCCUU-GGCUAC-
ptc-miR169b-3p      --GGCAGGU-UGUUCUU-GGCUAC-
ath-miR169b-3p      --GGCAAGU-UGUCCUUCGGCUACA
aly-miR169b-3p      --GGCAAGU-UGUCCUUCGGCUACA
zma-miR169r-3p      --GGCAAGU-UGUCCUU-GGCUACA
zma-miR169c-3p      --GGCAAGUCUGUCCUU-GGCUACA
aly-miR169a-3p      --GGCAAGU-UGUCCUU-GGCUACA
ath-miR169a-3p      --GGCAAGU-UGUCCUU-GGCUAC-
csi-miR169n-3p      --GGCAAGU-UGCCCUU-GGCUACA
osa-miR169p         UAGCCAAGGACAAACUU--GCCGG-
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