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-miR169b-3p

Organism

Arabidopsis lyrata

Species

Mature miRNA Sequence(5'-3')

GGCAAGUUGUCCUUCGGCUACA

miRBase

Precursor miRNA Sequence(5'-3')

GUGCCCAACGGAGUAGAAUUGCAUGAAGUGGAGUAGAGUAUAAUGCAGCCAAGGAUGACUUGCCGGAACGUUGUUAAUCAUACGUAUAAAUUAUGUGAUGAACAUAUUUCUGGCAAGUUGUCCUUCGGCUACAUUUUGCUCUCUUCUUCUCAUGCAAACUCUCUUUGGGAUAU

miRBase

Precursor miRNA Structure(5'-3') 

-GUG     C    U  AA        AGU    U      U    C    -                  CGU    A   AU     U 
    CCCAA GGAG AG  UUGCAUGA   GGAG AGAGUA AAUG AGCC AAGGAUGACUUGCCGGAA   UGUU AUC  ACGUA A
    ||||| |||| ||  ||||||||   |||| |||||| |||| |||| ||||||||||||||||||   |||| |||  ||||| A
    GGGUU UCUC UC  AACGUACU   CUUC UCUCGU UUAC UCGG UUCCUGUUGAACGGUCUU   ACAA UAG  UGUAU U
UAUA     -    -  -A        CUU    -      U    A    C                  UAU    G   --     U

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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