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

mpo-miR-b3.0r1-4273

Organism

Marchantia polymorpha

Species

Mature miRNA Sequence(5'-3')

CCGUGCCAAGCUGUGUGCAUC

Plant sRNA Gene (Penn State Uni)

Precursor miRNA Sequence(5'-3')

UGAACGCUGAGAGAUAUUGAGCUUCACGUGUCGGAUCAAUGCAUAUUCAUUGGUUACAUCCUGCAACGUCCUCUCCGUCUCGUCCAGUCAUGAUCCGAUUCAGUAAGAAGGUCUUCGGAUGCCGCAGUUUGGUACAACCUCCAGAUCCAUACUCUCGACCAUCUGCGCACCCGACUGCUGCUGCUGUAACUAGUUACAGCUUGCGUCGAGCGAGAUCUCGCAUGGGGAUGAACCUUUCGUGAGAGUUGGUGUAUGGGUGCCGUGCCAAGCUGUGUGCAUCCAAAGACUUUCAUUCUUCAAGCUUCAUAGCUCUA

Precursor miRNA Structure(5'-3') 

-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UGAAC    --A     AUU   CUUC    -  C    -----     CA 
                                                                                                                                                                                                                                  GCUG   GAGAU   GAG    ACGU GU GGAU     CAAUG  U
                                                                                                                                                                                                                                  ||||   |||||   |||    |||| || ||||     |||||   
                                                                                                                                                                                                                                  UGAC   CUCUG   CUC    UGCA CG CCUA     GUUAC  U
AUCUCGAUACUUCGAACUUCUUACUUUCAGAAACCUACGUGUGUCGAACCGUGCCGUGGGUAUGUGGUUGAGAGUGCUUUCCAAGUAGGGGUACGCUCUAGAGCGAGCUGCGUUCGACAUUGAUCAAUGUCGUCGUCGUCAGCCCACGCGUCUACCAGCUCUCAUACCUAGACCUCCAACAUGGUUUGACGCCGUAGGCUUCUGGAAGAAUGACUUAGCCUAGUAC    CUG     --C   -UCC    A  U    CAUUG     UU

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

ppt-miR536a              UUCGUGCCAAGCUGUGUGCAAC
ppt-miR536f              UUCGUGCCAAGCUGUGUGCA--
ppt-miR536b              UUCGUGCCAAGCUGUGUGCAAC
ppt-miR536d              UUCGUGCCAAGCUGUGUGCAAC
ppt-miR536e              UUCGUGCCAAGCUGUGUGCAAC
mpo-miR-b3.0r1-4273      -CCGUGCCAAGCUGUGUGCAUC
smo-miR536               -UCGUGUCAAGCUGUGUGCAUC
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