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-miR167d-3p

Organism

Arabidopsis lyrata

Species

Mature miRNA Sequence(5'-3')

AGGUCAUCCUGCAGCUUCAGU

miRBase

Precursor miRNA Sequence(5'-3')

GAUCUAUAUCUAUGCUGGUUUUUAGAGGCUGAAGCUGCCAGCAUGAUCUGGUAAUUGCUACAUACGACAUACACACAUAUACUAGUUAAUUUCCACACCUAUAAAAGUUUUUUUCCUACAACUUAAAGCUUUUUUCCUUCCUCUUUUUAAUAAUUAGUGAUCUCUAGUUCUUUGCCUACUUGUAAUAUAUAUUUACGGUGGAUUCAUGCAUGUGUGUAUAUAUAUACAUAGUUUACAUGCAUGCAUUUUGUGUAUGUGUGUGUGUAUAGAUAGUAGUACUAGGUCAUCCUGCAGCUUCAGUCACUAAAUCACCAACAAUAUCAAAUC

miRBase

Precursor miRNA Structure(5'-3') 

GAUCUAUAUCUA  C    -U     A            C  C           A      CA  CG                UAGUUAAUUUCCACACCUAUAAAAGUUUUUUUCCUACAACUUAAAGCUUUUUUCCUUCCUCUUUUUAAUAAUUAGUGAUCUC 
            UG UGGU  UUUAG GGCUGAAGCUGC AG AUGAUCUGGUA UUGCUA  UA  ACAUACACACAUAUAC                                                                                  U
            || ||||  ||||| |||||||||||| || ||||||||||| ||||||  ||  ||||||||||||||||                                                                                  A
            AC ACCA  AAAUC CUGACUUCGACG UC UACUGGAUCAU GAUGAU  AU  UGUGUGUGUGUAUGUG                                                                                  U
--CUAAACUAUA  A    CU     A            -  C           -      AG  -A                UUUUACGUACGUACAUUUGAUACAUAUAUAUAUGUGUGUACGUACUUAGGUGGCAUUUAUAUAUAAUGUUCAUCCGUUUCUU

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

csi-miR167c-3p      AGGUCAUCUUGCAGCUUCAAU
sly-miR167b-3p      AGGUCAUCUAGCAGCUUCAAU
aly-miR167d-3p      AGGUCAUCCUGCAGCUUCAGU
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