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

ppt-miR1030j

Organism

Physcomitrella patens

Species

Mature miRNA Sequence(5'-3')

CCUGCAUCUGCACCUGCACCA

miRBase

Precursor miRNA Sequence(5'-3')

AGCCUCCUCUUCAGCGCUGUAAUGCCAUGUUCCUGCAUCUGCACCUGCACCACACUUCUACGAGAGAAUGUGCAGAAGUCAGAGCGGUGUUGUGCGAAUCCUGCUCUCAGUCAAUUGCUGGGAUUGCGUUUCUCCAAUCUUCUUUCUCUGGGCUUUUCUCUGGCAUUGUGGUGGUGUAGGUGCUUAUGCAGAAAUAUUGCCUUGCAGCUUGCAGUUACUAGU

miRBase

Precursor miRNA Structure(5'-3') 

AGCCUCCU  U   C       U  C     C      CU             -  --UU   C       U  G    AGUCAGAGCGGUGUUGUGCGAAUCCUGCUCUCAG 
        CU CAG GCUGUAA GC AUGUU CUGCAU  GCACCUGCACCAC AC    CUA GAGAGAA GU CAGA                                  U
        || ||| ||||||| || ||||| ||||||  ||||||||||||| ||    ||| ||||||| || ||||                                   
        GA GUU CGACGUU CG UAUAA GACGUA  CGUGGAUGUGGUG UG    GGU CUCUUUU CG GUCU                                  A
UGAUCAUU  C   -       C  U     A      UU             G  UUAC   -       -  G    CUUUCUUCUAACCUCUUUGCGUUAGGGUCGUUAA

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

mpo-miR1030-b3.0r1-10150      UCUGCAUCUGCACCUGCACC-
ppt-miR1030h                  UCUGCAUCUGCACCUGCACCG
ppt-miR1030f                  UCUGCAUCUGCACCUGCACCA
ppt-miR1030g                  UCUGCAUCUGCACCUGCACCA
ppt-miR1030e                  UCUGCAUCUGCACCUGCACCA
ppt-miR1030d                  UCUGCAUCUGCACCUGCACCA
ppt-miR1030c                  UCUGCAUCUGCACCUGCACCA
ppt-miR1030b                  UCUGCAUCUGCACCUGCACCA
ppt-miR1030a                  UCUGCAUCUGCACCUGCACCA
ppt-miR1030j                  CCUGCAUCUGCACCUGCACCA
ppt-miR1030i                  CCUGCAUCUGCACCUGCACCG
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