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

bdi-miR2118b

Organism

Brachypodium distachyon

Species

Mature miRNA Sequence(5'-3')

UUCCUGAUGCCUCCCAUUCCUA

miRBase

Precursor miRNA Sequence(5'-3')

GAGGUGCAAAUAUUCAGUUUGGUGUUUUCCUGAUGCCUCCCAUUCCUAUGGUUCUUGAGCACUCCUUCCUCUUCCUUUUGGCCUGCGAAAUGGCUUAACGAAGAAAUUGUAGGUAUUUGUGCAUACUUUUAGACAAUGUGAGGCAGGUCGGGAAGAGGAAGAGAAGAGGGCCUUAGAGCAGUGGGAGUGGGAACAUGGAGGAAAGCCUGACUUGCUUUGUUUUCACCUC

miRBase

Precursor miRNA Structure(5'-3') 

      C     -UU   U    U        -G   CC            G     UGA  A   ----            UUU       GAA   GCUUAAC    AAAU    G U 
GAGGUG AAAUA   CAG UUGG GUUUUCCU  AUG  UCCCAUUCCUAU GUUCU   GC CUC    CUUCCUCUUCCU   GGCCUGC   AUG       GAAG    UGUA G A
|||||| |||||   ||| |||| ||||||||  |||  |||||||||||| |||||   || |||    ||||||||||||   |||||||   |||       ||||    |||| |  
CUCCAC UUUGU   GUU AGUC CGAAAGGA  UAC  AGGGUGAGGGUG CGAGA   CG GAG    GAAGGAGAAGGG   CUGGACG   UGU       UUUC    ACGU U U
      U     UUC   C    -        GG   -A            A     UUC  G   AAGA            ---       GAG   AACAGAU    --AU    G U

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

osa-miR2118m      UUCCUGAUGCCUCCCAUUCCUA
bdi-miR2118b      UUCCUGAUGCCUCCCAUUCCUA
osa-miR2118j      UUCCUGAUGCCUCCCAUUCCUA
osa-miR2118f      UUCCUGAUGCCUCCCAUUCCUA
zma-miR2118e      UUCCUGAUGUCUCCCAUUCCUA
osa-miR2118h      UUCCUGAUGCCUCUCAUUCCUA
osa-miR2118k      UUCCUGAUGCCUCUCAUUCCUA
zma-miR2118a      UUCCUGAUGCCUCUCAUUCCUA
osa-miR2118p      UUCCCGAUGCCUCCCAUGCCUA
osa-miR2118d      UUCCUGAUGCCUCCCAUGCCUA
osa-miR2118b      UUCCCGAUGCCUCCCAUUCCUA
osa-miR2118n      UUCCCGAUGCCUCCCAUUCCUA
zma-miR2118b      UUCCCGAUGCCUCCCAUUCCUA
osa-miR2118a      UUCUCGAUGCCUCCCAUUCCUA
bdi-miR2118a      UUUCCGAUGCCUCCCAUUCCUA
osa-miR2118c      UUCCCGAUGCCUCCUAUUCCUA
osa-miR2118q      UUCCCGAUGCCUCCUAUUCCUA
zma-miR2118g      UUCCUGAUGCCUCCUAUUCCUA
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