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

zma-miR390a-3p

Organism

Zea mays

Species

Mature miRNA Sequence(5'-3')

CGCUAUCUAUCCUGAGCUCCA

miRBase

Precursor miRNA Sequence(5'-3')

GAAGCUCAGGAGGGAUAGCGCCUAGGAAAACACAUAGAUCGGAGCCGGCCGCGAGGAGAAAGAAAGAGCCAAGAGAUAUGUGUGAUGAAUAAUCUACAUGGAUCUUGGCUAGCUUUUGUGUUCUCCUCUGGAGGCGUGGUUCUGUCUAUCAAUCUGAAGCGCUAUCUAUCCUGAGCUCCAC

miRBase

Precursor miRNA Structure(5'-3') 

-- A         G         CUA   AAACAC     U        -   --GC        --A     --        GA      U   G 
  G AGCUCAGGA GGAUAGCGC   GGA      AUAGA CGGAGCCG GCC    GAGGAGAA   GAAAG  AGCCAAGA  UAUGUG GAU A
  | ||||||||| |||||||||   |||      ||||| |||||||| |||    ||||||||   |||||  ||||||||  |||||| ||| A
  C UCGAGUCCU UCUAUCGCG   UCU      UAUCU GUCUUGGU CGG    CUCCUCUU   UUUUC  UCGGUUCU  GUACAU CUA A
CA C         A         AAG   ---AAC     -        G   AGGU        GUG     GA        AG      -   A

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

ptc-miR390d-3p      CGCUAUCCAUCCUGAGUUUUA
stu-miR390-3p       CGCUAUCCAUCUUGAGUUUUA
sly-miR390a-3p      CGCUAUCCAUCCUGAGUUUUA
ath-miR390a-3p      CGCUAUCCAUCCUGAGUUUCA
csi-miR390a-3p      CGCUAUCCAUCCUGAGUUUCA
sly-miR390b-3p      CGCUAUCCAUCCUGAGUUUCA
gma-miR390a-3p      CGCUAUCCAUCCUGAGUUUC-
gma-miR390c         CGCUAUCCAUCCUGAGUUUC-
mes-miR390          CGCUAUCCAUCCUGAGUUUC-
aly-miR390a-3p      CGCUAUCCAUCCUGAGUUUCA
ath-miR390b-3p      CGCUAUCCAUCCUGAGUUCC-
aly-miR390b-3p      CGCUAUCCAUCCUGAGUUCCA
zma-miR390a-3p      CGCUAUCUAUCCUGAGCUCCA
zma-miR390b-3p      CGCUAUCUAUCCUGAGCUCCA
bdi-miR390a-3p      CGCUAUCUAUCCUGAGCUCCA
osa-miR390-3p       CGCUAUCUAUCCUGAGCUCC-
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