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

sly-miR390a-3p

Organism

Solanum lycopersicum

Species

Mature miRNA Sequence(5'-3')

CGCUAUCCAUCCUGAGUUUUA

miRBase

Precursor miRNA Sequence(5'-3')

AGAGAUCAACUAUGAAUGUUGUUCUUGUGGAAAUGGCAUGGGGAAUCUAUAAAGCUCAGGAGGGAUAGCACCAUGAAUACAUCUUAAUGGCUAUCUAUAGCGCUAUCCAUCCUGAGUUUUAUGGCUUCUUCAUGCUCGCUUUUGGUGCUUCAUGUUGAUCUUU

miRBase

Precursor miRNA Structure(5'-3') 

A         U     U  UGUUCUU   GAAAU           U               G       ACCAUGAAUACAUCU 
 GAGAUCAAC AUGAA GU       GUG     GGCAUGGGGAA CUAUAAAGCUCAGGA GGAUAGC               U
 ||||||||| ||||| ||       |||     ||||||||||| ||||||||||||||| |||||||                
 UUCUAGUUG UACUU CG       CGC     UCGUACUUCUU GGUAUUUUGAGUCCU CCUAUCG               U
U         -     -  UGGUUUU   -----           C               A       CGAUAUCUAUCGGUA

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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