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-miR390a-3p

Organism

Brachypodium distachyon

Species

Mature miRNA Sequence(5'-3')

CGCUAUCUAUCCUGAGCUCCA

miRBase

Precursor miRNA Sequence(5'-3')

CCAAUCGAGAUCGGUAAGGAACAAUCCUUGAAGCUCAGGAGGGAUAGCGCCUAGGUUCACUGCAACCAACAAGAGAACCGGCCAUCGAUAUAUACAUAUAUAUGUCCUCGAUCGACCGAUCGAUCUCUUGCUGGUUCCGUCGAUCUGUUCGUCCGAAGCGCUAUCUAUCCUGAGCUCCACGGUUCGUUCGUUCUUACCAUGCCCACACA

miRBase

Precursor miRNA Structure(5'-3') 

CCAAUCGAGAUC      ---    AAU  U  A         G         CUAGGUUCACUGCAACCAACAAGAGAACCGGCCAUCGAUAUAUACAUAUAUA 
            GGUAAG   GAAC   CC UG AGCUCAGGA GGAUAGCGC                                                    U
            ||||||   ||||   || || ||||||||| |||||||||                                                    G
            CCAUUC   CUUG   GG AC UCGAGUCCU UCUAUCGCG                                                    C
-ACACACCCGUA      UUG    CUU  C  C         A         AAGCCUGCUUGUCUAGCUGCCUUGGUCGUUCUCUAGCUAGCCAGCUAGCUCC

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-
                    ******* *** **** *