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

osa-miR2118l

Organism

Oryza sativa

Species

Mature miRNA Sequence(5'-3')

UUCCUAAUGCUUCCCAUUCCUA

miRBase

Precursor miRNA Sequence(5'-3')

AGCGAGUUAGGAAGAGGAAGAAAUUGAGUGUCUAAGAACAGUGGGAAUGGAAACAUUAAGGAAAGCCUACAGUAUUUUCUUCUCCACUAGAAUUAGGGGUGGAGAUAAUUCUUUUGUGUUUUCCUAAUGCUUCCCAUUCCUAUUGUUGUUAGAUACUCCUUCCUCUUCCUUUUGGCU

miRBase

Precursor miRNA Structure(5'-3') 

   G  UU            AAAUU          G              -  A     A       CU    UAUUUUCU        AGA 
AGC AG  AGGAAGAGGAAG     GAGUGUCUAA AACAGUGGGAAUGG AA CAUUA GGAAAGC  ACAG        UCUCCACU   A
||| ||  ||||||||||||     |||||||||| |||||||||||||| || ||||| |||||||  ||||        ||||||||   U
UCG UU  UCCUUCUCCUUC     CUCAUAGAUU UUGUUAUCCUUACC UU GUAAU CCUUUUG  UGUU        AGAGGUGG   G
   G  -U            -----          G              C  C     -       --    UUCUUAAU        GGA

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

zma-miR2118c         UUCCUAAUGCCUCCCAUUCCUA-
osa-miR2118l         UUCCUAAUGCUUCCCAUUCCUA-
osa-miR2118i         UUCCUAGUGCCUCCCAUUCCUA-
vvi-miR3633a-3p      UUCCUA-UACCACCCAUUCCCUA
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