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

mdm-miR482a-5p

Organism

Malus domestica

Species

Mature miRNA Sequence(5'-3')

AGGAAUGGGCUGUUUGGGAAGA

miRBase

Precursor miRNA Sequence(5'-3')

GAGAAGAGGGAAAGGGAGAUUGGAGCUGCUGGAAGUUUUAGGAAUGGGCUGUUUGGGAAGAARGAAAAUUACAAGAAUAAUUGUCUUGUGGGGUUUCUUCCCAAGCCCGCCCAUUCCUAUGAUUUCCAGCUGUUCCUCCCUUUCCCUUGUAUCUC

miRBase

Precursor miRNA Structure(5'-3') 

    --A            GAUU     U          U           -U            RGAAAA        AU 
GAGA   GAGGGAAAGGGA    GGAGC GCUGGAAGUU UAGGAAUGGGC  GUUUGGGAAGAA      UUACAAGA  A
||||   ||||||||||||    ||||| |||||||||| |||||||||||  ||||||||||||      ||||||||  A
CUCU   UUCCCUUUCCCU    CCUUG CGACCUUUAG AUCCUUACCCG  CGAACCCUUCUU      GGUGUUCU  G
    AUG            ----     U          U           CC            ---UGG        GU

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

gra-miR482          UCUUUCCAAUUCCUCCCAUUCC------
fve-miR482a         UCUUUCCAAUUCCUCCCAUGCC------
csi-miR482a-3p      UCUUCCCUAUGCCUCCCAUUCC------
csi-miR482g-3p      UCUUCCCUAUGCCUCCCAUUCC------
pvu-miR482-3p       UCUUCCCAAUUCCGCCCAUUCC------
gma-miR482a-3p      UCUUCCCAAUUCCGCCCAUUCCUA----
gma-miR482c-3p      --UUCCCAAUUCCGCCCAUUCCU-----
sly-miR482a         --UUUCCAAUUCCACCCAUUCCUA----
stu-miR482a-3p      --UUUCCAAUUCCACCCAUUCCUA----
mtr-miR2118         --UUACCGAUUCCACCCAUUCCUA----
mdm-miR482a-3p      --UUCCCAAGCCCGCCCAUUCCUA----
ppe-miR482c-3p      --UUCCCAAGCCCGCCCAUUCCAA----
mes-miR482b         --UUCCCAAUGUCGCCCAUUCCGA----
ppe-miR482b-3p      -CUUCCCAA-ACCUCCCAUUCCUA----
osa-miR2118g        --UUCCUAAUGCCUCCCAUUCCUA----
stu-miR482e-3p      UCUUGCCAAUACCGCCCAUUCC------
sly-miR482c         UCUUGCCAAUACCGCCCAUUCC------
mdm-miR482a-5p      -----AGGAAUGGGCUGUUUGGGAAGA-
ppe-miR482c-5p      ------GGAAUGGGCUGUUUGGGAUG--
pvu-miR482-5p       ------GGAAUGGGCUGAUUGGGAAGCA
ppe-miR482b-5p      ------GGAAUGGGAGGAUUGGGAAAA-
                            *         *