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

mes-miR482b

Organism

Manihot esculenta

Species

Mature miRNA Sequence(5'-3')

UUCCCAAUGUCGCCCAUUCCGA

miRBase

Precursor miRNA Sequence(5'-3')

AGAUAGAGAGCUACUGGAAGUUGUAGGAAUGGGCGGUUUGGGAAAAAAUCAUAUACAUAAAUACGAUAACAGAUUACGUCGAAAAUCAAAUUAAGUGUAUACAAGUUUUCUUCCCAAUGUCGCCCAUUCCGAUGAUUUCCAGAAGCUCCUCCCUUUC

miRBase

Precursor miRNA Structure(5'-3') 

---  AU  A     A           A           -U       -     -CA       -A   AC   AACA     
   AG  AG GAGCU CUGGAAGUUGU GGAAUGGGCGG  UUGGGAA AAAAU   UAUACAU  AAU  GAU    GAUU 
   ||  || ||||| ||||||||||| |||||||||||  ||||||| |||||   |||||||  |||  |||    ||| A
   UC  UC CUCGA GACCUUUAGUA CCUUACCCGCU  AACCCUU UUUUG   AUAUGUG  UUA  CUA    CUGU 
CUU  CC  -     A           G           GU       C     AAC       AA   AA   AAAG

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-
                            *         *