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-miR2118g

Organism

Oryza sativa

Species

Mature miRNA Sequence(5'-3')

UUCCUAAUGCCUCCCAUUCCUA

miRBase

Precursor miRNA Sequence(5'-3')

GUGAACUUGGGAAGAGGAAGACAGAGGGUCUAAGAGCUGUAGGAAUGGGAACAUGGAGGAAAGUGCAAGCUCCAUGUUUGUGGAGACUUGGCUUGCAACUUUCCUAAUGCCUCCCAUUCCUAUUGUUCUUAGGUGCUCCUUCCUCUUCCUUUGGUCUCAC

miRBase

Precursor miRNA Structure(5'-3') 

    -   -U            ACA   G          U            -A   GG        -      ------     G 
GUGA ACU  GGGAAGAGGAAG   GAG GUCUAAGAGC GUAGGAAUGGGA  CAU  AGGAAAGU GCAAGC      UCCAU U
|||| |||  ||||||||||||   ||| |||||||||| ||||||||||||  |||  |||||||| ||||||      |||||  
CACU UGG  UCCUUCUCCUUC   CUC UGGAUUCUUG UAUCCUUACCCU  GUA  UCCUUUCA CGUUCG      AGGUG G
    C   UU            ---   G          U            CC   -A        A      GUUCAG     U

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-
                            *         *