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-miR2118r

Organism

Oryza sativa

Species

Mature miRNA Sequence(5'-3')

UUCCCAAUGCCUCCCAUGCCUA

miRBase

Precursor miRNA Sequence(5'-3')

GUGAGUCGGGAAGAGGAAGAAAAGAGGGUCUAAGAGCAGUGGGCAUGGGAACAUGGAGGAAGAACAUGUACUUUUCUUCCCUCUAAAUUUAGAGGUUGAGAUUUGCUAAGCAUUUUUCCCAAUGCCUCCCAUGCCUACAGUUCUUAGGUACUCCUUCCCCUUCCUGUUGGCUUGC

miRBase

Precursor miRNA Structure(5'-3') 

       ---      A     AAAA   GG         A            -A   --       GAACAU   CU    UUC      A 
GUGAGUC   GGGAAG GGAAG    GAG  UCUAAGAGC GUGGGCAUGGGA  CAU  GGAGGAA      GUA  UUUC   CCUCUA A
|||||||   |||||| |||||    |||  ||||||||| ||||||||||||  |||  |||||||      |||  ||||   ||||||  
CGUUCGG   UCCUUC CCUUC    CUC  GGAUUCUUG CAUCCGUACCCU  GUA  CCUUUUU      CGU  AGAG   GGAGAU U
       UUG      C     ----   AU         A            CC   AC       ACGAAU   UU    -UU      U

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

osa-miR2118e        -UUCCCAAUGCCUCCCAUGCCUA
zma-miR2118f        -UUCCCAAUGCCUUCCAUGCCUA
osa-miR2118r        -UUCCCAAUGCCUCCCAUGCCUA
mac-miR482b         -UUUCCAAUACCUCCCAUGCCAA
ptc-miR482b-3p      -UUACCAAUACCUCUCAUGCCAA
stu-miR482c         -UUUCCUAUUCCACCCAUGCCAA
sly-miR482d-3p      -UUUCCUAUUCCACCCAUGCCAA
ppe-miR482e         -UUGCCUAUUCCUCCCAUGCCAA
mac-miR482a         -UUUCCAAUGCCUCCCAUGCCAA
ptc-miR1448         CUUUCCAACGCCUCCCAUAC---
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