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

aly-miR472-3p

Organism

Arabidopsis lyrata

Species

Mature miRNA Sequence(5'-3')

UUUUUCCUACUCCGCCCAUACC

miRBase

Precursor miRNA Sequence(5'-3')

CCAAGGGGGAGUCAUAUUCUCAUCAAAGAUGGAUUCGGGGUUACGCCUCUGUAUGUAUGGUCGAAGUAGGCAAAAUCUCACCUUUCUAGCAGAUCAACAAUAGAUGCUUGAUUUAUAAAGGUUGUGGUGUUUGAAAGUGUUGAGAUCCGCAAGAUUUGAGUAAGAUUUUUCCUACUCCGCCCAUACCAUGCAUACACCUAAUCCUGAGUCCAUCUCUGAUGGGUUACUAUUGG

miRBase

Precursor miRNA Structure(5'-3') 

    G  GGAGUCAUAUU       A                 C CCUC            -----  A      C       C  - -UU   A  A  --      ---A        -U     A 
CCAA GG           CUCAUCA AGAUGGAUUCGGGGUUA G    UGUAUGUAUGGU     CG AGUAGG AAAAUCU AC C   UCU GC GA  UCAACA    UAGAUGCU  GAUUU U
|||| ||           ||||||| ||||||||||||||||| |    ||||||||||||     || |||||| ||||||| || |   ||| || ||  ||||||    ||||||||  |||||  
GGUU UC           GGGUAGU UCUACCUGAGUCCUAAU C    ACAUACGUACCA     GC UCAUCC UUUUAGA UG G   AGA CG CU  AGUUGU    GUUUGUGG  UUGGA A
    A  --------AUU       C                 C ----            UACCC  C      U       A  A UUU   A  C  AG      GAAA        UG     A

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

ptc-miR472b         --UUUUCCCAACUCCACCCAUCCC
csi-miR482f-3p      ---UUUUCCCACACCUCCCAUCCC
ptc-miR472a         --UUUUCCCUACUCCACCCAUCCC
mes-miR482          --UCUUCCCUACUCCACCCAUUCC
ath-miR472-3p       --UUUUUCCUACUCCGCCCAUACC
aly-miR472-3p       --UUUUUCCUACUCCGCCCAUACC
csi-miR482f-5p      ---GAUGGGUGAGUUGGGAAAAUA
csi-miR482d-5p      UGGUAUGGGUGAGUAGGGAAG---
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