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

ppt-miR536a

Organism

Physcomitrella patens

Species

Mature miRNA Sequence(5'-3')

UUCGUGCCAAGCUGUGUGCAAC

miRBase

Precursor miRNA Sequence(5'-3')

UGAUUCCACCCCUUGGAUGUCACUGCUUGGCACAAUCCUCUUAUUGUGAAUUUCAUGUCCUCUUUCGUGGUUAGUCGAUAGAGUUGUACUACCUUUAUUCAUCCAGUGUUAUAAAUGUUUGUCCAGUGCUAGCUCUUCACUUGGGGAUUGCACAACAGGGGGUUCGUGCCAAGCUGUGUGCAACCUAAGGGUGGUUUUA

miRBase

Precursor miRNA Structure(5'-3') 

   UU      CUU  A   -   U         -        UA     AAUUUCAU      UUUC    UUAGUCGAU      -     ------  C     -U     
UGA  CCACCC   GG UGU CAC GCUUGGCAC AAUCCUCU  UUGUG        GUCCUC    GUGG         AGAGUU GUACU      AC UUUAU  CAUC 
|||  ||||||   || ||| ||| ||||||||| ||||||||  |||||        ||||||    ||||         |||||| |||||      || |||||  ||| C
AUU  GGUGGG   CC ACG GUG CGAACCGUG UUGGGGGA  AACAC        UAGGGG    CACU         UCUCGA CGUGA      UG AAAUA  GUGU 
   UU      AAU  A   U   U         C        -C     ------GU      --UU    ---------      U     CCUGUU  U     UU

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

ppt-miR536a              UUCGUGCCAAGCUGUGUGCAAC
ppt-miR536f              UUCGUGCCAAGCUGUGUGCA--
ppt-miR536b              UUCGUGCCAAGCUGUGUGCAAC
ppt-miR536d              UUCGUGCCAAGCUGUGUGCAAC
ppt-miR536e              UUCGUGCCAAGCUGUGUGCAAC
mpo-miR-b3.0r1-4273      -CCGUGCCAAGCUGUGUGCAUC
smo-miR536               -UCGUGUCAAGCUGUGUGCAUC
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