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-miR477d

Organism

Physcomitrella patens

Species

Mature miRNA Sequence(5'-3')

CUCUCCCUCAAAGGCUUCCA

miRBase

Precursor miRNA Sequence(5'-3')

GUUGAUUUCGAUUAAACAGAUUGCUUGUUCCUCUCCCUCAAAGGCUUCCAACAACAGGUACUUGGUCUUGUUUUCACCAGCAAAGCUAAGGCCCGUCCCAGAUGUUAGAAGCCUCUGGGGGUGACGAAGCAGCAGCUGUAUGGGUGGUUCCCAU

miRBase

Precursor miRNA Structure(5'-3') 

GUUGAUUUCGAUUAA    A     UG   C  U      A       C    A A  U  UU      -     - A 
               ACAG UUGCU  UUC UC CCCUCA AGGCUUC AACA C GG AC  GGUCUU GUUUU C C
               |||| |||||  ||| || |||||| ||||||| |||| | || ||  |||||| ||||| |  
               UGUC GACGA  AAG AG GGGGGU UCCGAAG UUGU G CC UG  CCGGAA CGAAA G G
UACCCUUGGUGGGUA    -     CG   C  U      C       A    A A  C  -C      U     C A

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

ptc-miR477a-5p      -AUCUCCCUCAGAGGCUUCCAA-
ptc-miR477b         -AUCUCCCUCAGAGGCUUCCAA-
vvi-miR477a         -AUCUCCCUCAAAGGCUUCCAA-
mes-miR477f         -AUCUCCCUCAAAGGCUUCCA--
mes-miR477g         -AUCUCCCUCAAAGGCUUCCA--
ptc-miR477d-5p      -AUCUCCCUCAAAGGCUUCCUCU
ppt-miR477h         --UCUCCCUCAAAGGCUUCCA--
ppt-miR477c         -CUCUCCCUCAAAGGCUUCCA--
ppt-miR477a-5p      -CUCUCCCUCAAAGGCUUCCA--
ppt-miR477d         -CUCUCCCUCAAAGGCUUCCA--
ppt-miR477e         -CUCUCCCUCAAAGGCUUCCA--
ppt-miR477b         -CUCUCCCUCAAAGGCUUCCA--
csi-miR477b-5p      -CUCUCCCUCAAGGGCUUCUCU-
mes-miR477d         -CUCUCCCUCAAGGGCUUCUC--
stu-miR477a-5p      CCUCUCCCUCAAGGGCUUCUC--
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