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

dca-miR477-b2.0r1-4251

Organism

Daucus carota

Species

Mature miRNA Sequence(5'-3')

ACUCUCCCUCAAGGGCUUCUG

Plant sRNA Gene (Penn State Uni)

Precursor miRNA Sequence(5'-3')

UUUACUCUUCAAGGCAUUGGUUGCUUACUCUCCCUCAAGGGCUUCUGGAUUGGGCCAUUUAAUAGAAUUAUUCUAUUAAAAAGGGCUUGCUAGGAGCACUUUGAGGGGGAGUCAACAGCCCUUGCCUUGCUUAAUGCACUCUGCUGCAAACAAGUCAGGUGGUUGAUGAAGAUUUGAACAACAAUGGCUACAUAUCAUUGCUCACUCUCCCUCAAAGGCUUCCGAGAUAUUAUUCUGUCCUAUGGAAUCAUUUUUCCGGAAGCAGUUGGGGGCGAGUGGAUAAUGGUUUGCCAUGAUUAA

Precursor miRNA Structure(5'-3') 

------------------------------------------------------------------------------------------------------------------------------------------------------------------UUUACUCUUC      UU     CUU              -        AUU     --A            
                                                                                                                                                                            AAGGCA  GGUUG   ACUCUCCCUCAAGG GCUUCUGG   GGGCC   UUUAAUAGAAU 
                                                                                                                                                                            ||||||  |||||   |||||||||||||| ||||||||   |||||   |||||||||| U
                                                                                                                                                                            UUCCGU  CCGAC   UGAGGGGGAGUUUC CGAGGAUC   UUCGG   AAAUUAUCUUU 
AAUUAGUACCGUUUGGUAAUAGGUGAGCGGGGGUUGACGAAGGCCUUUUUACUAAGGUAUCCUGUCUUAUUAUAGAGCCUUCGGAAACUCCCUCUCACUCGUUACUAUACAUCGGUAACAACAAGUUUAGAAGUAGUUGGUGGACUGAACAAACGUCGUCUCACGUAAUUCG      UC     AAC              A        --G     GAA

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

mes-miR477c                 -CUCUCCCUCAAGGGCUUCUG-
mes-miR477e                 -CUCUCCCUCAAGGGCUUCUG-
mes-miR477b                 -CUCUCCCUCAAGGGCUUCUG-
mes-miR477a                 -CUCUCCCUCAAGGGCUUCUG-
csi-miR477e-5p              ACUCUCCCUCAAGGGCUUCUGA
dca-miR477-b2.0r1-4251      ACUCUCCCUCAAGGGCUUCUG-
stu-miR477b-5p              ACUCUCCCUCAAAGGCUUCUG-
mes-miR477i                 ACUCUCCCUCAAGGGCUUCCG-
mdm-miR477a                 ACUCUCCCUCAAGAGCUUCUC-
mes-miR477k                 ACUCUCCCUCAAGAGCUUCUC-
fve-miR477a                 ACUCUCCCUCAAGGGCUUCUC-
csi-miR477c-5p              ACUCUCCCUCAAGGGCUUCGC-
ptc-miR477e-5p              ACUCUCCCU-CAAGGCUUCCA-
mes-miR477j                 ACUCUCCCU-AAAGGCUUCAAC
mdm-miR477b                 ACUCUCCCUCAAGGGCUUCGAC
ptc-miR477f                 GCUCUCCCU-CAGGGCUUCCA-
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