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-miR408-5p

Organism

Arabidopsis lyrata

Species

Mature miRNA Sequence(5'-3')

CAGGGAACAAGCAGAGCAUGG

miRBase

Precursor miRNA Sequence(5'-3')

AAAGGUUAGAUUGGUAUUGCAAUGAAAGAAGUGGUAAUGAUAGAGAGAGACAGGGAACAAGCAGAGCAUGGAUUGAGUUUACUAAAACAUUAAACGACUCUGUUUUGUCUCUACCCAUGCACUGCCUCUUCCCUGGCUCCCUCUUUUCUCUCUCUCUCUCUCUCUCUCCCUCUCUCUAUUUCUUUCUCUCCUUUCAUUUCAAUGGAUUUUU

miRBase

Precursor miRNA Structure(5'-3') 

--AAAGGUUAGAUUGGUAUUGCAAU           UAAU  --U         -----------------------       CAA    A      AUU   UUU  U      UUAA 
                         GAAAGAAGUGG    GA   AGAGAGAGA                       CAGGGAA   GCAG GCAUGG   GAG   AC AAAACA    A
                         |||||||||||    ||   |||||||||                       |||||||   |||| ||||||   |||   || ||||||    C
                         CUUUCUUUAUC    CU   UCUCUCUCU                       GUCCCUU   CGUC CGUACC   CUC   UG UUUUGU    C
UUUUUAGGUAACUUUACUUUCCUCU           -UCU  CCC         CUCUCUCUCUCUUUUCUCCCUCG       CUC    A      CAU   ---  -      CUCA

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

ath-miR408-5p       ACAGGGAACAAGCAGAGCAUG-
aly-miR408-5p       -CAGGGAACAAGCAGAGCAUGG
mtr-miR408-5p       ACAGGGAACAUGCAGAGCAUG-
mdm-miR408b         ACAGGGAAGAGGUAGAGCAUG-
mdm-miR408c         ACAGGGAAGAGGUAGAGCAUG-
mdm-miR408d         ACAGGGAAGAGGUAGAGCAUG-
gma-miR408a-5p      CAGGGGAACAGGCAGAGCAUG-
gma-miR408c-5p      CAGGGGAACAGGCAGAGCAUG-
ptc-miR408-5p       -CGGGGAACAGGCAGAGCAUGG
csi-miR408-5p       ACGGGGAACAGGCAGAGCAUG-
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