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

ppe-miR399c

Organism

Prunus persica

Species

Mature miRNA Sequence(5'-3')

UGCCAAAGAAGAGUUGCCCUA

miRBase

Precursor miRNA Sequence(5'-3')

GCAUACUUGUCAAGUAAGCAAAGCAGUCAUAGGGCUCCUCCUUCUUGGCAGGCACUGGUGACUGAUGCAGCUACAAAUGUAAAAUCACUUUCAUUGACCUGCCAAAGAAGAGUUGCCCUACGAUUGCUUUGGCUUAAUGAAAUUUGC

miRBase

Precursor miRNA Structure(5'-3') 

   UACUUG   AG     -         A      UC   C     -      -  ---CU     CUGA    GCU 
GCA      UCA  UAAGC AAAGCAGUC UAGGGC  CUC UUCUU GGCAGG CA     GGUGA    UGCA   A
|||      |||  ||||| ||||||||| ||||||  ||| ||||| |||||| ||     |||||    ||||    
CGU      AGU  AUUCG UUUCGUUAG AUCCCG  GAG AAGAA CCGUCC GU     UCACU    AUGU   A
   --UUAA   -A     G         C      UU   -     A      A  UACUU     -AAA    AAA

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

ppe-miR399k         UGCCAAAGAAGAGUUGCCCUA
ppe-miR399l         UGCCAAAGAAGAGUUGCCCUA
ppe-miR399j         UGCCAAAGAAGAGUUGCCCUA
ppe-miR399i         UGCCAAAGAAGAGUUGCCCUA
ppe-miR399h         UGCCAAAGAAGAGUUGCCCUA
ppe-miR399g         UGCCAAAGAAGAGUUGCCCUA
ppe-miR399f         UGCCAAAGAAGAGUUGCCCUA
ppe-miR399e         UGCCAAAGAAGAGUUGCCCUA
ppe-miR399d         UGCCAAAGAAGAGUUGCCCUA
ppe-miR399c         UGCCAAAGAAGAGUUGCCCUA
stu-miR399i-3p      UGCCAAAGGAGAGUUGCCCUA
mdm-miR399d         UGCCAAAGGAGAGUUGCCCUA
csi-miR399b-3p      UGCCAAAGGAGAGUUGCCCUA
sly-miR399          UGCCAAAGGAGAGUUGCCCUA
bra-miR399h         UGCCAAAGGAGAGUUGCCCU-
mdm-miR399k         UGCCAAAGGAGAGUUGCCCUU
mac-miR399a         -GCCAAAGGAGACUUGCCCUA
ptc-miR399e         CGCCAAAGGAGAGUUGCCCUC
ppe-miR399a         CGCCAAAGGAGAGUUGCCCUU
vvi-miR399i         CGCCAAAGGAGAGUUGCCCUG
tcc-miR399a         CGCCAAAGGAGAGUUGCCCUG
tcc-miR399e         CGCCAAAGGAGAAUUGCCCUG
csi-miR399f-3p      CGCCAAAGGAGAAUUGCCCUG
stu-miR399j-3p      CGCCAAAGGAGAGCUGCCCUG
stu-miR399k-3p      CGCCAAAGGAGAGCUGCCCUG
stu-miR399l-3p      CGCCAAAGGAGAGCUGCCCUG
stu-miR399m-3p      CGCCAAAGGAGAGCUGCCCUG
stu-miR399n-3p      CGCCAAAGGAGAGCUGCCCUG
stu-miR399o-3p      CGCCAAAGGAGAGCUGCCCUG
stu-miR399g-3p      CGCCAAAGGGGAGCUGCCCUA
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