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

stu-miR399n-3p

Organism

Solanum tuberosum

Species

Mature miRNA Sequence(5'-3')

CGCCAAAGGAGAGCUGCCCUG

miRBase

Precursor miRNA Sequence(5'-3')

GGGCUACUCUCUAUUGGCAUGCAUUUGUAUGUUUCAGCUGACACGCCAAAGGAGAGCUGCCCUG

miRBase

Precursor miRNA Structure(5'-3') 

--    UA      A     A  -  U   UA 
  GGGC  CUCUCU UUGGC UG CA UUG  U
  ||||  |||||| ||||| || || |||  G
  CCCG  GAGAGG AACCG AC GU GAC  U
GU    UC      A     C  A  C   UU

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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