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

vvi-miR535b

Organism

Vitis vinifera

Species

Mature miRNA Sequence(5'-3')

UGACAACGAGAGAGAGCACGC

miRBase

Precursor miRNA Sequence(5'-3')

UGUAAUUGCUUGACAACGAGAGAGAGCACGCUAGUCAGCAUUCAUGCGAGGAACAUGACUGUGUACAGGCGUGCUCUCUCUCGCUGUCAUACAAUCUUCUC

miRBase

Precursor miRNA Structure(5'-3') 

--UGUA    CU     A                A  CA   U     CG 
      AUUG  UGACA CGAGAGAGAGCACGCU GU  GCA UCAUG  A
      ||||  ||||| |||||||||||||||| ||  ||| |||||  G
      UAAC  ACUGU GCUCUCUCUCGUGCGG CA  UGU AGUAC  A
CUCUUC    AU     C                A  UG   C     AA

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

mdm-miR535b         -UGACAAGGAGAGAGAGCACGC
mdm-miR535c         -UGACAAGGAGAGAGAGCACGC
mac-miR535b         -UGACGACGAGAGAGAGCACGC
mdm-miR535d         -UGACGACGAGAGAGAGCACGC
ppe-miR535b         -UGACGACGAGAGAGAGCACGC
mes-miR535d         UUGACGACGAGAGAGAGCACG-
atr-miR535          -UGACAACGAGAGAGAGCACGC
tcc-miR535          -UGACAACGAUAGAGAGCACGC
cpa-miR535          -UGACAACGAGAGAGAGCACGC
ppe-miR535a         -UGACAACGAGAGAGAGCACGC
mdm-miR535a         -UGACAACGAGAGAGAGCACGC
rco-miR535          -UGACAACGAGAGAGAGCACGC
vvi-miR535c         -UGACAACGAGAGAGAGCACGC
vvi-miR535b         -UGACAACGAGAGAGAGCACGC
vvi-miR535a         -UGACAACGAGAGAGAGCACGC
ppt-miR535d         -UGACAACGAGAGAGAGCACGC
osa-miR535-5p       -UGACAACGAGAGAGAGCACGC
ppt-miR535c         -UGACAACGAGAGAGAGCACGC
ppt-miR535b         -UGACAACGAGAGAGAGCACGC
ppt-miR535a         -UGACAACGAGAGAGAGCACGC
sit-miR535          -UGACAACGAGAGAGAGCACGC
pvi-miR535b         -UGACAACGAGAGAGAGCACGC
pvi-miR535a         -UGACAACGAGAGAGAGCACGC
pha-miR535          -UGACAACGAGAGAGAGCACGC
mac-miR535h         -UGACAACGAGAGAGAGCACGC
mac-miR535g         -UGACAACGAGAGAGAGCACGC
mac-miR535f         -UGACAACGAGAGAGAGCACGC
mac-miR535e         -UGACAACGAGAGAGAGCACGC
mac-miR535d         -UGACAACGAGAGAGAGCACGC
mac-miR535c         -UGACAACGAGAGAGAGCACGC
mac-miR535a         -UGACAACGAGAGAGAGCACGC
mes-miR535a         -UGACAACGAGAGAGAGCACGU
mes-miR535b         -UGACAACGAGAGAGAGCACGG
csi-miR535a         -UGACAAUGAGAGAGAGCACAC
csi-miR535b-5p      -UGACAAUGAGAGAGAGCACAC
csi-miR535c-5p      -UGACAAUGAGAGAGAGCACAC
csi-miR535d-5p      -UGACAAUGAGAGAGAGCACAC
csi-miR535e-5p      -UGACAAUGAGAGAGAGCACAC
csi-miR535f-5p      -UGACAAUGAGAGAGAGCACAC
fve-miR535a         -UGACGAUGAGAGAGAGCACGC
fve-miR535b         -UGACGAUGAGAGAGAGCACGC
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