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

rco-miR535

Organism

Ricinus communis

Species

Mature miRNA Sequence(5'-3')

UGACAACGAGAGAGAGCACGC

miRBase

Precursor miRNA Sequence(5'-3')

UUUGUUGACAACGAGAGAGAGCACGCUUGUUAGCCUUCAUGUAAGGAACAUGGUUGCACACCAGCGUGCUCCCUAUCGUUGUCAAUGAGAU

miRBase

Precursor miRNA Structure(5'-3') 

--              G  A         U  UA  CU      A 
  UUUGUUGACAACGA AG GAGCACGCU GU  GC  UCAUGU A
  |||||||||||||| || ||||||||| ||  ||  |||||| G
  GAGUAACUGUUGCU UC CUCGUGCGA CA  CG  GGUACA A
UA              A  C         C  CA  UU      A

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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