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Table 5 Analysis of functional consequences of SNPs on Dicer processing sites using PHDcleav.

From: PHDcleav: a SVM based method for predicting human Dicer cleavage sites using sequence and secondary structure of miRNA precursors

miRBase 19
ID
Reference Genetic variant
  Cleavage
Position
PHDcleav
Score
Variation dbSNP ID SNP location on hairpin Cleavage Position PHDcleav Score Effect on Dicer cleavage site
hsa-mir-196a-2 47 2.326 g.78C>T rs11614913 Mature 47 2.326 remain same
  46 2.055     46 2.055  
  48 1.614     48 1.614  
hsa-mir-335 39 2.855 g.39T>C MIR335_00001* Mature 37 1.653 loss of site
  38 1.367     36 1.337  
  37 1.338     35 1.027  
hsa-mir-570 46 2.025 g.34T>C rs9860655 Stem 46 2.025 remain same
  45 1.126     45 1.126  
  39 0.908     40 0.994  
hsa-mir-650 35 1.366 g.71C>G rs59996397 Stem 35 1.366 remain same
  36 1.349     36 1.349  
  38 1.271     38 1.271  
hsa-mir-941-3 57 2.095 g.69C>G rs12625445 Mature 57 2.398 altered
  55 1.011     56 1.034  
  56 0.750     55 1.023  
  1. Top three scores of PHDcleav with their corresponding cleavage sites are given in the table, higher score indicates most probable Dicer cleave site. miRBase annotated canonical cleavage site is shown in bold, while altered cleavage site is shown in bold and italics.
  2. *miRvar DB-ID [43].