The SD–Score represents a common logarithm of the frequency of a specific 5’splice site in the human genome.
For example‚ "CAG|GTGAGG" is observed at 2‚562 sites among the 189‚249 splice donor sites in the NCBI RefSeq Database Build 36.2‚ and its SD–Score is log (2‚562/189‚249) = –1.868. The SD–Score of a splice site sequence that never appears in the human genome is arbitrarily defined as log (0.25/189‚249) = –5.879 to simplify calculations. The SD–Score algorithm predicts if a mutation at the 5’splice site causes aberrant splicing or not with the sensitivity of 97.1% and the specificity of 94.7%.


  1. Enter the wild–type and mutant genomic sequences below and press the "analyze" button.
  2. Alternatively‚ enter the wild–type and mutant sequences spanning nine nucleotides from exon –3 to intron +6 separated by line breaks.
  3. Click on the excised nine nucleotide sequences in the results to predict splicing consequences of simulated mutations.

Wild–type sequence

Mutant sequence

A reference to be cited

K. Sahashi‚ A. Masuda‚ T. Matsuura‚ J. Shinmi‚ Z. Zhang‚ Y. Takeshima‚ M. Matsuo‚ G. Sobue‚ K. Ohno. In vitro and in silico analysis reveals an efficient algorithm to predict the splicing consequences of mutations at the 5' splice sites. Nucleic Acids Res 35: 5995–6003‚ 2007 [PMID: 17726045].


The SD–Score algorithm and the service program are made available by KAKENHI (Grant–in–Aid for Scientific Research) on Priority Areas "Systems Genomics" from the Ministry of Education‚ Culture‚ Sports‚ Science and Technology of Japan.