SNPSplicer

SNPSplicer analyzes single nucleotide polymorphisms (SNPs) that influence pre-mRNA splicing by interpreting genotyped cDNA to functionally annotate splice-altering variants.

Key Features:

• High-throughput functional annotation: Performs systematic, high-throughput annotation of SNP effects on splicing regulatory elements and splice sites.
• Integration with genotyped cDNA: Uses matched DNA and cDNA from genotyped tissue samples to interpret RT-PCR screening experiments.
• Detection of splice-altering consequences: Identifies splice outcomes including activation of cryptic splice sites, exon skipping, and exon inclusion mediated by exonic splice enhancers (ESE), intronic/exonic splicing enhancers/silencers (ISE, ESS, ISS).
• Variant case examples: Reports specific examples such as rs2076530:A>G (donor splice site → cryptic splice site usage), rs3816989:G>A (donor splice site → exon skipping), and rs2274987:C/T (exonic splice enhancer → inclusion of a new exon).

Scientific Applications:

• Functional annotation of noncoding variants: Assigns functional splicing consequences to SNPs that do not change amino acid sequence or cause frameshifts.
• RT-PCR interpretation: Supports interpretation of RT-PCR screening experiments that compare matched DNA and cDNA to detect splice-altering variants.
• Gene expression and protein-impact studies: Enables investigation of how genotype-dependent splicing changes affect gene expression and protein function.
• Genetic studies of disease and precision medicine: Applies to research on disease mechanisms and personalized medicine through characterization of regulatory SNPs.

Methodology:

Interprets RT-PCR screening results from matched DNA and cDNA of genotyped tissue samples to identify SNP-associated splice changes such as cryptic splice site activation, exon skipping, and novel exon inclusion.