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Table 1 In vitro observed and in silico predicted mRNA splicing phenotypes associated with the two canonical splice site variants and four intronic variants prioritized for quantitative RT-PCR analysis

From: In silico prioritization and further functional characterization of SPINK1 intronic variants

Intron SPINK1 variant SpliceSiteFinder-like (0–100) MaxEntScan (0–12) NNSPLICE (0–1) Human Splicing Finder (0–100) In vitro observed mRNA splicing phenotypea
Canonical splice donor site variants
 2 c.87 + 1G > A dss 79.8 → 0 dss 8.3 → 0 dss 0.9 → 0 dss 84.1 → 0 Complete exon 2 skipping
 3 c.194 + 2T > C dss 82.6 → 72.3 dss 11.1 → 0 dss 1.0 → 0 dss 92.1 → 0 Partial exon 3 skipping
Variants prioritized for quantitative RT-PCR analysis
 2 c.87 + 363A > G dss 0 → 65.5 Normal
ass 0 → 83.3
 3 c.194 + 13T > G dss 0 → 82.0 dss 0 → 9.5 dss 0 → 0.9 dss 0 → 86.9 Normal
 3 c.194 + 1504A > G dss 0 → 77.2 dss 0 → 0.7 dss 0 → 83.2 Normal
 3 c.195-323C > T dss 0 → 6.3 dss 0 → 0.7 dss 0 → 75.1 Normal
  1. Abbreviations: dss donor splice site, ass acceptor splice site
  2. aIn accordance with Zou et al. [2, 3]