Table 1.
Nucleotide sequences of 3' splice sites in 22 informative transcript pairs and exon skipping preferences of their -3C/T alleles
| Gene | Mutation | 3'ss that prefers ESa | RNA sequence across 3'ssb | Conformation at -3C/-3Uc | ES (%) of -3C:-3Ud |
|---|---|---|---|---|---|
| EPS15 | c.652-3 T/C | CAG | UACUGUUUUUUUUCCUCCCUGCAG/UGGGUUGUAUC | P/Pw | 7:0 |
| ABCA4 | c.5899-3 T > C | CAG | GGCUAGCUCUGUGUUUUCUCCCAG/UGCUUUGGCCU | P/Pw | 46:0 |
| CAPS | c.84-3 T/C | CAG | UCCAACCGUGUCCCCUGCCUCCAG/GUUUUUCCGCC | P/P | 40:28 |
| UHRF1 | c.887-3 T/C | CAG | CUGACCCUGCCGCCCCGUGCCCAG/GGAAGAGCGGG | P/B | 80:21 |
| CXXC1 | c.460-3 C/T | UAG | UCUGUUCUGGGCCCCCUCCUGUAG/CAUCACCAGCA | P/Pw | 1:5 |
| SRI | c.249-3 C/T | UAG | CUCUAAUCCUUGAUUACAGUUUAG/AGAGAUAUGUC | P/P | 79:96 |
| NOX5 | c.175-3 C/T | UAG | GUCUUCCACCCUUCUCGCCCAUAG/UCCUUCUUUGC | U/U | 4:16 |
| CRACR2A | c.229-3 C/T | UAG | CAGUACACUCUGGGUUGUUUUUAG/AGGCUGCAUAA | U/U | 2:7 |
| HGD | c.650-3 C/T | UAG | GACUUUUGGGUUACUGUUUUCUAG/GGGCCAAUGGC | P/U | 0:5 |
| F8 | c.5999-3 C/T | UAG | UUCUUCACUGUCCCUUUAAAAUAG/AUUUGGCCAGG | P/P | 4:22 |
| UBE2F | c.215-3 T/C | UAG | GUUUUGUUUUGUGUUUUUUGAUAG/AUGAGGGUUAC | P/U | 21:70f |
| SMN1 | c.835-3 T/C | UAG | UAACUUCCUUUAUUUUCCUUAUAG/GGUUUCAGACA | U/U | 0:27 |
| OTC | c.867-3 T > C | UAG | GUGGUCUUAUCCCCAUCUCUUUAG/ACUGCUAAAGU | U/P | 12:93 |
| PKHD1 | c.2141-3 T > C | UAG | AGUAAUUGGAUCACUGGUCUCUAG/UUUCUCAAGCU | P/U | 0:9 |
| SGCE | c.391-3 T > C | UAG | AAUAUGGUUUUCCUUUUAUAAUAG/AUAACUGCCUA | U/U | 0:4 |
| CFTRe | c.165-3 C > T | UAG | GUCCCACUUUUUAUUCUUUUGUAG/AGAAUGGGAUA | U/P | 0:24 |
| CRB2 | c.941-3 C > T | UAG | GACCCACAGCUGGGCCUCUUAUAG/GAGCCGACUGC | U/U | 17:83 |
| FRMD7 | c.498-3 C > T | UAG | CUCAUAAAUUCUUUCCCCUUUUAG/UGGCAGGAGCC | P/Pw | 0:3 |
| KIF5A | c.2993-3 C > T | UAG | UGUUCUCAAUGAUGAUCUCUUUAG/GAAAUGCCACA | U/U | 21:100 |
| NIPBL | c.3856-3 C > T | UAG | UUCAUUAACAAUACUGUUUUAUAG/AAUAACGAUAC | P/P | 4:100 |
| PARN | c.178-3 C > T | UAG | AGAUGUUUUAUUUCCCUUUUCUAG/CAUUCCAUGGA | U/U | 12:34 |
| AMELX | c.103-3 T > C | UAG | UUUACCUUCUUCUUUCUUUUGUAG/AACUCACAUUC | U/U | 13:98 |
aCAG or UAG 3'ss that showed higher exon skipping (ES) than their mutated versions in 22 tested minigene pairs (Fig. 1a). The sequence of minigene pairs differed only by pyrimidine at position -3 relative to 3'ss of the middle exon. Only the less efficient allele is shown per transcript pair. CAG 3'ss that showed higher ES than their UAG 3'ss counterparts (laggard CAG 3'ss) are at the top (n = 4); UAG 3'ss that showed higher ES than CAG 3'ss counterparts are at the bottom (n = 18)
bIntron-exon junctions are denoted by a slash; position -3 is underlined. Compilation of all disease-associated pyrimidine-to-pyrimidine mutations at position -3 as and their wild-type sequences are in Tables S5 and S6 of ref. [18]
cPaired (P), wobble (Pw), bulged (B), and unpaired (U) conformation of -3C and -3U bases in the most stable minimum free energy models
dExon skipping (%) of the two alleles (CAG:UAG) was measured previously [18]
eCFTR refers to CFTR exon 3 in ref. [18]
fExon skipping was induced only by weakening both 3’ss with a mutated PUF60 [18]