Table 1 –
Sixteen splice variants (SVs) spanning 15 genes selected by our pipeline to be enriched and prevalent in clear cell renal cell carcinoma
| SV | SV locusa | Gene name | Strand | Alternative splicing classification |
|---|---|---|---|---|
| PTPN14 | 1:214638300–214649697 | ENSG00000152104;PTPN14 | − | A5 |
| HPCAL1 | 2:10529703–10536960 | ENSG00000115756;HPCAL1 | + | A5 |
| COBLL1 | 2:165561615–165577187 | ENSG00000082438; COBLL1 | − | A5 |
| MCCC1 | 3:182756923–182757100 | ENSG00000078070;MCCC1 | + | A5 |
| SYNPO | 5:150019047–150027505 | ENSG00000171992;SYNPO | + | A5 |
| PDZD2 | 5:31995744–32000244 | ENSG00000133401;PDZD2 | + | A5 |
| RNASET2-beta | 6:167369679–167370715 | ENSG00000026297;RNASET2 | − | A5 |
| EGFR | 7:55259222–55259411 | ENSG00000146648;EGFR | + | A5 |
| FAM107B | 10:14664173–14709632 | ENSG00000065809;FAM107B | − | A3 |
| MVK | 12:110032624–110032832 | ENSG00000110921;MVK | + | A5 |
| MVK-beta | 12:110032708–110032832 | ENSG00000110921;MVK | + | A5 |
| SLC15A4 | 12:129299615–129307792 | ENSG00000139370;SLC15A4 | − | A5 |
| KDELC1 | 13:103444486–103445690 | ENSG00000134901;KDELC1 | − | ES |
| PARN | 16:14576684–14605072 | ENSG00000140694;PARN | − | A5 |
| GAL3ST1-gamma | 22:30953388–30959216 | ENSG00000128242;GAL3ST1 | − | Alt exon usage |
| FGD1 | X:54497920–54500960 | ENSG00000102302;FGD1 | − | A5 |
A3 = alternative 30-splice site; A5 = alternative 50-splice site; Alt exon usage = alternative exon usage; ES = exon skipping.
a
Loci are based on reference genome sequence hs37d5.