Extended Data Fig. 5: Splicing consequences of FGD4 and GALNT2 essential splice mutations.
From: Non-additive association analysis using proxy phenotypes identifies novel cattle syndromes
Mammary RNA-seq alignments for the FGD4 (a) and GALNT2 (b) genes, showing wildtype and carrier animals for the FGD4 c.1671+1G>A and GALNT2 c.1561-1G>A splice mutations (two animals representing each genotype class per gene). Intron and exon numbers reference the ENSBTAT00000007175.5 and ENSBTAT00000006404.5 transcript annotations for the FGD4 and GALNT2 genes respectively. Right-most panels show intron-exon boundaries of the mutation-implicated splice junction, left-most panels show kilobase-level views of the whole intron and adjoining exon junction. Coverage tracks demonstrate clear intron retention for FGD4 heterozygous mutants, without obvious cryptic splicing. Animals heterozygous for GALNT2 mutant transcripts show less uniform intron retention, though at least three recurrent cryptic splice sites indicated by the purple arrows (green arrows show annotated junctions). c Putative translations for these alternatively spliced transcripts are indicated (light blue=reference splice, red=mis-splice), where the first base of the new acceptor exon boundaries are: cryptic 1 chr28 g.1309085; cryptic 2 chr28 g.1312087; cryptic 3 chr28 g.1312203. Note that all intron retention and cryptic splices are predicted to cause premature termination, with the exception of the ‘GALNT2 cryptic 3’ isoform that encodes a 44aa 5’ frame-extension of exon 16.
