Fig. 1

a Sample principal components clustering based on exon expression. Circles on the plot were ellipses drawn based on tissue types at the confidence interval = 0.95. Tissue types with which the non-overlapping ellipses were drawn were emphasised with underscored text labelling. Ellipses that were drawn based on experiments can be found in Additional file 2: Figure S4. b The significant splicing events between breeds and between genotypes (cis splicing quantitative trait loci, sQTLs) for CSN3 in the milk cell transcriptome. In the upper panel, from left to right: the 1st pair of bars are the least square means of normalised expression level of the gene (ENSBTAG00000039787) in Holstein and Jersey breeds; the 2nd pair of bars are the normalised expression level of the 5th exon (Chr6:87392578–87392750) in Holstein and Jersey breeds; the 3rd pair of bars are the normalised inclusion ratio of the 5th exon in Holstein and Jersey breeds; and 4th pair of bars is the frequency of the B allele of the sQTL (Chr6:87392580) for CSN3 in Holstein and Jersey breeds. The standard errors bars are indicated. In the lower panel, from left to right: the 1st bar is the effects (signed t values, b/se) of the sQTL (Chr6:87392580) B allele on the normalised expression of the gene; the 2nd bar is the sQTL B allele effect on the normalised expression of the 5th exon; and the 3rd bar was the sQTL B allele effects on the normalised inclusion ratio of the 5th exon