Table 2.

Glossary of Terms. Glossary of common terms and their definitions used in this article

Term	Description
High-TS genes	We identified isoforms with high TS scores (>0.5) and refer to them as High-TS genes. A value of 0.5 was chosen since this gave significant shape differences on manual visual inspection whilst maintaining a sufficiently large number of multi protein genes for statistical tests.
Primary isoform	The transcript of a gene with the maximum average expression.
Secondary isoform	The transcript of a gene with a different protein sequence to the primary isoform and with the next highest average expression level.
Minor isoform	Any transcript with a different protein sequence to the primary isoform.
Multi protein gene	A gene coding for at least two different protein isoforms. In this study we also filtered to only include isoforms if they were expressed >1FPKM in at least one developmental stage.
Intron Retention (IR)	Intron retention occurs when the intron of gene fails to be removed from the between neighbouring exons.
Exon Gain/Loss	Splicing events where a whole exon is gained or lost in one transcript relative to another.
Conservation Index (CI)	The conservation index as defined in the modENCODE validation paper measures the evolutionary distance at which a genomic element (e.g. exon) can be identified as expressed by RNAseq data. Greater values indicate greater evolutionary distances.
FPKM	FPKM (Fragments per kilobase of exon per million reads mapped) is a standard measure of expression for RNAseq data.