Alternative splicing is regulated by a number of factors. One is the strength of the snRNP binding sites, the U1 and U2 sites of the splice donor and splice receptor of the major splicosome. Non-consensus splice sites bind snRNPs less strongly and so are less likely to dominate splicing. Variations in splicing over time are usually determined by changes in the concentrations of splice regulatory proteins that bind to regulatory target sites on the pre-mRNA, such as intronic splice suppressors or exonic splice enhancers. The activity of the proteins that bind these sites can be regulated physiologically.
Alternative transcripts can be identified by RT-PCR with appropriate primers. For an example see the following paper in which the investigators forced changes in splicing using Morpholino antisense oligos and then assayed the results by RT-PCR:
Draper BW, Morcos PA, Kimmel CB. Inhibition of zebrafish fgf8 pre-mRNA splicing with morpholino oligos: A quantifiable method for gene knockdown. Genesis. 2001 Jul;30(3):154-6. http://www.gene-tools.com/files/draper_etal.pdf