In AltAnalyze a probeset associated with an intron is predicted to alter protein domain composition of the protein, but in DomainGraph why don't I see the probeset?

Answer: AltAnalyze uses both Ensembl and UCSC mRNAs (those in the all_mrna.txt annotation file) to determine which regions of a gene encode for possible exons. Thus, intron-retention can be identified from a non-Ensembl transcript. Indeed, Ensembl tends to be fairly conservative when adding a transcript to their database, such that valid alternative isoforms (with mRNA evidence) can be missing. In such a case, a probeset would not map to an Ensembl transcript and would not be shown in DomainGraph.

Furthermore, AltAnalyze searches for probesets that directly overlap with a domain/motif in mRNAs but also search for indirectly overlapping (in an intron that dissects a domain) and probesets that alter the domain composition by indirectly altering protein sequence. An example of which is the introduction of a premature stop codon that prevents the expression of a particular protein domain or motif. These annotations are present in the "exon-inclusion" result files in the folder AltResults/AlternativeOutput after completion of an AltAnalyze analysis.