How does an MPSS tag relate to a gene or transcript?
The position of the MPSS tag for a given gene or transcript should coincide with the first Sau3A site 5′ of the polyadenylation site. There are only two biological reasons for variation in the location of this site: small variations in the polyadenylation site, shifting it 5′ or 3′ of a Sau3A site (and thus splitting the total abundance count for that transcript among two or more signatures; or alternative polyadenylation due to alternative splicing and variable stop codons. The latter case is easier to demonstrate if you find two abundant signatures separated by an unused or less-used potential signature.
