title: Large-scale analysis of human alternative protein isoforms: pattern classification and correlation with subcellular localization signals.
abstract: We investigated human alternative protein isoforms of >2600 genes based on full-length cDNA clones and SwissProt. We classified the isoforms and examined their co-occurrence for each gene. Further, we investigated potential relationships between these changes and differential subcellular localization. The two most abundant patterns were the one with different C-terminal regions and the one with an internal insertion, which together account for 43% of the total. Although changes of the N-terminal region are less common than those of the C-terminal region, extension of the C-terminal region is much less common than that of the N-terminal region, probably because of the difficulty of removing stop codons in one isoform. We also found that there are some frequently used combinations of co-occurrence in alternative isoforms. We interpret this as evidence that there is some structural relationship which produces a repertoire of isoformal patterns. Finally, many terminal changes are predicted to cause differential subcellular localization, especially in targeting either peroxisomes or mitochondria. Our study sheds new light on the enrichment of the human proteome through alternative splicing and related events. Our database of alternative protein isoforms is available through the internet.
authors.affiliation: Human Genome Center, Institute of Medical Science, University of Tokyo Tokyo, Japan.
authors.forename: Mitsuteru
authors.initials: M
authors.lastname: Nakao
authors.forename: Roberto A
authors.initials: RA
authors.lastname: Barrero
authors.forename: Yuri
authors.initials: Y
authors.lastname: Mukai
authors.forename: Chie
authors.initials: C
authors.lastname: Motono
authors.forename: Makiko
authors.initials: M
authors.lastname: Suwa
authors.forename: Kenta
authors.initials: K
authors.lastname: Nakai
mesh_terms: D017398:Alternative Splicing; D030562:Databases, Protein; D006801:Humans; D020033:Protein Isoforms / Q000032:analysis / Q000737:chemistry* / Q000145:classification* / Q000235:genetics; D021382:Protein Sorting Signals; D040901:Proteomics; D020539:Sequence Analysis, Protein
chemical_list: D020033:Protein Isoforms; D021382:Protein Sorting Signals