title: Bioinformatic approaches for the identification of serpin genes with multiple reactive site loop coding exons.
abstract: In several branches of the tree of life, alternative splicing of a single primary transcript may give rise to multiple serpin isoforms exhibiting different target enzyme specificities. Though the continuously increasing number of genome sequencing projects has been paralleled by a rapidly rising number of serpin genes, the full spectrum of isoforms that some of these genes can encode has often not been recognized in routine database searches. In this chapter, we introduce procedures that enable the systematic extraction of multi-isoform generating serpin genes from genomic sequences. Spot checking of a model organism demonstrates that the phyletic distribution of such genes appears to be largely underestimated. The bioinformatic approach presented here may help to dissect the complete antiproteolytic spectrum of a genome's serpin complement and to register the occurrence of multitasking serpin genes in eukaryotes for functional and evolutionary studies.
authors.affiliation: Department of Biotechnology, Faculty of Technology, Bielefeld University, Bielefeld, Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Börner
authors.forename: Hermann
authors.initials: H
authors.lastname: Ragg
mesh_terms: D000465:Algorithms; D017398:Alternative Splicing; D000595:Amino Acid Sequence; D000818:Animals; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods* / Q000706:statistics & numerical data; D030541:Databases, Genetic; D005091:Exons / Q000235:genetics; D016678:Genome; D006801:Humans; D007438:Introns; D008390:Markov Chains; D008969:Molecular Sequence Data; D010802:Phylogeny; D010944:Plants; D011485:Protein Binding; D020033:Protein Isoforms / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D012333:RNA, Messenger; D016415:Sequence Alignment; D015843:Serpins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D012984:Software; D013379:Substrate Specificity
chemical_list: D020033:Protein Isoforms; D012333:RNA, Messenger; D015843:Serpins