title: Cryptic splice sites and split genes.
abstract: We describe a new program called cryptic splice finder (CSF) that can reliably identify cryptic splice sites (css), so providing a useful tool to help investigate splicing mutations in genetic disease. We report that many css are not entirely dormant and are often already active at low levels in normal genes prior to their enhancement in genetic disease. We also report a fascinating correlation between the positions of css and introns, whereby css within the exons of one species frequently match the exact position of introns in equivalent genes from another species. These results strongly indicate that many introns were inserted into css during evolution and they also imply that the splicing information that lies outside some introns can be independently recognized by the splicing machinery and was in place prior to intron insertion. This indicates that non-intronic splicing information had a key role in shaping the split structure of eukaryote genes.
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20814, USA. yurikapustin@gmail.com
authors.forename: Yuri
authors.initials: Y
authors.lastname: Kapustin
authors.forename: Elcie
authors.initials: E
authors.lastname: Chan
authors.forename: Rupa
authors.initials: R
authors.lastname: Sarkar
authors.forename: Frederick
authors.initials: F
authors.lastname: Wong
authors.forename: Igor
authors.initials: I
authors.lastname: Vorechovsky
authors.forename: Robert M
authors.initials: RM
authors.lastname: Winston
authors.forename: Tatiana
authors.initials: T
authors.lastname: Tatusova
authors.forename: Nick J
authors.initials: NJ
authors.lastname: Dibb
mesh_terms: D001483:Base Sequence; D016384:Consensus Sequence; D019143:Evolution, Molecular; D020224:Expressed Sequence Tags / Q000737:chemistry; D005796:Genes; D030342:Genetic Diseases, Inborn / Q000235:genetics; D023281:Genomics / Q000379:methods; D006801:Humans; D007438:Introns; D022821:RNA Splice Sites; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein; D012984:Software
chemical_list: D022821:RNA Splice Sites