{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,1]],"date-time":"2026-06-01T17:13:39Z","timestamp":1780334019736,"version":"3.54.1"},"reference-count":67,"publisher":"Public Library of Science (PLoS)","issue":"8","license":[{"start":{"date-parts":[[2008,8,8]],"date-time":"2008-08-08T00:00:00Z","timestamp":1218153600000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1000147","type":"journal-article","created":{"date-parts":[[2008,8,7]],"date-time":"2008-08-07T22:00:25Z","timestamp":1218146425000},"page":"e1000147","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":220,"title":["A General Definition and Nomenclature for Alternative Splicing Events"],"prefix":"10.1371","volume":"4","author":[{"given":"Michael","family":"Sammeth","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sylvain","family":"Foissac","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Roderic","family":"Guig\u00f3","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2008,8,8]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1146\/annurev.biochem.72.121801.161720","article-title":"Mechanisms of alternative pre-messenger RNA splicing.","volume":"72","author":"DL Black","year":"2003","journal-title":"Annu Rev Biochem"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1146\/annurev.genet.32.1.279","article-title":"Alternative splicing of pre-mRNA: developmental consequences and mechanisms of regulation.","volume":"32","author":"AJ Lopez","year":"1998","journal-title":"Annu Rev Genet"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1016\/S0968-0004(00)01604-2","article-title":"Alternative pre-mRNA splicing: the logic of combinatorial control.","volume":"25","author":"CW Smith","year":"2000","journal-title":"Trends Biochem Sci"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"860","DOI":"10.1038\/35057062","article-title":"Initial sequencing and analysis of the human genome.","volume":"409","author":"ES Lander","year":"2001","journal-title":"Nature"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1093\/bib\/bbk005","article-title":"Bioinformatics of alternative splicing and its regulation.","volume":"7","author":"L Florea","year":"2006","journal-title":"Brief Bioinform"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1038\/nrg1896","article-title":"Alternative splicing and RNA selection pressure\u2014evolutionary consequences for eukaryotic genomes.","volume":"7","author":"Y Xing","year":"2006","journal-title":"Nat Rev Genet"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"362","DOI":"10.1016\/j.sbi.2006.05.002","article-title":"The types and prevalence of alternative splice forms.","volume":"16","author":"M Zavolan","year":"2006","journal-title":"Curr Opin Struct Biol"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"2141","DOI":"10.1126\/science.1090100","article-title":"Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays.","volume":"302","author":"JM Johnson","year":"2003","journal-title":"Science"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"915","DOI":"10.1038\/ng0904-915","article-title":"Estimating rates of alternative splicing in mammals and invertebrates.","volume":"36","author":"H Kim","year":"2004","journal-title":"Nat Genet"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"467","DOI":"10.1146\/annurev.bi.56.070187.002343","article-title":"Alternative splicing: a ubiquitous mechanism for the generation of multiple protein isoforms from single genes.","volume":"56","author":"RE Breithart","year":"1987","journal-title":"Annu Rev Biochem"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"799","DOI":"10.1038\/nature05874","article-title":"Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.","volume":"447","year":"2007","journal-title":"Nature"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"D61","DOI":"10.1093\/nar\/gkl842","article-title":"NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins.","volume":"35","author":"KD Pruitt","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"739","DOI":"10.1089\/104454900750058107","article-title":"An alternative-exon database and its statistical analysis.","volume":"19","author":"S Stamm","year":"2000","journal-title":"DNA Cell Biol"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"D46","DOI":"10.1093\/nar\/gkj031","article-title":"ASD: a bioinformatics resource on alternative splicing.","volume":"34","author":"S Stamm","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1186\/1471-2105-7-169","article-title":"AltTrans: transcript pattern variants annotated for both alternative splicing and alternative polyadenylation.","volume":"7","author":"V Le Texier","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"D56","DOI":"10.1093\/nar\/gkj048","article-title":"HOLLYWOOD: a comparative relational database of alternative splicing.","volume":"34","author":"D Holste","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"584","DOI":"10.1016\/S0888-7543(03)00204-0","article-title":"Database and analyses of known alternatively spliced genes in plants.","volume":"82","author":"Y Zhou","year":"2003","journal-title":"Genomics"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1016\/S0168-9525(01)02525-2","article-title":"SpliceNest: visualization of gene structure and alternative splicing based on EST clusters.","volume":"18","author":"E Coward","year":"2002","journal-title":"Trends Genet"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"186","DOI":"10.1093\/nar\/30.1.186","article-title":"PALS db: Putative Alternative Splicing database.","volume":"30","author":"YH Huang","year":"2002","journal-title":"Nucleic Acids Res"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1093\/nar\/29.1.255","article-title":"SpliceDB: database of canonical and non-canonical mammalian splice sites.","volume":"29","author":"M Burset","year":"2001","journal-title":"Nucleic Acids Res"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"260","DOI":"10.1093\/nar\/29.1.260","article-title":"AsMamDB: an alternative splice database of mammals.","volume":"29","author":"H Ji","year":"2001","journal-title":"Nucleic Acids Res"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"2850","DOI":"10.1093\/nar\/29.13.2850","article-title":"Genome-wide detection of alternative splicing in expressed sequences of human genes.","volume":"29","author":"B Modrek","year":"2001","journal-title":"Nucleic Acids Res"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"R29","DOI":"10.1186\/gb-2003-4-4-r29","article-title":"ProSplicer: a database of putative alternative splicing information derived from protein, mRNA and expressed sequence tag sequence data.","volume":"4","author":"HD Huang","year":"2003","journal-title":"Genome Biol"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"1815","DOI":"10.1093\/bioinformatics\/btm084","article-title":"EuSplice: a unified resource for the analysis of splice signals and alternative splicing in eukaryotic genes.","volume":"23","author":"A Bhasi","year":"2007","journal-title":"Bioinformatics"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"D93","DOI":"10.1093\/nar\/gkl884","article-title":"The ASAP II database: analysis and comparative genomics of alternative splicing in 15 animal species.","volume":"35","author":"N Kim","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"505","DOI":"10.1101\/gr.4236606","article-title":"Evolution of exon\u2013intron structure and alternative splicing in fruit flies and malarial mosquito genomes.","volume":"16","author":"DB Malko","year":"2006","journal-title":"Genome Res"},{"key":"ref27","first-page":"901","article-title":"Proceedings of the SMBE Tri-National Young Investigators&apos; Workshop 2005. Investigating the intron recognition mechanism in eukaryotes.","volume":"23","author":"L Collins","year":"2006","journal-title":"Mol Biol Evol"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"16176","DOI":"10.1073\/pnas.0508489102","article-title":"The architecture of pre-mRNAs affects mechanisms of splice-site pairing.","volume":"102","author":"KL Fox-Walsh","year":"2005","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1016\/j.gene.2005.07.027","article-title":"Species-specific variation of alternative splicing and transcriptional initiation in six eukaryotes.","volume":"364","author":"H Nagasaki","year":"2005","journal-title":"Gene"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"3494","DOI":"10.1093\/nar\/gkl498","article-title":"Defective splicing, disease and therapy: searching for master checkpoints in exon definition.","volume":"34","author":"E Buratti","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"1489","DOI":"10.1261\/rna.7100104","article-title":"Multiple links between transcription and splicing.","volume":"10","author":"AR Kornblihtt","year":"2004","journal-title":"RNA"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"815","DOI":"10.1038\/nsmb1135","article-title":"Cotranscriptional coupling of splicing factor recruitment and precursor messenger RNA splicing in mammalian cells.","volume":"13","author":"I Listerman","year":"2006","journal-title":"Nat Struct Mol Biol"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"1288","DOI":"10.1101\/gr.9.12.1288","article-title":"Frequent alternative splicing of human genes.","volume":"9","author":"AA Mironov","year":"1999","journal-title":"Genome Res"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1186\/1471-2105-6-131","article-title":"Gene finding in the chicken genome.","volume":"6","author":"E Eyras","year":"2005","journal-title":"BMC Bioinformatics"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"S181","DOI":"10.1093\/bioinformatics\/18.suppl_1.S181","article-title":"Splicing graphs and EST assembly problem.","volume":"18","author":"S Heber","year":"2002","journal-title":"Bioinformatics"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"D509","DOI":"10.1093\/nar\/gkh067","article-title":"trome, trEST and trGEN: databases of predicted protein sequences.","volume":"32","author":"P Sperisen","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"ref37","first-page":"66","article-title":"Transcriptome and genome conservation of alternative splicing events in humans and mice.","author":"CW Sugnet","year":"2004","journal-title":"Pac Symp Biocomput"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"W444","DOI":"10.1093\/nar\/gkl268","article-title":"ASGS: an alternative splicing graph web service.","volume":"34","author":"D Bollina","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"2579","DOI":"10.1093\/bioinformatics\/bth288","article-title":"Genome wide identification and classification of alternative splicing based on EST data.","volume":"20","author":"S Gupta","year":"2004","journal-title":"Bioinformatics"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"566","DOI":"10.1101\/gr.3030405","article-title":"ECgene: genome-based EST clustering and gene modeling for alternative splicing.","volume":"15","author":"N Kim","year":"2005","journal-title":"Genome Res"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1186\/1471-2105-5-189","article-title":"DEDB: a database of Drosophila melanogaster exons in splicing graph form.","volume":"5","author":"BT Lee","year":"2004","journal-title":"BMC Bioinformatics"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"W297","DOI":"10.1093\/nar\/gkm311","article-title":"ASTALAVISTA: dynamic and flexible analysis of alternative splicing events in custom gene datasets.","volume":"35","author":"S Foissac","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1016\/S0168-9525(02)00029-X","article-title":"Evolution of alternative splicing: deletions, insertions and origin of functional parts of proteins from intron sequences.","volume":"19","author":"FA Kondrashov","year":"2003","journal-title":"Trends Genet"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"e15","DOI":"10.1371\/journal.pcbi.0020015","article-title":"Large-scale trends in the evolution of gene structures within 11 animal genomes.","volume":"2","author":"M Yandell","year":"2006","journal-title":"PLoS Comput Biol"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"912","DOI":"10.1101\/gr.5211806","article-title":"Genomic localization of RNA binding proteins reveals links between pre-mRNA processing and transcription.","volume":"16","author":"IA Swinburne","year":"2006","journal-title":"Genome Res"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"D25","DOI":"10.1093\/nar\/gkm929","article-title":"GenBank.","volume":"36","author":"DA Benson","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"332","DOI":"10.1038\/ng0893-332","article-title":"dbEST\u2014database for \u201cexpressed sequence tags\u201d.","volume":"4","author":"MS Boguski","year":"1993","journal-title":"Nat Genet"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"D610","DOI":"10.1093\/nar\/gkl996","article-title":"Ensembl 2007.","volume":"35","author":"TJ Hubbard","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"S4.1","DOI":"10.1186\/gb-2006-7-s1-s4","article-title":"GENCODE: Producing a reference annotation for ENCODE.","volume":"7","author":"J Harrow","year":"2006","journal-title":"Genome Biol"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1093\/nar\/gkj408","article-title":"Alternative splicing regulation at tandem 3\u2032 splice sites.","volume":"34","author":"M Akerman","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"e45","DOI":"10.1371\/journal.pgen.0020045","article-title":"A simple physical model predicts small exon length variations.","volume":"2","author":"TM Chern","year":"2006","journal-title":"PLoS Genet"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"1255","DOI":"10.1038\/ng1469","article-title":"Widespread occurrence of alternative splicing at NAGNAG acceptors contributes to proteome plasticity.","volume":"36","author":"M Hiller","year":"2004","journal-title":"Nat Genet"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"1129","DOI":"10.1073\/pnas.85.4.1129","article-title":"Possible evolution of splice-junction signals in eukaryotic genes from stop codons.","volume":"85","author":"P Senapathy","year":"1988","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"1642","DOI":"10.1101\/gr.520702","article-title":"Signatures of domain shuffling in the human genome.","volume":"12","author":"H Kaessmann","year":"2002","journal-title":"Genome Res"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1093\/nar\/gkl924","article-title":"Different levels of alternative splicing among eukaryotes.","volume":"35","author":"E Kim","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.","volume":"25","author":"M Ashburner","year":"2000","journal-title":"Nat Genet"},{"key":"ref57","doi-asserted-by":"crossref","first-page":"669","DOI":"10.1101\/gr.6339607","article-title":"What is a gene, post-ENCODE? History and updated definition.","volume":"17","author":"MB Gerstein","year":"2007","journal-title":"Genome Res"},{"key":"ref58","doi-asserted-by":"crossref","first-page":"398","DOI":"10.1038\/441398a","article-title":"Genetics: what is a gene?","volume":"441","author":"H Pearson","year":"2006","journal-title":"Nature"},{"key":"ref59","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1101\/gr.4137606","article-title":"Transcription-mediated gene fusion in the human genome.","volume":"16","author":"P Akiva","year":"2006","journal-title":"Genome Res"},{"key":"ref60","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1101\/gr.4145906","article-title":"Tandem chimerism as a means to increase protein complexity in the human genome.","volume":"16","author":"G Parra","year":"2006","journal-title":"Genome Res"},{"key":"ref61","doi-asserted-by":"crossref","first-page":"746","DOI":"10.1101\/gr.5660607","article-title":"Prominent use of distal 5\u2032 transcription start sites and discovery of a large number of additional exons in ENCODE regions.","volume":"17","author":"F Denoeud","year":"2006","journal-title":"Genome Res"},{"key":"ref62","doi-asserted-by":"crossref","first-page":"3917","DOI":"10.1093\/nar\/gkl507","article-title":"Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56,419 completely sequenced and manually annotated full-length cDNAs.","volume":"34","author":"J Takeda","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"ref63","doi-asserted-by":"crossref","first-page":"799","DOI":"10.1038\/nature05874","article-title":"Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.","volume":"447","author":"E Birney","year":"2007","journal-title":"Nature"},{"key":"ref64","doi-asserted-by":"crossref","first-page":"3456","DOI":"10.1093\/nar\/22.17.3456","article-title":"FlyBase\u2014the Drosophila database.","volume":"22","year":"1994","journal-title":"Nucleic Acids Res"},{"key":"ref65","doi-asserted-by":"crossref","first-page":"82","DOI":"10.1093\/nar\/29.1.82","article-title":"WormBase: network access to the genome and biology of Caenorhabditis elegans.","volume":"29","author":"L Stein","year":"2001","journal-title":"Nucleic Acids Res"},{"key":"ref66","doi-asserted-by":"crossref","first-page":"1188","DOI":"10.1101\/gr.849004","article-title":"WebLogo: a sequence logo generator.","volume":"14","author":"GE Crooks","year":"2004","journal-title":"Genome Res"},{"key":"ref67","doi-asserted-by":"crossref","first-page":"838","DOI":"10.1038\/nrg929","article-title":"The origin and evolution of model organisms.","volume":"3","author":"SB Hedges","year":"2002","journal-title":"Nat Rev Genet"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1000147","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,5,9]],"date-time":"2020-05-09T04:44:35Z","timestamp":1588999475000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1000147"}},"subtitle":[],"editor":[{"given":"Michael R.","family":"Brent","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2008,8,8]]},"references-count":67,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2008,8,8]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1000147","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2008,8,8]]}}}