{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,30]],"date-time":"2025-09-30T04:08:43Z","timestamp":1759205323145},"reference-count":73,"publisher":"Public Library of Science (PLoS)","issue":"1","license":[{"start":{"date-parts":[[2008,1,25]],"date-time":"2008-01-25T00:00:00Z","timestamp":1201219200000},"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.0040021","type":"journal-article","created":{"date-parts":[[2008,1,22]],"date-time":"2008-01-22T21:00:49Z","timestamp":1201035649000},"page":"e21","update-policy":"http:\/\/dx.doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":15,"title":["Strategies for Identifying RNA Splicing Regulatory Motifs and Predicting Alternative Splicing Events"],"prefix":"10.1371","volume":"4","author":[{"given":"Dirk","family":"Holste","sequence":"first","affiliation":[]},{"given":"Uwe","family":"Ohler","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2008,1,25]]},"reference":[{"key":"pcbi-0040021-b001","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1038\/416499a","article-title":"An extensive network of coupling among gene expression machines.","volume":"416","year":"2002","journal-title":"Nature"},{"key":"pcbi-0040021-b002","unstructured":"BurgeCTuschlTSharpP\n\t\t\t\t\t1999\n\t\t\t\t\tSplicing of precursors to mRNAs by the spliceosomes.\n\t\t\t\t\tIn:\n\t\t\t\t\tGestelandRCechTAtkinsJ\n\t\t\t\t\tThe RNA world. 2nd edition\n\t\t\t\t\tCold Spring Harbor (New York)\n\t\t\t\t\tCold Spring Harbor Laboratory Press\n\t\t\t\t\t525\n\t\t\t\t\t560"},{"key":"pcbi-0040021-b003","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","year":"1998","journal-title":"Annu Rev Genet"},{"key":"pcbi-0040021-b004","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","year":"2003","journal-title":"Annu Rev Biochem"},{"key":"pcbi-0040021-b005","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1016\/S1097-2765(03)00270-3","article-title":"Pre-mRNA splicing: Awash in a sea of proteins.","volume":"12","year":"2003","journal-title":"Mol Cell"},{"key":"pcbi-0040021-b006","doi-asserted-by":"crossref","first-page":"1147","DOI":"10.1002\/bies.10394","article-title":"The spliceosome: The most complex macromolecular machine in the cell?","volume":"25","year":"2003","journal-title":"Bioessays"},{"key":"pcbi-0040021-b007","doi-asserted-by":"crossref","first-page":"100","DOI":"10.1016\/S0168-9525(00)02176-4","article-title":"Alternative splicing: Increasing diversity in the proteomic world.","volume":"17","year":"2001","journal-title":"Trends Genet"},{"key":"pcbi-0040021-b008","doi-asserted-by":"crossref","first-page":"860","DOI":"10.1038\/35057062","article-title":"Initial sequencing and analysis of the human genome.","volume":"409","year":"2001","journal-title":"Nature"},{"key":"pcbi-0040021-b009","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1038\/ng1159","article-title":"Alternative splicing in the human, mouse and rat genomes is associated with an increased frequency of exon creation and\/or loss.","volume":"34","year":"2003","journal-title":"Nat Genet"},{"key":"pcbi-0040021-b010","doi-asserted-by":"crossref","first-page":"D56","DOI":"10.1093\/nar\/gkj048","article-title":"HOLLYWOOD: A comparative relational database of alternative splicing.","volume":"34","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"pcbi-0040021-b011","doi-asserted-by":"crossref","first-page":"419","DOI":"10.1101\/gad.1048803","article-title":"Pre-mRNA splicing and human disease.","volume":"17","year":"2003","journal-title":"Genes Dev"},{"key":"pcbi-0040021-b012","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1016\/j.ceb.2005.03.002","article-title":"Mechanistic links between nonsense-mediated mRNA decay and pre-mRNA splicing in mammalian cells.","volume":"17","year":"2005","journal-title":"Curr Opin Cell Biol"},{"key":"pcbi-0040021-b013","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1073\/pnas.0136770100","article-title":"Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans.","volume":"100","year":"2003","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi-0040021-b014","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1101\/gad.1382806","article-title":"Quantitative microarray profiling provides evidence against widespread coupling of alternative splicing with nonsense-mediated mRNA decay to control gene expression.","volume":"20","year":"2006","journal-title":"Genes Dev"},{"key":"pcbi-0040021-b015","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1016\/j.sbi.2004.05.002","article-title":"The evolving roles of alternative splicing.","volume":"14","year":"2004","journal-title":"Curr Opin Struct Biol"},{"key":"pcbi-0040021-b016","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1093\/bib\/6.1.23","article-title":"Bioinformatics analysis of alternative splicing.","volume":"6","year":"2005","journal-title":"Brief Bioinform"},{"key":"pcbi-0040021-b017","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1038\/nrg775","article-title":"Listening to silence and understanding nonsense: Exonic mutations that affect splicing.","volume":"3","year":"2002","journal-title":"Nat Rev Genet"},{"key":"pcbi-0040021-b018","doi-asserted-by":"crossref","first-page":"386","DOI":"10.1038\/nrm1645","article-title":"Understanding alternative splicing: Towards a cellular code.","volume":"6","year":"2005","journal-title":"Nat Rev Mol Cell Biol"},{"key":"pcbi-0040021-b019","doi-asserted-by":"crossref","first-page":"773","DOI":"10.1038\/nrg1451","article-title":"How did alternative splicing evolve?","volume":"5","year":"2004","journal-title":"Nat Rev Genetics"},{"key":"pcbi-0040021-b020","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","year":"2006","journal-title":"Nat Rev Genet"},{"key":"pcbi-0040021-b021","doi-asserted-by":"crossref","first-page":"1837","DOI":"10.1101\/gr.764102","article-title":"Selecting for functional alternative splices in ESTs.","volume":"12","year":"2002","journal-title":"Genome Res"},{"key":"pcbi-0040021-b022","doi-asserted-by":"crossref","first-page":"R74","DOI":"10.1186\/gb-2004-5-10-r74","article-title":"Variation in alternative splicing across human tissues.","volume":"5","year":"2004","journal-title":"Genome Biol"},{"key":"pcbi-0040021-b023","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1093\/nar\/gkl924","article-title":"Different levels of alternative splicing among eukaryotes.","volume":"35","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"pcbi-0040021-b024","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1038\/ng803","article-title":"Alternative splicing and genome complexity.","volume":"30","year":"2002","journal-title":"Nat Genet"},{"key":"pcbi-0040021-b025","doi-asserted-by":"crossref","first-page":"11193","DOI":"10.1073\/pnas.201407298","article-title":"A computational analysis of sequence features involved in recognition of short introns.","volume":"98","year":"2001","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi-0040021-b026","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1016\/j.tig.2007.04.001","article-title":"Coevolution of genomic intron number and splice sites.","volume":"23","year":"2007","journal-title":"Trends Genet"},{"key":"pcbi-0040021-b027","doi-asserted-by":"crossref","first-page":"831","DOI":"10.1016\/j.cell.2004.11.010","article-title":"Systematic identification and analysis of exonic splicing silencers.","volume":"119","year":"2004","journal-title":"Cell"},{"key":"pcbi-0040021-b028","doi-asserted-by":"crossref","first-page":"1007","DOI":"10.1126\/science.1073774","article-title":"Predictive identification of exonic splicing enhancers in human genes.","volume":"297","year":"2002","journal-title":"Science"},{"key":"pcbi-0040021-b029","doi-asserted-by":"crossref","first-page":"1777","DOI":"10.1261\/rna.2660805","article-title":"Characteristics and regulatory elements defining constitutive splicing and different modes of alternative splicing in human and mouse.","volume":"11","year":"2005","journal-title":"Rna"},{"key":"pcbi-0040021-b030","doi-asserted-by":"crossref","first-page":"5053","DOI":"10.1093\/nar\/gki810","article-title":"Distribution of SR protein exonic splicing enhancer motifs in human protein-coding genes.","volume":"33","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"pcbi-0040021-b031","doi-asserted-by":"crossref","first-page":"278","DOI":"10.1007\/BF02254432","article-title":"Regulation of alternative RNA splicing by exon definition and exon sequences in viral and mammalian gene expression.","volume":"11","year":"2004","journal-title":"J Biomed Sci"},{"key":"pcbi-0040021-b032","first-page":"reviews0008","article-title":"Finding signals that regulate alternative splicing in the post-genomic era.","volume":"3","year":"2002","journal-title":"Genome Biol"},{"key":"pcbi-0040021-b033","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1016\/S0896-6273(00)80900-9","article-title":"Nova-1 regulates neuron-specific alternative splicing and is essential for neuronal viability.","volume":"25","year":"2000","journal-title":"Neuron"},{"key":"pcbi-0040021-b034","doi-asserted-by":"crossref","first-page":"254","DOI":"10.1016\/S0896-6273(00)80888-0","article-title":"Genetic evidence for a Nova regulator of alternative splicing in the brain.","volume":"25","year":"2000","journal-title":"Neuron"},{"key":"pcbi-0040021-b035","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1006\/geno.2002.6826","article-title":"Alternative splicing of brain-specific PTB defines a tissue-specific isoform pattern that predicts distinct functional roles.","volume":"80","year":"2002","journal-title":"Genomics"},{"key":"pcbi-0040021-b036","doi-asserted-by":"crossref","first-page":"905","DOI":"10.1093\/emboj\/cdg089","article-title":"A vertebrate RNA-binding protein Fox-1 regulates tissue-specific splicing via the pentanucleotide GCAUG.","volume":"22","year":"2003","journal-title":"EMBO J"},{"key":"pcbi-0040021-b037","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/nar\/gki338","article-title":"Tissue-dependent isoforms of mammalian Fox-1 homologs are associated with tissue-specific splicing activities.","volume":"33","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"pcbi-0040021-b038","doi-asserted-by":"crossref","first-page":"2338","DOI":"10.1093\/nar\/29.11.2338","article-title":"Computational analysis of candidate intron regulatory elements for tissue-specific alternative pre-mRNA splicing.","volume":"29","year":"2001","journal-title":"Nucleic Acids Res"},{"key":"pcbi-0040021-b039","doi-asserted-by":"crossref","first-page":"1998","DOI":"10.1101\/gad.12.13.1998","article-title":"Identification of functional exonic splicing enhancer motifs recognized by individual SR proteins.","volume":"12","year":"1998","journal-title":"Genes Dev"},{"key":"pcbi-0040021-b040","doi-asserted-by":"crossref","first-page":"3568","DOI":"10.1093\/nar\/gkg616","article-title":"ESEfinder: A web resource to identify exonic splicing enhancers.","volume":"31","year":"2003","journal-title":"Nucleic Acids Res"},{"key":"pcbi-0040021-b041","article-title":"Single nucleotide polymorphism-based validation of exonic splicing enhancers.","volume":"2","year":"2004","journal-title":"PLoS Biol"},{"key":"pcbi-0040021-b042","doi-asserted-by":"crossref","first-page":"1241","DOI":"10.1101\/gad.1195304","article-title":"Computational definition of sequence motifs governing constitutive exon splicing.","volume":"18","year":"2004","journal-title":"Genes Dev"},{"key":"pcbi-0040021-b043","doi-asserted-by":"crossref","first-page":"769","DOI":"10.1016\/j.molcel.2006.05.008","article-title":"Comparative analysis identifies exonic splicing regulatory sequences\u2014The complex definition of enhancers and silencers.","volume":"22","year":"2006","journal-title":"Mol Cell"},{"key":"pcbi-0040021-b044","article-title":"Discovery and analysis of evolutionarily conserved intronic splicing regulatory elements.","volume":"3","year":"2007","journal-title":"PLoS Genet"},{"key":"pcbi-0040021-b045","article-title":"Intronic alternative splicing regulators identified by comparative genomics in nematodes.","volume":"2","year":"2006","journal-title":"PLoS Comput Biol"},{"key":"pcbi-0040021-b046","article-title":"Inference of splicing regulatory activities by sequence neighborhood analysis.","volume":"2","year":"2006","journal-title":"PLoS Genet"},{"key":"pcbi-0040021-b047","doi-asserted-by":"crossref","first-page":"12813","DOI":"10.1073\/pnas.0506139102","article-title":"Sequence conservation, relative isoform frequencies, and nonsense-mediated decay in evolutionarily conserved alternative splicing.","volume":"102","year":"2005","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi-0040021-b048","doi-asserted-by":"crossref","first-page":"1258","DOI":"10.1101\/gr.3929705","article-title":"Origin and evolution of new exons in rodents.","volume":"15","year":"2005","journal-title":"Genome Res"},{"key":"pcbi-0040021-b049","doi-asserted-by":"crossref","first-page":"2392","DOI":"10.1093\/molbev\/msl111","article-title":"Intron size, abundance, and distribution within untranslated regions of genes.","volume":"23","year":"2006","journal-title":"Mol Biol Evol"},{"key":"pcbi-0040021-b050","doi-asserted-by":"crossref","first-page":"2850","DOI":"10.1073\/pnas.0409742102","article-title":"Identification and analysis of alternative splicing events conserved in human and mouse.","volume":"102","year":"2005","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi-0040021-b051","doi-asserted-by":"crossref","first-page":"1313","DOI":"10.1093\/hmg\/ddg137","article-title":"Low conservation of alternative splicing patterns in the human and mouse genomes.","volume":"12","year":"2003","journal-title":"Hum Mol Genet"},{"key":"pcbi-0040021-b052","doi-asserted-by":"crossref","first-page":"2544","DOI":"10.1093\/nar\/gkg355","article-title":"Conservation of human alternative splice events in mouse.","volume":"31","year":"2003","journal-title":"Nucleic Acids Res"},{"key":"pcbi-0040021-b053","doi-asserted-by":"crossref","first-page":"1631","DOI":"10.1101\/gr.1208803","article-title":"Intronic sequences flanking alternatively spliced exons are conserved between human and mouse.","volume":"13","year":"2003","journal-title":"Genome Res"},{"issue":"Supplement 1","key":"pcbi-0040021-b054","first-page":"i369","article-title":"RASE: recognition of alternatively spliced exons in C. elegans.","volume":"21","year":"2005","journal-title":"Bioinformatics"},{"key":"pcbi-0040021-b055","doi-asserted-by":"crossref","first-page":"1838","DOI":"10.1261\/rna.7136104","article-title":"A computational and experimental approach toward a priori identification of alternatively spliced exons.","volume":"10","year":"2004","journal-title":"Rna"},{"key":"pcbi-0040021-b056","doi-asserted-by":"crossref","first-page":"1617","DOI":"10.1101\/gr.2572604","article-title":"A non-EST-based method for exon-skipping prediction.","volume":"14","year":"2004","journal-title":"Genome Res"},{"key":"pcbi-0040021-b057","doi-asserted-by":"crossref","first-page":"897","DOI":"10.1093\/bioinformatics\/bti132","article-title":"Accurate identification of alternatively spliced exons using support vector machine.","volume":"21","year":"2005","journal-title":"Bioinformatics"},{"issue":"Supplement 1","key":"pcbi-0040021-b058","first-page":"i387","article-title":"A motif-based framework for recognizing sequence families.","volume":"21","year":"2005","journal-title":"Bioinformatics"},{"key":"pcbi-0040021-b059","first-page":"113","article-title":"Recognition of unknown conserved alternatively spliced exons.","volume":"1","year":"2005","journal-title":"PLoS Comput Biol"},{"key":"pcbi-0040021-b060","unstructured":"DurbinREddySRKroghAMitchisonG\n\t\t\t\t\t1998\n\t\t\t\t\tBiological sequence analysis: Probabilistic models of proteins and nucleic acids\n\t\t\t\t\tCambridge (United Kingdom)\n\t\t\t\t\tCambridge University Press"},{"key":"pcbi-0040021-b061","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1186\/1748-7188-1-14","article-title":"A phylogenetic generalized hidden Markov model for predicting alternatively spliced exons.","volume":"1","year":"2006","journal-title":"Algorithms Mol Biol"},{"key":"pcbi-0040021-b062","doi-asserted-by":"crossref","first-page":"1561","DOI":"10.1093\/hmg\/11.13.1561","article-title":"Common exon duplication in animals and its role in alternative splicing.","volume":"11","year":"2002","journal-title":"Hum Mol Genet"},{"key":"pcbi-0040021-b063","doi-asserted-by":"crossref","first-page":"5611","DOI":"10.1093\/nar\/gki870","article-title":"Non-EST based prediction of exon skipping and intron retention events using Pfam information.","volume":"33","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"pcbi-0040021-b064","doi-asserted-by":"crossref","first-page":"3192","DOI":"10.1093\/nar\/gkm187","article-title":"Non-EST-based prediction of novel alternatively spliced cassette exons with cell signaling function in Caenorhabditis elegans and human.","volume":"35","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"pcbi-0040021-b065","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1186\/1471-2164-7-273","article-title":"Assessing the number of ancestral alternatively spliced exons in the human genome.","volume":"7","year":"2006","journal-title":"BMC Genomics"},{"issue":"Supplement 2","key":"pcbi-0040021-b066","first-page":"II36","article-title":"HMM sampling and applications to gene finding and alternative splicing.","volume":"19","year":"2003","journal-title":"Bioinformatics"},{"issue":"Supplement 1","key":"pcbi-0040021-b067","first-page":"1","article-title":"Using several pair-wise informant sequences for de novo prediction of alternatively spliced transcripts.","volume":"7","year":"2006","journal-title":"Genome Biol"},{"key":"pcbi-0040021-b068","article-title":"Improving the Caenorhabditis elegans genome annotation using machine learning.","volume":"3","year":"2007","journal-title":"PLoS Comput Biol"},{"key":"pcbi-0040021-b069","doi-asserted-by":"crossref","first-page":"739","DOI":"10.1089\/104454900750058107","article-title":"An alternative-exon database and its statistical analysis.","volume":"19","year":"2000","journal-title":"DNA Cell Biol"},{"key":"pcbi-0040021-b070","article-title":"Extraction of transcript diversity from scientific literature.","volume":"1","year":"2005","journal-title":"PLoS Comput Biol"},{"key":"pcbi-0040021-b071","doi-asserted-by":"crossref","first-page":"457","DOI":"10.1042\/BST0330457","article-title":"Regulation of alternative splicing by PTB and associated factors.","volume":"33","year":"2005","journal-title":"Biochem Soc Trans"},{"key":"pcbi-0040021-b072","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1016\/S1097-2765(03)00502-1","article-title":"Autoregulation of polypyrimidine tract binding protein by alternative splicing leading to nonsense-mediated decay.","volume":"13","year":"2004","journal-title":"Mol Cell"},{"key":"pcbi-0040021-b073","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1016\/j.cell.2005.07.028","article-title":"Mutually exclusive splicing of the insect Dscam pre-mRNA directed by competing intronic RNA secondary structures.","volume":"123","year":"2005","journal-title":"Cell"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.0040021","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,5,6]],"date-time":"2020-05-06T22:33:45Z","timestamp":1588804425000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.0040021"}},"subtitle":[],"editor":[{"given":"Fran","family":"Lewitter","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2008,1,25]]},"references-count":73,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2008,1,25]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.0040021","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2008,1,25]]}}}