{"id":"https://openalex.org/W2139582154","doi":"https://doi.org/10.1093/bioinformatics/btr280","title":"A cautionary note for retrocopy identification: DNA-based duplication of intron-containing genes significantly contributes to the origination of single exon genes","display_name":"A cautionary note for retrocopy identification: DNA-based duplication of intron-containing genes significantly contributes to the origination of single exon genes","publication_year":2011,"publication_date":"2011-05-05","ids":{"openalex":"https://openalex.org/W2139582154","doi":"https://doi.org/10.1093/bioinformatics/btr280","mag":"2139582154","pmid":"https://pubmed.ncbi.nlm.nih.gov/21551137"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btr280","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr280","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/13/1749/48869011/bioinformatics_27_13_1749.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/27/13/1749/48869011/bioinformatics_27_13_1749.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5077864427","display_name":"Yong E. Zhang","orcid":"https://orcid.org/0000-0003-3770-2383"},"institutions":[{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yong E. Zhang","raw_affiliation_strings":["1 Department of Ecology and Evolution, The University of Chicago, 1101 E 57th Street, 2Department of Molecular Genetics and Cell Biology, The University of Chicago, 920 E 58th Street and 3Committee on Evolutionary Biology, The University of Chicago, 1025 E 57th Street, Chicago, IL 60637, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Ecology and Evolution, The University of Chicago, 1101 E 57th Street, 2Department of Molecular Genetics and Cell Biology, The University of Chicago, 920 E 58th Street and 3Committee on Evolutionary Biology, The University of Chicago, 1025 E 57th Street, Chicago, IL 60637, USA","institution_ids":["https://openalex.org/I40347166"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012845493","display_name":"Maria D. Vibranovski","orcid":"https://orcid.org/0000-0001-8313-9726"},"institutions":[{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Maria D. Vibranovski","raw_affiliation_strings":["1 Department of Ecology and Evolution, The University of Chicago, 1101 E 57th Street, 2Department of Molecular Genetics and Cell Biology, The University of Chicago, 920 E 58th Street and 3Committee on Evolutionary Biology, The University of Chicago, 1025 E 57th Street, Chicago, IL 60637, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Ecology and Evolution, The University of Chicago, 1101 E 57th Street, 2Department of Molecular Genetics and Cell Biology, The University of Chicago, 920 E 58th Street and 3Committee on Evolutionary Biology, The University of Chicago, 1025 E 57th Street, Chicago, IL 60637, USA","institution_ids":["https://openalex.org/I40347166"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076687767","display_name":"Benjamin H. Krinsky","orcid":null},"institutions":[{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Benjamin H. Krinsky","raw_affiliation_strings":["1 Department of Ecology and Evolution, The University of Chicago, 1101 E 57th Street, 2Department of Molecular Genetics and Cell Biology, The University of Chicago, 920 E 58th Street and 3Committee on Evolutionary Biology, The University of Chicago, 1025 E 57th Street, Chicago, IL 60637, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Ecology and Evolution, The University of Chicago, 1101 E 57th Street, 2Department of Molecular Genetics and Cell Biology, The University of Chicago, 920 E 58th Street and 3Committee on Evolutionary Biology, The University of Chicago, 1025 E 57th Street, Chicago, IL 60637, USA","institution_ids":["https://openalex.org/I40347166"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5037432233","display_name":"Manyuan Long","orcid":"https://orcid.org/0000-0002-6755-197X"},"institutions":[{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Manyuan Long","raw_affiliation_strings":["1 Department of Ecology and Evolution, The University of Chicago, 1101 E 57th Street, 2Department of Molecular Genetics and Cell Biology, The University of Chicago, 920 E 58th Street and 3Committee on Evolutionary Biology, The University of Chicago, 1025 E 57th Street, Chicago, IL 60637, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Ecology and Evolution, The University of Chicago, 1101 E 57th Street, 2Department of Molecular Genetics and Cell Biology, The University of Chicago, 920 E 58th Street and 3Committee on Evolutionary Biology, The University of Chicago, 1025 E 57th Street, Chicago, IL 60637, USA","institution_ids":["https://openalex.org/I40347166"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5077864427"],"corresponding_institution_ids":["https://openalex.org/I40347166"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.0636,"has_fulltext":true,"cited_by_count":20,"citation_normalized_percentile":{"value":0.76484855,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"27","issue":"13","first_page":"1749","last_page":"1753"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11482","display_name":"RNA modifications and cancer","score":0.9991000294685364,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/intron","display_name":"Intron","score":0.8492736220359802},{"id":"https://openalex.org/keywords/gene-duplication","display_name":"Gene duplication","score":0.809100866317749},{"id":"https://openalex.org/keywords/exon","display_name":"Exon","score":0.7695838809013367},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.7661272287368774},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.7318543195724487},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.7210875153541565},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.6775954961776733},{"id":"https://openalex.org/keywords/tandem-exon-duplication","display_name":"Tandem exon duplication","score":0.5129539370536804},{"id":"https://openalex.org/keywords/human-genome","display_name":"Human genome","score":0.4130551517009735},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.33246445655822754}],"concepts":[{"id":"https://openalex.org/C94671646","wikidata":"https://www.wikidata.org/wiki/Q207551","display_name":"Intron","level":3,"score":0.8492736220359802},{"id":"https://openalex.org/C7602840","wikidata":"https://www.wikidata.org/wiki/Q746284","display_name":"Gene duplication","level":3,"score":0.809100866317749},{"id":"https://openalex.org/C36823959","wikidata":"https://www.wikidata.org/wiki/Q373027","display_name":"Exon","level":3,"score":0.7695838809013367},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7661272287368774},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.7318543195724487},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.7210875153541565},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6775954961776733},{"id":"https://openalex.org/C156446351","wikidata":"https://www.wikidata.org/wiki/Q7682435","display_name":"Tandem exon duplication","level":4,"score":0.5129539370536804},{"id":"https://openalex.org/C197077220","wikidata":"https://www.wikidata.org/wiki/Q720988","display_name":"Human genome","level":4,"score":0.4130551517009735},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.33246445655822754}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004331","descriptor_name":"Drosophila melanogaster","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004331","descriptor_name":"Drosophila melanogaster","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004331","descriptor_name":"Drosophila melanogaster","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005091","descriptor_name":"Exons","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005091","descriptor_name":"Exons","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005091","descriptor_name":"Exons","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007438","descriptor_name":"Introns","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007438","descriptor_name":"Introns","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007438","descriptor_name":"Introns","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008297","descriptor_name":"Male","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008297","descriptor_name":"Male","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008297","descriptor_name":"Male","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018626","descriptor_name":"Retroelements","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018626","descriptor_name":"Retroelements","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018626","descriptor_name":"Retroelements","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020440","descriptor_name":"Gene Duplication","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020440","descriptor_name":"Gene Duplication","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020440","descriptor_name":"Gene Duplication","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btr280","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr280","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/13/1749/48869011/bioinformatics_27_13_1749.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:21551137","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21551137","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:27/13/1749","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/27/13/1749","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"},{"id":"pmh:oai:pubmedcentral.nih.gov:3117337","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3117337","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btr280","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr280","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/13/1749/48869011/bioinformatics_27_13_1749.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3611247453","display_name":null,"funder_award_id":"R01GM","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3650008479","display_name":null,"funder_award_id":"00719","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4603818126","display_name":null,"funder_award_id":"1026200","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G848032724","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306278","display_name":"Chicago Community Trust","ror":"https://ror.org/01fcdd135"},{"id":"https://openalex.org/F4320317058","display_name":"Chicago Biomedical Consortium","ror":null},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2139582154.pdf","grobid_xml":"https://content.openalex.org/works/W2139582154.grobid-xml"},"referenced_works_count":33,"referenced_works":["https://openalex.org/W1552368341","https://openalex.org/W1796631315","https://openalex.org/W1993827187","https://openalex.org/W2025794959","https://openalex.org/W2028190503","https://openalex.org/W2033114461","https://openalex.org/W2042661483","https://openalex.org/W2046183549","https://openalex.org/W2057998009","https://openalex.org/W2059583250","https://openalex.org/W2063535371","https://openalex.org/W2073552485","https://openalex.org/W2075347516","https://openalex.org/W2086152457","https://openalex.org/W2096525273","https://openalex.org/W2098155430","https://openalex.org/W2100518496","https://openalex.org/W2102881062","https://openalex.org/W2110335151","https://openalex.org/W2113623526","https://openalex.org/W2120362978","https://openalex.org/W2122598328","https://openalex.org/W2124560890","https://openalex.org/W2127640118","https://openalex.org/W2130883600","https://openalex.org/W2135827569","https://openalex.org/W2136289616","https://openalex.org/W2150934173","https://openalex.org/W2158714788","https://openalex.org/W2160697532","https://openalex.org/W2916427899","https://openalex.org/W4232946036","https://openalex.org/W4239678514"],"related_works":["https://openalex.org/W1539107620","https://openalex.org/W2014905760","https://openalex.org/W1984349060","https://openalex.org/W1978448871","https://openalex.org/W2036368800","https://openalex.org/W2082856106","https://openalex.org/W2118812285","https://openalex.org/W1973164572","https://openalex.org/W2015491422","https://openalex.org/W2083833254"],"abstract_inverted_index":{"mlong@uchicago.edu;":[0],"zhangy@uchicago.edu":[1]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":4}],"updated_date":"2026-03-16T09:10:04.655348","created_date":"2025-10-10T00:00:00"}
