Gene Model Annotations for Drosophila melanogaster: The Rule-Benders
Abstract In the context of the FlyBase annotated gene models in Drosophila melanogaster, we describe the many exceptional cases we have curated from the literature or identified in the course of FlyBase analysis. These range from atypical but common examples such as dicistronic and polycistronic tra...
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| Veröffentlicht in: | G3 : genes - genomes - genetics 2015-06, Vol.5 (8), p.1737-1749 |
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| container_title | G3 : genes - genomes - genetics |
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| creator | Crosby, Madeline A Gramates, L Sian dos Santos, Gilberto Matthews, Beverley B St. Pierre, Susan E Zhou, Pinglei Schroeder, Andrew J Falls, Kathleen Emmert, David B Russo, Susan M Gelbart, William M |
| description | Abstract
In the context of the FlyBase annotated gene models in Drosophila melanogaster, we describe the many exceptional cases we have curated from the literature or identified in the course of FlyBase analysis. These range from atypical but common examples such as dicistronic and polycistronic transcripts, noncanonical splices, trans-spliced transcripts, noncanonical translation starts, and stop-codon readthroughs, to single exceptional cases such as ribosomal frameshifting and HAC1-type intron processing. In FlyBase, exceptional genes and transcripts are flagged with Sequence Ontology terms and/or standardized comments. Because some of the rule-benders create problems for handlers of high-throughput data, we discuss plans for flagging these cases in bulk data downloads. |
| doi_str_mv | 10.1534/g3.115.018937 |
| format | Article |
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In the context of the FlyBase annotated gene models in Drosophila melanogaster, we describe the many exceptional cases we have curated from the literature or identified in the course of FlyBase analysis. These range from atypical but common examples such as dicistronic and polycistronic transcripts, noncanonical splices, trans-spliced transcripts, noncanonical translation starts, and stop-codon readthroughs, to single exceptional cases such as ribosomal frameshifting and HAC1-type intron processing. In FlyBase, exceptional genes and transcripts are flagged with Sequence Ontology terms and/or standardized comments. Because some of the rule-benders create problems for handlers of high-throughput data, we discuss plans for flagging these cases in bulk data downloads.</description><identifier>ISSN: 2160-1836</identifier><identifier>EISSN: 2160-1836</identifier><identifier>DOI: 10.1534/g3.115.018937</identifier><identifier>PMID: 26109356</identifier><language>eng</language><publisher>United States: Oxford University Press</publisher><subject>Animals ; Base Sequence ; Codon, Terminator ; Databases, Genetic ; Drosophila melanogaster - genetics ; Investigations ; Mitochondria - genetics ; Mitochondria - metabolism ; Models, Genetic ; Molecular Sequence Annotation ; Protein Biosynthesis ; RNA Editing ; RNA Splice Sites</subject><ispartof>G3 : genes - genomes - genetics, 2015-06, Vol.5 (8), p.1737-1749</ispartof><rights>2015 Crosby et al. 2015</rights><rights>Copyright © 2015 Crosby et al.</rights><rights>Copyright © 2015 Crosby 2015</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c381t-d1bb736751244890757a7d45f4406c52ef28157c75954bddc49e9f156a149d623</citedby><cites>FETCH-LOGICAL-c381t-d1bb736751244890757a7d45f4406c52ef28157c75954bddc49e9f156a149d623</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4528330/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4528330/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,27901,27902,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/26109356$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Crosby, Madeline A</creatorcontrib><creatorcontrib>Gramates, L Sian</creatorcontrib><creatorcontrib>dos Santos, Gilberto</creatorcontrib><creatorcontrib>Matthews, Beverley B</creatorcontrib><creatorcontrib>St. Pierre, Susan E</creatorcontrib><creatorcontrib>Zhou, Pinglei</creatorcontrib><creatorcontrib>Schroeder, Andrew J</creatorcontrib><creatorcontrib>Falls, Kathleen</creatorcontrib><creatorcontrib>Emmert, David B</creatorcontrib><creatorcontrib>Russo, Susan M</creatorcontrib><creatorcontrib>Gelbart, William M</creatorcontrib><creatorcontrib>FlyBase Consortium</creatorcontrib><creatorcontrib>the FlyBase Consortium</creatorcontrib><title>Gene Model Annotations for Drosophila melanogaster: The Rule-Benders</title><title>G3 : genes - genomes - genetics</title><addtitle>G3 (Bethesda)</addtitle><description>Abstract
In the context of the FlyBase annotated gene models in Drosophila melanogaster, we describe the many exceptional cases we have curated from the literature or identified in the course of FlyBase analysis. These range from atypical but common examples such as dicistronic and polycistronic transcripts, noncanonical splices, trans-spliced transcripts, noncanonical translation starts, and stop-codon readthroughs, to single exceptional cases such as ribosomal frameshifting and HAC1-type intron processing. In FlyBase, exceptional genes and transcripts are flagged with Sequence Ontology terms and/or standardized comments. Because some of the rule-benders create problems for handlers of high-throughput data, we discuss plans for flagging these cases in bulk data downloads.</description><subject>Animals</subject><subject>Base Sequence</subject><subject>Codon, Terminator</subject><subject>Databases, Genetic</subject><subject>Drosophila melanogaster - genetics</subject><subject>Investigations</subject><subject>Mitochondria - genetics</subject><subject>Mitochondria - metabolism</subject><subject>Models, Genetic</subject><subject>Molecular Sequence Annotation</subject><subject>Protein Biosynthesis</subject><subject>RNA Editing</subject><subject>RNA Splice Sites</subject><issn>2160-1836</issn><issn>2160-1836</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2015</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkM1Lw0AQxRdRbKk9epUcvaTu9yYehNpqFSqC1POySSZpJMnW3UTwvzelterJuczAPN6b-SF0TvCECMavCjYhREwwiWKmjtCQEolDEjF5_GseoLH3b7gvIaTk8hQNqCQ4ZkIO0XwBDQRPNoMqmDaNbU1b2sYHuXXB3FlvN-uyMkENlWlsYXwL7jpYrSF46SoIb6HJwPkzdJKbysN430fo9f5uNXsIl8-Lx9l0GaYsIm2YkSRRTCpBKOdRjJVQRmVc5JxjmQoKOY2IUKkSseBJlqU8hjgnQhrC40xSNkI3O99Nl9SQpdC0zlR648rauE9tTan_bppyrQv7obmgEWO4N7jcGzj73oFvdV36FKr-ObCd10RhKgVWeCsNd9K0p-Ad5IcYgvUWvi6Y7uHrHfxef_H7toP6G_VPtu02_3h9AT8DinI</recordid><startdate>20150624</startdate><enddate>20150624</enddate><creator>Crosby, Madeline A</creator><creator>Gramates, L Sian</creator><creator>dos Santos, Gilberto</creator><creator>Matthews, Beverley B</creator><creator>St. Pierre, Susan E</creator><creator>Zhou, Pinglei</creator><creator>Schroeder, Andrew J</creator><creator>Falls, Kathleen</creator><creator>Emmert, David B</creator><creator>Russo, Susan M</creator><creator>Gelbart, William M</creator><general>Oxford University Press</general><general>Genetics Society of America</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20150624</creationdate><title>Gene Model Annotations for Drosophila melanogaster: The Rule-Benders</title><author>Crosby, Madeline A ; Gramates, L Sian ; dos Santos, Gilberto ; Matthews, Beverley B ; St. Pierre, Susan E ; Zhou, Pinglei ; Schroeder, Andrew J ; Falls, Kathleen ; Emmert, David B ; Russo, Susan M ; Gelbart, William M</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c381t-d1bb736751244890757a7d45f4406c52ef28157c75954bddc49e9f156a149d623</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><topic>Animals</topic><topic>Base Sequence</topic><topic>Codon, Terminator</topic><topic>Databases, Genetic</topic><topic>Drosophila melanogaster - genetics</topic><topic>Investigations</topic><topic>Mitochondria - genetics</topic><topic>Mitochondria - metabolism</topic><topic>Models, Genetic</topic><topic>Molecular Sequence Annotation</topic><topic>Protein Biosynthesis</topic><topic>RNA Editing</topic><topic>RNA Splice Sites</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Crosby, Madeline A</creatorcontrib><creatorcontrib>Gramates, L Sian</creatorcontrib><creatorcontrib>dos Santos, Gilberto</creatorcontrib><creatorcontrib>Matthews, Beverley B</creatorcontrib><creatorcontrib>St. Pierre, Susan E</creatorcontrib><creatorcontrib>Zhou, Pinglei</creatorcontrib><creatorcontrib>Schroeder, Andrew J</creatorcontrib><creatorcontrib>Falls, Kathleen</creatorcontrib><creatorcontrib>Emmert, David B</creatorcontrib><creatorcontrib>Russo, Susan M</creatorcontrib><creatorcontrib>Gelbart, William M</creatorcontrib><creatorcontrib>FlyBase Consortium</creatorcontrib><creatorcontrib>the FlyBase Consortium</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>G3 : genes - genomes - genetics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Crosby, Madeline A</au><au>Gramates, L Sian</au><au>dos Santos, Gilberto</au><au>Matthews, Beverley B</au><au>St. Pierre, Susan E</au><au>Zhou, Pinglei</au><au>Schroeder, Andrew J</au><au>Falls, Kathleen</au><au>Emmert, David B</au><au>Russo, Susan M</au><au>Gelbart, William M</au><aucorp>FlyBase Consortium</aucorp><aucorp>the FlyBase Consortium</aucorp><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Gene Model Annotations for Drosophila melanogaster: The Rule-Benders</atitle><jtitle>G3 : genes - genomes - genetics</jtitle><addtitle>G3 (Bethesda)</addtitle><date>2015-06-24</date><risdate>2015</risdate><volume>5</volume><issue>8</issue><spage>1737</spage><epage>1749</epage><pages>1737-1749</pages><issn>2160-1836</issn><eissn>2160-1836</eissn><abstract>Abstract
In the context of the FlyBase annotated gene models in Drosophila melanogaster, we describe the many exceptional cases we have curated from the literature or identified in the course of FlyBase analysis. These range from atypical but common examples such as dicistronic and polycistronic transcripts, noncanonical splices, trans-spliced transcripts, noncanonical translation starts, and stop-codon readthroughs, to single exceptional cases such as ribosomal frameshifting and HAC1-type intron processing. In FlyBase, exceptional genes and transcripts are flagged with Sequence Ontology terms and/or standardized comments. Because some of the rule-benders create problems for handlers of high-throughput data, we discuss plans for flagging these cases in bulk data downloads.</abstract><cop>United States</cop><pub>Oxford University Press</pub><pmid>26109356</pmid><doi>10.1534/g3.115.018937</doi><tpages>13</tpages><oa>free_for_read</oa></addata></record> |
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| source | Oxford Journals Open Access Collection; MEDLINE; DOAJ Directory of Open Access Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central |
| subjects | Animals Base Sequence Codon, Terminator Databases, Genetic Drosophila melanogaster - genetics Investigations Mitochondria - genetics Mitochondria - metabolism Models, Genetic Molecular Sequence Annotation Protein Biosynthesis RNA Editing RNA Splice Sites |
| title | Gene Model Annotations for Drosophila melanogaster: The Rule-Benders |
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