Genome-scale analysis of human mRNA 5′ coding sequences based on expressed sequence tag (EST) database
The “5′ end mRNA artifact” issue refers to the incorrect assignment of the first AUG codon in an mRNA, due to the incomplete determination of its 5′ end sequence. We performed a systematic identification of coding regions at the 5′ end of all human known mRNAs, using an automated expressed sequence...
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| Veröffentlicht in: | Genomics (San Diego, Calif.) Calif.), 2012-08, Vol.100 (2), p.125-130 |
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| creator | Casadei, Raffaella Piovesan, Allison Vitale, Lorenza Facchin, Federica Pelleri, Maria Chiara Canaider, Silvia Bianconi, Eva Frabetti, Flavia Strippoli, Pierluigi |
| description | The “5′ end mRNA artifact” issue refers to the incorrect assignment of the first AUG codon in an mRNA, due to the incomplete determination of its 5′ end sequence. We performed a systematic identification of coding regions at the 5′ end of all human known mRNAs, using an automated expressed sequence tag (EST)-based approach. Following parsing of more than 7million BLAT alignments, we found 477 human loci, out of 18,665 analyzed, in which an extension of the mRNA 5′ coding region was identified. Proof-of-concept confirmation was obtained by in vitro cloning and sequencing for GNB2L1, QARS and TDP2 cDNAs, and the consequences for the functional studies of these loci are discussed. We also generated a list of 20,775 human mRNAs where the presence of an in-frame stop codon upstream of the known start codon indicates completeness of the coding sequence at 5′ in the current form.
► Start codon may be incorrectly assigned if mRNA sequence is not complete at 5′ end. ► An EST-based computational approach identifies extended 5′ coding regions. ► The mRNA 5′ coding region is extended in 477 human loci out of 18,665 analyzed. ► Experimental confirmation has been obtained for GNB2L1, QARS and TDP2. ► 20,775 human mRNAs have a coding region not further extendable by EST sequences. |
| doi_str_mv | 10.1016/j.ygeno.2012.05.012 |
| format | Article |
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► Start codon may be incorrectly assigned if mRNA sequence is not complete at 5′ end. ► An EST-based computational approach identifies extended 5′ coding regions. ► The mRNA 5′ coding region is extended in 477 human loci out of 18,665 analyzed. ► Experimental confirmation has been obtained for GNB2L1, QARS and TDP2. ► 20,775 human mRNAs have a coding region not further extendable by EST sequences.</description><identifier>ISSN: 0888-7543</identifier><identifier>EISSN: 1089-8646</identifier><identifier>DOI: 10.1016/j.ygeno.2012.05.012</identifier><identifier>PMID: 22659028</identifier><language>eng</language><publisher>Amsterdam: Elsevier Inc</publisher><subject>5' Untranslated Regions - genetics ; 5′ Untranslated region (5′ UTR) ; Amino Acid Sequence ; Biological and medical sciences ; Cloning, Molecular ; Codon, Initiator ; complementary DNA ; Computational Biology ; Databases, Genetic ; Diverse techniques ; DNA, Complementary ; Expressed sequence tag (EST) ; Expressed Sequence Tags ; Fundamental and applied biological sciences. Psychology ; Genes. Genome ; Genetic Association Studies - methods ; Genetic Loci ; Genetics of eukaryotes. Biological and molecular evolution ; Genome, Human ; Human genome ; Humans ; loci ; messenger RNA ; Molecular and cellular biology ; Molecular genetics ; Molecular Sequence Data ; mRNA 5′ coding sequence ; Open Reading Frames ; RNA, Messenger - genetics ; Sequence Alignment ; Sequence Analysis, DNA ; start codon ; stop codon ; Translation start codon</subject><ispartof>Genomics (San Diego, Calif.), 2012-08, Vol.100 (2), p.125-130</ispartof><rights>2012 Elsevier Inc.</rights><rights>2015 INIST-CNRS</rights><rights>Copyright © 2012 Elsevier Inc. All rights reserved.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c458t-28271fb9442659b1e8a9013cac2f515414c73c954a94de2cb853139b9dc513283</citedby><cites>FETCH-LOGICAL-c458t-28271fb9442659b1e8a9013cac2f515414c73c954a94de2cb853139b9dc513283</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://dx.doi.org/10.1016/j.ygeno.2012.05.012$$EHTML$$P50$$Gelsevier$$Hfree_for_read</linktohtml><link.rule.ids>314,778,782,3539,27911,27912,45982</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=26255947$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/22659028$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Casadei, Raffaella</creatorcontrib><creatorcontrib>Piovesan, Allison</creatorcontrib><creatorcontrib>Vitale, Lorenza</creatorcontrib><creatorcontrib>Facchin, Federica</creatorcontrib><creatorcontrib>Pelleri, Maria Chiara</creatorcontrib><creatorcontrib>Canaider, Silvia</creatorcontrib><creatorcontrib>Bianconi, Eva</creatorcontrib><creatorcontrib>Frabetti, Flavia</creatorcontrib><creatorcontrib>Strippoli, Pierluigi</creatorcontrib><title>Genome-scale analysis of human mRNA 5′ coding sequences based on expressed sequence tag (EST) database</title><title>Genomics (San Diego, Calif.)</title><addtitle>Genomics</addtitle><description>The “5′ end mRNA artifact” issue refers to the incorrect assignment of the first AUG codon in an mRNA, due to the incomplete determination of its 5′ end sequence. We performed a systematic identification of coding regions at the 5′ end of all human known mRNAs, using an automated expressed sequence tag (EST)-based approach. Following parsing of more than 7million BLAT alignments, we found 477 human loci, out of 18,665 analyzed, in which an extension of the mRNA 5′ coding region was identified. Proof-of-concept confirmation was obtained by in vitro cloning and sequencing for GNB2L1, QARS and TDP2 cDNAs, and the consequences for the functional studies of these loci are discussed. We also generated a list of 20,775 human mRNAs where the presence of an in-frame stop codon upstream of the known start codon indicates completeness of the coding sequence at 5′ in the current form.
► Start codon may be incorrectly assigned if mRNA sequence is not complete at 5′ end. ► An EST-based computational approach identifies extended 5′ coding regions. ► The mRNA 5′ coding region is extended in 477 human loci out of 18,665 analyzed. ► Experimental confirmation has been obtained for GNB2L1, QARS and TDP2. ► 20,775 human mRNAs have a coding region not further extendable by EST sequences.</description><subject>5' Untranslated Regions - genetics</subject><subject>5′ Untranslated region (5′ UTR)</subject><subject>Amino Acid Sequence</subject><subject>Biological and medical sciences</subject><subject>Cloning, Molecular</subject><subject>Codon, Initiator</subject><subject>complementary DNA</subject><subject>Computational Biology</subject><subject>Databases, Genetic</subject><subject>Diverse techniques</subject><subject>DNA, Complementary</subject><subject>Expressed sequence tag (EST)</subject><subject>Expressed Sequence Tags</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Genes. Genome</subject><subject>Genetic Association Studies - methods</subject><subject>Genetic Loci</subject><subject>Genetics of eukaryotes. Biological and molecular evolution</subject><subject>Genome, Human</subject><subject>Human genome</subject><subject>Humans</subject><subject>loci</subject><subject>messenger RNA</subject><subject>Molecular and cellular biology</subject><subject>Molecular genetics</subject><subject>Molecular Sequence Data</subject><subject>mRNA 5′ coding sequence</subject><subject>Open Reading Frames</subject><subject>RNA, Messenger - genetics</subject><subject>Sequence Alignment</subject><subject>Sequence Analysis, DNA</subject><subject>start codon</subject><subject>stop codon</subject><subject>Translation start codon</subject><issn>0888-7543</issn><issn>1089-8646</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2012</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp9kc9u1DAQhy0EosvCEyCBL0jtIcF_E_vQQ1WVglSBRNuz5TiTrVdJvNhZxN54Jh6JJ6nDbsutp5Hlb2Z-_ozQW0pKSmj1cV3uVjCGkhHKSiLLXJ6hBSVKF6oS1XO0IEqpopaCH6FXKa0JIZor9hIdMVZJTZhaoLvLPGKAIjnbA7aj7XfJJxw6fLcd7IiH71_PsPz7-w92ofXjCif4sYXRQcKNTdDiMGL4tYmQ5sPDJZ7sCh9fXN-c4NZOdiZfoxed7RO8OdQluv10cXP-ubj6dvnl_OyqcEKqqWCK1bRrtBBzxIaCsppQ7qxjnaRSUOFq7rQUVosWmGuU5JTrRrdOUs4UX6Lj_dxNDDlMmszgk4O-tyOEbTKUsLpShOa-JeJ71MWQUoTObKIfbNxlyMyKzdr8U2xmxYZIk0vuendYsG0GaB97Hpxm4MMBsLPVLtrR-fSfq5iUWtSZe7_nOhuMXcXM3F7nTTL_k2D5UZk43ROQhf30EE1yfvbb-ghuMm3wT0a9B8ABozw</recordid><startdate>20120801</startdate><enddate>20120801</enddate><creator>Casadei, Raffaella</creator><creator>Piovesan, Allison</creator><creator>Vitale, Lorenza</creator><creator>Facchin, Federica</creator><creator>Pelleri, Maria Chiara</creator><creator>Canaider, Silvia</creator><creator>Bianconi, Eva</creator><creator>Frabetti, Flavia</creator><creator>Strippoli, Pierluigi</creator><general>Elsevier Inc</general><general>Elsevier</general><scope>6I.</scope><scope>AAFTH</scope><scope>FBQ</scope><scope>IQODW</scope><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></search><sort><creationdate>20120801</creationdate><title>Genome-scale analysis of human mRNA 5′ coding sequences based on expressed sequence tag (EST) database</title><author>Casadei, Raffaella ; Piovesan, Allison ; Vitale, Lorenza ; Facchin, Federica ; Pelleri, Maria Chiara ; Canaider, Silvia ; Bianconi, Eva ; Frabetti, Flavia ; Strippoli, Pierluigi</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c458t-28271fb9442659b1e8a9013cac2f515414c73c954a94de2cb853139b9dc513283</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2012</creationdate><topic>5' Untranslated Regions - genetics</topic><topic>5′ Untranslated region (5′ UTR)</topic><topic>Amino Acid Sequence</topic><topic>Biological and medical sciences</topic><topic>Cloning, Molecular</topic><topic>Codon, Initiator</topic><topic>complementary DNA</topic><topic>Computational Biology</topic><topic>Databases, Genetic</topic><topic>Diverse techniques</topic><topic>DNA, Complementary</topic><topic>Expressed sequence tag (EST)</topic><topic>Expressed Sequence Tags</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Genes. Genome</topic><topic>Genetic Association Studies - methods</topic><topic>Genetic Loci</topic><topic>Genetics of eukaryotes. Biological and molecular evolution</topic><topic>Genome, Human</topic><topic>Human genome</topic><topic>Humans</topic><topic>loci</topic><topic>messenger RNA</topic><topic>Molecular and cellular biology</topic><topic>Molecular genetics</topic><topic>Molecular Sequence Data</topic><topic>mRNA 5′ coding sequence</topic><topic>Open Reading Frames</topic><topic>RNA, Messenger - genetics</topic><topic>Sequence Alignment</topic><topic>Sequence Analysis, DNA</topic><topic>start codon</topic><topic>stop codon</topic><topic>Translation start codon</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Casadei, Raffaella</creatorcontrib><creatorcontrib>Piovesan, Allison</creatorcontrib><creatorcontrib>Vitale, Lorenza</creatorcontrib><creatorcontrib>Facchin, Federica</creatorcontrib><creatorcontrib>Pelleri, Maria Chiara</creatorcontrib><creatorcontrib>Canaider, Silvia</creatorcontrib><creatorcontrib>Bianconi, Eva</creatorcontrib><creatorcontrib>Frabetti, Flavia</creatorcontrib><creatorcontrib>Strippoli, Pierluigi</creatorcontrib><collection>ScienceDirect Open Access Titles</collection><collection>Elsevier:ScienceDirect:Open Access</collection><collection>AGRIS</collection><collection>Pascal-Francis</collection><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><jtitle>Genomics (San Diego, Calif.)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Casadei, Raffaella</au><au>Piovesan, Allison</au><au>Vitale, Lorenza</au><au>Facchin, Federica</au><au>Pelleri, Maria Chiara</au><au>Canaider, Silvia</au><au>Bianconi, Eva</au><au>Frabetti, Flavia</au><au>Strippoli, Pierluigi</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genome-scale analysis of human mRNA 5′ coding sequences based on expressed sequence tag (EST) database</atitle><jtitle>Genomics (San Diego, Calif.)</jtitle><addtitle>Genomics</addtitle><date>2012-08-01</date><risdate>2012</risdate><volume>100</volume><issue>2</issue><spage>125</spage><epage>130</epage><pages>125-130</pages><issn>0888-7543</issn><eissn>1089-8646</eissn><abstract>The “5′ end mRNA artifact” issue refers to the incorrect assignment of the first AUG codon in an mRNA, due to the incomplete determination of its 5′ end sequence. We performed a systematic identification of coding regions at the 5′ end of all human known mRNAs, using an automated expressed sequence tag (EST)-based approach. Following parsing of more than 7million BLAT alignments, we found 477 human loci, out of 18,665 analyzed, in which an extension of the mRNA 5′ coding region was identified. Proof-of-concept confirmation was obtained by in vitro cloning and sequencing for GNB2L1, QARS and TDP2 cDNAs, and the consequences for the functional studies of these loci are discussed. We also generated a list of 20,775 human mRNAs where the presence of an in-frame stop codon upstream of the known start codon indicates completeness of the coding sequence at 5′ in the current form.
► Start codon may be incorrectly assigned if mRNA sequence is not complete at 5′ end. ► An EST-based computational approach identifies extended 5′ coding regions. ► The mRNA 5′ coding region is extended in 477 human loci out of 18,665 analyzed. ► Experimental confirmation has been obtained for GNB2L1, QARS and TDP2. ► 20,775 human mRNAs have a coding region not further extendable by EST sequences.</abstract><cop>Amsterdam</cop><pub>Elsevier Inc</pub><pmid>22659028</pmid><doi>10.1016/j.ygeno.2012.05.012</doi><tpages>6</tpages><oa>free_for_read</oa></addata></record> |
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| ispartof | Genomics (San Diego, Calif.), 2012-08, Vol.100 (2), p.125-130 |
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| subjects | 5' Untranslated Regions - genetics 5′ Untranslated region (5′ UTR) Amino Acid Sequence Biological and medical sciences Cloning, Molecular Codon, Initiator complementary DNA Computational Biology Databases, Genetic Diverse techniques DNA, Complementary Expressed sequence tag (EST) Expressed Sequence Tags Fundamental and applied biological sciences. Psychology Genes. Genome Genetic Association Studies - methods Genetic Loci Genetics of eukaryotes. Biological and molecular evolution Genome, Human Human genome Humans loci messenger RNA Molecular and cellular biology Molecular genetics Molecular Sequence Data mRNA 5′ coding sequence Open Reading Frames RNA, Messenger - genetics Sequence Alignment Sequence Analysis, DNA start codon stop codon Translation start codon |
| title | Genome-scale analysis of human mRNA 5′ coding sequences based on expressed sequence tag (EST) database |
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