Statistical Analysis of the 5′ Untranslated Region of Human mRNA Using “Oligo-Capped” cDNA Libraries
We constructed 34 types of human “full-length enriched” and “5′-end enriched” cDNA libraries based on the “Oligo-Capping” method. We randomly picked and sequenced 10,000 clones from these libraries. BLAST analysis showed that about 50% of the cDNAs were identical to known genes. Among them, we selec...
Gespeichert in:
| Veröffentlicht in: | Genomics (San Diego, Calif.) Calif.), 2000-03, Vol.64 (3), p.286-297 |
|---|---|
| Hauptverfasser: | , , , , , , , , , , , |
| Format: | Artikel |
| Sprache: | eng |
| Schlagworte: | |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | 297 |
|---|---|
| container_issue | 3 |
| container_start_page | 286 |
| container_title | Genomics (San Diego, Calif.) |
| container_volume | 64 |
| creator | Suzuki, Yutaka Ishihara, Daisuke Sasaki, Masahide Nakagawa, Haruhito Hata, Hiroko Tsunoda, Takeshi Watanabe, Manabu Komatsu, Takami Ota, Toshio Isogai, Takao Suyama, Akira Sugano, Sumio |
| description | We constructed 34 types of human “full-length enriched” and “5′-end enriched” cDNA libraries based on the “Oligo-Capping” method. We randomly picked and sequenced 10,000 clones from these libraries. BLAST analysis showed that about 50% of the cDNAs were identical to known genes. Among them, we selected 954 species of cDNA that should represent the entire sequence from the mRNA start sites. Compared with previously reported sequences, they were on average 45 bp longer in the 5′-end. Using these cDNA data, we statistically analyzed the sequence features of the 5′UTR. The average length of the 5′UTR was 125 bp, and there was little correlation with the corresponding mRNA length (correlation coefficiency = 0.26). Of the 954 species of 5′UTR, 459 contained no in-frame terminator codon, which is against the common belief. Two hundred seventy-eight species contained at least one ATG codon upstream of the initiator ATG codon. We identified 569 upstream ATGs, in total, 63% of which adequately satisfied Kozak's criteria. These findings are contrary to the typical translation initiation model, which states that translation is initiated from the “first” ATG codon. |
| doi_str_mv | 10.1006/geno.2000.6076 |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_cross</sourceid><recordid>TN_cdi_proquest_miscellaneous_71029336</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><els_id>S0888754300960762</els_id><sourcerecordid>71029336</sourcerecordid><originalsourceid>FETCH-LOGICAL-c466t-c4639d4cdf0bc2487a646886bd4dcda4db420bae482304d5bc97d90f63927ef03</originalsourceid><addsrcrecordid>eNqFkcFuEzEQhi0EoiFw5Yh8QNw29dper_cYpUCRolZqydny2rPB1a432A5Sb3kQeAkeKU-CV4kEF9TL-DDfjMbfj9DbkixKQsTlFvy4oISQhSC1eIZmJZFNIQUXz9GMSCmLuuLsAr2K8SFTDZP0JbooSV0J0ogZerhPOrmYnNE9XnrdP0YX8djh9A1wdTz8xhufgvax1wksvoOtG_3Uv94P2uPh7maJN9H5LT4eft72bjsWK73bgT0efmFzlbtr1wYdHMTX6EWn-whvzu8cbT59_Lq6Lta3n7-sluvCcCHSVFljubEdaQ3lstb5M1KK1nJrrOa25ZS0GrikjHBbtaapbUO6PEVr6Aibow-nvbswft9DTGpw0UDfaw_jPqq6JLRhTDwJlnVFKc365mhxAk0YYwzQqV1wgw6PqiRqikFNMagpBjXFkAfenTfv2wHsP_jJewbenwEds_kuGzYu_uUYoxVjGZMnDLKvHw6CisaBN2BdAJOUHd3_TvgDW0mleg</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>17522254</pqid></control><display><type>article</type><title>Statistical Analysis of the 5′ Untranslated Region of Human mRNA Using “Oligo-Capped” cDNA Libraries</title><source>MEDLINE</source><source>Elsevier ScienceDirect Journals Complete</source><creator>Suzuki, Yutaka ; Ishihara, Daisuke ; Sasaki, Masahide ; Nakagawa, Haruhito ; Hata, Hiroko ; Tsunoda, Takeshi ; Watanabe, Manabu ; Komatsu, Takami ; Ota, Toshio ; Isogai, Takao ; Suyama, Akira ; Sugano, Sumio</creator><creatorcontrib>Suzuki, Yutaka ; Ishihara, Daisuke ; Sasaki, Masahide ; Nakagawa, Haruhito ; Hata, Hiroko ; Tsunoda, Takeshi ; Watanabe, Manabu ; Komatsu, Takami ; Ota, Toshio ; Isogai, Takao ; Suyama, Akira ; Sugano, Sumio</creatorcontrib><description>We constructed 34 types of human “full-length enriched” and “5′-end enriched” cDNA libraries based on the “Oligo-Capping” method. We randomly picked and sequenced 10,000 clones from these libraries. BLAST analysis showed that about 50% of the cDNAs were identical to known genes. Among them, we selected 954 species of cDNA that should represent the entire sequence from the mRNA start sites. Compared with previously reported sequences, they were on average 45 bp longer in the 5′-end. Using these cDNA data, we statistically analyzed the sequence features of the 5′UTR. The average length of the 5′UTR was 125 bp, and there was little correlation with the corresponding mRNA length (correlation coefficiency = 0.26). Of the 954 species of 5′UTR, 459 contained no in-frame terminator codon, which is against the common belief. Two hundred seventy-eight species contained at least one ATG codon upstream of the initiator ATG codon. We identified 569 upstream ATGs, in total, 63% of which adequately satisfied Kozak's criteria. These findings are contrary to the typical translation initiation model, which states that translation is initiated from the “first” ATG codon.</description><identifier>ISSN: 0888-7543</identifier><identifier>EISSN: 1089-8646</identifier><identifier>DOI: 10.1006/geno.2000.6076</identifier><identifier>PMID: 10756096</identifier><language>eng</language><publisher>San Diego, CA: Elsevier Inc</publisher><subject>5' Untranslated Regions ; Biological and medical sciences ; Data Interpretation, Statistical ; Fundamental and applied biological sciences. Psychology ; Gene Library ; Humans ; Molecular and cellular biology ; Molecular genetics ; Molecular Sequence Data ; Oligonucleotides - chemistry ; Polymerase Chain Reaction ; RNA Caps - chemistry ; Sequence Analysis, RNA ; Translation. Translation factors. Protein processing</subject><ispartof>Genomics (San Diego, Calif.), 2000-03, Vol.64 (3), p.286-297</ispartof><rights>2000 Academic Press</rights><rights>2000 INIST-CNRS</rights><rights>Copyright 2000 Academic Press.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c466t-c4639d4cdf0bc2487a646886bd4dcda4db420bae482304d5bc97d90f63927ef03</citedby><cites>FETCH-LOGICAL-c466t-c4639d4cdf0bc2487a646886bd4dcda4db420bae482304d5bc97d90f63927ef03</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://dx.doi.org/10.1006/geno.2000.6076$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>314,780,784,3550,27924,27925,45995</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=1332533$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/10756096$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Suzuki, Yutaka</creatorcontrib><creatorcontrib>Ishihara, Daisuke</creatorcontrib><creatorcontrib>Sasaki, Masahide</creatorcontrib><creatorcontrib>Nakagawa, Haruhito</creatorcontrib><creatorcontrib>Hata, Hiroko</creatorcontrib><creatorcontrib>Tsunoda, Takeshi</creatorcontrib><creatorcontrib>Watanabe, Manabu</creatorcontrib><creatorcontrib>Komatsu, Takami</creatorcontrib><creatorcontrib>Ota, Toshio</creatorcontrib><creatorcontrib>Isogai, Takao</creatorcontrib><creatorcontrib>Suyama, Akira</creatorcontrib><creatorcontrib>Sugano, Sumio</creatorcontrib><title>Statistical Analysis of the 5′ Untranslated Region of Human mRNA Using “Oligo-Capped” cDNA Libraries</title><title>Genomics (San Diego, Calif.)</title><addtitle>Genomics</addtitle><description>We constructed 34 types of human “full-length enriched” and “5′-end enriched” cDNA libraries based on the “Oligo-Capping” method. We randomly picked and sequenced 10,000 clones from these libraries. BLAST analysis showed that about 50% of the cDNAs were identical to known genes. Among them, we selected 954 species of cDNA that should represent the entire sequence from the mRNA start sites. Compared with previously reported sequences, they were on average 45 bp longer in the 5′-end. Using these cDNA data, we statistically analyzed the sequence features of the 5′UTR. The average length of the 5′UTR was 125 bp, and there was little correlation with the corresponding mRNA length (correlation coefficiency = 0.26). Of the 954 species of 5′UTR, 459 contained no in-frame terminator codon, which is against the common belief. Two hundred seventy-eight species contained at least one ATG codon upstream of the initiator ATG codon. We identified 569 upstream ATGs, in total, 63% of which adequately satisfied Kozak's criteria. These findings are contrary to the typical translation initiation model, which states that translation is initiated from the “first” ATG codon.</description><subject>5' Untranslated Regions</subject><subject>Biological and medical sciences</subject><subject>Data Interpretation, Statistical</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Gene Library</subject><subject>Humans</subject><subject>Molecular and cellular biology</subject><subject>Molecular genetics</subject><subject>Molecular Sequence Data</subject><subject>Oligonucleotides - chemistry</subject><subject>Polymerase Chain Reaction</subject><subject>RNA Caps - chemistry</subject><subject>Sequence Analysis, RNA</subject><subject>Translation. Translation factors. Protein processing</subject><issn>0888-7543</issn><issn>1089-8646</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2000</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkcFuEzEQhi0EoiFw5Yh8QNw29dper_cYpUCRolZqydny2rPB1a432A5Sb3kQeAkeKU-CV4kEF9TL-DDfjMbfj9DbkixKQsTlFvy4oISQhSC1eIZmJZFNIQUXz9GMSCmLuuLsAr2K8SFTDZP0JbooSV0J0ogZerhPOrmYnNE9XnrdP0YX8djh9A1wdTz8xhufgvax1wksvoOtG_3Uv94P2uPh7maJN9H5LT4eft72bjsWK73bgT0efmFzlbtr1wYdHMTX6EWn-whvzu8cbT59_Lq6Lta3n7-sluvCcCHSVFljubEdaQ3lstb5M1KK1nJrrOa25ZS0GrikjHBbtaapbUO6PEVr6Aibow-nvbswft9DTGpw0UDfaw_jPqq6JLRhTDwJlnVFKc365mhxAk0YYwzQqV1wgw6PqiRqikFNMagpBjXFkAfenTfv2wHsP_jJewbenwEds_kuGzYu_uUYoxVjGZMnDLKvHw6CisaBN2BdAJOUHd3_TvgDW0mleg</recordid><startdate>20000315</startdate><enddate>20000315</enddate><creator>Suzuki, Yutaka</creator><creator>Ishihara, Daisuke</creator><creator>Sasaki, Masahide</creator><creator>Nakagawa, Haruhito</creator><creator>Hata, Hiroko</creator><creator>Tsunoda, Takeshi</creator><creator>Watanabe, Manabu</creator><creator>Komatsu, Takami</creator><creator>Ota, Toshio</creator><creator>Isogai, Takao</creator><creator>Suyama, Akira</creator><creator>Sugano, Sumio</creator><general>Elsevier Inc</general><general>Elsevier</general><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>8FD</scope><scope>FR3</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope></search><sort><creationdate>20000315</creationdate><title>Statistical Analysis of the 5′ Untranslated Region of Human mRNA Using “Oligo-Capped” cDNA Libraries</title><author>Suzuki, Yutaka ; Ishihara, Daisuke ; Sasaki, Masahide ; Nakagawa, Haruhito ; Hata, Hiroko ; Tsunoda, Takeshi ; Watanabe, Manabu ; Komatsu, Takami ; Ota, Toshio ; Isogai, Takao ; Suyama, Akira ; Sugano, Sumio</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c466t-c4639d4cdf0bc2487a646886bd4dcda4db420bae482304d5bc97d90f63927ef03</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2000</creationdate><topic>5' Untranslated Regions</topic><topic>Biological and medical sciences</topic><topic>Data Interpretation, Statistical</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Gene Library</topic><topic>Humans</topic><topic>Molecular and cellular biology</topic><topic>Molecular genetics</topic><topic>Molecular Sequence Data</topic><topic>Oligonucleotides - chemistry</topic><topic>Polymerase Chain Reaction</topic><topic>RNA Caps - chemistry</topic><topic>Sequence Analysis, RNA</topic><topic>Translation. Translation factors. Protein processing</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Suzuki, Yutaka</creatorcontrib><creatorcontrib>Ishihara, Daisuke</creatorcontrib><creatorcontrib>Sasaki, Masahide</creatorcontrib><creatorcontrib>Nakagawa, Haruhito</creatorcontrib><creatorcontrib>Hata, Hiroko</creatorcontrib><creatorcontrib>Tsunoda, Takeshi</creatorcontrib><creatorcontrib>Watanabe, Manabu</creatorcontrib><creatorcontrib>Komatsu, Takami</creatorcontrib><creatorcontrib>Ota, Toshio</creatorcontrib><creatorcontrib>Isogai, Takao</creatorcontrib><creatorcontrib>Suyama, Akira</creatorcontrib><creatorcontrib>Sugano, Sumio</creatorcontrib><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>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Genomics (San Diego, Calif.)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Suzuki, Yutaka</au><au>Ishihara, Daisuke</au><au>Sasaki, Masahide</au><au>Nakagawa, Haruhito</au><au>Hata, Hiroko</au><au>Tsunoda, Takeshi</au><au>Watanabe, Manabu</au><au>Komatsu, Takami</au><au>Ota, Toshio</au><au>Isogai, Takao</au><au>Suyama, Akira</au><au>Sugano, Sumio</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Statistical Analysis of the 5′ Untranslated Region of Human mRNA Using “Oligo-Capped” cDNA Libraries</atitle><jtitle>Genomics (San Diego, Calif.)</jtitle><addtitle>Genomics</addtitle><date>2000-03-15</date><risdate>2000</risdate><volume>64</volume><issue>3</issue><spage>286</spage><epage>297</epage><pages>286-297</pages><issn>0888-7543</issn><eissn>1089-8646</eissn><abstract>We constructed 34 types of human “full-length enriched” and “5′-end enriched” cDNA libraries based on the “Oligo-Capping” method. We randomly picked and sequenced 10,000 clones from these libraries. BLAST analysis showed that about 50% of the cDNAs were identical to known genes. Among them, we selected 954 species of cDNA that should represent the entire sequence from the mRNA start sites. Compared with previously reported sequences, they were on average 45 bp longer in the 5′-end. Using these cDNA data, we statistically analyzed the sequence features of the 5′UTR. The average length of the 5′UTR was 125 bp, and there was little correlation with the corresponding mRNA length (correlation coefficiency = 0.26). Of the 954 species of 5′UTR, 459 contained no in-frame terminator codon, which is against the common belief. Two hundred seventy-eight species contained at least one ATG codon upstream of the initiator ATG codon. We identified 569 upstream ATGs, in total, 63% of which adequately satisfied Kozak's criteria. These findings are contrary to the typical translation initiation model, which states that translation is initiated from the “first” ATG codon.</abstract><cop>San Diego, CA</cop><pub>Elsevier Inc</pub><pmid>10756096</pmid><doi>10.1006/geno.2000.6076</doi><tpages>12</tpages></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 0888-7543 |
| ispartof | Genomics (San Diego, Calif.), 2000-03, Vol.64 (3), p.286-297 |
| issn | 0888-7543 1089-8646 |
| language | eng |
| recordid | cdi_proquest_miscellaneous_71029336 |
| source | MEDLINE; Elsevier ScienceDirect Journals Complete |
| subjects | 5' Untranslated Regions Biological and medical sciences Data Interpretation, Statistical Fundamental and applied biological sciences. Psychology Gene Library Humans Molecular and cellular biology Molecular genetics Molecular Sequence Data Oligonucleotides - chemistry Polymerase Chain Reaction RNA Caps - chemistry Sequence Analysis, RNA Translation. Translation factors. Protein processing |
| title | Statistical Analysis of the 5′ Untranslated Region of Human mRNA Using “Oligo-Capped” cDNA Libraries |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-04T18%3A58%3A11IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_cross&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Statistical%20Analysis%20of%20the%205%E2%80%B2%20Untranslated%20Region%20of%20Human%20mRNA%20Using%20%E2%80%9COligo-Capped%E2%80%9D%20cDNA%20Libraries&rft.jtitle=Genomics%20(San%20Diego,%20Calif.)&rft.au=Suzuki,%20Yutaka&rft.date=2000-03-15&rft.volume=64&rft.issue=3&rft.spage=286&rft.epage=297&rft.pages=286-297&rft.issn=0888-7543&rft.eissn=1089-8646&rft_id=info:doi/10.1006/geno.2000.6076&rft_dat=%3Cproquest_cross%3E71029336%3C/proquest_cross%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=17522254&rft_id=info:pmid/10756096&rft_els_id=S0888754300960762&rfr_iscdi=true |