{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T09:14:05Z","timestamp":1773306845235,"version":"3.50.1"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2803,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Selenoproteins contain the 21st amino acid selenocysteine which is encoded by an inframe UGA codon, usually read as a stop. In eukaryotes, its co-translational recoding requires the presence of an RNA stem\u2013loop structure, the SECIS element in the 3 untranslated region of (UTR) selenoprotein mRNAs. Despite little sequence conservation, SECIS elements share the same overall secondary structure. Until recently, the lack of a significantly high number of selenoprotein mRNA sequences hampered the identification of other potential sequence conservation. In this work, the web-based tool SECISaln provides for the first time an extensive structure-based sequence alignment of SECIS elements resulting from the well-defined secondary structure of the SECIS RNA and the increased size of the eukaryotic selenoproteome. We have used SECISaln to improve our knowledge of SECIS secondary structure and to discover novel, conserved nucleotide positions and we believe it will be a useful tool for the selenoprotein and RNA scientific communities.<\/jats:p>\n               <jats:p>Availability: SECISaln is freely available as a web-based tool at http:\/\/genome.crg.es\/software\/secisaln\/.<\/jats:p>\n               <jats:p>Contact: \u00a0charles.chapple@crg.es<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp020","type":"journal-article","created":{"date-parts":[[2009,1,30]],"date-time":"2009-01-30T01:24:46Z","timestamp":1233278686000},"page":"674-675","source":"Crossref","is-referenced-by-count":34,"title":["SECISaln, a web-based tool for the creation of structure-based alignments of eukaryotic SECIS elements"],"prefix":"10.1093","volume":"25","author":[{"given":"Charles E.","family":"Chapple","sequence":"first","affiliation":[{"name":"1 Institut Municipal d'Investigaci\u00f3 M\u00e9dica, 2Centre de Regulaci\u00f3 Gen\u00f3mica, Universitat Pompeu Fabra and Parc de Recerca Biomedica de Barcelona, Carrer del Doctor Aiguader 88, 08003, Barcelona, Catalonia, Spain and 3Unit\u00e9 Architecture et R\u00e9activit\u00e9 de l\u2032ARN, Universit\u00e9 Louis Pasteur de Strasbourg, CNRS, 15 rue Ren\u00e9 Descartes, F-67084 Strasbourg, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Roderic","family":"Guig\u00f3","sequence":"additional","affiliation":[{"name":"1 Institut Municipal d'Investigaci\u00f3 M\u00e9dica, 2Centre de Regulaci\u00f3 Gen\u00f3mica, Universitat Pompeu Fabra and Parc de Recerca Biomedica de Barcelona, Carrer del Doctor Aiguader 88, 08003, Barcelona, Catalonia, Spain and 3Unit\u00e9 Architecture et R\u00e9activit\u00e9 de l\u2032ARN, Universit\u00e9 Louis Pasteur de Strasbourg, CNRS, 15 rue Ren\u00e9 Descartes, F-67084 Strasbourg, France"},{"name":"1 Institut Municipal d'Investigaci\u00f3 M\u00e9dica, 2Centre de Regulaci\u00f3 Gen\u00f3mica, Universitat Pompeu Fabra and Parc de Recerca Biomedica de Barcelona, Carrer del Doctor Aiguader 88, 08003, Barcelona, Catalonia, Spain and 3Unit\u00e9 Architecture et R\u00e9activit\u00e9 de l\u2032ARN, Universit\u00e9 Louis Pasteur de Strasbourg, CNRS, 15 rue Ren\u00e9 Descartes, F-67084 Strasbourg, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alain","family":"Krol","sequence":"additional","affiliation":[{"name":"1 Institut Municipal d'Investigaci\u00f3 M\u00e9dica, 2Centre de Regulaci\u00f3 Gen\u00f3mica, Universitat Pompeu Fabra and Parc de Recerca Biomedica de Barcelona, Carrer del Doctor Aiguader 88, 08003, Barcelona, Catalonia, Spain and 3Unit\u00e9 Architecture et R\u00e9activit\u00e9 de l\u2032ARN, Universit\u00e9 Louis Pasteur de Strasbourg, CNRS, 15 rue Ren\u00e9 Descartes, F-67084 Strasbourg, France"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2009,1,29]]},"reference":[{"key":"2023013110114534400_B1","doi-asserted-by":"crossref","first-page":"21598","DOI":"10.1074\/jbc.274.31.21598","article-title":"The Caenorhabditis elegans homologue of thioredoxin reductase contains a selenocysteine insertion sequence (secis) element that differs from mammalian secis elements but directs selenocysteine incorporation","volume":"274","author":"Buettner","year":"1999","journal-title":"J. Biol. Chem."},{"key":"2023013110114534400_B2","doi-asserted-by":"crossref","first-page":"697","DOI":"10.1093\/embo-reports\/kve151","article-title":"In silico identification of novel selenoproteins in the Drosophila melanogaster genome","volume":"2","author":"Castellano","year":"2001","journal-title":"EMBO Rep."},{"key":"2023013110114534400_B3","doi-asserted-by":"crossref","first-page":"e2968","DOI":"10.1371\/journal.pone.0002968","article-title":"Relaxation of selective constraints causes independent selenoprotein extinction in insect genomes","volume":"3","author":"Chapple","year":"2008","journal-title":"PLoS ONE"},{"key":"2023013110114534400_B4","doi-asserted-by":"crossref","first-page":"1868","DOI":"10.1093\/nar\/gkm066","article-title":"An improved definition of the rna-binding specificity of secis-binding protein 2, an essential component of the selenocysteine incorporation machinery","volume":"35","author":"Cl\u00e9ry","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"2023013110114534400_B5","doi-asserted-by":"crossref","first-page":"2679","DOI":"10.1093\/nar\/28.14.2679","article-title":"Structural analysis of new local features in secis RNA hairpins","volume":"28","author":"Fagegaltier","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"2023013110114534400_B6","first-page":"1442","article-title":"The selenocysteine incorporation machinery: interactions between the secis RNA and the secis-binding protein sbp2","volume":"7","author":"Fletcher","year":"2001","journal-title":"RNA"},{"key":"2023013110114534400_B7","doi-asserted-by":"crossref","first-page":"625","DOI":"10.1017\/S1355838299981542","article-title":"Two distinct secis structures capable of directing selenocysteine incorporation in eukaryotes","volume":"5","author":"Grundner-Culemann","year":"1999","journal-title":"RNA"},{"key":"2023013110114534400_B8","doi-asserted-by":"crossref","first-page":"33888","DOI":"10.1074\/jbc.274.48.33888","article-title":"New mammalian selenocysteine-containing proteins identified with an algorithm that searches for selenocysteine insertion sequence elements","volume":"274","author":"Kryukov","year":"1999","journal-title":"J. Biol. Chem."},{"key":"2023013110114534400_B9","doi-asserted-by":"crossref","first-page":"1439","DOI":"10.1126\/science.1083516","article-title":"Characterization of mammalian selenoproteomes","volume":"300","author":"Kryukov","year":"2003","journal-title":"Science"},{"key":"2023013110114534400_B10","doi-asserted-by":"crossref","first-page":"38147","DOI":"10.1074\/jbc.274.53.38147","article-title":"Novel selenoproteins identified in silico and in vivo by using a conserved rna structural motif","volume":"274","author":"Lescure","year":"1999","journal-title":"J. Biol. Chem."},{"key":"2023013110114534400_B11","doi-asserted-by":"crossref","first-page":"R198","DOI":"10.1186\/gb-2007-8-9-r198","article-title":"Evolutionary dynamics of eukaryotic selenoproteomes: large selenoproteomes may associate with aquatic life and small with terrestrial life","volume":"8","author":"Lobanov","year":"2007","journal-title":"Genome Biol."},{"key":"2023013110114534400_B12","doi-asserted-by":"crossref","first-page":"7857","DOI":"10.1073\/pnas.0610683104","article-title":"A highly efficient form of the selenocysteine insertion sequence element in protozoan parasites and its use in mammalian cells","volume":"104","author":"Novoselov","year":"2007","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023013110114534400_B13","first-page":"367","article-title":"A novel RNA structural motif in the selenocysteine insertion element of eukaryotic selenoprotein mRNAs","volume":"2","author":"Walczak","year":"1996","journal-title":"RNA"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/5\/674\/48985108\/bioinformatics_25_5_674.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/5\/674\/48985108\/bioinformatics_25_5_674.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T19:50:56Z","timestamp":1675194656000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/25\/5\/674\/182876"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,1,29]]},"references-count":13,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2009,3,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btp020","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2009,3,1]]},"published":{"date-parts":[[2009,1,29]]}}}