{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,6]],"date-time":"2026-03-06T06:01:51Z","timestamp":1772776911940,"version":"3.50.1"},"reference-count":38,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2022,11,18]],"date-time":"2022-11-18T00:00:00Z","timestamp":1668729600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"European Life-science Infrastructure for Biological Information Italy"},{"name":"ELIXIR-CONVERGE","award":["H2020-INFRADEV-2019-2"],"award-info":[{"award-number":["H2020-INFRADEV-2019-2"]}]},{"name":"ELIXIR","award":["GA 871075"],"award-info":[{"award-number":["GA 871075"]}]},{"name":"Ministero dell\u2019Universit\u00e0 e Ricerca","award":["AIM1893457"],"award-info":[{"award-number":["AIM1893457"]}]},{"name":"Italian Ministry of Education, University and Research"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The 5\u2032 and 3\u2032 untranslated regions of eukaryotic mRNAs (UTRs) play crucial roles in the post-transcriptional regulation of gene expression through the modulation of nucleo-cytoplasmic mRNA transport, translation efficiency, subcellular localization, and message stability. Since 1996, we have developed and maintained UTRdb, a specialized database of UTR sequences. Here we present UTRdb 2.0, a major update of UTRdb featuring an extensive collection of eukaryotic 5\u2032 and 3\u2032 UTR sequences, including over 26 million entries from over 6 million genes and 573 species, enriched with a curated set of functional annotations. Annotations include CAGE tags and polyA signals to label the completeness of 5\u2032 and 3\u2032UTRs, respectively. In addition, uORFs and IRES are annotated in 5\u2032UTRs as well as experimentally validated miRNA targets in 3\u2032UTRs. Further annotations include evolutionarily conserved blocks, Rfam motifs, ADAR-mediated RNA editing events, and m6A modifications. A web interface allowing a flexible selection and retrieval of specific subsets of UTRs, selected according to a combination of criteria, has been implemented which also provides comprehensive download facilities. UTRdb 2.0 is accessible at http:\/\/utrdb.cloud.ba.infn.it\/utrdb\/<\/jats:p>","DOI":"10.1093\/nar\/gkac1016","type":"journal-article","created":{"date-parts":[[2022,11,18]],"date-time":"2022-11-18T18:30:32Z","timestamp":1668796232000},"page":"D337-D344","source":"Crossref","is-referenced-by-count":30,"title":["UTRdb 2.0: a comprehensive, expert curated catalog of eukaryotic mRNAs untranslated regions"],"prefix":"10.1093","volume":"51","author":[{"given":"Claudio","family":"Lo\u00a0Giudice","sequence":"first","affiliation":[{"name":"Department of Biosciences, Biotechnology and Environment, University of Bari A. Moro , 70126 Bari, Italy"}]},{"given":"Federico","family":"Zambelli","sequence":"additional","affiliation":[{"name":"Department of Biosciences, University of Milan , 20133 Milan, Italy"},{"name":"Institute of Biomembranes, Bioenergetics and Molecular Biotechnology , Consiglio Nazionale delle Ricerche, 70126 Bari, Italy"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3983-4961","authenticated-orcid":false,"given":"Matteo","family":"Chiara","sequence":"additional","affiliation":[{"name":"Department of Biosciences, University of Milan , 20133 Milan, Italy"},{"name":"Institute of Biomembranes, Bioenergetics and Molecular Biotechnology , Consiglio Nazionale delle Ricerche, 70126 Bari, Italy"}]},{"given":"Giulio","family":"Pavesi","sequence":"additional","affiliation":[{"name":"Department of Biosciences, University of Milan , 20133 Milan, Italy"},{"name":"Institute of Biomembranes, Bioenergetics and Molecular Biotechnology , Consiglio Nazionale delle Ricerche, 70126 Bari, Italy"}]},{"given":"Marco\u00a0Antonio","family":"Tangaro","sequence":"additional","affiliation":[{"name":"Institute of Biomembranes, Bioenergetics and Molecular Biotechnology , Consiglio Nazionale delle Ricerche, 70126 Bari, Italy"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6549-0114","authenticated-orcid":false,"given":"Ernesto","family":"Picardi","sequence":"additional","affiliation":[{"name":"Department of Biosciences, Biotechnology and Environment, University of Bari A. Moro , 70126 Bari, Italy"},{"name":"Institute of Biomembranes, Bioenergetics and Molecular Biotechnology , Consiglio Nazionale delle Ricerche, 70126 Bari, Italy"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3663-0859","authenticated-orcid":false,"given":"Graziano","family":"Pesole","sequence":"additional","affiliation":[{"name":"Department of Biosciences, Biotechnology and Environment, University of Bari A. Moro , 70126 Bari, Italy"},{"name":"Institute of Biomembranes, Bioenergetics and Molecular Biotechnology , Consiglio Nazionale delle Ricerche, 70126 Bari, Italy"}]}],"member":"286","published-online":{"date-parts":[[2022,11,18]]},"reference":[{"key":"2023010804231340400_B1","doi-asserted-by":"crossref","first-page":"580","DOI":"10.1038\/ng.2653","article-title":"The genotype-tissue expression (GTEx) project","volume":"45","author":"Lonsdale","year":"2013","journal-title":"Nat. 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Biol."},{"key":"2023010804231340400_B7","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1038\/s41576-018-0008-z","article-title":"Heterogeneity and specialized functions of translation machinery: from genes to organisms","volume":"19","author":"Genuth","year":"2018","journal-title":"Nat. Rev. Genet."},{"key":"2023010804231340400_B8","doi-asserted-by":"crossref","first-page":"e1653","DOI":"10.1002\/wrna.1653","article-title":"On the function and relevance of alternative 3\u2032-UTRs in gene expression regulation","volume":"12","author":"Pereira-Castro","year":"2021","journal-title":"WIREs RNA"},{"key":"2023010804231340400_B9","doi-asserted-by":"crossref","first-page":"158","DOI":"10.1038\/nrm.2017.103","article-title":"Functional 5\u2032 UTR mRNA structures in eukaryotic translation regulation and how to find them","volume":"19","author":"Leppek","year":"2018","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"2023010804231340400_B10","doi-asserted-by":"crossref","first-page":"322","DOI":"10.1038\/s41594-019-0200-7","article-title":"RNA structure maps across mammalian cellular compartments","volume":"26","author":"Sun","year":"2019","journal-title":"Nat. Struct. Mol. 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Ther."},{"key":"2023010804231340400_B32","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1093\/bioinformatics\/btu613","article-title":"The ensembl REST API: ensembl data for any language","volume":"31","author":"Yates","year":"2015","journal-title":"Bioinformatics"},{"key":"2023010804231340400_B33","doi-asserted-by":"crossref","first-page":"D1005","DOI":"10.1093\/nar\/gky1120","article-title":"The NHGRI-EBI GWAS catalog of published genome-wide association studies, targeted arrays and summary statistics 2019","volume":"47","author":"Buniello","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2023010804231340400_B34","doi-asserted-by":"crossref","first-page":"D1115","DOI":"10.1093\/nar\/gkab959","article-title":"The UCSC genome browser database: 2022 update","volume":"50","author":"Lee","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"2023010804231340400_B35","doi-asserted-by":"crossref","first-page":"D590","DOI":"10.1093\/nar\/gkj144","article-title":"The UCSC genome browser database: update 2006","volume":"34","author":"Hinrichs","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"2023010804231340400_B36","doi-asserted-by":"crossref","first-page":"R1","DOI":"10.1186\/gb-2003-5-1-r1","article-title":"MicroRNA targets in Drosophila","volume":"5","author":"Enright","year":"2003","journal-title":"Genome Biol."},{"key":"2023010804231340400_B37","article-title":"PySAM (Python Wrapper for system advisor model \u2018SAM\u2019)","author":"Gilman","year":"2019"},{"key":"2023010804231340400_B38","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1016\/j.gene.2004.11.041","article-title":"uAUG and uORFs in human and rodent 5\u2032untranslated mRNAs","volume":"349","author":"Iacono","year":"2005","journal-title":"Gene"}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/51\/D1\/D337\/48440789\/gkac1016.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/51\/D1\/D337\/48440789\/gkac1016.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,8]],"date-time":"2023-01-08T04:23:54Z","timestamp":1673151834000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/51\/D1\/D337\/6833245"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,11,18]]},"references-count":38,"journal-issue":{"issue":"D1","published-online":{"date-parts":[[2022,11,18]]},"published-print":{"date-parts":[[2023,1,6]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkac1016","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2023,1,6]]},"published":{"date-parts":[[2022,11,18]]}}}