{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,21]],"date-time":"2026-01-21T06:03:23Z","timestamp":1768975403394,"version":"3.49.0"},"reference-count":18,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2021,1,28]],"date-time":"2021-01-28T00:00:00Z","timestamp":1611792000000},"content-version":"vor","delay-in-days":27,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100002850","name":"Fondo Nacional de Desarrollo Cient\u00edfico y Tecnol\u00f3gico","doi-asserted-by":"publisher","award":["1090451, 1130683 and 1181717"],"award-info":[{"award-number":["1090451, 1130683 and 1181717"]}],"id":[{"id":"10.13039\/501100002850","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Programa de Apoyo a Centros con Financiamiento Basal","award":["AFB170004"],"award-info":[{"award-number":["AFB170004"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,1,28]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Single-exon coding sequences (CDSs), also known as \u2018single-exon genes\u2019 (SEGs), are defined as nuclear, protein-coding genes that lack introns in their CDSs. They have been studied not only to determine their origin and evolution but also because their expression has been linked to several types of human cancers and neurological\/developmental disorders, and many exhibit tissue-specific transcription. We developed SinEx DB that houses DNA and protein sequence information of SEGs from 10 mammalian genomes including human. SinEx DB includes their functional predictions (KOG (euKaryotic Orthologous Groups)) and the relative distribution of these functions within species. Here, we report SinEx 2.0, a major update of SinEx DB that includes information of the occurrence, distribution and functional prediction of SEGs from 60 completely sequenced eukaryotic genomes, representing animals, fungi, protists and plants. The information is stored in a relational database built with MySQL Server 5.7, and the complete dataset of SEG sequences and their GO (Gene Ontology) functional assignations are available for downloading. SinEx DB 2.0 was built with a novel pipeline that helps disambiguate single-exon isoforms from SEGs. SinEx DB 2.0 is the largest available database for SEGs and provides a rich source of information for advancing our understanding of the evolution, function of SEGs and their associations with disorders including cancers and neurological and developmental diseases.<\/jats:p>\n               <jats:p>Database URL: http:\/\/v2.sinex.cl\/<\/jats:p>","DOI":"10.1093\/database\/baab002","type":"journal-article","created":{"date-parts":[[2021,1,5]],"date-time":"2021-01-05T21:25:50Z","timestamp":1609881950000},"source":"Crossref","is-referenced-by-count":5,"title":["SinEx DB 2.0 update 2020: database for eukaryotic single-exon coding sequences"],"prefix":"10.1093","volume":"2021","author":[{"given":"R","family":"Jorquera","sequence":"first","affiliation":[{"name":"Center for Bioinformatics and Genome Biology, Fundacion Ciencia & Vida, Za\u00f1artu 1482, \u00d1u\u00f1oa Santiago 7780132, Chile"},{"name":"Laboratorio Medicina Traslacional, Fundaci\u00f3n Arturo L\u00f3pez P\u00e9rez, Jos\u00e9 Manuel Infante 805, Providencia, Santiago 7500691, Chile"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"C","family":"Gonz\u00e1lez","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics and Genome Biology, Fundacion Ciencia & Vida, Za\u00f1artu 1482, \u00d1u\u00f1oa Santiago 7780132, Chile"},{"name":"Centro de Gen\u00f3mica y Bioinform\u00e1tica, Universidad Mayor, Camino la pir\u00e1mide 5750, Huechuraba, Santiago 8580745, Chile"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"P T L C","family":"Clausen","sequence":"additional","affiliation":[{"name":"Department of Global Surveillance, Technical University of Denmark, Kemitorvet building 204, 2800 Kgs. Lyngby, Denmark"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2472-8317","authenticated-orcid":false,"given":"B","family":"Petersen","sequence":"additional","affiliation":[{"name":"Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Hovedstaden, \u00d8ster Voldgade 5\u20137, Copenhagen 1350, Denmark"},{"name":"Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), AIMST University, Batu 3 1\/2, Jalan Bukit Air Nasi, 08100 Bedong, Kedah, Malaysia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9555-138X","authenticated-orcid":false,"given":"D S","family":"Holmes","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics and Genome Biology, Fundacion Ciencia & Vida, Za\u00f1artu 1482, \u00d1u\u00f1oa Santiago 7780132, Chile"},{"name":"Centro de Gen\u00f3mica y Bioinform\u00e1tica, Universidad Mayor, Camino la pir\u00e1mide 5750, Huechuraba, Santiago 8580745, Chile"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2021,1,28]]},"reference":[{"issue":"baw095","key":"2021012815252287900_R1","first-page":"1","article-title":"SinEx DB: a database for single exon coding sequences in mammalian genomes","volume":"2016","author":"Jorquera","year":"2016","journal-title":"Database (Oxford)"},{"issue":"bay089","key":"2021012815252287900_R2","first-page":"1","article-title":"Improved ontology for eukaryotic single-exon coding sequences in biological databases","volume":"2018","author":"Jorquera","year":"2018","journal-title":"Database"},{"key":"2021012815252287900_R3","article-title":"Tumor-suppressor gene SOX1 is a methylation-specific expression gene in cervical adenocarcinoma","volume":"98","author":"Yuan","year":"2019","journal-title":"Medicine (United States)"},{"key":"2021012815252287900_R4","doi-asserted-by":"crossref","first-page":"6101","DOI":"10.1158\/0008-5472.CAN-19-1019","article-title":"Histone-related genes are hypermethylated in lung cancer and hypermethylated HIST1H4F could serve as a pan-cancer biomarker","volume":"79","author":"Dong","year":"2019","journal-title":"Cancer Res"},{"key":"2021012815252287900_R5","doi-asserted-by":"crossref","first-page":"1862","DOI":"10.3390\/ijms19071862","article-title":"The reprimo gene family: a novel gene lineage in gastric cancer with tumor suppressive properties","volume":"19","author":"Amigo","year":"2018","journal-title":"Int. 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