{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,12]],"date-time":"2025-10-12T04:13:31Z","timestamp":1760242411274,"version":"build-2065373602"},"reference-count":37,"publisher":"MDPI AG","issue":"3","license":[{"start":{"date-parts":[[2017,7,5]],"date-time":"2017-07-05T00:00:00Z","timestamp":1499212800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100004875","name":"DFG","doi-asserted-by":"publisher","award":["NO 920\/6-1"],"award-info":[{"award-number":["NO 920\/6-1"]}],"id":[{"id":"10.13039\/100004875","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001655","name":"Deutscher Akademischer Austauschdienst","doi-asserted-by":"publisher","award":["PhD stipend"],"award-info":[{"award-number":["PhD stipend"]}],"id":[{"id":"10.13039\/501100001655","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["ncRNA"],"abstract":"<jats:p>Long non-coding RNAs (lncRNAs) form a substantial component of the transcriptome and are involved in a wide variety of regulatory mechanisms. Compared to protein-coding genes, they are often expressed at low levels and are restricted to a narrow range of cell types or developmental stages. As a consequence, the diversity of their isoforms is still far from being recorded and catalogued in its entirety, and the debate is ongoing about what fraction of non-coding RNAs truly conveys biological function rather than being \u201cjunk\u201d. Here, using a collection of more than 100 transcriptomes from related B cell lymphoma, we show that lncRNA loci produce a very defined set of splice variants. While some of them are so rare that they become recognizable only in the superposition of dozens or hundreds of transcriptome datasets and not infrequently include introns or exons that have not been included in available genome annotation data, there is still a very limited number of processing products for any given locus. The combined depth of our sequencing data is large enough to effectively exhaust the isoform diversity: the overwhelming majority of splice junctions that are observed at all are represented by multiple junction-spanning reads. We conclude that the human transcriptome produces virtually no background of RNAs that are processed at effectively random positions, but is\u2014under normal circumstances\u2014confined to a well defined set of splice variants.<\/jats:p>","DOI":"10.3390\/ncrna3030023","type":"journal-article","created":{"date-parts":[[2017,7,5]],"date-time":"2017-07-05T11:26:04Z","timestamp":1499253964000},"page":"23","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["Rare Splice Variants in Long Non-Coding RNAs"],"prefix":"10.3390","volume":"3","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5980-5565","authenticated-orcid":false,"given":"Rituparno","family":"Sen","sequence":"first","affiliation":[{"name":"Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University Leipzig, H\u00e4rtelstrasse 16-18, D-04107 Leipzig, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gero","family":"Doose","sequence":"additional","affiliation":[{"name":"ecSeq Bioinformatics, Brandvorwerkstra\u00dfe 43, D-04275 Leipzig, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5016-5191","authenticated-orcid":false,"given":"Peter","family":"Stadler","sequence":"additional","affiliation":[{"name":"Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University Leipzig, H\u00e4rtelstrasse 16-18, D-04107 Leipzig, Germany"},{"name":"ecSeq Bioinformatics, Brandvorwerkstra\u00dfe 43, D-04275 Leipzig, Germany"},{"name":"German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Competence Center for Scalable Data Services and Solutions, Leipzig Research Center for Civilization Diseases, and Leipzig Research Center for Civilization Diseases (LIFE), University Leipzig, H\u00e4rtelstrasse 16-18, D-04107 Leipzig, Germany"},{"name":"Max Planck Institute for Mathematics in the Sciences, Inselstra\u00dfe 22, D-04103 Leipzig, Germany"},{"name":"Fraunhofer Institute for Cell Therapy and Immunology, Perlickstrasse 1, D-04103 Leipzig, Germany"},{"name":"Center for RNA in Technology and Health, University Copenhagen, Gr\u00f8nneg\u00e5rdsvej 3, 1870 Frederiksberg C, Denmark"},{"name":"Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2017,7,5]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Clark, M.B., Amaral, P.P., Schlesinger, F.J., Dinger, M.E., Taft, R.J., Rinn, J.L., Ponting, C.P., Stadler, P.F., Morris, K.J., and Morillon, A. 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