Please use this identifier to cite or link to this item: http://hdl.handle.net/2381/39801
Title: L1Base 2: more retrotransposition-active LINE-1s, more mammalian genomes
Authors: Penzkofer, Tobias
Jäger, Marten
Figlerowicz, Marek
Badge, Richard
Mundlos, Stefan
Robinson, Peter N.
Zemojtel, Tomasz
First Published: 18-Oct-2016
Publisher: Oxford University Press (OUP)
Citation: Nucleic Acids Research, 2017, 45 (D1), pp. D68-D73
Abstract: LINE-1 (L1) insertions comprise as much as 17% of the human genome sequence, and similar proportions have been recorded for other mammalian species. Given the established role of L1 retrotransposons in shaping mammalian genomes, it becomes an important task to track and annotate the sources of this activity: full length elements, able to encode the cis and trans acting components of the retrotransposition machinery. The L1Base database (http://l1base.charite.de) contains annotated full-length sequences of LINE-1 transposons including putatively active L1s. For the new version of L1Base, a LINE-1 annotation tool, L1Xplorer, has been used to mine potentially active L1 retrotransposons from the reference genome sequences of 17 mammals. The current release of the human genome, GRCh38, contains 146 putatively active L1 elements or full length intact L1 elements (FLIs). The newest versions of the mouse, GRCm38 and the rat, Rnor_6.0, genomes contain 2811 and 492 FLIs, respectively. Most likely reflecting the current level of completeness of the genome project, the latest reference sequence of the common chimpanzee genome, PT 2.19, only contains 19 FLIs. Of note, the current assemblies of the dog, CF 3.1 and the sheep, OA 3.1, genomes contain 264 and 598 FLIs, respectively. Further developments in the new version of L1Base include an updated website with implementation of modern web server technologies. including a more responsive design for an improved user experience, as well as the addition of data sharing capabilities for L1Xplorer annotation.
DOI Link: 10.1093/nar/gkw925
ISSN: 0305-1048
eISSN: 1362-4962
Links: https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkw925
http://hdl.handle.net/2381/39801
Version: Publisher Version
Status: Peer-reviewed
Type: Journal Article
Rights: Copyright © the authors, 2016. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-commercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits unrestricted use, distribution, and reproduction in any medium non-commercially, provided the original author and source are credited.
Appears in Collections:Published Articles, Dept. of Genetics

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