title: L1Base 2: more retrotransposition-active LINE-1s, more mammalian genomes.
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.
authors.affiliation: Department of Radiology, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany.
authors.forename: Tobias
authors.initials: T
authors.lastname: Penzkofer
authors.affiliation: Institut für Medizinische Genetik und Humangenetik, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany.
authors.forename: Marten
authors.initials: M
authors.lastname: Jäger
authors.affiliation: Institute of Bioorganic Chemistry, Polish Academy of Sciences, 60-569 Poznan, Poland.
authors.forename: Marek
authors.initials: M
authors.lastname: Figlerowicz
authors.affiliation: Department of Genetics, University of Leicester, Leicester, LE1 7RH, UK.
authors.forename: Richard
authors.initials: R
authors.lastname: Badge
authors.affiliation: Institut für Medizinische Genetik und Humangenetik, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Mundlos
authors.affiliation: Institut für Medizinische Genetik und Humangenetik, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany.|The Jackson Laboratory for Genomic medicine, 10 Discovery Drive, Farmington, CT 06032, USA.
authors.forename: Peter N
authors.initials: PN
authors.lastname: Robinson
authors.affiliation: Institut für Medizinische Genetik und Humangenetik, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany tomasz.zemojtel@charite.de.|Institute of Bioorganic Chemistry, Polish Academy of Sciences, 60-569 Poznan, Poland.
authors.forename: Tomasz
authors.initials: T
authors.lastname: Zemojtel
mesh_terms: D000818:Animals; D030561:Databases, Nucleic Acid; D016678:Genome; D006801:Humans; D020084:Long Interspersed Nucleotide Elements; D008322:Mammals / Q000235:genetics; D051379:Mice; D058977:Molecular Sequence Annotation; D051381:Rats