ArticleNucleic acids research2017
L1Base 2: more retrotransposition-active LINE-1s, more mammalian genomes.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 96 papers.
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Who cites it
96 citing papers in PubMed, 161 citations in OpenAlex.
- Interactions of LINE-1 ORF1p with proteins and chromatin suggest a role in neuronal physiology.Life science alliance · 2026Article
- LINE-1 CpG methylation in canine blood and cortical DNA tracks epigenetic changes with age.GeroScience · 2026Article
- Transcriptional perturbation of LINE-1 elements reveals their cis-regulatory potential.EMBO reports · 2026Article
- Fiber-TEnCATS reveals haplotype-specific chromatin accessibility and DNA methylation at human L1HS loci.bioRxiv : the preprint server for biology · 2026Article
- Characterizing cytosine methylation of polymorphic transposable element insertions using the human pangenome resources.Genome research · 2026Article
- SIRT6 overexpression counteracts chromatin aging in the male murine liver.Nature communications · 2026Article
- Transposable elements as drivers of genome evolution in Drosophila virilis.Nucleic acids research · 2026Article
- Human CCR4-NOT suppresses pervasive transcription and retrotransposable elements.bioRxiv : the preprint server for biology · 2026Article
- Repeats mimic pathogen-associated patterns across a vast evolutionary landscape.Cell genomics · 2025Article
- A tandem repeat atlas for the genome of inbred mouse strains: A genetic variation resource.iScience · 2025Article
- mScience China. Life sciences · 2025Article
- Article
- Transposable element dynamics in glioblastoma stem cells: insights from locus-specific quantification.Mobile DNA · 2025Article
- Sequence Diversity and Encoded Enzymatic Differences of Monocistronic L1 ORF2 mRNA Variants in the Aged Normal and Alzheimer's Disease Brain.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2025Article
- A Tandem Repeat Atlas for the Genome of Inbred Mouse Strains: A Genetic Variation Resource.bioRxiv : the preprint server for biology · 2025Article
- LINE1 elements at distal junctions of rDNA repeats regulate nucleolar organization in human embryonic stem cells.Genes & development · 2025Article
- Multi-ancestry GWAS reveals loci linked to human variation in LINE-1- and Alu-insertion numbers.bioRxiv : the preprint server for biology · 2025Article
- Retrotransposition-competent L1s are increased in the genomes of individuals with amyotrophic lateral sclerosis.Experimental biology and medicine (Maywood, N.J.) · 2025Article
- MORE-RNAseq: a pipeline for quantifying retrotransposition-capable LINE1 expression based on RNA-seq data.Frontiers in bioinformatics · 2025Article
- Multi-ancestry GWAS reveals loci linked to human variation in LINE-1- and Alu-insertion numbers.Translational medicine of aging · 2025Article
36 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors at 4 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.