L1Base: from Functional Annotation to Prediction of Active LINE-1 Elements

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2004 Dec 21

PMID 15608246

Citations 69

Authors

Tobias Penzkofer

Thomas Dandekar

Tomasz Zemojtel

Affiliations

Soon will be listed here.

Abstract

L1Base is a dedicated database containing putatively active LINE-1 (L1) insertions residing in human and rodent genomes that are as follows: (i) intact in the two open reading frames (ORFs), full-length L1s (FLI-L1s) and (ii) intact ORF2 but disrupted ORF1 (ORF2-L1s). In addition, due to their regulatory potential, the full-length (>6000 bp) non-intact L1s (FLnI-L1s) were also included in the database. Application of a novel annotation methodology, L1Xplorer, allowed in-depth annotation of functional sequence features important for L1 activity, such as transcription factor binding sites and amino acid residues. The L1Base is available online at http://l1base.molgen.mpg.de. In addition, the data stored in the database can be accessed from the Ensembl web browser via a DAS service (http://l1das.molgen.mpg.de:8080/das).

Citing Articles

Interchromosomal translocation in neural progenitor cells exposed to L1 retrotransposition.

Muotri A Genet Mol Biol. 2023; 46(1):e20220268.

PMID: 36734369 PMC: 9936793. DOI: 10.1590/1678-4685-GMB-2022-0268.

Pattern matching for high precision detection of LINE-1s in human genomes.

Lopez J, Seguel J, Chamorro A, Ramos K BMC Bioinformatics. 2022; 23(1):375.

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The Tumor-Specific Expression of L1 Retrotransposons Independently Correlates with Time to Relapse in Hormone-Negative Breast Cancer Patients.

Berrino E, Miglio U, Bellomo S, Debernardi C, Bragoni A, Petrelli A Cells. 2022; 11(12).

PMID: 35741073 PMC: 9221920. DOI: 10.3390/cells11121944.

Locus specific reduction of L1 expression in the cortices of individuals with amyotrophic lateral sclerosis.

Pfaff A, Bubb V, Quinn J, Koks S Mol Brain. 2022; 15(1):25.

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Genome surveillance by HUSH-mediated silencing of intronless mobile elements.

Seczynska M, Bloor S, Martinez Cuesta S, Lehner P Nature. 2021; 601(7893):440-445.

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