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Protocols

L1Base specifications

Information


Unique identifier OMICS_14159
Name L1Base
Alternative name L1Base2
Restrictions to use None
Database management system MySQL
Community driven No
Data access Browse
User data submission Not allowed
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/L1Base

Taxon


  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus
    • Rattus norvegicus

Subtool


  • L1Xplorer

Maintainer


  • person_outline Tomasz Zemojtel

Publications for L1Base

L1Base citations

 (10)
library_books

Exonization of an Intronic LINE 1 Element Causing Becker Muscular Dystrophy as a Novel Mutational Mechanism in Dystrophin Gene

2017
Genes
PMCID: 5664103
PMID: 28972564
DOI: 10.3390/genes8100253

[…] Genome similarity sequence search was conducted using the Basic Local Alignment Search Tool (BLASTN v2.2.32) []. Analysis of repetitive elements was performed using CENSOR [], RepeatMasker [] and L1Xplorer []. Potential acceptor splice-sites and branchpoints were assessed using different algorithms available in Alamut Visual software (v2.8, Interactive Biosoftware, Rouen, France) (). […]

library_books

Patterns of Transposable Element Expression and Insertion in Cancer

2016
Front Mol Biosci
PMCID: 5110550
PMID: 27900322
DOI: 10.3389/fmolb.2016.00076

[…] more reliable measures of TE transcription levels compared to previously published methods, such as HTSeq-count, Cufflinks, and RepEnrich (Trapnell et al., ; Criscione et al., ; Anders et al., ). The L1Base database was used to identify the genomic locations of 145 full length, intact elements from the most recently active L1 subfamily (Penzkofer et al., ). The set of full-length intact L1 sequenc […]

library_books

The endonuclease domain of the LINE 1 ORF2 protein can tolerate multiple mutations

2016
Mob DNA
PMCID: 4837594
PMID: 27099633
DOI: 10.1186/s13100-016-0064-x

[…] Using L1Base [], we analyzed the sequences of full-length L1 loci present in the human genome to identify naturally occurring mutations in the ORF2 endonuclease domain. Our search parameters were set to ide […]

call_split

Resolving rates of mutation in the brain using single neuron genomics

2016
eLife
PMCID: 4805530
PMID: 26901440
DOI: 10.7554/eLife.12966.016
call_split See protocol

[…] ences were analyzed with the aid of standard tools, including the UCSC genome browser (), Blat (), NCBI BLAST (http://blast.ncbi.nlm.nih.gov/Blast.cgi), RepeatMasker (), RepBase (), ClustalW2 (), and L1Xplorer (). […]

library_books

Differential LINE 1 regulation in pluripotent stem cells of humans and other great apes

2013
Nature
PMCID: 4064720
PMID: 24153179
DOI: 10.1038/nature12686

[…] ee L1-EGFP reporter plasmid, we followed a modification of the strategy previously described. Intact L1Pt elements were identified in the Chimpanzee genome (CSAC 2.1.4/panTro4, UCSC) through Blat and L1Xplorer analyses. Among the identified intact full-length L1Pt elements, we amplified the L1 element located in chromosome 7: 11771100-11777132 of the chimpanzee genome from 0.2 ng of genomic DNA ex […]

library_books

High Levels of Sequence Diversity in the 5′ UTRs of Human Specific L1 Elements

2012
Comp Funct Genomics
PMCID: 3286893
PMID: 22400009
DOI: 10.1155/2012/129416

[…] All of the human-specific L1 elements were divided into their 5′ UTR, ORF1, ORF2, and 3′ UTR components using a combination of the L1Xplorer (http://line1.bioapps.biozentrum.uni-wuerzburg.de/l1xplorer.php) annotation tool [] and manual inspection. The sizes of the 5′ UTR, ORF1, ORF2, and 3′ UTR were 897, 1017, 3828, and 202 bp, r […]

Citations

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L1Base institution(s)
Department of Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Berlin, Germany; Department of Bioinformatics, University of Wuerzburg, Am Hubland, Wuerzburg, Germany
L1Base funding source(s)
This work has been a part of BioSapiens project funded by the European Commission within its FP6 Programme, under the thematic area ‘Life sciences, genomics and biotechnology for health’, contract number LHSG-CT-2003-503265.

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