L1Base: from functional annotation to prediction of active LINE-1 elements - PubMed (original) (raw)

. 2005 Jan 1;33(Database issue):D498-500.

doi: 10.1093/nar/gki044.

Affiliations

• PMID: 15608246
• PMCID: PMC539998
• DOI: 10.1093/nar/gki044

L1Base: from functional annotation to prediction of active LINE-1 elements

Tobias Penzkofer et al. Nucleic Acids Res. 2005.

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).

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