L1Base: from functional annotation to prediction of active LINE-1 elements.
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).
Penzkofer
Tobias
T
Department of Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Ihnestrasse 73, D-14195 Berlin, Germany.
Dandekar
Thomas
T
Zemojtel
Tomasz
T
D000818:Animals; D001665:Binding Sites; D030561:Databases, Nucleic Acid; D023281:Genomics; D006801:Humans; D020084:Long Interspersed Nucleotide Elements; D051379:Mice; D016366:Open Reading Frames; D051381:Rats; D014157:Transcription Factors / Q000378:metabolism; D014584:User-Computer Interface
D014157:Transcription Factors