Nucleic Acids Research, 2004, Vol. 32, Database issue D471-D475
© 2004 Oxford University Press
FREP: a database of functional repeats in mouse cDNAs
1 Biomedical Knowledge Discovery Team, Bioinformatics Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan, 2 Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Toyonaka, Osaka 560-8531, Japan, 3 Autoimmunity Research Unit, The Canberra Hospital, Woden ACT 2605, Australia, 4 John Curtin School of Medical Research, Australian National University, Canberra ACT 2601, Australia, 5 Genome Research Exploration (GER) Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan, 6 Genome Science Laboratory, RIKEN, Hirosawa, Wako, Saitama 351-0198, Japan and 7 Bioinformatics Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
*To whom correspondence should be addressed. Tel: +81 45 503 9303; Fax: +81 45 503 9552; Email: schoen{at}gsc.riken.jp
RIKEN GER Group and Genome Science Laoratory (GSL) Members are: Takeya Kasukawa, Takahiro Arakawa, Piero Carninci, Jun Kawai and Yoshihide Hayashizaki
The FREP database (http://facts.gsc.riken.go.jp/FREP/) contains 31 396 RepeatMasker-identified non-redundant variant repeat sequences derived from 16 527 mouse cDNAs with protein-coding potential. The repeats were computationally associated with potential effects on transcriptional variation, translation, protein function or involvement in disease to identify Functional REPeats (FREPs). FREPs are defined by the (i) occurrence of exon–exon boundaries in repeats, (ii) presence of polyadenylation sites in 3'UTR-located repeats, (iii) effect on translation, (iv) position in the protein- coding region or protein domains or (v) conditional association with disease MeSH terms. Currently the database contains 9261 (29.5%) inferred FREPs derived from 6861 (41.5%) mouse cDNAs. Integrated evidence of the functional assignments and dynamically generated sequence similarity search results support the exploration and annotation of functional, ancestral or taxon-specific repeats. Keyword and pre-selected feature searches (e.g. coding sequence–repeat or splice site–repeat relations) support intuitive database querying as well as the retrieval of repeat sequences. Integrated sequence search and alignment tools allow the analysis of known or identification of new functional repeat candidates. FREP is a unique resource for illuminating the role of transposons and repetitive sequences in shaping the coding part of the mouse transcriptome and for selecting the appropriate experimental model to study diseases with suspected repeat etiology contributions.
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