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FREP: a database of functional repeats in mouse cDNAs
Takeshi Nagashima1, Hideo Matsuda, Diego G Silva
1Biomedical Knowledge Discovery Team, Bioinformatics Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
Nucleic Acids Research
|December 19, 2003
Summary
The Functional REPeats (FREPs) database identifies mouse repeat sequences impacting gene function and disease. It aids research into repetitive elements in the mouse transcriptome and disease models.
Area of Science:
- Genomics
- Bioinformatics
- Molecular Biology
Background:
- Repetitive elements are abundant in genomes and can influence gene regulation and function.
- Understanding the functional impact of these repeats is crucial for deciphering complex biological processes and diseases.
Purpose of the Study:
- To create and curate the Functional REPeats (FREP) database, cataloging mouse repeat sequences with potential functional roles.
- To provide a resource for identifying and analyzing functional repeats in the mouse transcriptome.
Main Methods:
- Identification of non-redundant variant repeat sequences in mouse cDNAs using RepeatMasker.
- Computational association of repeats with potential effects on transcription, translation, protein function, or disease.
- Definition of Functional REPeats (FREPs) based on criteria including exon-exon boundaries, polyadenylation sites, translational effects, and disease associations.
Main Results:
- The FREP database contains 31,396 repeat sequences from 16,527 mouse cDNAs.
- 9,261 (29.5%) inferred FREPs were identified, derived from 6,861 (41.5%) mouse cDNAs.
- The database integrates evidence for functional assignments and provides sequence similarity search results.
Conclusions:
- The FREP database is a valuable resource for studying the role of transposons and repetitive sequences in the mouse transcriptome.
- It facilitates the exploration of functional repeats and aids in selecting appropriate experimental models for diseases with suspected repeat contributions.