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SinEx DB: a database for single exon coding sequences in mammalian genomes.

Roddy Jorquera1, Rodrigo Ortiz1, F Ossandon1

  • 1Center for Bioinformatics and Genome Biology, Fundacion Ciencia & Vida and Facultad de Ciencias Biologicas, Universidad Andres Bello, Avda Zañartu 1482, Santiago, Chile.

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This study introduces SinEx DB, a new database for single exon genes (SEGs) in mammals. It provides valuable data for understanding the evolution and function of these unique protein-coding genes.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Eukaryotic genes often contain introns, but some lack them in their coding sequence (CDS), known as single exon genes (SEGs).
  • Existing specialized databases for SEGs are limited, necessitating a more comprehensive resource.

Purpose of the Study:

  • To create SinEx DB, a publicly accessible, searchable database of predicted SEGs from 10 mammalian genomes.
  • To provide DNA and protein sequences, functional predictions (KOG), and distribution data for SEGs.

Main Methods:

  • Definition of SEGs as nuclear, protein-coding genes lacking introns in their CDS.
  • Development of a relational database using MySQL Server 5.1.33.
  • Inclusion of data from 10 completely sequenced mammalian genomes, including human.

Main Results:

  • SinEx DB houses predicted SEG sequences and functional information.
  • The database is searchable via phylogenetic browsing, BLAST, and advanced keyword/function searches.
  • Complete SEG datasets are available for download.

Conclusions:

  • SinEx DB serves as a rich resource for studying SEG evolution and function.
  • The database enhances the accessibility and diversity of SEG information for researchers.