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RPG: the Ribosomal Protein Gene database.

Akihiro Nakao1, Maki Yoshihama, Naoya Kenmochi

  • 1Department of Biotechnology, Research Center for Frontier Bioscience, Miyazaki University, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan.

Nucleic Acids Research
|December 19, 2003
PubMed
Summary

The Ribosomal Protein Gene (RPG) database offers comprehensive data on ribosomal protein genes across multiple organisms. This resource facilitates comparative genomics and the study of small nucleolar RNAs within ribosomal protein gene introns.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Ribosomal proteins (RPs) are essential components of ribosomes, crucial for protein synthesis.
  • Understanding RP genes and their regulation is vital for cellular function and disease research.
  • Existing databases may lack comprehensive, comparative data on RP genes across diverse species.

Purpose of the Study:

  • To introduce the Ribosomal Protein Gene (RPG) database, a novel resource for RP gene information.
  • To provide a centralized platform for detailed data on RP genes from various organisms.
  • To enable comparative analysis of RP gene structures and related non-coding RNAs.

Main Methods:

  • Database development integrating genomic, cDNA, and amino acid sequences.

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  • Inclusion of data from model organisms (human, Drosophila, C. elegans, S. cerevisiae, M. jannaschii, E. coli).
  • Implementation of search functionalities by gene name and organism, with comparative tools.

    • Main Results:

    • RPG database established with detailed information on RP genes and their orthologs.
    • Features include sequence data, intron/exon structures, genomic locations, and ortholog information.
    • Comparative tools for gene structure visualization and multiple amino acid sequence alignments are available.

    Conclusions:

    • The RPG database serves as a valuable resource for researchers studying ribosomal proteins and gene regulation.
    • It facilitates cross-species comparisons of RP gene organization and evolution.
    • The database also highlights the significance of small nucleolar RNAs (snoRNAs) encoded within RP gene introns.