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Imprinted Gene Catalogue


NAR Molecular Biology Database Collection entry number 294
Morison, I.M.1, Glaser, R.2
1Cancer Genetics Laboratory, Department of Biochemistry, University of Otago, P O Box 56, Dunedin, New Zealand
2Department of Biology, Massachusetts College of Liberal Arts, North Adams, MA 01247, USA

Database Description

The imprinted gene and parent-of-origin effect database (http://www.otago.ac.nz/IGC) consists of two sections. One section catalogues the current literature on imprinted genes in humans and animals. The second, and new, section catalogues current reports of parental origin of de novo mutations in humans alone. The database includes descriptions of 85 imprinted genes from several mammalian species, over 300 entries on reported parent-of-origin effects in animals, and 1700 mutations (found in 59 different genes) with a parent-of-origin effect. Data is accessed through a search engine and references are hyperlinked to PubMed, UCSC Genome Browser and Ensembl.

Recent Developments

We have recently added a comprehensive section on spontaneous mutations that show a bias with respect to their parental origin. This new part of the database can be searched according to mutation type, disorder, chromosomal location, gene name, and inheritance pattern. Outcomes of the search are presented in a tabular format with the following information: disorder, inheritance pattern, incidence of disorder, gene name, chromosomal location, evidence of a paternal or maternal age effect, mutation type and any recurrent mutations associated with a parent-of-origin effect, number of paternal mutations, number of maternal mutations, and PubMed reference. Data for base substitutions are separated according to the type of base substitution (missense mutation, nonsense mutation or splice site mutation), whether the mutation is a transition or transversion mutation, and whether the base substitution falls within a CpG dinucleotide. The distinction is made between large deletions and insertions (>20 base pairs) and small deletions and insertions (< 20 base pairs). This size distinction is made based upon the possibility of different mechanisms contributing to these different types of mutations, and therefore potentially different parental origins.

Acknowledgements

Sue Harvey provides ongoing support and manages the database.

References

1. Reik W., and Walter, J. (2001) Genomic imprinting: parental influence on the genome. Nature Rev. Genet. 2, 21-32.
2. Glaser R.L, and Jabs, E.W. (2004) Dear Old Dad. Sci. Aging Knowl. Environ., 3.
3. Crow, J.F. (2000) The origins, patterns and implications of human spontaneous mutation. Nature Rev. Genet. 1, 40-47.
4. Morison I.M. and Reeve A.E. (1998) A catalogue of imprinted genes and parent-of-origin effects in humans and animals. Hum. Mol. Genet., 7, 1599-1609.
5. Morison I.M., Paton C.J., Cleverly S.D. (2001) The imprinted gene and parent-of-origin effect database. Nucleic Acids Res. 29, 275-276.
6. Morison I.M., Ramsay J.P., Spencer H.G. (2005) A census of mammalian imprinting. Trends Genet. 21, 457-465.


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