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Update on the olfactory receptor (OR) gene superfamily

DOI: 10.1186/1479-7364-3-1-87

Keywords: classification of gene families and subfamilies, OR gene superfamily, CYP gene superfamily, nasal olfactory neurone, olfaction, olfactory receptor gene superfamily, allelic exclusion, opossum genome, platypus genome

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Abstract:

Before 1980, the names of genes and classification of their encoded proteins were highly variable and non-systematic -- especially to anyone slightly outside a particular field or to a new graduate student entering the field. Professor Margaret Oakley Dayhoff was a pioneer in attempting to create order out of chaos in the naming of genes and gene families by means of computerised protein alignments [1]. She was widely recognised as the founder in this new field of gene/protein classification, before her untimely death in 1983.Cytochrome P450 (CYP) genes are conveniently arranged into families and subfamilies based on the percentage amino acid sequence identity [2-7]. Enzymes that share approximately ≥ 40 per cent identity are assigned to a particular family designated by an Arabic numeral, whereas those sharing approximately ≥ 55 per cent identity are grouped into a particular subfamily designated by a letter. For example, the sterol 27-hydroxylase enzyme and the 25-hydroxy-vitamin D3 1α-hydroxylase enzyme are both assigned to the CYP27 family because they share > 40 per cent sequence identity. Furthermore, the sterol 27-hydroxylase is assigned to the CYP27 'A' subfamily and the 25-hydroxy-vitamin D3 1 α-hydroxylase to the CYP27 'B' subfamily because their protein sequences are < 55 per cent identical. If an additional enzyme were to be discovered that shared > 55 per cent identity with the sterol 27-hydroxylase, then it would be named CYP27A2. If an additional enzyme were to be discovered that shared < 55 per cent but > 40 per cent identity with the sterol 27-hydroxylase as well as the 25-hydroxy-vitamin D3 1α-hydroxylase, then it would be named CYP27C1. The development and application of this delightfully logical system of nomenclature to the genes of many animals, plants and bacteria [8] has eliminated the confusion that often had plagued the naming of gene families and superfamilies. Subsequently, this 'divergent evolution' nomenclature system was adopted for se

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