Chimerical nature of the gene annotated as Zebra finch (Taeniopygia guttata) glucokinase (hexokinase IV) has been proved in this study. N-half of the protein encoded by that gene shows similarity with glucokinase from other vertebrates, while its C-half shows similarity with C-halves of hexokinases II. We mapped 7 new exons coding for N-half of hexokinase II and 4 new exons coding for glucokinase of Zebra finch. Finally, we reconstructed normal genes coding for Zebra finch glucokinase and hexokinase II which are situated in “head-to-tail” orientation on the chromosome 22. Because of the error in gene annotation, exons encoding N-half of normal glucokinase have been fused with exons encoding C-half of normal hexokinase II, even though they are separated from each other by the sequence 98066 nucleotides in length. 1. Introduction Methods of phylogenetic analysis are usually used for reconstruction of the relations between distinct species or between families of homologous proteins. Nucleotide sequences of homologous genes are used as a material for fundamental works in computational biology and phylogenetic. In this study, the situation is quite different. Methods of phylogenetic analysis and methods of computational biology helped to find an error in gene annotation. The volume of nucleotide sequences including those of complete prokaryotic and eukaryotic genomes is increasing in geometric progression in the last decade. There are many different automatic gene finding algorithms developed to annotate those sequences. Even though most of the annotations are correct, there are still some mistakes which may lead to wrong conclusions. The material from public databases should not be taken as something absolutely correct. In case if something is wrong with phylogenetic trees one should carefully recheck all the nucleotide sequences used. There are five types of hexokinase encoded by five different genes in genomes of vertebrates: hexokinase I (HKI); hexokinase II (HKII), hexokinase III (HKIII), hexokinase domain containing protein I (HKDCI), and glucokinase (GK) [1]. HKI, HKII, HKIII, and HKDCI consist of two homologous halves. GK, which is often referred to as hexokinase IV, contains only a single “half” of hexokinase. It was shown that N-halves of HKI and HKIII are not catalytically active, unlike their C-halves [2]. In contrast, both halves of HKII are able to catalyze phosphorylation of hexoses [3]. Phylogenetic relations between glucokinase and two halves of hexokinase have been studied previously with the aim to reconstruct evolutionary history of the
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