| Summary: | <p>Abstract</p> <p>Background</p> <p>Sequencing of the human genome has identified numerous chromosome copy number additions and subtractions that include stable partial gene duplications and pseudogenes that when not properly annotated can interfere with genetic analysis. As an example of this problem, an evolutionary chromosome event in the primate ancestral chromosome 18 produced a partial duplication and inversion of rho-associated protein kinase 1 (<it>ROCK1 </it>-18q11.1, 33 exons) in the subtelomeric region of the p arm of chromosome 18 detectable only in humans. <it>ROCK1 </it>and the partial gene copy, which the gene databases also currently call <it>ROCK1</it>, include non-unique single nucleotide polymorphisms (SNPs).</p> <p>Results</p> <p>Here, we characterize this partial gene copy of the human <it>ROCK1</it>, termed <it>Little ROCK</it>, located at 18p11.32. <it>Little ROCK </it>includes five exons, four of which share 99% identity with the terminal four exons of <it>ROCK1 </it>and one of which is unique to <it>Little ROCK</it>. In human while <it>ROCK1 </it>is expressed in many organs, <it>Little ROCK </it>expression is restricted to vascular smooth muscle cell (VSMC) lines and organs rich in smooth muscle. The single nucleotide polymorphism database (dbSNP) lists multiple variants contained in the region shared by <it>ROCK1 </it>and <it>Little ROCK</it>. Using gene and cDNA sequence analysis we clarified the origins of two non-synonymous SNPs annotated in the genome to actually be fixed differences between the <it>ROCK1 </it>and the <it>Little ROCK </it>gene sequences. Two additional coding SNPs were valid polymorphisms selectively within <it>Little ROCK</it>. Little ROCK-Green Fluorescent fusion proteins were highly unstable and degraded by the ubiquitin-proteasome system <it>in vitro</it>.</p> <p>Conclusion</p> <p>In this report we have characterized <it>Little ROCK </it>(<it>ROCK1P1</it>), a human expressed pseudogene derived from partial duplication of <it>ROCK1</it>. The large number of pseudogenes in the human genome creates significant genetic diversity. Our findings emphasize the importance of taking into consideration pseudogenes in all candidate gene and genome-wide association studies, as well as the need for complete annotation of human pseudogenome.</p>
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