Nature Genetics
- 38, 1216 - 1220 (2006)
Published online: 24 September 2006; | doi:10.1038/ng1888
Mammalian ultraconserved elements are strongly depleted among segmental duplications and copy number variantsAdnan Derti1, 2, 3, 4, Frederick P Roth1, 5, George M Church2, 3 & C-ting Wu61
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA. 2
Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. 3
Lipper Center for Computational Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. 4
Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA. 5
Center for Cancer Systems Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA. 6
Divisions of Genetics and Molecular Medicine, Harvard Medical School, Boston, Massachusetts 02115, USA.
Correspondence should be addressed to C-ting Wu twu@genetics.med.harvard.edu An earlier search in the human, mouse and rat genomes for sequences that are 100% conserved in orthologous segments and  200 bp in length identified 481 distinct sequences1. These human-mouse-rat sequences, which represent ultraconserved elements (UCEs), are believed to be important for functions involving DNA binding, RNA processing and the regulation of transcription and development. In vivo and additional computational studies of UCEs and other highly conserved sequences are consistent with these functional associations, with some observations indicating enhancer-like activity for these elements1,
2,
3,
4,
5,
6,
7,
8,
9. Here, we show that UCEs are significantly depleted among segmental duplications and copy number variants. Notably, of the UCEs that are found in segmental duplications or copy number variants, the majority overlap exons, indicating, along with other findings presented, that UCEs overlapping exons represent a distinct subset.
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