An earlier search in the human, mouse and rat genomes for sequences that are 
100% conserved in orthologous segments and > or = 200 bp in length identified 
481 distinct sequences. 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 elements. 
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.