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Originally published in Science Express on 6 May 2004
Science 28 May 2004:
Vol. 304. no. 5675, pp. 1321 - 1325
DOI: 10.1126/science.1098119
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Reports

Ultraconserved Elements in the Human Genome

Gill Bejerano,1* Michael Pheasant,3 Igor Makunin,3 Stuart Stephen,3 W. James Kent,1 John S. Mattick,3 David Haussler2*

There are 481 segments longer than 200 base pairs (bp) that are absolutely conserved (100% identity with no insertions or deletions) between orthologous regions of the human, rat, and mouse genomes. Nearly all of these segments are also conserved in the chicken and dog genomes, with an average of 95 and 99% identity, respectively. Many are also significantly conserved in fish. These ultraconserved elements of the human genome are most often located either overlapping exons in genes involved in RNA processing or in introns or nearby genes involved in the regulation of transcription and development. Along with more than 5000 sequences of over 100 bp that are absolutely conserved among the three sequenced mammals, these represent a class of genetic elements whose functions and evolutionary origins are yet to be determined, but which are more highly conserved between these species than are proteins and appear to be essential for the ontogeny of mammals and other vertebrates.

1 Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
2 Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
3 ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia.

* To whom correspondence should be addressed. E-mail: jill{at}soe.ucsc.edu (G.B.); haussler{at}soe.ucsc.edu (D.H.).

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