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Published online before print November 21, 2007, 10.1101/gr.6859308
Genome Res. 18:77-87, 2008
©2008 by Cold Spring Harbor Laboratory Press; ISSN 1088-9051/08 $5.00
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Letter

Features of 5'-splice-site efficiency derived from disease-causing mutations and comparative genomics

Xavier Roca1, Andrew J. Olson1, Atmakuri R. Rao1,6, Espen Enerly2,3, Vessela N. Kristensen2,3, Anne-Lise Børresen-Dale2,3, Brage S. Andresen4,5, Adrian R. Krainer1, and Ravi Sachidanandam1,7

1 Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA; 2 Department of Genetics, Institute for Cancer Research, Rikshospitalet-Radiumhospitalet Medical Centre, Montebello 0310, Oslo, Norway; 3 Faculty of Medicine, University of Oslo, Norway; 4 Department of Human Genetics, Aarhus University, Aarhus 8000C, Denmark; 5 Aarhus University Hospital, Sygehus 8000N, Denmark

Many human diseases, including Fanconi anemia, hemophilia B, neurofibromatosis, and phenylketonuria, can be caused by 5'-splice-site (5'ss) mutations that are not predicted to disrupt splicing, according to position weight matrices. By using comparative genomics, we identify pairwise dependencies between 5'ss nucleotides as a conserved feature of the entire set of 5'ss. These dependencies are also conserved in human–mouse pairs of orthologous 5'ss. Many disease-associated 5'ss mutations disrupt these dependencies, as can some human SNPs that appear to alter splicing. The consistency of the evidence signifies the relevance of this approach and suggests that 5'ss SNPs play a role in complex diseases.

6 Present address: IASRI, New Delhi 110012, India.

7 Corresponding author.

E-mail sachidan{at}cshl.edu; fax (516) 367-8389.

[Supplemental material is available online at www.genome.org.]

Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.6859308


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