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Open Access Research article

Frequency of intron loss correlates with processed pseudogene abundance: a novel strategy to test the reverse transcriptase model of intron loss

Tao Zhu12 and Deng-Ke Niu12*

Author Affiliations

1 Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Xinjiekouwai Street 19, Beijing 100875, China

2 Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Xinjiekouwai Street 19, Beijing 100875, China

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BMC Biology 2013, 11:23  doi:10.1186/1741-7007-11-23

Published: 5 March 2013

Additional files

Additional file 1:

Phylogenetic tree of all mammalian species used in this study.

Format: DOC Size: 63KB Download file

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Additional file 2:

Correlation of intron loss and abundance of processed pseudogenes. (A) Percentage of mouse and rat genes producing processed pseudogenes. (B) Comparison of the abundance of processed pseudogenes and mRNA lengths between intron-lost genes and no-intron-lost genes in mice. (C) Comparison of lost introns and mRNA lengths between parents of processed pseudogenes and other genes in mice.

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Additional file 3:

Imprecise intron loss events mediated by genomic deletion. (A) Sequence alignments around seven lost introns. (B, C) Another case of intron loss that may be mis-recognized as imprecise deletion.

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Additional file 4:

Comparison of expression levels between intron-lost genes and no-intron-lost genes.

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Additional file 5:

Processed pseudogenes obtained from http://pseudogene.org webcite.

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Additional file 6:

16,241 intron-containing orthologous genes between mice and rats.

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Additional file 7:

Details for lost introns.

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Additional file 8:

List of intron-lost genes and no-intron-lost genes in mice and rats.

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