Research
Evidence for conserved post-transcriptional roles of unitary pseudogenes and for frequent bifunctionality of mRNAs
1 MRC Functional Genomics Unit, University of Oxford, Department of Physiology, Anatomy and Genetics, South Parks Road, Oxford, OX1 3PT, UK
2 University of Oxford, Department of Physiology, Anatomy and Genetics, South Parks Road, Oxford, OX1 3PT, UK
Genome Biology 2012, 13:R102 doi:10.1186/gb-2012-13-11-r102
Published: 15 November 2012Additional files
Additional file 2:
Human CPO peptide complete pairwise alignments.
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Additional file 3:
Mouse unitary pseudogene transcripts (mm9) using [35].
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Additional file 4:
Mouse unitary pseudogene transcripts (mm9) using [37].
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Additional file 5:
Codon substitution pattern of unitary pseudogenes. The coding substitution pattern unitary pseudogene (green) is significantly smaller (***P < 0.001) than that of protein-coding transcript fragments (blue) with matching size. Only transcripts with a sequence allowing reliable prediction of an open reading frame (94 and 722 unitary pseudogenes and protein-coding transcripts, respectively) were considered.
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Additional file 6:
Unitary transcribed pseudogene and protein-coding expression. (a, b) Median normalized expression (log 2 fragments per kilobase of exon per million read) (a) and maximum tissue specificity (maxTS) (b) across six mouse adult tissue unitary transcribed pseudogenes (green) and protein-coding genes (blue).
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Additional file 7:
Expression level and tissue specificity of transcribed unitary pseudogenes.
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Additional file 8:
Tissue expression correlation between mouse and human loci. Distribution of mouse-human expression correlation (Pearson) between 1,000 mouse-human random pairs of non-orthologous protein-coding genes (grey) and mouse unitary pseudogene protein-coding orthologs (green). The P-value associated with the comparison between these distributions is 0.23.
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Additional file 10:
Selected protein-coding candidates for validation of miR-185 binding in mouse and humans.
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