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Evidence for conserved post-transcriptional roles of unitary pseudogenes and for frequent bifunctionality of mRNAs

Ana C Marques12*, Jennifer Tan12, Sheena Lee2, Lesheng Kong1, Andreas Heger1 and Chris P Ponting12

Author Affiliations

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

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Genome Biology 2012, 13:R102  doi:10.1186/gb-2012-13-11-r102

Published: 15 November 2012

Additional files

Additional file 1:

Rodent-specific unitary pseudogenes.

Format: XLSX Size: 13KB Download file

Open Data

Additional file 2:

Human CPO peptide complete pairwise alignments.

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Additional file 3:

Mouse unitary pseudogene transcripts (mm9) using [35].

Format: GTF Size: 20KB Download file

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Additional file 4:

Mouse unitary pseudogene transcripts (mm9) using [37].

Format: GTF Size: 51KB Download file

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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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Open Data

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 9:

Custom oligonucleotide sequences.

Format: XLSX Size: 12KB Download file

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Additional file 10:

Selected protein-coding candidates for validation of miR-185 binding in mouse and humans.

Format: XLSX Size: 12KB Download file

Open Data