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Genome-wide identification of pseudogenes that can be transcribed

Genome-wide identification of pseudogenes that can be transcribed. The idea. Recently shown that some pseudogenes in mouse genome are transcribed To scan the entire Mouse genome for identification of other pseudogenes that can be transcribed.

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Genome-wide identification of pseudogenes that can be transcribed

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  1. Genome-wide identification of pseudogenes that can be transcribed

  2. The idea • Recently shown that some pseudogenes in mouse genome are transcribed • To scan the entire Mouse genome for identification of other pseudogenes that can be transcribed. • To be used for further analysis like their conservation, selection etc.

  3. Materials and Methods • Downloaded the sequences of all the pseudogenes that have been shown to be transcribed (+/- 500 nucleotides). • 137 pgenes • Ran Eponine to evaluate its TSS prediction performance

  4. Eponine • Models based on position weight matrices built from Eukaryotic Promoter Database (EPD) • Elements of the models • Preference for CpG enrichment downstream • TATAAA motif around position -30 • GC rich matrices flanking the TATA box

  5. Length of the Pseudogenes

  6. Results

  7. Next • Try other TSS prediction tools (PromoterInspector, tfscan from Emboss) • Extract sequence motifs from the seqs using Gibbs Motif Sampler and MEME

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