Genome-wide identification of pseudogenes that can be transcribed

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