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"Common Characteristic of Sequences of Ribosomal Protein Gene Introns in Saccharomyces cerevisiae"

"Common Characteristic of Sequences of Ribosomal Protein Gene Introns in Saccharomyces cerevisiae". Michal Wolff Advisors: Prof. Martin Kupiec (TAU) DR. Ron Unger. Why? -there is something special about them. Number of intron containing genes = 242

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"Common Characteristic of Sequences of Ribosomal Protein Gene Introns in Saccharomyces cerevisiae"

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  1. "Common Characteristic of Sequences of Ribosomal Protein Gene Introns in Saccharomyces cerevisiae" Michal Wolff Advisors: Prof. Martin Kupiec (TAU) DR. Ron Unger

  2. Why? -there is something special about them • Number of intron containing genes = 242 • Number of ribosomal protein intron containing genes = 105 = 43% • Number of ribosomal protein genes = 140 • Ribosomal protein gene introns in the yeast are larger • On average the ribosomal intron length is 405 while the non-ribosomal is 151

  3. Why?

  4. What? - The sequence homology, consensus, all the intron, areas in the intron, nucleotides.

  5. What? - Secondary structure

  6. Where? - Ares lab Yeast Intron Database

  7. How? – Perl & Bioinformatics Tools • Perl - originally designed for text processing • EMBOSS – sequence alignment • mfold – secondary structure • BLAST – all against all

  8. How? – Data Analysis • Microsoft Excel • charts • sort • graphs • χ² - expected – non-ribosomal behavior

  9. Results – upstream the intronglutamine

  10. Results – downstream the intronlysine

  11. Results – in the intron • Hexamers -The biggest difference (30-40%) is in the AU rich sequences for the ribosomal sequences. • Octamer - The ribosomal introns had more poly U octamers then the non-ribosomal ones.

  12. Results - in the intron • 10-20 nucleotides upstream from the 3’ end the ribosomal introns have a high probability to contain a polyU sequence. • The area between the branchpoint and the 3’ splice site is around 30 bases long. • UUU,AUU,UUA

  13. Results - in the intron

  14. Results – in the branchpoint-3’

  15. Results – in the branchpoint-3’ • common subsequences • A-polyU • polyU • polyU-A • U subsequence with a mutation – • In the area – more in the ribosomal introns • In the whole intron – more in the non-ribosomal

  16. Results – in the branchpoint-3’

  17. Conclusion • The branchpoint-3’ splice site area might be homologues – all against all blast. • The difference between ribosomal and non-ribosomal may be connected with a polyU sequence. • The ribosomal gene introns and the non-ribosomal gene introns are not similar.

  18. Thanks for listening!

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