1. Tutorial 7 Genome browser

2. Free, open source, on-line broswer for genomes Contains ~100 genomes, from nematodes to human. Many tools that can be used to analyze genomic data Genome browser

3. http://genome.ucsc.edu/ Genome browser

4. How to find a gene of interest?

5. clade genome Genome assembly location Gene name OR

6. Lets take a look at the gene

7. Sequences +Links to other databases Information about the gene

8. Expression data Structural information

9. Basic tracks

10. RefSeq id Other names Summary on the gene Sequences Genomic position Gene length

11. mRNA length Protein sequence, mRNA sequence

12. Basic tracks

13. Zooming in can help us identifying alternative splicing events

14. Other tracks

16. How to download a gene sequence?

17. position Group and track “Known genes” table Choose “sequence” Clade, genome, assembly

18. Different parts of the gene

19. Class work

20. 1. In which chromosome can you find the CFTR gene in human?

21. 2. In which chromosome can you find the CFTR gene in mouse?

22. 3. How many exons does the CFTR gene have?

23. 4. Suggest a way to discover exons without searching for mRNA

24. 5. Which animo acid(s) will join the protein if the termination codon will be mutated?

25. 6. Which genes are close to CFTR on chromosome 7?

26. 7. What is the orientation of the gene? Plus or minus?

27. 8. download the promoter area of the CFTR gene (1000 bp)

28. 9. How many polyadenylation sites are known on the CFTR gene?

29. 10. Are there microsatellites on the CFTR gene?