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Tutorial 7

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  1. Tutorial 7 Genome browser

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

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

  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. Information about the gene Sequences +Links to other databases

  8. Expression data Structural information

  9. Basic tracks

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

  11. mRNA length Protein sequence, mRNA sequence

  12. Basic tracks

  13. Zooming in can help us identifying alternative splicing events

  14. Other tracks

  15. How to download a gene sequence?

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

  17. Different parts of the gene

  18. Class work

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

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

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

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

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

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

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

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

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

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