Tutorial 7 Genome browser. Free, open source, on-line broswer for genomes Contains ~100 genomes, from nematodes to human. Many tools that can be used.

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Tutorial 7 Genome browser

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

Genome browser

How to find a gene of interest?

clade genome Genome assembly location Gene name OR

Lets take a look at the gene

Sequences +Links to other databases Information about the gene

Expression data Structural information

Basic tracks

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

mRNA length Protein sequence, mRNA sequence

Basic tracks

Zooming in can help us identifying alternative splicing events

Other tracks

How to download a gene sequence?

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

Different parts of the gene

Class work

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

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

3. How many exons does the CFTR gene have?

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

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

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

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

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

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

10. Are there microsatellites on the CFTR gene?