Tutorial 7

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

Genome browser

http://genome.ucsc.edu/

Genome browser

How to find a gene of interest?

clade

genome

Genome assembly

location Gene nameOR

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?