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
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
RefSeq id
Other names
Summary on the gene
Sequences
Genomic position
Gene length
mRNA length
Protein sequence,mRNA sequence
Zooming in can help us identifying alternative splicing events
How to download a gene sequence?
position
Group and track
“Known genes” table
Choose “sequence”
Clade, genome, assembly
Different parts of the gene
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?