1. Gene Safari (Biological Databases)
BI420 – Introduction to Bioinformatics
Gene Safari (Biological Databases)

2. In-class lab: Find out everything possible about the interleukin 2 (IL2) gene

3. NCBI -- Entrez http://www.ncbi.nlm.nih.gov/sites/entrez

4. NCBI – Pubmed Central Literature search on IL2.
Task: What is the last article on IL2 to appear in
BMC: Genomics?

5. NCBI – Genes
Task: On what chromosome is Interleukin2 in human, mouse, rat, and chimp?
Why do the chromosome numbers differ?

6. NCBI – Protein
Task: What is the protein sequence of interleukin2?

7. NCBI – Nucleotide
How many bases long is the IL2 sequence in mouse?

8. NCBI – Homologene
Task: Name 5 species with gene homologs to IL2.

9. NCBI – Structure
Task: What does the structure of interleukin 2 look like?

10. Ensembl – Main (ensembl.org)
Searching Ensembl (Homo sapiens division) for IL2 gene

11. Ensembl – Homologues
Task: How many homologs to IL2 are available in Ensembl?

12. Ensembl – Homologues

13. Ensembl – Sequence markup

14. Ensembl – Annotation

15. Ensembl – Variations
How many SNPs are there in the vicinity of IL2?

16. dbSNP – SNPs
Find a SNP in the vicinity of IL2 on dbSNP. What is the polymorphism?

17. Gene SNPs Search SeattleSNPs collection for IL2 gene

18. Gene view
What features can be adjusted in this view?

19. Resources

20. Variation markup
Find the page showing sequence level variation

21. Genotypes
Find the page showing variation and heterozygosity.

22. Diseases
Name a disease that might result from a lack of IL2.

23. Pharmaco-genetics

24. Pharmaco-genetics

25. UCSC – Main genome.ucsc.edu: What features can you see on the
UCSC browser about IL2?

26. UCSC – Main How many exons are there?
Click on IL2 in the Refseq track. Find the alignment between human and marmoset.
How many SNPs does UCSC show in the vicinity of IL2?
Are there any known Neandertal sequences that match to this gene?