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

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

NCBI -- Entrez http://www.ncbi.nlm.nih.gov/sites/entrez http://www.ncbi.nlm.nih.gov/sites/gquery?itool=toolbar

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

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

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

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

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

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

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

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

Ensembl – Homologues

Ensembl – Sequence markup

Ensembl – Annotation

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

dbSNP – SNPs Find a SNP in the vicinity of IL2 on dbSNP. What is the polymorphism? http://www.ncbi.nlm.nih.gov/projects/SNP/

Gene SNPs Search SeattleSNPs collection for IL2 gene http://pga.mbt.washington.edu/

Gene view What features can be adjusted in this view?

Resources

Variation markup Find the page showing sequence level variation

Genotypes Find the page showing variation and heterozygosity.

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

Pharmaco-genetics

Pharmaco-genetics

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

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?