Biological Databases Exercises
You have an EMBL entry with the accession number: X03225, and you are required to extract information about this gene and the corresponding protein. Search the relevant databases and follow the necessary links to answer the questions below for 2 marks each.
1. What organism is this gene from? What is the taxon ID of the genus level of this organism?
2. Write down the description of the gene and its official HGNC gene symbol.
3. What is the corresponding Ensembl gene identifier for this gene and its chromosome location?
4. Does the gene undergo any alternative splicing? If so, how many different protein coding transcripts does it produce according to Ensembl?
5. Identify and list the potential orthologous genes in mouse and dog. How many transcripts does the orthologous mouse gene produce?
6. List the corresponding UniProt protein accession number for this gene, and its protein name.
7. Does the protein undergo any post-translational modifications, if so name one?
8. Is this gene product involved in any diseases, if so, which disease?
9. List one publication that investigates alternative splicing of this gene
10. In the last reported publication in the entry [56], van Rossum EFC reports on a polymorphism in this protein. Based on this author's publications in PubMed, would you say he is an expert on this protein? List one of his related publications.
11. Where is this protein located in the cell? Does this differ between isoforms?
12. What is interesting about the protein's isoform Beta-2 in terms of introns?
13. What amino acid change has been noted as a natural variant at position 23 of the protein sequence and what is the dbSNP identifier?
14. Has this gene appeared in any publicly deposited microarray experiments? If so, describe in one sentence one of the experiments (e.g. which conditions/cell types/disease states etc. were studied).
15. How many protein interaction partners does this protein have in the MINT protein-protein interaction database?