The goal of this exercise is for you to become familiar with GenBank and Entrez for retrieving DNA and protein sequences.

1.) Use NCBI Entrez to find the cDNA sequence for the human zona pellucida glycoprotein 3 gene. What is the accession number? Is the gene a complete cDNA sequence (start and stop codon) or a partial sequence? There should be a complete cDNA sequence in the database. Is there a mouse zona pellucida glycoprotein 3 gene? What is the mouse accession number?

2.) Use NCBI Blast to compare the ZP3 human gene against the NR database? What primate sequences are available - the the chimpanzee gene? Blast the human ZP3 gene against the HTGS sequence database. Are any additional primate sequences available?

3.) Search GenBank for a protein coding gene of interest to you. Start with a general search (i.e. human sperm) and then refine the search using Boolean operators (i.e. “human sperm” or “human sperm” NOT BAC). Record how many databases files come up with each search? How did using Boolean operators help narrow down the results? Be sure to search for a gene of your interest, not just the sperm example above.

4.) Once you find a GenBank entry of interest, follow the related links. Is there a publication associated with the entry? Is there a protein sequence, nucleotide sequence, 3D structure, ect? Download the CDS (coding sequence) for the gene in fasta format.

5.) Use Blast to identify homologs for your gene of interest from other species (try to find ~6 genes). Download the CDS sequence for each gene and put in muliple-fasta formated file with your initial gene from #4 above. We will use this file to make a multiple alignment.

6.) Browse some of the organism specific databases. Find one gene and try to find it localized on the chromosome. For example, try the search ACP* in the Drosophila database or try to search for ZP3 in the human genome. What genes are nearby?