1. Search for the gene encoding your target protein in Genbank. Find and paste the Genbank page for JUST the sequence of your gene (NOT the entire genome!!!) into your document. This CANNOT be the mRNA sequence, you must find the original DNA version of the gene. Also, tell us what is the common name (if there is one) for your organism. For example, for the bacterium Escherichia coli, there is no ‘common name’ other than an abbreviation (E. coli). However, the common name for Quercus rubra is a red oak tree.

Answer: The gene provided to me is notch 1 of Mus musculus . The gene is protein coding and is present on Chromosome 2. The gene id for the above said is 18128. The common name of genus Mus musculus is house mouse.

Several things to think about:
a. Note that databases do contain spelling errors, as well as different (British versus American) spellings. For example haemoglobin versus hemoglobin.

Answer: The difference is the dialect in which it is used. I, a Briton, would call it haemoglobin, whereas an American would call it hemoglobin and so the difference in spellings.

c. Note that the DNA sequence of the gene might be MUCH larger than the actual coding sequence (why is this?). You should include the entire DNA sequence of your gene. However, do NOT paste in an entire genome!! Nor should you include an entire “CONTIG” if that is where you find the sequence. (What is a contig?) You only want the sequence of your gene.
i. Underline the DNA sequence encoding the protein (ONLY the coding sequence)
ii. Highlight the start and stop codons

Answer: A Contiguous sequence of DNA formed by assembling overlapping sequenced fragments of a chromosome. A cluster of clones represents overlapping regions of the genome. A contig is a chromosome map screening the locations of that area of a chromosome where contiguous DNA segments overlap. Contig maps are significant as they provide the capability to study an entire, and often large, segment of the genome by probing a series of overlapping clones which then offer a continuous succession of information about that region.

2. For each primer you designed, use the website and the guideline...