1. Conservation in Evolution
-HOX genes Vestigial structures

2. Please answer 2 pre-lab questions

3. You are the manager of a new animal food supply company
You are the manager of a new animal food supply company. You need to find out if vitamin C needs to be included in the food for dogs, cows, cats, mice, and guinea pigs
???
Hypothesis?

4. Part A--Is the GULO gene present in various mammals?

6. This is the nucleotide sequence found in Gene #1
This is the nucleotide sequence found in Gene #1. Do NOT alter any of the parameters used on this page.
This setting indicates that all the databases will be searched.
Selecting the human database + transcript would only yield similar sequences found in humans. By selecting others all of the genomes in the BLAST database will be searched.
Click “BLAST.”

7. The turquoise bar represents the gene sequence you entered into BLAST.
The red bars represent the top results in the query and how well aligned each result is with the gene sequence you uploaded.

8. To see an alignment for a particular hit on the search, click the red bar and then click Alignment. You’ll jump down the page to see it.
Click “DISTANCE TREE OF RESULTS” to see a cladogram of these results. NOTE: This is now at top of page (as of fall 2014).

9. Click the “accession” ID for a specific sequence to learn more about that sequence.
This is the species and genus name that matches the gene of interest. Phenotype is sometimes identified as well.
The score (bits) refers to how many gaps or substitutions are associated with the sequence. The higher the score, the more similar the alignment.
The E value is the likelihood that a match occurred purely by chance. The lower the value, the better the match.

10. Under the BLAST table is a full report of each result.
This describes the number of identical nucleotides found in this sequence.
This part shows the exact pattern of alignment.
The top line is the gene of interest and the bottom line is the matching sequence.
This indicates the species the aligned sequence is found in and the gene/phenotype.

11. How to view a tree of your results: Scroll to the top and click [Distance tree of results]

12. Part B—Does human GULO gene produce a function protein?

14. Questions
Why do you think that primates have lost the ability to produce Vitamin C?
Explain why the GULO gene in humans may be considered vestigial.
What can you infer about the GULO BLAST results between humans and chimps?
Would you give Vitamin C supplement to dogs, cows, cats, mice, and guinea pigs?

15. Part 3: Search the databases and create your own phylogeny
Pick 1 protein (aqaporins, ATP synthase, catalase, etc)
Minimum 15 organisms and the proteins—FASTA format
1 page conclusion