Part I. You are interested in sequence conservation and function of the androgen receptor (AR) across vertebrate species. The first thing you will want to do is collect protein sequences of the AR from these selected species: Homo sapiens (human), Pan troglodytes (chimp), Mus muculus (mouse), Canis familiaris (dog), Gallus gallus (chicken), Danio rerio (zebrafish). To find these protein sequences I set up the search of the protein database with the search terms "androgen receptor" "AR" and then the appropriate genus and species. Choose the hit with the longest amino acid sequence, likely to be the complete sequence of the protein. Prepare a summary of your comparison as if you were making a presentation to a class (OK, a ClustalOmega with some text as the minimum). Be sure to include 1. An analysis of the molecular evolution of this gene across vertebrate species. What is the variation in sequence by region of the protein likely to mean? 2. Anything intriguing about particular "poly-amino-acid repeats" you see? That is, the familiar "poly-Q" that is the site of disease alleles in huntingtin, or any other case of a repeating amino acid? (I personally noted 3 such regions; this is open-ended but your score on this section will depend on the quality of your assessment and presentation) Part II. Clearly, there is a region of the AR that is highly conserved across vertebrates! Does this encode one or more functional domains that might also be conserved in female hormone receptors? (In particular, receptors for the female sex hormones estrogen and/or progesterone.) In other words, are there domain features that maybe overlap in both male and female hormone receptors?! Hint: the starting point for Part II will be a protein BLAST using a region of the human AR protein sequence where the sequence conservation with other AR receptors begins: look for CLICGDEASGCHYG=>to the carboxyl end of the protein as the query (the text box for submitting the search). Limit the search to the proteins of the species you used in Part I! Now look for "hits" that are female sex hormone receptors. Note that hits will be found in especially the progesterone receptor in distant vertebrate relatives! How would I personally close out Part II? With an interesting ClustalOmega that compares the complete human AR protein squence with the complete female receptor sequences of some other vertebrate species. Again, open-ended, your choice of who to compare, but make it interesting and include some interpretation.
Part I. You are interested in sequence conservation and function of the androgen receptor (AR) across vertebrate species. The first thing you will want to do is collect protein sequences of the AR from these selected species: Homo sapiens (human), Pan troglodytes (chimp), Mus muculus (mouse), Canis familiaris (dog), Gallus gallus (chicken), Danio rerio (zebrafish). To find these protein sequences I set up the search of the protein database with the search terms "androgen receptor" "AR" and then the appropriate genus and species. Choose the hit with the longest amino acid sequence, likely to be the complete sequence of the protein. Prepare a summary of your comparison as if you were making a presentation to a class (OK, a ClustalOmega with some text as the minimum). Be sure to include 1. An analysis of the molecular evolution of this gene across vertebrate species. What is the variation in sequence by region of the protein likely to mean? 2. Anything intriguing about particular "poly-amino-acid repeats" you see? That is, the familiar "poly-Q" that is the site of disease alleles in huntingtin, or any other case of a repeating amino acid? (I personally noted 3 such regions; this is open-ended but your score on this section will depend on the quality of your assessment and presentation) Part II. Clearly, there is a region of the AR that is highly conserved across vertebrates! Does this encode one or more functional domains that might also be conserved in female hormone receptors? (In particular, receptors for the female sex hormones estrogen and/or progesterone.) In other words, are there domain features that maybe overlap in both male and female hormone receptors?! Hint: the starting point for Part II will be a protein BLAST using a region of the human AR protein sequence where the sequence conservation with other AR receptors begins: look for CLICGDEASGCHYG=>to the carboxyl end of the protein as the query (the text box for submitting the search). Limit the search to the proteins of the species you used in Part I! Now look for "hits" that are female sex hormone receptors. Note that hits will be found in especially the progesterone receptor in distant vertebrate relatives! How would I personally close out Part II? With an interesting ClustalOmega that compares the complete human AR protein squence with the complete female receptor sequences of some other vertebrate species. Again, open-ended, your choice of who to compare, but make it interesting and include some interpretation.
