The DNA sequence that has been emailed to you is a mutant cDNA sequence derived from an organism that displays an altered phenotype to wild type organisms.
Using appropriate bioinformatic software and databases determine the following.
(1) What species is the wild type sequence derived from (give Linnaean and common species names)?
(2) What protein does the wild type sequence code for?
(3) Align the mutant and wild type cDNAs and answer the following questions.
a. How do the mutant and wild type DNA sequences differ?
b. What is the nucleotide position of the change in the mutant?
(4) Use appropriate software to deduce the protein sequence that the mutant cDNA encodes and align it with the wild type. Answer the following questions.
a. What is the codon position of the change in the mutant sequence?
b. What amino acid substitution results from the mutation?
(5) Briefly comment on the effect you think the mutation might have on the protein function using the results obtained in part 4.
(6) Use appropriate bioinformatic resources to find the most closely related human protein homolog of the wild type sequence.
(i) What is the percentage similarity between the wild type protein and the human protein?
(ii) Use appropriate literature to find out the subchromosomal location of the human gene encoding this protein and how many exons it has.
(7) Select 15 orthologs of NADH dehydrogenase subunit 3 protein sequence from an evolutionary diverse cross section of bilateria species including human and align these using Clustal. Show the Clustal alignment output obtained. Use appropriate journal literature to find features and amino acids and highlight these in the alignment. Comment on the evolutionary conservation of these in less than 150 words.
(8) Using the data obtained in question 7 select an appropriate protein sequence as an outgroup and draw a phylogenetic tree. Comment on whether mammals, birds, amphibians and fish are monophyletic.
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