Albinism+Discussion

Sequence and Phylogenetic Tree Analysis:

In the nucleotide sequence, a good amount of similarity between organisms is shown by the star above the sequences. In this snapshot, the human sequence 1 matches up perfectly with the human sequence 2, however, there were very slight differences at some points. The Sumatran orangutan also shows a perfect match up with human 1 and human 2, however there were slight differences. All other organisms show differences from the human nucleotide in the snapshot.
 * Nucleotide**

By looking at the neighbor joining phylogenetic tree, we can see all boot strap values are above 85, therefore, the tree shows good topology. The external nodes are the tips of the tree, or the organisms themselves. The internal nodes are points in the tree where a branch goes in two different directions. Human 1 and Human 2 are most closely related to each other, which we would expect because they are the same species. Human 1 and Human 2 are both equally related to the Sumatran orangutan. We can also say that humans are most closely related to the orangutan, out of the organisms on this tree. The human and orangutan are both equally related to the wild boar. The mouse is more closely related to the group containing the wild boar, orangutan, and human, than to the chicken. Both the Mexican tetra and the Japanese rice fish are an outgroup to the rest of the organisms. We can see that the primates are grouped together to show their similarity. The other mammals are more closely related to the primates than the fish are. The primates and mammals form a clade, while the outgroup contains the fish.

In the protein sequence, there is very little similarity between organisms, even between human 1 and human 2. There are only two instances shown in this snapshot where the sequence matches up between all organisms.
 * Protein Sequence**

By looking at the neighbor joining phylogenetic tree, we can see that all boot strap values are above 85, meaning the tree shows good topology. This is surprising because the protein sequence seems as if it does not match up. The organisms show the same relationships to each other as they do in the nucleotide phylogenetic tree.

STRING: We can see that the OCA2 protein interacts with ten other proteins, meaning that a mutation in any one of these other proteins could potentially lead to albinism. For example, of these 10 other proteins, three of them (TYR, TYRP1, and SLC45A2) are also known genes for causing oculocutaneous albinism and one of the 10 other proteins (GPR143) is a known gene for causing ocular albinism. The OCA2 protein specifically is involved in the transport of tyrosine which is needed for melanin synthesis. OCA2 "may serve as a key control point at which ethnic skin color variation is determined and is a major determinant of brown and/ or blue eye color."

By looing at the "evidence view" we can see where the information comes from that links the proteins together. All of the edges coming off of the OCA2 node are yellow meaning that all of the evidence comes from text by carefully studying patterns. By looking at the "confidence view" we can see how confident researchers are in the linkage information they discovered. All edges coming from the OCA2 node, and going to other nodes, show the highest level of confidence, meaning researchers are confident in their work.

Protein Data Bank: A better understanding of the tyrosinase protein was obtained by observing the crystal structure of the protein (4J6U). Protein function is directly affected by protein structure. Tyrosinase contains a dinuclear copper center. These copper ions are essential for the activity of tyrosinase. All tyrosinase molecules, across different species, have a copper center.

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