{"id":45,"date":"2024-04-22T21:14:59","date_gmt":"2024-04-22T21:14:59","guid":{"rendered":"https:\/\/student.wp.odu.edu\/aadam040\/?p=45"},"modified":"2024-04-22T21:14:59","modified_gmt":"2024-04-22T21:14:59","slug":"genome-assignment","status":"publish","type":"post","link":"https:\/\/student.wp.odu.edu\/aadam040\/2024\/04\/22\/genome-assignment\/","title":{"rendered":"Genome Assignment"},"content":{"rendered":"\n

Chromosome Maps<\/strong>
1. What chromosome did you choose?
I chose Chromosome 19.<\/mark>
2. State the number of genes on the chromosome you chose.
Chromosome 19 contains over 1700 genes.<\/mark>
3. State the number of base pairs on the chromosome you chose.
Chromosome 19 contains 60 million base pairs.<\/mark>
4. List one gene that is located on this chromosome.
A gene that is located on this chromosome is Jak3.<\/mark>
5. State the function of the gene you listed in #4. It is important that you state the
physiological function of the gene product you select, not the disease listed for the gene.
Jak3, or Janus kinase 3, is a gene that plays a significant role in providing instructions for making a protein essential for the immune system’s development and operation. It functions by transmitting chemical signals from outside the cell to the nucleus, which helps regulate the growth and maturity of specific white blood cells like T cells and B cells. One disease linked to this gene is severe combined immunodeficiency (SCID), which seriously affects the immune system’s ability to fight infections. (JAK3 Gene: MedlinePlus Genetics, n.d.)<\/mark>
Introduction to Nucleotide BLAST<\/strong>
6. What is the second sequence description match for your query sequence?
The second sequence description match for the query sequence is: Homo sapiens CFTR (CFTR) gene, partial cds.<\/mark>
7. What does the encoded protein do in the body?
The encoded protein acts as a chloride channel, unlike other proteins in its family. This regulates ion and water movement in the epithelial tissues. Its activation involves phosphorylation of regulatory domains, ATP binding and ATP hydrolysis. This suggests that it plays an important role in maintaining tissue ion and water balance.<\/mark><\/p>\n\n\n\n

8. For what disease is a mutated form of this gene responsible?
Mutations in this gene can lead to cystic fibrosis (DeltaF508) which can result in impaired folding and trafficking of the encoded protein.<\/mark>
9. On what chromosome is the gene located?
This gene is located on chromosome 7<\/mark>.
10. Choose a species (state the scientific name) other than Homo Sapiens that also has a 100% identity for this sequence?
I chose Pongo abelii.<\/mark>
11. What is the common name for this species?
The common name for this species is Sumatran orangutan<\/mark>
12. Does it surprise you that this species also has a 100% similarity in identity? Why or why not?
I was not surprised by this because humans and chimpanzees share a lot of similarities in their DNA, which explains the close relation.<\/mark>
13. Find the first meath that has less than 100% similarity identity. Click on the description to
answer this question.
13a. What is the genus and species with this nucleotide sequences?
The genus and species with these nucleotide sequences is Nomascus leucogenys.<\/mark>
13b. What is the common name?
The common name is Northern White-Cheeked Gibbon.<\/mark>
13c. Are there any gaps between the two sequences (the one you originally submitted and one that has less than 100% query cover)?
Both of these sequences have 0 gaps (0\/120).<\/mark>
14. What is a gap in sequence alignments?
In sequence alignment, gaps pop up when DNA or protein sequences don’t align smoothly, leading to the use of padding or null characters to match similar residues. These gaps crop up due to insertions or deletions in the sequences, causing mismatches.<\/mark>
15. For each, state what the gene is (#15-18). NM_145556
Mus musculus TAR DNA binding protein (Tardbp), transcript variant 1, mRNA<\/mark>
16. NM_013444
Homo sapiens ubiquilin 2 (UBQLN2), mRNA<\/mark><\/p>\n\n\n\n

17. NM_001010850
Homo sapiens fusion (involved in t(12;16) in malignant liposarcoma) (FUS), transcript variant 2, mRNA<\/mark>
18. KJ174530
Homo sapiens superoxide dismutase-1 (SOD-1) gene, exon 1 and partial cds<\/mark>
19. What disease is associated with mutations of the genes referenced in #15-#18? What is a \u201ccommon name\u201d of the disease?
The common name of the disease is ALS.<\/mark>
20. What is GenBank?
GenBack is a vast database storing publicly accessible nucleotide sequences from over 300,000 organisms, which are identified at the genus level or lower. These sequences are primarily sourced from submissions by individual research labs and bulk submissions from large-scale sequencing initiatives. (Benson et al., 2009)<\/mark>
Introduction to Protein BLAST<\/strong>
21. What is cDNA?
Complementary DNA, often abbreviated as cDNA, refers to synthetic DNA molecules generated by transcribing a specific messenger RNA (mRNA).<\/mark>
22. What is the sequence match?
The sequence match is beta-globin [Homo sapiens].<\/mark>
23. Do you see any difference between the two amino acids?
I found two differences between the amino acids, there was a gap and a dash in query 779.<\/mark>
24. If you saw a difference, what were they?
I found a gap and a dash.<\/mark>
25. Are there any gaps in the sequence alignment?
Yes, there were gaps in the sequence alignment.<\/mark>
26. What gene encodes for the polypeptide you were analyzing?
This gene encoded a member of the fibroblast growth factor receptor (FGFR) family.<\/mark>
27. What is the function of this protein?
The function of this protein is to bind to acidic and basic fibroblast growth hormones, which plays a role in bone development and maintenance<\/mark><\/p>\n\n\n\n

28. What human disease is caused by a mutation in the gene?
Skeletal dysplasia is caused by a mutation in this gene.<\/mark>
29. What is the connection among the following: NIH, NLM, NCBI, AND HHS?
The link between the National Institutes of Health (NIH), the National Library of Medicine (NLM), the National Center for Biotechnology Information (NCBI), and the Department of Health and Human Services (HHS) is their shared involvement within the U.S. government to promote medical research. These institutions collaborate to advance biomedical knowledge and facilitate public health initiatives.<\/mark>
30. What was one positive thing and one negative thing you encountered while doing this assignment?
One positive thing I found while working on this assignment was discovering the GenBank database, where I could explore a ton of reliable information on nucleotide sequences from over 300,000 organisms. One negative thing I encountered was learning about the FGFR3 gene. It turns out that mutations in this gene can slow down bone formation and lead to skeletal dysplasia. Learning about genetic conditions like this is challenging and sometimes uncomfortable, but it’s important to understand them for medical research and improving patient care.<\/mark><\/p>\n\n\n\n

References<\/strong>
Benson, D. A., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J., & Sayers, E. W. (2009). GenBank. Nucleic Acids Research, 38(suppl_1), D46\u2013D51. https:\/\/doi.org\/10.1093\/nar\/gkp1024<\/p>\n\n\n\n


JAK3 gene: MedlinePlus Genetics. (n.d.). Medlineplus.gov. Retrieved April 22, 2024, from https:\/\/medlineplus.gov\/genetics\/gene\/jak3\/#:~:text=Normal%20Function&text=Signals %20relayed%20by%20the%20JAK<\/p>\n\"Facebook\"<\/a>\"twitter\"<\/a>\"linkedin\"<\/a>\"instagram\"<\/a>\"flickr\"<\/a>\"foursquare\"<\/a>\"mail\"<\/a>","protected":false},"excerpt":{"rendered":"

Chromosome Maps1. What chromosome did you choose?I chose Chromosome 19.2. State the number of genes on the chromosome you chose.Chromosome 19 contains over 1700 genes.3. State the number of base pairs on the chromosome you chose.Chromosome 19 contains 60 million… Continue Reading →<\/a><\/p>\n","protected":false},"author":25108,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":"","wds_primary_category":0},"categories":[1],"tags":[],"_links":{"self":[{"href":"https:\/\/student.wp.odu.edu\/aadam040\/wp-json\/wp\/v2\/posts\/45"}],"collection":[{"href":"https:\/\/student.wp.odu.edu\/aadam040\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/student.wp.odu.edu\/aadam040\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/student.wp.odu.edu\/aadam040\/wp-json\/wp\/v2\/users\/25108"}],"replies":[{"embeddable":true,"href":"https:\/\/student.wp.odu.edu\/aadam040\/wp-json\/wp\/v2\/comments?post=45"}],"version-history":[{"count":1,"href":"https:\/\/student.wp.odu.edu\/aadam040\/wp-json\/wp\/v2\/posts\/45\/revisions"}],"predecessor-version":[{"id":46,"href":"https:\/\/student.wp.odu.edu\/aadam040\/wp-json\/wp\/v2\/posts\/45\/revisions\/46"}],"wp:attachment":[{"href":"https:\/\/student.wp.odu.edu\/aadam040\/wp-json\/wp\/v2\/media?parent=45"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/student.wp.odu.edu\/aadam040\/wp-json\/wp\/v2\/categories?post=45"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/student.wp.odu.edu\/aadam040\/wp-json\/wp\/v2\/tags?post=45"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}