{"id":206,"date":"2022-12-10T04:46:21","date_gmt":"2022-12-10T04:46:21","guid":{"rendered":"https:\/\/sites.wp.odu.edu\/kelsysmithbiol294\/?p=206"},"modified":"2022-12-10T04:46:26","modified_gmt":"2022-12-10T04:46:26","slug":"genome-assignment","status":"publish","type":"post","link":"https:\/\/sites.wp.odu.edu\/kelsysmithbiol294\/2022\/12\/10\/genome-assignment\/","title":{"rendered":"Genome Assignment"},"content":{"rendered":"\n

Chromosome Maps
1. Which Chromosome did you choose? I choose chromosome 12.
2\/3. How many number of genes and base pairs on the chromosome? 130 million base pairs and over
1600 genes.
4. List one gene which is located on this chromosome? PXR1.
5. State the normal Function of the gene listed in previous question? The PXR1 receptor is important
for the import of enzymes into the peroxisomes, if this is not functioning properly the peroxisomes
can not use the enzymes to carry out their functions.
Introduction to BLAST
6. What is the top sequence description math for your query sequence? Homo sapiens CFTR promoter
region (LOC111674463) on chromosome 7.
7. Is this a sequence for a protein or another part of the gene? I believe this is a sequence for a protein this
region represents the promoter and proximal regulatory regions of the cystic fibrosis transmembrane
conductance regulator (CFTR) gene.
8. What does the encoded protein associated with the above sequence do in the body? Pathogenic variants
of the CFTR gene are responsible for broad phenotypic spectrum characterized by malfunction of some
exocrine tissues, with an autosomal recessive mode of inheritance.
https:\/\/www.sciencedirect.com\/science\/article\/abs\/pii\/S0929693X20300440?via%3Dihub
9. A mutated form of this gene is responsible for a well-studied disease what is that disease? Cystic
fibrosis.
10. On what chromosome is the gene located? Chromosome 7.
11. What species (state the scientific name) other than HOME SAPIENS also has a 100% identity for this
sequence? Pongo pygmaeus abelii.
12. What is the common name for this species? Sumatran Orangutan.
13. Does is surprise you that this species also has a 100% similarity in identity? It does not surprise me
that the Sumatran orangutan has a 100% similarity in identity because I know from previous biology
classes that we share about 97% of the same DNA with orangutan.
14. Describe the first match that has less than 100% query cover but is not predicted or homo sapiens,
state scientific and common names. Saimiri boliviensis boliviensis, common name: Bolivian squirrel
monkey.
15. How many gaps occur between the two sequences? 1\/119(0%)
16. What is a gap in the sequence alignments? A gap in sequence alignments is when one or more amino
acid residues have been deleted from the sequence, or an insertion in the next sequence. <\/a><\/p>\n\n\n\n

<\/p>\n\n\n\n

For each state what the gene is
17. NM_14556? TAR DNA binding protein, gene type: protein coding. Enables RNA polymerase II cis-
regulatory region sequence-specific DNA binding activity and pre-mRNA intronic binding activity.
Product is the majority of RNA sequences.
18. NM_013444? UBQLN2, mainly involved in protein homeostasis.
19. NM_001010850? FUS gene this gene encodes a multifunctional protein component of the
heterogeneous nucleoprotein complex, helps promote cell growth.
20. KJ174530? SOD1 gene this gene The protein encoded by this gene binds to zinc and copper ions and
is one of two isozymes responsible for destroying free superoxide radicals in the body. Produces enzyme
called superoxide dismutase.
21. What disease is associated with mutations in the genes referenced above? ALS or Lou Gehrig\u2019s
disease.
22. What is GENBANK? GenBank is an open access sequence database collection of public nucleotide
sequences and their protein translations.
Introduction to Swiss-Prot to Study Protein Sequences
23. What is cDNA how can we obtain cDNA in the lab? cDNA is complementary DNA, which is DNA
synthesized from a single stranded RNA template. It is obtained by mRNA molecules treated with the
enzyme reverse transcriptase which is used to make a DNA copy of mRNA.
24. Using the same program you used in the introduction to blast above what is the sequence match?
Homo sapiens partial HBB gene for hemoglobin beta chain, exon 1, isolate 04593664.
ACATTTGCTTCTGACACAATTGTGTTCACTAGCAACCTCAAACAGACACCATGGTGCATC
25. What is an open reading frame(ORFs)? Open reading frames are defined as spans of DNA sequence
between the start and stop codons.
26. All of the proposed open reading frames (highlighted in red) start with the amino acid M. From what
you know about polypeptide4s, what is M? Methionine, an essential amino acid in humans it helps with
the metabolism and health of many species including humans.
27. Which 5\u2019 to 3\u2019 frame is most likely to be an open reading frame?
MVHLTPEEKSAVTALWGKVNVDEVGGEALG I choose this one because it is the longest.
Amino Acid Sequence Comparisons
28. Do you see any differences between the two amino acid sequences? Yes there is a difference.<\/p>\n\n\n\n

<\/p>\n\n\n\n

29. If you saw a difference what were they? There was the absence of asterisks on the last line of the
sequence, the absent of a S on one of the sequences.
30. What is the function of this protein? FGFR3 is a gene that is involved in cell division, cell
maturation, and the formation of new blood vessels.
31. What human disease is caused by a mutation in this gene? Mutations in this gene lead to
craniosynostosis and multiple types of skeletal dysplasia.
32. I believe by completing this assignment I learned how to read genome sequences more clearly than
before by having this hands on assignment. I also learned the diseases of some mutations in genes.


Citations
https:\/\/www.cancer.gov\/publications\/dictionaries\/cancer-terms\/def\/fgfr3-gene
https:\/\/www.genome.gov\/genetics-glossary\/Copy-DNA<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"

Chromosome Maps1. Which Chromosome did you choose? I choose chromosome 12.2\/3. How many number of genes and base pairs on the chromosome? 130 million base pairs and over1600 genes.4. List one gene which is located on this chromosome? PXR1.5. State… Continue Reading →<\/a><\/p>\n","protected":false},"author":20498,"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:\/\/sites.wp.odu.edu\/kelsysmithbiol294\/wp-json\/wp\/v2\/posts\/206"}],"collection":[{"href":"https:\/\/sites.wp.odu.edu\/kelsysmithbiol294\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/sites.wp.odu.edu\/kelsysmithbiol294\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/sites.wp.odu.edu\/kelsysmithbiol294\/wp-json\/wp\/v2\/users\/20498"}],"replies":[{"embeddable":true,"href":"https:\/\/sites.wp.odu.edu\/kelsysmithbiol294\/wp-json\/wp\/v2\/comments?post=206"}],"version-history":[{"count":1,"href":"https:\/\/sites.wp.odu.edu\/kelsysmithbiol294\/wp-json\/wp\/v2\/posts\/206\/revisions"}],"predecessor-version":[{"id":207,"href":"https:\/\/sites.wp.odu.edu\/kelsysmithbiol294\/wp-json\/wp\/v2\/posts\/206\/revisions\/207"}],"wp:attachment":[{"href":"https:\/\/sites.wp.odu.edu\/kelsysmithbiol294\/wp-json\/wp\/v2\/media?parent=206"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/sites.wp.odu.edu\/kelsysmithbiol294\/wp-json\/wp\/v2\/categories?post=206"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/sites.wp.odu.edu\/kelsysmithbiol294\/wp-json\/wp\/v2\/tags?post=206"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}