- What chromosome did you choose?
-Chromosome 13
- State the number of genes.
-Roughly 800 genes are in chromosome 13
- Number of base pairs on the chromosome you choose?
-There are over 110 million base pairs on chromosome 13
- List one gene that is located on this chromosome?
-ATP7B
- State the normal function of the gene you listed in #4.
– Regulate copper homeostasis within the brain and liver
Nucleotide BLAST
- What is the second sequence description match for your query sequence?
-Homo sapiens CFTR (CFTR) gene, partial cds.
-Homosapien, Mac score: 217, query cover: 100% e-value: 4e-52
- What does the encoded protein do in the body?
-The encoded protein functions as a chloride channel, controlling the ion and water secretion and absorption in epithelial tissues.
- For what disease is a mutated form of this gene responsible?
-Mutations to this gene will cause cystic fibrosis. Which is the impaired folding and trafficking of the encoded protein.
- On what chromosome is the gene located?
-It is located on chromosome 7
- What species other than the Homo sapiens also have a 100% identity for this sequence
-Pongo abelii is another species besides Homo sapiens that have 100% identity
- What is the common name for the species?
-Sumatran Orangutan
- Does it surprise you that this/these species also has 100% similarity in identity?
-I’m surprised by this observation because it means we have something similar to orangutans, which I never knew about.
-
- What is the gene and species with this nucleotide sequence?
– Sapajus Apella, gene: CFTR
- What is the common name?
-Tuft Capuchin
- Are there any gaps between the two sequences?
-1/119 (0%)
- What is a gap sequence?
-A gap sequence means that there are one or more amino acids that have been deleted from the sequence.
- NM_145556: Mus musculus Tar DNA binding protein
- NM_013444: Homo Sapiens ubiquilin 2 (UBQLN2), mRNA
- NM_001010850: Homo sapiens fusion (FUS), transcript variant 2, mRNA
- KJ174530: Homo sapiens superoxide dismutase-1 (SOD-1) gene, exon 1 and partial cds
- What disease is associated with mutations of the genes?
-NM_145556 – Amyotrophic lateral sclerosis, Lou Gehrig’s Disease
-NM_013444 – Amyotrophic lateral sclerosis, Lou Gehrig’s Disease
-NM_001010850 – Amyotrophic lateral sclerosis, Lou Gehrig’s Disease
-KJ174530 – Amyotrophic lateral sclerosis, Lou Gehrig’s Disease
- What is genbank?
-Genbank is basically a genetic sequence database that possesses an archive of publicly available nucleotide sequences.
Protein BLAST
- What is cDNA?
-cDNA is complementary DNA and is reverse transcribed from an RNA sequence.
- What is the sequence match?
-Closes match is hypothetical protein PANDA_015769 (EFB18430)
- Do you see any differences between the two amino sequences?
-Yes there is a difference between the two sequences
- If you saw any, what are they?
-There is a gap between 380 and 382, with sequence one having a G at 381 and sequence two having an R at 381
- Are there any gaps in the sequence alignment?
Yes and it occurs at 381
- What gene encodes for the polypeptide you were analyzing?
-FGFR3 Fibroblast growth factor receptor 3
- What is the function of this protein?
-The function of the gene is to bind acidic and basic fibroblast growth hormones and plays a role in bone development.
- What disease is caused by a mutation of this gene?
-Mutations of this gene lead to craniosynostosis and skeletal dysplasia.
- What is the connection among: NIH, NLM, NCBI, and HHS?
-National institute of health, NIH, oversees medical and behavioral research conducted within the United States. NLM is the national library of medicine and conducts and supports research in methods of recording, retrieving, preserving, and communicating health information. NCBI is the national center for biotechnology information and oversees the creation of automated systems for storing and analyzing knowledge about biology and its related disciplines. HHS is the health and human services and they oversee the health and wellbeing of the citizens of the United States. All of these organizations are connected and work together, NIH conducts research, NLM helps store the information from experiments, NCBI creates the digital technology for accessing the information, and HHS uses this information for the wellbeing of the United States.
- What was one positive thing and one negative thing you encountered while doing this assignment
-A positive thing about this assignment is that I got to do some hands-on activities about doing research about different chromosomes, genes on the chromosomes, and finding the genes associated with DNA polymers and nucleotide sequences. A negative of this assignment is that I do not fully understand what is being provided in the description of the genes, like the graphs and interactive diagrams at the bottom, but one day I will understand what all that means.