Worksheet: NCBI See the handout on our website. Name: Shayna Russell GSI & Sect # Dale 108 Station # 5
1. Name three databases other than Entrez Gene that you can use to find information related to your gene. What kind of information is available on these databases? Genbank protein database BLAST gene information OMIM articles about the gene 2. a) What are the score and E-value for your top hit? Score = 66 and e-value = 1x10-11 b) What is the percent identity between your query and top hit? 100% c) How many amino acids align? 20 3. a) What is the official symbol and full name of your gene? PSEN1 presenilin 1 b) What specific biochemical processes does the protein encoded by your gene perform? Alzheimer's disease (AD) patients with an inherited form of the disease carry mutations in the presenilin proteins. These disease-linked mutations result in increased production of the longer form of amyloid-beta. Also, it is thought that the presenilins are involved in the cleavage of the Notch receptor, such that they either directly regulate gammasecretase activity or themselves are protease enzymes. c) Name one fact from the published literature relevant to your gene. The majority of early-onset cases of familial Alzheimer's disease are linked to mutations in two related genes, PS1 and PS2, located on chromosome 14 and 1, respectively. 4. a) List the disease(s) associated with your gene. Alzheimers Disease b) Describe how mutations in a single gene could cause multiple diseases. A single gene mutation causing any of the various types of mutations, missense, nonsense, or frameshift could have severe consequences with protein production, and inherently cause disease. A single gene could provide the genetic information for multiple mRNAs producing many different proteins; many proteins can come from one gene. If there are many protein production failures, there could be multiple diseases arising from one genetic mutation.
c) Briefly describe a disease associated with your gene. Include clinical features like age of onset when available. Describe new or medical terms in your own words. Alzheimers Disease is the most common form of dementia. It is diagnosed around age 65, although it could be found earlier or later. As of September 2009, there are 35 million plus people worldwide affected by AD. It is a degenerative, terminal disease that has symptoms that are mistaken for age issues or stress manifestation. 5. a) How one can genomic sequence encode multiple protein products? One gene produces multiple mRNAs due to alternate splicing of exons in the final product. Different mRNAs make different proteins. b) List the genes located near yours. RBM25 and NUMB c) Record the gene map locus of your gene. chromosome: 14; Location: 14q24.3 6. a) What is the GenBank record number of the mRNA for your gene? NM_000021 b) How many base pairs are in the mRNA sequence? 6107bp 7. a) Which reading frame gives the correct protein? 53 Frame 3 b) How many amino acids are in the virtual sequence? 375 Amino Acids c) What is the molecular weight of the protein? 42082 g/mol d) Name one function of an untranslated region. It separates the different exons so that multiple mRNAs can be made through alternative splicing. 8. a) After deleting a block of nucleotides from the mRNA sequence of your gene, describe the mutated protein product in terms of number of amino acid residues and molecular weight compared to the wild type protein. 384 AA and 43087 g/mol b) When you make a single base pair substitution, why are silent mutations so common? There are 3 nucleotides for every AA code; there are multiple nucleotide groups that code specific AA.
c) List the amino acid change for a missense mutation using proper notation (for example, A223V signifies that the 223rd amino acid residue has been changed from alanine to valine.) V420G d) How can an insertion or deletion in the mRNA not affect the protein sequence? If there is an irregularity in an untranslated region, entron, it will not affect the protein because it is spliced out. 9. a) Discuss the phenotype of mutations in your gene in another organism.
In the Norway Rat (Rattus norvegicus) may mediate retinal lamination and pattern formation.
b) How different is the mouse ortholog of your gene? 92.7% c) Why does d increase across the species listed, while dN/dS hits a plateau? D increases due to speciation and changes in genetic information. Dn hits a plateau because if there were an increasing amount of nonsynonymous it would create a new species or the organism would die from having messed up genes. d) Which would you expect to have a higher dN/dS, orthologs or paralogs? Why? I would expect orthologs to have a higher ratio of non-synonymous switches because they have gone through much evolution. Paralogs are on the starting path to evolution; it is a duplication of the original gene with some mutations.