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1. OMIM Exercises
1. How many entries are there in the OMIM database that contain information about genes on the Y
chromosome?
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Click the “limits” tab
Tick Y chromosome
Press Go
Results page has 46 entries
2. How many entries are there that contain the term “Hypertension”? How does it affect the results if
the search is limited to those entries where “hypertension” is in the title field only?
Part 1:
 Hypertension as search term
 Press Go
 Results page has 366 entries
Part 2:
 Click the “limits” tab
 Tick Title
 Press Go
 Results page has 28 entries
3. The NOS3 gene appears to be related to hypertension. What other disorders has this gene been
linked to?
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Either choose the NOS3 entry from the results list from question 2 or use NOS3 as a search
term
Click on the entry +163729 to get the NOS3 details
Diseases mentioned in the summary at the top of the page:
i. Coronary spasms
ii. Alzheimer disease, late-onset
iii. Hypertension, pregnancy-induced
iv. Hypertension, resistant to conventional therapy
4. What is the chromosomal location of the NOS3 gene?
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7q36
5. How many GenBank entries are there for the NOS3 gene, and how many of these are mRNA
sequences?
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Click on the G link on the left hand side of the page
This shows 18 entries
9 are mRNA
2. SRS and Genome Browser Exercises
1. Using SRS, search the UniProtKB database for SerpinA3. How many results are there? How many
of these are human protein sequences? If there are any sequences that look as though they are not
SerpinA3, can you explain why they are coming up in your search?
Part 1:
 Choose UniProtKB from library page
 Go to Query page
 Use SerpinA3 as search term in ‘all text’
 Results page shows 23 entries
Part 2:
 Use SerpinA3 in ‘all text’
 Add human in ‘organism name’
 Results page shows 3 entries
Part 3:
 Second entry is for Ubiquitin cross-reactive protein precursor
 Click to look at the entry in more detail
 SerpinA3 mentioned in comments section: “Targets include SERPINA3G/SPI2A, JAK1,
MAPK3/ERK1 and PLCG1.”
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Searching for SerpinA3 in ‘gene name’ with human in ‘organism name’ gives 2 relevant results.
2. Using Ensembl, search for the gene annotation for human SerpinA3. You should get 2 matches – a
gene from Ensembl and a gene from Vega. Answer the following questions from each entry in turn to
compare them.
a. How many exons does the SerpinA3 gene have?
Ensembl: 9
Vega: 5
b. What is the length of the transcript?
Ensembl: 2646bp
Vega: 1576bp
c.
What is the length of the protein?
Ensembl: 429 amino acids
Vega: 445 amino acids
3. Use NCBI Map Viewer to search for human SerpinA3.
a. What are the two genes immediately adjacent to SerpinA3?
SerpinA5 is upstream, LOC390503 is downstream.
b. Is the SerpinA3 gene located on the positive or negative strand of the DNA?
Positive strand (downwards arrow in orientation column)
4. Use the UCSC browser to find SerpinA3.
a. What is the subcellular location of SerpinA3?
Extracellular
b. What is the main site of synthesis?
Liver
c. How many exons are there?
5
d. What is the length of the protein?
423 amino acids