NCBI Gene: Finding the Gene in the Genome
NCBI Gene is a portal to information about a gene from different sources.
This tutorial shows how to find where the gene is located in the genome.
Click Next for an example scenario.
Example Scenario
According to a lab report, my patient has a deletion of chromosome 8q (nts 111137305-119897611).
How do I find out what genes are involved?
Step 1: Search for Organism
Type (or copy and paste) human[orgn] into search box and click Search.
This tells the database to search for sequences where the organism is identified as human.
You should retrieve around 190,000 results.
Step 2: Filter by Chromosome Location
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Click Show additional filters from the menu on the left side of the results page.
Step 2: Filter by Chromosome Location
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Select Chromosome locations and click the Show button.
Step 2: Filter by Chromosome Location
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Click more... under Chromosome locations.
The Chromosome locations menu appears.
Step 2: Filter by Chromosome Location
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Select an organism by typing or scrolling to Homo sapiens.
You have been given the information that the deletion is:
- Chromosome 8
- nt range from 111137305 to 119897611
Enter this information into the boxes at the bottom of the window.
Click Apply.
You should retrieve around 180 results.
Step 3: Sort by Chromosome
You now have the list of all genes reported on chromosome 8, in the nt range from 111137305 to 119897611 bases. This is the data you were seeking.
Change the Display Settings to Sort by: Chromosome.
This sorts your search results in the order of the genes on the chromosome, from p-arm end to q-arm end.
Another Way to Search (Direct Search)
You can also do a direct search in Gene with this query (copy and paste into the search box):
human[orgn] AND 8[chr] AND 111137305:119897611[chrpos]
You should retrieve the same (about 180) results.
Step 4: Save and Share Results
If you would like to save this search:
- Use the Save search link below the search box (sign into your NCBI account to create an alert), or
- Save results with the Send to: drop down menu (right side of the screen).
Conclusion
In summary, to find all the genes in a particular location in a chromosome:
- Step 1: Search the Organism
- Step 2: Filter by Chromosome Location
- Step 3: Sort by Chromosome
- Step 4: Save or Share Results
For additional help, visit NCBI Gene Help Resources.
Congratulations! You've completed this exercise on using NCBI Gene to find the gene in the genome.
You can now close the NLM Navigator windows.