NCBI Gene: Where is the gene located in the genome?

Open https://www.ncbi.nlm.nih.gov/gene

in another browser window to work through this tutorial side by side.

Introduction

NCBI Gene is a portal to gene-centered information from different sources. 

This tutorial shows how to answer the question:

Where is the gene located in the genome?

NOTE: Use the Single-page view to do this lesson or the database Sort may not work properly.

Single-page view

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

1. Type human[orgn] into search box and click Search

This tells the database to search for the organism

Tip

You should retrieve around 60,000 results 

Step 2: Filter by chromosome location and nt range

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2. Click Show additional filters from the menu on the left side of the results page.

show additional filters

Step 2: Filter by chromosome location and nt range

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Select Chromosome locations and click the Show button:

chromosome locations

Step 2: Filter by chromosome location and nt range

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Click more under Chromosome locations.

more

The Chromosome locations menu appears.

Step 2: Filter by chromosome location and nt range

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chromosome location selection box

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, so enter this into the boxes at the bottom of the Window.

Click Apply.

You should retrieve around 80 results. 

Step 3 - Sort by Chromosome

3. 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

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.

chromosome arms

Another way to search (direct search in Gene)

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]

Long-hand chromosome search

You should retrieve the same (about 80) results.

4. Save and Share Results

4. Save the search using the link below the search box.  You will need to sign into your NCBI account to create an alert.

OR 

Save results with the Send to: drop down menu (right side of the screen).

save search

 

Conclusion

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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.

Conclusion

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You have reached the end of the tutorial for the question Where is the gene located in the genome?

NCBI Gene Help Resources 

Continue to Chapter 5. What are the Reference genomic, transcript and protein sequences for the gene?

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