Human Genome Resources
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Find the chromosomal location of a gene using the genome view.

  Sample User Question
Analysis/Comments
Flow Chart
Step By Step Guide
Additional Notes
 

Sample User Question back to top

Find the chromosomal location of the gene EDN1 (endothelin 1).

Analysis/Comments back to top

It can be very useful to the researcher to identify the chromosomal location of a gene, particularly when a gene has been initially studied by mRNA/cDNA techniques. Now that the full genomic sequences of many organisms are available, the process of obtaining the complete genomic sequence of a gene is much easier. This allows localization of introns, promoters, and other flanking sequences. Often, the expression of a gene is impacted by the sequences surrounding it. Further, by using the available maps, the researcher can identify neighboring genes, markers, mapped disease loci, ESTs, and SNPs that are localized near or within the target gene.

Flow Chart back to top

  1. MapViewer Search/Browse Page - This is a basic search. An advanced search with additional options is also available.

  2. Entrez Gene - It is often useful to look up the gene in Entrez Gene first, in order to learn more about it and make certain that you are choosing the correct gene.

Step By Step Guide back to top

MapViewer Search

  • Start with a simple keyword search for "endothelin."
  • The correct hit is the gene "endothelin 1" (EDN1).
  • Notice that you find hits from both the NCBI reference assembly and the Celera assembly. Try using the assembly dropdown menu on the top of the page to select the NCBI's reference assembly and eliminate the others. Click on Find once you've selected the correct assembly. Also note that you find multiple entries of type gene. Look through them to find the one that says "endothelin 1" and has the Map Element "EDN1"
  • You have the option of clicking on the map element "EDN1" or on one of two maps, the Genes_Cyto and the Genes_Seq. You can also click on the number of the chromosome EDN1 is on (Chromosome 6) in the graphical display. Each choice will result in a slightly different display in the Map Viewer, but that display can be modified to your choice later.
Entrez Gene

  • Search for human Endothelin in Entrez Gene: endothelin[title] AND human[organism]
  • Find and view the record for EDN1. How far down the list is it?
  • Find the "Genomic context" section.
  • Click on the link to the MapViewer to activate it ("See EDN1 in MapViewer")

Additional Notes back to top

Be cautious of using numbers in gene names; MapViewer may confuse them with a chromosome number.


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Revised 07/12/2007