We are going to try to find the map position and adjacent genes of
the human calcitonin receptor gene.
Go to the Entrez Gene main page.
Click on the 'Preview/Index' button. Change the pulldown menu in the 'Add Term(s) to Query or View Index:' section
to say "Organism" and enter "human" into the textbox. Click the 'AND' button. Human is now added
to your query in the main query box at the top of the page. Now change the pulldown menu
to "Gene/Protein name" and enter "calcitonin receptor" into the text box. To make sure that we
are adding the right phrase, click on 'Index'. The calcitonin receptor keyword has 41 matches to
entries in the Entrez Gene database.
Show RECEPTOR KEYWORD image
Alternatively, if you already know that the symbol for the calcitonin receptor is CALCR, you can
enter that under the "Gene name" keyword.
Click 'AND' to add the term to the query line, and then click 'Go'.
If you chose to input the words calcitonin receptor, you will get 5 matches, which all
include the words calcitonin and receptor in the description of that locus. The calcitonin
receptor that we are looking for is the first match, CALCR (GeneID: 799). If you just used CALCR as input,
you will get a page with just that single match.
Show CALCR RESULTS image
To view all the information about the calcitonin receptor, we now click on the CALCR link.
This brings us to the Entrez Gene page about this gene. There is a huge amount of information
available in Entrez Gene, ranging from the gene sequence (and its products, to map information,
to functional information, to interaction information. There is a list of links at the right of
the page which link to other databases in Entrez with information about this gene. For example,
the SNP link will take you to the list of SNPs annotated in the calcitonin receptor gene.
Since we want to find the map position and adjacent genes for the calcitonin receptor, we scroll
down to the Genomic context section. Here, the location is given as 7q21.3.
Show CALCR LOCATION image
To find adjacent genes, click on the 'See CALCR in MapViewer' link. If the gene has been
included in a genomic annotation, this takes you to a page which indicates the
location of the gene on the
relevant chromosome (in this case, chromosome 7). If available, it will also show schematics
of the syntenic region for other organisms. In this case, we have regions displayed for cow, chicken, mouse, rat and pig.
If there are many genomes available, it may be difficult to view all the information simultaneously, so you can hide some maps by clicking the 'X' button at the top of the relevant map.
Show CALCR MAP VIEW image
To see the genes adjacent to CALCR, click on the zoom box to the left of the page. The further
out you zoom, the more genes you will see (although, if you zoom out too much, you will no longer be able to guarantee that the genes you see are actually adjacent since as you zoom out, more and more genes are shown, and they can't all be fitted onto the same page.
You can get a table view of all the genes in the pictured region of the chromosome by clicking on
the 'Table View' link for the 'Genes On Sequence' map. This will give you a list not only
of the genes that were shown on the chromosome diagram, but also all those which could not be
shown. The table view also gives you exact nucleotide start and stop positions for each gene (where known) and gene orientation on the chromosome.
Show CALCR ADJACENT GENES TABLE image
Thus, we can say that CALCR is mapped to 7q21.3, and is mapped to the
same region as the CDK6, SAMD9, TFPI2, GNGT1 and GNG11 genes.
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