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The Human Genome… genes on chromosomes

08 Sep

I was spending some time on stack exchange’s biology section the other day, when I saw an interesting question that someone had about how genes are arranged on chromosomes.

In answering his question, I picked up a couple of screen shots and links that I thought I should share here.

The query was included the following (paraphrased):

How are genes  arranged on the chromosome, are they were all in a single direction and how does the cell ‘know’ which direction they are in?

The best way to approach this question is to take advantage of the amazing amount of resources compiled at the NIH’s National Library of Medicine…

One fun place to start is the Genome Page, which looks like this:

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Note the 22+ X and Y chromosomes on the lefthand side of the page. Each chromosome is clickable and will take you to a chromosome page that looks like this:

Image

Map view of H. sapiens Chromosome 14

Genes are listed on the right side of this map with locations of each indicated through a set of nested maps on the left. Each gene is clickable, providing links to the research done supporting these map placements and functions of the gene/protein. You can also easily use this information to jump to the homologous gene found in any of a number of fully sequenced organisms.

Below the map of the chromosome is a legend that indicates additional information and shows how much detail that each of the maps you are observing provides.

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The amount of data is overwhelming, but you can adjust how much detail is shown in order to get the ‘lay of the land’ for a specific chromosome without getting too lost. If you have a gene you want to find, you can also pinpoint it this way and see what other genes are located nearby (and therefor ‘linked’ to your gene).

Image

huMMR gene, chromosome 10

I searched for the Human Macrophage Mannose Receptor (a protein I made antibodies against when I worked for Medarex). This gene is located on chromosome 10, as indicated by the red dots. 212 references provide sequence information about this gene and protein.

If you keep going down the rabbit hole, you can see each of the DNA sequences that were used to identify and locate this gene on the chromosome (I omitted providing an illustration of this page because it is hard to get anything from it if shrunk down of prevented piecemeal. However, you can go to this page by following this link).

Finally, you are given the links to the complete coding sequence (cds), which has the actual sequence of the gene and protein as well as notes about how it is put together. In my mind, these are the bread and butter of this site, and probably the oldest reference pages that have provided gene hunters data for several decades now. 

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Ahh, data I can use!!

 …

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A slice of sequence info

It’s easy to see this as way too much information to be useful (hence the problem of ‘Big Data’ in Biology), but it’s also extremely cool, and I have to admit that I’ve gotten just as lost in tracing the data on genes using this site as I did walking from topic to topic in the Encyclopedia when I was a kid.

So… to answer the questions posed above, you can use this site to see that many genes lie in different direction along the chromosome. Why the cell doesn’t get ‘confused’ is because the cell doesn’t try to arrange data like we do in volumes of books meant to be read in order. Each gene is regulated, transcribed and translated according to its own local rules, as if ‘unaware’ of all that’s going on around it.

 

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Posted by on September 8, 2013 in Uncategorized

 

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