Location of a gene in several chromosomes_Is that possible? - (Apr/12/2007 )

Hello, everybody
I would like to ask how often you see in mouse or mammals in general, the phenomenon of observing one gene on several chromosomes and if you think that this is possible (any example?)?

To be more specific after a microarray experiment i observe a probe set that it is annotated to hybridize to a transcript, that i found to be high and specific for one specific organ. My problem is that when i looked for potential location of this trascript on the DNA, more than one chromosomes came as a result. Is that possible?

I read that retroviral elements, like gag, pol, env have these kind of characteristics.
As a matter of fact my potentially interesting trancript has 95% of repeats and i also looked in the sequence quality file, where i show that in general the quality is high expect from a part in tha middle.

Thanks in advance,
piki

Could be pseudogenes, which are known to be spread in different chromosomes. What part of the gene is the probe from? One potential way to increase your specificity for the true gene, and remove the pseudogenes is to include an exon/intron boundary in the probe (pseudogenes don't have any) or the 5' UTR.

You may be detecting processed pseudogenes that lack introns. Swanny's suggestion would be good to discount these. Non-processed pseudogenes contain introns, though. You may also be detecting other members of a gene family whose sequences are similar to your probe's. Gene duplication events are responsible for both paralogues and pseudogenes, and the time between the duplication event and now will determine the specificity of your probe. Try making your hybridisation conditions more stringent.

Hi there,
Thanks for the help.
The point on pseudogenes is a good one.
But now listen to this....I looked up in Esbml the genomic regions that could be recognized by these probes that i have in the probe set (group of 11 probes, that are designed to recognize the 3end of an mRNA-this is somehing fixed from the company that i cannot change). So these 11 probes of 25bp each, can hybridize at least to 5 diffetrent chromosomes and also in that chromosomes at least in one chromosomal locations. The regions that the probes can hybridize are introns.
Then i checked for protential cDNAs in these regions and i ended up with a cDNA( the one onserved more often than others in diffrent regions), which has been also cloned and sequenced. The mRNA that this cDNA comes from has only one exon. So i think the point about processed pseudogenes that lack introns it has some relation to this.
However, I disigned external and internal primers for this seqeunce and i managed to amplify it. So it is something expressed. I thought that pseudogenes don't give any mRNA.
Finally i blast this sequence and all probes seperately and i found high similarity with a gag retoviral protein.
So after all this description what to you thing about the case of looking at a gag endogenous retroviral protein.
I am not sure but i think that viewing this transcript of one exon in several chrmosomes could be attributed to random insertion of retroviral elements in the mouse genome, accumlated over the years.

What do you think on this version of the story? Is it possible that i am really looking to an endogenous retroviral element?
Thanks, piki