[rat-forum] RE: Chromosome 7 and Ohno's Law?

ggopinat nobody at no-reply.mcw.edu
Thu Mar 20 08:52:02 CST 2003


Hi-

You have not indicated which comparison maps you have looked at.

But if you do use VCMap from RGD website ( http://rgd.mcw.edu/VCMAP/)
you can find the following profile for syntenic regions. 

Rat X compared to human and mouse:
syntenic regions are located on only the X chromosomes in mouse and human.

http://rgd.mcw.edu/tools/vcmap/vcmap.cgi?Ver=5.0_HS&Species=Rat&Chr=21&MapName=maps

If you click on the link below you will get the VCMap predictions and known genes. You can see that all the visible rat genes have their homologs located on X chromosomes in the other two species:

http://rgd.mcw.edu/tools/vcmap/vcmap.cgi?MapName=Rat+VirtualMap+5.0_HS&Chr=21&FirstPos=0&SecondPos=845

Interestingly, if you look at Human X chr syntenic profile at:
http://rgd.mcw.edu/tools/vcmap/vcmap.cgi?Ver=5.0_HS&Species=Human&Chr=X&MapName=maps

you can see that while in mouse it is localized to X chromosome, in rats, the syntenic regions are dispersed in: chromosomes X, 01 and 05.

The list of predicted and known genes in these three species too, as expected, corresponds to this observation:

http://rgd.mcw.edu/tools/vcmap/vcmap.cgi?MapName=Human+VirtualMap+5.0_HS&Chr=X&FirstPos=1&SecondPos=350

Finally, in mouse, the syntenic profile looks like:

http://rgd.mcw.edu/tools/vcmap/vcmap.cgi?Ver=5.0_HS&Species=Mouse&Chr=X&MapName=maps

where syntenic regions are localized to X chromosome (in human ) and dispersed in 01,04 and X chromosomes.

The predicted and known genes match this observation:

http://rgd.mcw.edu/tools/vcmap/vcmap.cgi?MapName=Mouse+VirtualMap+5.0_HS&Chr=X&FirstPos=0&SecondPos=200

.From these, you get a preliminary answer to your question: Is it really true that the rat X is so different from ouse and human X? 
The answer inferred from  VCMap:  Apparently so.

But, VCMap observations do not indicate any syntenic relationship between Rat chr 07 and human/mouse chr X, in any direction. One way to resolve the location of individual genes, I think, would be to use UCSC genome browser tool at:
http://genome-test.cse.ucsc.edu/cgi-bin/hgGateway?org=rat

This great tool maps individual genes to the genome of the selected (in this case rat) species.

You may first want to prepare the list of genes from human/mouse X chromosome and use this browser to map them on rat genome to see whether they really are located on rat chr 07.  You can use RGD or LocusLink resources to get the gene symbols/related IDs for all the three species.

If you want more help, please do not hesitate to write to the Rat Genome Database (http://rgd.mcw.edu/contact/index.shtml). The members of RGD bioinformatics and curation team will only be happy to assist you in your search.

- Gopal
Curator,
RGD



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