Fisher Pricing
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Re: Fisher Pricing
For identifying exons, my favorite database is Ensemble Genome Browser:
http://uswest.ensembl.org/index.html" onclick="window.open(this.href);return false;
Go to the link, then select "Horse" from the drop down menu at the top left. In the box next to the menu, type the name of the gene you want (like EDNRB) and click go. You will get a Results Summary, and click on the link that says "Gene" under "By Feature Type", then click "Equus Caballus". (I have no idea why they have you click so many things.) That will bring up a link to the gene. Click on that, and you'll get to a summary page for the gene. In the box-type thing at the top, click on the link under "Transcript ID".
Now you're in a page where you can look at the transcript of the gene. There's lots you can do--see the menu at the left of your screen. You'll see under "sequence" that it says "Exons" and gives you the number of them. If all you want is to know the number of exons, you can quit right now! Or you can click on Exons and it will actually show you the sequence of all of them. You might care about that if you want to see exactly where a mutation occurs, for example.
Re: Fisher Pricing
LOL - It's not like the video from Jurassic Park!
I can search using a wildcard and get too many hits, but I don't understand why it will let you search on heart disease on a human but not lethal White on a horse - maybe just a matter of getting the right words in, but the visual of it as a graph is not one I'd have thought of. It is helpful though for us visual learners....
The ones that have no mappings found - does that mean they've not been mapped yet?
Re: Fisher Pricing
It's actually much more useful to search by genes rather than by phenotype. It can only give you the location of and information on known genes...it is a database put together so that researchers can easily find info on genes they're interested in. So when I think that a particular gene might cause some phenotype I'm interested in, I can pull the sequence for that gene, note where the exons are, and design assays to sequence the coding regions of the gene. Then, when I have the sequence, Ensembl can tell me the protein sequence and show me where mutations I've found would have an effect.
I suggested it to lilith because she was looking for information on genes known to cause particular coat colors...MC1R, ASIP, MATP, EDNRB, KIT...all of those will be easily searchable.
Re: Fisher Pricing
Sorry to necro an old thread but I thought it made more sense than starting a new one. I can't seem to find MCR1 and MAPT has 4 different transcripts with different numbers of exons, am I being dense?
On a thankyou so much for that site note horsegen I have found the rest of the information I wanted there :)
If anyone hears a sniff of info about an agouti paper on brown or a paper on pearl comming out I will dance :)
Re: Fisher Pricing
Oh really blonde moment, MCR1 isnt there but oddly enough the correct order of letters MC1R is :oops:
Still kinda confused by 4 transcripts for MAPT ranging from 13 to 17 exons though.
Edited to add - Ensembl has 2 options under KIT one says there are 8 Exons on KIT while the deuncentralstation website shows 21, and the other has 3 transcripts that range from 20-22 exons I am confused.
Re: Fisher Pricing
Obviously horsegen will give you a better answer, but in the meantime you could go to
[url]http://genome.ucsc.edu/cgi-bin/hgGatewa…]
select "horse" under genome, and enter the name of the gene in the "position or search term" box.
For example if you search for EDNRB the first hit you get is endothelin B receptor precursor, the gene mutated in frame. If you click on the first hit, you get a diagram of the gene. This stuff -<-<-<- is intron, fat line is exon, and skinnier line is untranslated part of exon (not spliced out like intron but doesn't code for protein).
Hope this helps.