Daniel Smith
Posts: 970
Joined: Sep. 2007
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| Quote (JAM @ Oct. 16 2007,21:44) | | Quote (Daniel Smith @ Oct. 16 2007,18:44) | | My prediction was that exactly the same frame shift will occur - so I'm guessing it will be #1. |
Wrong! Completely different, nonhomologous gene. Would you like to see the data?
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Yes, I would be interested in seeing that. | Quote |
| Quote | | Quote | | P.S. Did you check out the mouse vs. rat sequences yet? |
I've been there several times. Let me give you a blow by blow of my most recent visit:
I want to see the mouse and rat genomes side by side so I go to VISTA and select the Mouse Feb. 2006 genome as a base genome, then I figure the best place to start is at the beginning,... |
Probably not. There are repeats, called telomeres, at the ends. |
I'd like to see those - just for my own curiosity. | Quote |
| Quote | | so I select ch1:1-1000000 and click GO, I get an error saying "No such contig. or chromosome". This is a bit confusing. How can the mouse genome not have a chromosome 1? |
There's probably no contig for that region. The repeats make it complicated. |
What is "contig"? | Quote |
| Quote | | So then I select ch2:1-1000000 and get the same error. Ch3 and 4 give the same results. So then I decided to try the Rat June 2003 and go with the default chr10:10000001-10100000, which then gives me some results. |
Yes, because you're in the middle, away from the junk at the ends that you thought would be conserved.
| Quote | | I click on Browse alignment so I can see the coding (the Cs, As, Ts, and Gs). I zoom in on a spot and when I put my mouse over the Rat code, it gives the number 10034062, when I cursor over the Mouse genome in the same spot, it gives the number 5312532. I'm assuming these are the numbers for the position of that site within the chromosome. |
Correct, but it's not the same chromosome number. Why do you think that I tried to explain synteny to you?
| Quote | | So, (if that's the case) it's not showing me the Rat and Mouse genomes, side by side - starting at position 10000001 and ending at position 10100000. If it was, they'd both give the number 10034062 - wouldn't they? |
No, because contra your hypothesis, they aren't colinear. The autosomes are numbered according to their length, not their content. In fact, the place in which you were looking on rat chr10 has been inverted, and lines up with a bit of mouse chromosome 16, as VISTA tells you. These relationships are illustrated here:
http://www.softberry.com/synt_pl....chr_2=*
and in a different way, as well as conversely, here:
http://www.informatics.jax.org/reports/homologymap/mouse_rat.shtml
| Quote | | So, like I said, I'm not sure what I'm looking at and I'm not sure the correct way to use the site, but it doesn't appear to be giving me what I was looking for. |
Since your hypothesis is incorrect, what you're looking for doesn't exist. Rat chromosome 10 doesn't align with mouse chromosome 1, it aligns with chunks of mouse chromosomes 16, 17, and 11. Those represent translocations and inversions from the past. Therefore, none of those breakpoints have been conserved, and your hypothesis is incorrect. But all you had to do was look at the graph to see that between rat and mouse, there are big regions of no conservation between the pink lumps that are 80-100% conserved.
| Quote | | So, if you have something you want me to see, you'll have to specifically tell me what it is I'm looking at and how it reflects on my hypothesis. |
Why are there gaps between the pink lumps that are the conserved sequences when we align orthologous sequences from two species within the same lineage? |
Thank you for the explanations and the data. The second page you cited really helped me understand what I was looking at (and not understanding) in the VISTA program.
Let me ask you this:
The rat genome appears to be a re-arrangement of the mouse genome, so how do we know that the "junk" (as you call it) wasn't rearranged in similar manner?
Does the VISTA program check for this?
Or does it only compare genes?
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"If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance." Orville Wright
"The presence or absence of a creative super-intelligence is unequivocally a scientific question." Richard Dawkins
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