Base change in genes/ mutations

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liswil
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Base change in genes/ mutations

Post by liswil » Wed Jul 02, 2008 11:08 am

Hello,
I have a question concerning mutations/ base change. In an publication they have found point mutations in some genes. They have listed up the name on the genes, the base change they found in them, in addition to the amino acid change the mutations result in. For example they say that the base change occurs in 811 T>C which leads to the amino acid change C271R. I want to find where in the gene this mutation is. Is it in a specific exon? Where do I search for that kind of problems? What do they mean with the number 811? :?: Do they count from the start of the gene? Do you usually exclude the introns when you want to describe where you found the mutation? Do some of you recommend a specific data base where I can find this kind of information about the gene sequences? I really hope some of you will help me! :)
Best, Lise

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canalon
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Post by canalon » Thu Jul 03, 2008 1:17 am

Usually the accession number to the sequence is given in the paper, and the number refers to that sequence. The number for the amino acid is given with respect to the translated protein.
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victor
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Post by victor » Thu Jul 03, 2008 1:44 am

Well, I can say that it happens in a specified exon which they'd make their own sequence (and the mutation happens in nucleotide 811 from T into C in their own numbering version). In the case, it's mentioned that the mutation yields an amino acid change (misense mutation). So, this mutation happens in the exon, yielding a change from cysteine into arginine in amino acid position 271.
I can think like this: cystein is encoded by codon UGC and UGU, thus the DNA sequence are TGC and TGT respectively. While arginine is encoded by AGG, AGA, CG(GACU); thus the DNA sequence are AGG, AGA, and CG(GACT) respectively. If the mutation cause changes from T into C, and the resulting amino acid changes from Cys into Arg, then the mutation is located at the first letter of the triplet:
TGC (Cys) ---> CGC (Arg)
TGT (Cys) ---> CGT (Arg)

About the sequence data, I think it's written maybe in the supplemental material of the publication.
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liswil
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Re: Base change in genes/ mutations

Post by liswil » Thu Jul 03, 2008 6:42 am

Thank you for responding my query. Now I understand that I have to get the accession number or the sequence data from the author of the publication. It says in the paper that primers for PCR are available upon request, but I thougt I could find my own primers just to now their mutation findings (811 T>C and so on...). I have been in contact with the auther, but they have problems finding the data... :shock: This is the first time I am using this forum - but not the last time! Thank you! :D

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