When comparing a gene nucleotide sequences from my sample and reference from NCBI (same fungi), i found several SNPs, can i assume that it is due to different strain/variety?
When i analyze the protein sequence using geneious software, both of them actually yield the same protein sequence (due to different combination of nucleotide that yield the same amino acid), so does that mean that the protein produced from my sample will be exactly the same as the protein from the reference ?
Any opinion and suggestion is much appreciated! Thank you.
if they do both produce a protein it should be the same protein but consider also that a single base change in the coding sequence might also make a better splice site than the original splice site for that protein in which case a new truncated or elongated protein will be produced which will be very different from the original one
You will also think about codon bias, degeneracy increases SNP tolerance for protein sequence but under certain conditions, the amino acid pool around the ribosomes gain priorities for entry but some do not. So those SNPs appeared in your sequence might cause changes in the amount of protein translated or even other properties of this protein.
1. Before you make all the claims such as two SNPs are present, you need to make sure that those so-called SNPs are really SNPs, not sequecing errors.
2. Each amino acid has several 'codons' (see attached table). So, two different DNA codon sequences (in two DNA sequences) can yield two identical amino acids.
3. Since your 'protein (amino acid) sequences' are the same, so they should behave the same. This is the same situation as we 'optimize' a bacterial gene codons to make it better express in plant genome (termed 'codon usage'). In codon optimization, the some amino acid codons have been changed but the final protein (amino acid) sequence stay the same.
Dear Paul Rutland,
Splicing can occur when codon sequence change. But, Vikki already had checked these two proteins with a reference protein sequence deposited in NCBI (found with a few SNPs). So, I think that there should have no 'truncation' and 'elongation' problem in this case.
A good point Yau. I understood the question to mean that on comparison of his sequences with the reference sequences she found changes ( SNPs) in her sequences only and was assuming that as they do not code for different amino acids that they must be SNPs and not functional changes and it is true that this is a much rarer situation than the changes being simple SNPs
HI Paul,
If the SNPs are real, and if the occurrance of SNP turns the site into a specific restriction site (or vise versa, loss a restriction site due to SNP), people can acturally detect them by restriction digestion. I have seen people done so. But I am not sure if the occurrance of the SNP in the gene from Vikki has turned the site into a restriction site (or lost a RS). I think this can tell whether the SNP is real or just a sequencing error. Just a piece of info to share. See attached picture (A)***.
*** Explaination of the figure: "CYP2C9 SNP structure and sample characterization/genotyping. A: A single nucleotide polymorphism (SNP) in the CYP2C9 gene contains a C (allele 1) or T (allele 2) at the locus. The C→T alteration destroys an AvaII (GGACC) site"
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