Discussion of all aspects of biological molecules, biochemical processes and laboratory procedures in the field.
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I'm reading a paper on the pseudogenization of certain genes through gene conversion, but the paper contains some terminology that I'm a little new to, and neither the internet or my book seem to give a very good explanation of it. So could anyone give me a general idea about what intragenic and interlocus conversion rates represent, and exactly what a haplotype is?
Since all gene conversion occurs between two different loci, the "interlocus conversion rate" must simply mean the frequency of occurrence of gene conversion. There's no such thing as intragenic gene conversion, so I assume they are referring to the rate of recombination. A haplotype is the haploid genotype. Any single chromosome, being a single molecule, represents a haplotype. SNP A in gene 1, SNP H in gene 2, and SNP L in gene 3 on the maternal chromosome have the AHL haplotype. Maybe the paternal chromosome has SNP R in gene 2, so its haplotype would be ARL. Haplotypes don't have to be the entire chromosome, though. They are just the collection of the different polymorphisms at different loci that are all physically linked together by virtue of being on the same molecule. Gene conversion and recombination interupt haplotypes (and can create new ones). Hope this helps.
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