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Question: [Beginners question]: What determines the number at the end of a gene? (example: CTX-M-15, CTX-M-55, CTX-M-28)
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What do the numbers at the end of a gene stand for?

Do they represent the location, or something else?

ADD COMMENTlink 4.6 years ago lumramabaja • 10 • updated 4.6 years ago seidel 6.8k
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The numbers at the end of gene names reflect arbitrary conventions chosen by the person(s) who named them. It is different for different organisms because different people work on different organisms, and different people work on those organisms in different ways. In yeast, for example, genes (open reading frames along the chromosome) were originally named based on what chromosome they were on, which arm of the chromosome, their chromosomal order away from the centromere, and what strand of the DNA. So, a name such as YFL039C is on the Left arm of the 6th chromosome (F is the 6th letter of the alphabet), and is the 39th reading frame on the Crick strand. However, this gene also goes by ACT1, and genes named this way are often chosen based on a mutant hunt, and reflect the order of characterization from a screen. Obviously human genes are not named like yeast genes, nor are flatworm genes. There are often good reasons for this (there may be no assembled chromosomal sequence for your organism, no named chromosomes, etc.).

There is no general convention that is broadly applied, so people derive their own. And since people working with a system usually (!) try to make sensible choices in terms of coming up with conventions, if you see some order (as is evident in your examples) it suggests some kind of ordering - but you simply have to discover or enquire of the creators, because there are no rules that apply across the board.

ADD COMMENTlink 4.6 years ago seidel 6.8k
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Something else that this question/answer highlights, is the benefit of using unique identifiers for a given biological entity (gene, protein, splice form etc.) - e.g. there are two human proteins in UniProt with the name "COX2" http://www.uniprot.org/uniprot/P00403 http://www.uniprot.org/uniprot/P35354, but they can be distinguished in UniProt using their distinct accession numbers i.e. P00403 and P35354. If you're talking to someone about the protein you're working on, you could reduce ambiguity by referring it e.g. by both 'name' and accession number, so that you can both be sure you're talking about the same entity.

ADD REPLYlink 4.6 years ago
aidan-budd
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If they were proteins it would be the order that they where classified. If I remember correctly genes are the same way. I am sure if I am wrong some one will correct me.
ADD COMMENTlink 4.6 years ago skbrimer • 530

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