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New to genes, and have to read literature to find candidate genes for a particular study. I cannot for the life of my understand if all genes are placed into either the "nuclear" or "mitochondrial" category...are there more categories? Some are easy, like cytochrome subunit genes are always written as "mitochondrial" and then rhodopsin are written as nuclear...but other genes like ATPase etc. don't have those descriptions. When I search online further, it still does not clarify, so I am wondering now if there are just more categories to this?

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  • $\begingroup$ Welcome to SE Biology. It will help people to answer your question if you note what resources you are using to confirm whether you are dealing with a genomic or mitochondrial gene. The databases vary in where they report this information. $\endgroup$ – Michael_A Nov 26 '16 at 2:52
  • $\begingroup$ I am still very early on in my research, so I am going through journal articles dealing with genes that differ in species found in one habitat vs. another. As of right now my only resource are journal articles. I am not sure what you mean by genomic or mitochondrial gene...i.e. the COI genes were obtained from genomic DNA, so I am not sure how to answer that. $\endgroup$ – CuriousDude Nov 26 '16 at 2:58
  • $\begingroup$ I don't know what you mean by COI genes. I understood your question as a query about the location of genes; genome or mitochondrial genome. If you want to know the likely subcellular location of proteins, your question should ask about proteins and not genes. $\endgroup$ – Michael_A Nov 26 '16 at 3:15
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    $\begingroup$ biology.stackexchange.com/questions/40331/… Would this be helpful? $\endgroup$ – Malhar Khushu Nov 26 '16 at 3:19
  • $\begingroup$ Ahh okay, sorry this is me developing my vocabulary properly. I did mean the location of genes, nuclear or mitochondrial. I meant to use COI as an example where in the literature they always just outright call it mitochondrial. Then I come across something like ATP1 which is just called a membrane protein - so I didn't know if that meant just nuclear membrane or potentially mitochondrial membrane. $\endgroup$ – CuriousDude Nov 26 '16 at 3:29
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I have limited my answer to refer to humans, but the advice generalises to other eukaryotic cells.

In human cells, almost all of the genes that code for proteins are located in the genome, which is located in the nucleus. The mitochondria have their own genetic material, however, the mitochondrial genes only encode for 14 proteins. The answer to this question also notes the existence of extrachromosomal circular DNA. There are also a number of proteins (1192) that are verified to exist but their genomic location is currently unconfirmed.

In your comments you mention ATP1 and note that it is called a membrane protein. The gene is located on chromosome 19 in the nucleus. The protein, that is encoded by the gene, can be found in a variety of places, including the nucleus and also the mitochondrion. The gene for Cytochrome c oxidase subunit 1 (CO1/COX1) is encoded in the mitochondrial genome and it localises to the inner membrane of the mitochondrion.

The links in this answer all point to Uniprot. This is what I use to get an idea of the basic functions of proteins. The database includes information genes but its primary purpose is to describe proteins and their functions. The information is roughly correct, it is not perfect. It includes a many species and links to a number of tools, including the gene ontology which attempts to characterise proteins using a controlled vocabulary.

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