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With respect to this paper:

Identification of Host Proteins Required for HIV Infection Through a Functional Genomic Screen

In the abstract, I found names such as Rab6 and Vps35 and TNPO3. So Rab6 and Vps35 are proteins and TNPO3 is a gene? So the strings written in full caps are the genes and those strings whose just first letter is capital and the rest of the letters are small is a protein?

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  • $\begingroup$ Thats a really tough one due to the scope of things.. here's a resource as to gene nomenclature, and here's another one for proteins. $\endgroup$ – CKM Mar 11 '15 at 4:09
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Genes, conventionally, are always written in italic (e.g. SHH) which is not the case for proteins (in the former example SHH). That should allow you to tell apart gene and protein symbols (SHH vs SHH).

The capitalization of gene/protein names is a bit more in the grey area. Usually one will use capitalized gene and protein symbols for human and primates (e.g. SHH and SHH) and use non-capitalized symbols for mice and rat genes (e.g. Shh but still SHH for the protein). This is dependent on the organism and journals usually have specific guidelines on how to exactly write gene and protein symbols.

In your case the article refers to Rab6, Vps53 (not 35) and TNPO3 as proteins, if not clearly stated differently, such as the Rab6 siRNA, not only in the abstract alone but over the entire article. They use italic names for genes as shown in one of the sentence:

... and 48 hours later staining for p24, produced from the HIV gag gene...

Just as a footnote, full gene names (e.g. the sonic hedgehog gene) are not italicized.

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