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NCBI general protein information

I am still a little confused on how Genbank annotates its genes.

For example, if I look at this gene: LOC110845878 [ Folsomia candida ], NCBI will list it as uncharacterized.

However, if you scroll down and look at the general protein information, it calls it a pyruvate kinase PKLR.

So in this case, it would be fair to just consider the LOC110845878 uncharacterized gene as pyruvate kinase PKLR?

ncbi
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updated by GenoMax GenoMax • written by 100dustedclays • 100dustedclays

About LOC gene designation (From LINK):

Symbols beginning with LOC. When a published symbol is not available, and orthologs have not yet been determined, Gene will provide a symbol that is constructed as 'LOC' + the GeneID. This is not retained when a replacement symbol has been identified, although queries by the LOC term are still supported. In other words, a record with the symbol LOC12345 is equivalent to GeneID = 12345. So if the symbol changes, the record can still be retrieved on the web using LOC12345 as a query, or from any file using GeneID = 12345.

As for

it would be fair to just consider the LOC110845878 uncharacterized gene as pyruvate kinase PKLR?

If you trust the annotation provided by the submitter (VU Amsterdam) then yes. NCBI has not yet done their due diligence for it.

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written by GenoMax GenoMax

Thank you. That makes a bit more sense now.

So LOC110845878 will continue to be labelled as uncharacterized until someone at NCBI personally verifies the annotation?

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written by 100dustedclays • 100dustedclays

LOC designation in this case is actually coming from Ensembl's rapid release of genomes but the intent is more than likely the same as one from NCBI. Until some validation occurs this ID will stay as LOC. But it should remain searchable in future if you want to use it for something.

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written by GenoMax GenoMax

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