Is number after "LOC" genes equal to its Entrez id ?

Question

[takoyaki]

Hi everyone!

I want to ask about genes that start from "LOC", just like "LOC134466"

I wonder whether the number after "LOC" is equal to its linked Entrez id.

I searched this gene in the NCBI gene and detected several different genes.

If it is "LOC134466", does this mean that this locus is officially linked to the gene with 134466 Entrez id? So, in this case, "LOC134466" is the locus of ZNF300P1 which Entrez id is 134466 ?

If NCBI shows official comment or any documents, websites, would you share that information ?

[lieven.sterck]

which species are we talking here?

I don't think (but could be wrong here) that those are official omni-applicable , and might thus even be present for several species (rice has those LOC ids as well if recall correctly)

[takoyaki]

Thank you for your reply !

So, genes defined by this "LOC + ids" can be different between species. I was talking about human genes, but we have to care about ,,,

Answer 1

[Sej Modha]

I think LOC+GeneID is the typical convention. See more: https://www.ncbi.nlm.nih.gov/books/NBK3840/

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.

[GenoMax]

Indeed. Both searches below using EntrezDirect retrieve identical results:

$ efetch -db gene -id "134466"

or

$ efetch -db gene -id "LOC134466"

1. ZNF300P1
Official Symbol: ZNF300P1 and Name: zinc finger protein 300 pseudogene 1 [Homo sapiens (human)]
Other Designations: zinc finger protein 300 pseudogene 1 (functional)
Chromosome: 5; Location: 5q33.1
Annotation: Chromosome 5 NC_000005.10 (150930436..150946584, complement)
ID: 134466

[takoyaki]

Oh, we can confirm by EntrezDirect. thanks :)

[takoyaki]

Thank you so much !