The reason two identical sequences have different accession numbers and different loci

Question

[Michel Edwar]

I am currently working on a certain gene. I was looking for it in pigs among other species. In all the species investigated, I found a single copy. However, when I inspected the pigs genome,

I found two identical copies that, although have different genes accession numbers(XP_xx11, XP_xx2), and appear in two different loci (loci 1, loci 2) , their nucleotide sequences are identical. Would that suggest that the two genes are really identical ( two copies of the same gene ) or that could be a sequencing error?

Answer 1

[h.mon]

These genes may be assembly errors, but if they were given different GIs, it is more likely there is enough evidence they are real duplicates.

You don't describe anything about them and the context they are: are they located in short, fragmented contigs? Do they belong to olfactory, immunological, or other pathway where duplications are common? Did you investigate the flanking regions?