Dealing with assembly versions

Question

[thjnant]

Hello,

I have a set of genes of chicken but the IDs belong to an older version of chicken assembly, however now I am using galgal4 and I see several of the IDs, the names have changed.

For example when I search one gene I get this message:

Ensembl gene ENSGALG00000008643 is no longer in the database but it has been mapped....

and that the new version is named : ENSGALG00000008643.3

I was wondering if there is a way to update gene IDs for a large number of genes as I can't do this process for many genes manually.

Thanks.

[iraun]

I do not understand very well your question, what do you mean with "ENSGALG00000008643 is no longer in the database but it has been mapped"? When you look for ENSGALG00000008643 in Ensembl, can you find the gene no? Normally the gene names between assemblies do not vary. Anyway if the modification between assemblies is only the ".3" you can add ".3" to your ID list easily using any programming language.

Answer 1

[Emily]

I assume you're looking at this page. When it says "Latest Version: "ENSGALG00000008643.3" it doesn't mean that is the current version, but that that ID was the last version of the gene to be in the database. If you click on the link for the gene, you'll see that it takes you to an archive site for Ensembl release 70. The graphic at the bottom of the page shows you that it last existed in release 70, and was removed from the database since.

The ".3" at the end of the ID is just the version number. The graphic shows that we updated to this version in release 42 (which was while we were using the WASHUC2 assembly).

If you have a list of old Ensembl IDs, you can find their current equivalents (or if they don't have them) using the ID history converter tool, which you can find on the tools page here.

[thjnant]

Such great help! Thank you very much.