Hi, I am currently working on a project to compare one-to-one orthologs between two species (human and pig) via BLAST. I am trying to do this between all possible one-to-one orthologs between both species that is currently available. I was able to retrieve a list of one to one orthologs from ensembl, but I have an issue where multiple human transcript IDs are orthologs to the same pig transcript ID.
For example, in my list of one-to-one orthologs, there are 7 one-to-one orthologous zinc finger genes. The human gene stable ID is ENSG00000067646, there are 7 human Transcript stable IDs all of which with different ID numbers. However, the pig transcript stable IDs for each one-to-one ortholog is the same number (ENSSSCP00000012966). I attached a image showcasing this in case what I’m saying was not explained good.
I understand that this is probably due to the pig genome not being as fleshed out as say human or mouse genomes. I was wondering if anyone has any information on how I can get one-to-one orthologs from humans and pigs but with only unprocessed cDNAs. Any help would be much appreciated and thank you!!
You are not likely to get one-to-one pre-computed ortholog lists like you want.
You should consider using a representative transcript for each human gene from MANE project. Find its
EnsemblID and the go with that from the table above, if you want to have a strict one-to-one list.