I have some transcript IDs mapped with Ensembl 67. I want to study the corresponding proteins but some of the IDs are not present in the newest Ensembl release and Protein databases are usually updated to the most recent annotations (or previous annotation but anyway more recent than the 67). Moreover, as I'm studying protein variants of a same gene, I would exclude those protein that actually are not product of alternative splicing, so I would exclude proteins and transcripts which are not annotated in the newest release. ID history converter doesn't find any match ID in the new release for my old IDs, but in some cases I have transcript which encode a protein with similar length to one included in the newest release (for example ENSMUST00000191212 and ENSMUST00000112313) is it wrong to assume that the latter has been converted in the former? or that anyway what I mapped as ENSMUST00000112313 is indeed ENSMUST00000191212 which wasn't present in Ensembl 67? If not what is what I mapped as ENSMUST00000112313?
In other cases both bp and aa length are nearly identical in two IDs of Ensembl 67 but in Ensembl 80 only one of the two is present. Again, is it wrong to assume that the reads mapped on the retired IDs are actually of the newest IDs?
Thanks a lot!