I am having some problems with Ensembl. I have some exons and their coordinates annotated with Ensembl 61 (mouse). As I couldn't find the permanent link to Ensembl 61 I used the release 66 to get the sequences and I used Emboss sixpack and Interporscan5 to see the corresponding protein domains, but I couldn't find any match. I also tried to submit the aa sequence given by biomart in Ensembl 66 and I didn't have any result. When I tried the same approach with Ensembl 67 I obtained different nucleotide sequences and the corresponding protein domains found with Interproscan 5 were correct (or at least made sense with the corresponding gene studied). I also tried to translate my coordinates to the latest release, Ensembl 79, and again both the nucleotide and the aa sequences when put in Interposcan5 gave results identical to those obtained with Ensembl 67. Why there are these differences between Ensembl 66 and Ensembl 67, given that they both refer to mm9? Can I be confident that I am retrieving the right sequence, since the annotation has been made with Ensembl 61? Where can I find Ensembl 61, given that what should be its permanent link (http://feb2012.archive.ensembl.org) leads to Ensembl 66?