In Ensembl release 110, we have introduced changes to the way that the location of human genes located on patches are annotated and stored in the Ensembl databases.
In previous Ensembl releases, genes on patches were projected from their scaffold sequences (e.g. HSCHR6_MHC_APD_CTG1) and stored onto chromosome-based sequences (e.g. CHR_HSCHR6_MHC_APD_CTG1) which were ultimately used to visualise patches on the Ensembl Browser with all their associated features. For example, the gene(s) on this example patch were projected onto a sequence with coordinate positions in the context of human chromosome 6.
From Ensembl release 110, human genes (and their associated features) will remain on their original scaffold patch sequence as part of a long-term project to harmonise the available Ensembl and GENCODE FTP files and will also allow for more simple comparisons of annotation between Ensembl and NCBI RefSeq.
If you have any questions, please get in touch via the Ensembl helpdesk.