NCBI's Comparative Genome Viewer (CGV), allow you to view the alignments between two assemblies to see differences in genomic sequence and structure, including deletions, inversions, and translocations. Currently, you can compare assemblies from over 50 annotated animal and plant genomes. Example: Mus caroli CAROLI_EIJ_v1.1 (GCF_900094665.1) and Mus musculus GRCm39 (GCF_000001635.27).
The latest update allows you to search for a gene in NCBI’s Comparative Genome Viewer (CGV) and navigate directly to its location in the viewer and compare orthologous regions in the aligned assemblies. Details at NCBI Insights. Please try it out and let us know what you think.