Usually exon sequences are likely to be shared within a species like mouse, with only minor differences from strain to strain. Intron sequences vary much more; that was the reason over 20 years ago to use "isogenic" libraries for K.O. experiments to achieve a better homology for recombinant events in embryonic stem (ES) cells. I wonder if the EMBL-database would have accepted data from overlapping lambda phages, but from different mouse strains. Journals at that time wanted some Embl accession number for genetic information, but --- my impression was and is --- there never was a chance to get such information as a mix of different strains. Therefore it would have been "wise" to not mention the mix to get a manuscript published fast (and to avoid another round of screening for getting the missing part from the original library).