The rat Gene And Position Prediction map was based on orthologous rat-mouse gene pairs obtained from the rat genome database, RATMAP and the mouse genome database MGD. Combined with mouse-on-rat zoo-FISH analysis a total of 49 autosomal and 4 X-chromosomal Evolutionarily Conserved Segments (ECS) were defined.

All ECSs were anchored to the physical rat chromosomes by combining FISH and zoo-FISH. Assuming that the genome organization, including gene order, is essentially conserved within the ECSs a tentative subchromosomal map positions was assigned for rat genes for which no regional mapping information was available. Furthermore, the concept of prediction mapping was extended to unmapped rat homologs of genes, which in the mouse are situated inside or in the vicinity of an ECS.

In a few cases (RNO4, 6, 7, 11 and 15), the breaks between two ECSs occur on the same pair of chromosomes as a result of an inversion in one of the two species. In this presentation these ECSs appear to cover the same regions but this is only due to the limited resolution in the present data set. That is, too few genes in these ECSs have been mapped to a cytogenetic banding postion on the rat chromosome and so the search from the grapically presented chromosome becomes fuzzy. However, this does not interfere with the gene order predicted for these ECSs since it is based on the mouse gene order.