Table 2. Sequence variants and allele distribution of genes in six rat MHC haplotypes.

Gene a	Size b	SNP c	del d	Allele 1 e	Allele 2	Allele 3	Allele 4	Allele 5	Allele 6	Subs f	Isof g
Btnl2 h	1542	4	0	a n	u					3	2
RT1-Da	768	7	0	a f i h n	u					1	2
RT1-Db2	861	2	3	a f	i	n	u			0	2
RT1-Db1	795	76	9	a f i	h n	u				35	3
RT1-Ba	768	66	3	a i	h n	f	u			40	4
RT1-Bb	792	72	0	a i	h n	f	u			38	4
RT1-DOb i	819	19	0	a i	h n	f	u			7	4
Tap2	2112	61	0	a i	h n	f	u			28	4
Psmb8	831	14	0	a i	h n	f	u			3	3
Tap1	2178	26	0	a	f	i	h	n	u	10	6
Psmb9	661	5	0	n i	f u	a	h			1	2
RT1-DMb	785	8	0	n i	a	f	h	u		1	2
RT1-DMa	783	5	0	a f h	n i	u				0	1
Tapbp	1563	2	0	a f n	h i	u				1	2

^aAll genes except RT1-DMa and Tapbp are encoded within the Tcs2 locus.

^bSize of the coding sequences (cds) in bp.

^cTotal number of synonymous and nonsynonymous SNPs in the cds.

^dTotal number of insertions/deletions on gene level.

^eAllele distribution between MHC haplotypes; DA (RT1^a), DA.1F (RT1^f), DA.1I (RT1ⁱ), DA.1H (RT1^h), DA.1U (RT1^u). Sequence information for RT1ⁿ was obtained from NCBI GenBank.

^fTotal number of amino acid substitutions.

^gNumber of alternative isoforms at the protein level.

^h Btnl2 was analyzed in only two strains.

^ISequence information for RT1-DOb refers to the full-length transcript of this gene (see Fig. S1 for alternative transcript).