<p>Figure legends and information to online supplementary material </p><p>Fig 6. PipMaker output file generated with 4122 kb of rat genomic sequence. The sequence includes 201 kb of working draft sequence generated at Baylor College that provides a link between our two sequence contigs consisting of 3828 kb (Accession number BX11170) and 93kb</p><p>(Accession number AL603724) finished-quality sequence. We used MultiPipMaker which allows the input sequence to be compared against several sequences at once. We compared the RT1 sequence against a draft of the mouse MHC and the finished human MHC (see legend to Fig. 1 for details). Because of space constraints, several annotated features are represented by symbols in the PipMaker output file. *:Sacm2l-ps1; *1: Sacm2l-ps2; *2: E230034O05Rik; *3:</p><p>2539a1a2/Rcrg1-ps11; *4: 2600a1a2; *5: Nerg-8; *6: 2738a1a2/Rcrg1-ps21; *7: 2920a1a2; *8:</p><p>2941a1a2/Rcrg1-ps35; *9: Rcrg1-ps37/2981a1a2; *10: RT1-M1-1; *11: RT1-M1-5; *12: Or11.</p><p>No symbols are associated with the following annotated features (position on the map in brackets): Nerg-ps4 (2500kb), 2619a1 (2619kb), 2759a1 (2759kb), Rcrg1-ps25 (2799kb),</p><p>2800a1a2 (2800kb), 2879a1 (2879kb), 2959a1 (2959kb), Rcrg1-ps40 (3020kb).</p><p>Data file: Exon annotation file for rat sequence 4122 kb </p><p>Fig. 7. Gene Tree analysis using UPGMA of class I gene fragments located in RT1-N on the basis of 120 bp derived from the 3' end of exon 2 (part of 1-domain). All rat class I genes identified by us that contain an exon 2 from different class I gene containing blocks were included in the analysis. Class I gene fragments are identified by their position on the map and domain homologies (see legend to Fig. 2). Clustering of fragments is correlated to their position within a module. Asterisks and open cirles indicate bootstrap levels (500 replicates) of 95% and 70%, respectively.</p><p>Fig. 8. Dot-matrix analysis of the MHC sequence of rat, mouse and human. Dotplots were produced using the Advanced PipMaker option to obtain a dotplot form of the alignment. We compared 3828kb rat MHC sequence (our finished rat sequenced submitted as accession number</p><p>BX11170) (a) against itself, (b) against mouse and (c) against human. Selected framework genes are highlighted for the rat sequence. For details on mouse and human MHC sequences, see legend to Fig. 1. A comparison at higher resolution is available from the PipMaker pdf file in Fig. 6.</p><p>Fig. 9. Degree of diversity for two class Ia genes, RT1-A1 and RT1-A2, of the RT1-A region and the class RT1-B and RT1-D genes encoding class II molecules. For class Ia genes exon 2 and 3 sequences are shown separately for peptide-binding and non peptide-binding codons. For class II genes only sequences of exon 2, separately for peptide-binding and non peptide-binding codons, are included. Data are based on cDNA sequences of standard RT1 haplotypes, 14 for RT1-A and</p><p>11 for RT1-B/D; n indicates the number of alleles found (for details see Günther and Walter</p><p>2001). </p><p>Table 1. Gene list and annotated features in the rat MHC. Column A, position on genomic sequence; B, Gene name; C, Accession numbers of genes used for annotation of rat genomic sequence; D, species from which sequences for annotation were derived; E, orientation of annotated feature: +, forward strand; -, reverse strand; F, number of exons in annotated gene; G, synonyms in rat, mouse and human; H, full gene name and designation.</p>