1
Busch, Waser, & DeWoody Kangaroo rat MHC
Fig. S1 Seven MhcDisp-DRB sequences aligned against other mammals. Dots represent identity to the top sequence (Disp-DRB*01); dashes represent deletions [including codons missing in DRB*06 (nt 319-321) and DRB*07 (nt 277-279)]; asterisks denote undetermined sequences. Exon boundaries are based on HLA-DRB1 (NM_002124) and highlighted with vertical gray bars. Primers anchored in the 5’ and 3’UTR are labeled and their positions shaded with horizontal gray bars (oligo sequences may be found in Table S1 under the section “cDNA PCR & sequencing”). All sequences have been deposited in GenBank under accession numbers EU817479-EU817485. Abbreviations and GenBank accession numbers of comparison sequences were: DLA-DRB1 (dog, NP_001014768); HLA-DRB1 (human, NP_002115); Caja-DRB1 (common marmoset, CAJ34981); Scab-DRB (Abert’s squirrel, AAA42356).
5’UTR -50 -40 -30 -20 -10
....|....|....|....|....|....|....|....|....|....|....|....
Disp-DRB1 5’UTR_DRB1-F AGAGAAGGGTTCAT------TCTGATCTCCAGC
Disp-DRB2 ...... ------......
Disp-DRB3 ...... ------......
Disp-DRB4 5’UTR_DRB4+5-F ...... A...AGTTCTCACTGCACTCTTCTAACTAGTTTTCTC......
Disp-DRB5 ...... A...AGTTCTCACTGCTCTCTTCTAACTAGTTTTCTC......
Disp-DRB6 5’UTR_DRB6-F *TGCTCACTCAGTGAGGCTGGTCTACAGATCTGACACCCCTCCTCTC..CT......
Disp-DRB7 5’UTR_DRB7-F *******GGTTCAT------......
exon1 10 20 30 40 50 60 70 80 90
....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|
Disp-DRB1 ATGCTGTGCCCATGGCTCCCTGGAGGCTTCCACATGGCAGTTCTGATGGTGCTGCTGATGGTGCTGAGCCCGCCTGTGGCTTTGACCTGG
Disp-DRB2 ......
Disp-DRB3 ......
Disp-DRB4 ...... TG...... G...... T...... A..
Disp-DRB5 ...... TG...... G...... T...... C....A..
Disp-DRB6 ...G...... T...... CA.CA.TCC.TT..A....AC...A.CCC..A...... C.T...... T...... TT.A..
Disp-DRB7 ...G...AT...A...... AC...... T.TT...T...... A..
Scab-DRB ...G..G.T.TG..T....G....A...C.TG...... G.....CAT..A.A...... CA...... TT..CC...... G..A..
DLA-DRB1 ...G....T.TG..TT.T.T...... C.TGG...A...C...... C..A.A...... A...T..CT.C....G.G..A..
Caja-DRB1 ...G...ATATGA...... C.TG...... G....CA...A...... T.C..AC...... G.TG..
HLA-DRB1 ...G....T.TGAA...... C.TG....A...CG....CA...ACA...... T.C..AC...... T.TG..
100 exon2 110 120 130 140 150 160 170 180
....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|
Disp-DRB1 GACCTTCAATCGCGGTTCCTGGAGCAAGCTAAGGGCGAGTGTCACTTCCTCAACGGGACGCAGCGGGTGCGGTTTGTGCGGAGATACATC
Disp-DRB2 ...... C...... T.....A...... TCT...... C.AC......
Disp-DRB3 ......
Disp-DRB4 ...... C...... A...TT...... C..AC..GT.....T....
Disp-DRB5 ...... C...... A....TC.GACA...... C.A.C..GACG.....T..
Disp-DRB6 ...ACC.G.C.A..C...A..C....GTTG.....T...... T.T....C...T.....CG..G.A...T..AGC...ATC...C.....
Disp-DRB7 ...T.....C.A..T...... TTA.....G...A...... T...T...... A.....AT..GTC...A..GA....CG....
Scab-DRB ...ACCAG...T..C...T...... CAA.T.....C..T...TA...... CC..GA...... T..
DLA-DRB1 ...ACC.C.C.A.AT...T.....GTG..A...TC...... CT.T...AC...... G...... C...GAA......
Caja-DRB1 ...ACC.G.C.A..T...T.....T.TAGC.C.TCT...... T...T...... G...... C.CC..GAA......
HLA-DRB1 ...ACC.G.C.A..T...... TG...GC.....A.G...... T...T....T...... G...... CC..GAC...... T..
190 200 210 220 230 240 250 260 270
....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|
Disp-DRB1 TACAACCGGGAGGAGTTCCTGCGCTTCGACAGCGAGGTCGGGGAGTACCGCGCGGTGAATGAGCTGGGGCGGCCCATCGCCAAGGACTGG
Disp-DRB2 ...... C......
Disp-DRB3 ...... C......
Disp-DRB4 ...... CC......
Disp-DRB5 ...... A.G...... AT...... GC...... GGGA....G..T.....
Disp-DRB6 ...... A.A...G...... T...... C..T...... T...... TCA..C...... T...... G....ACTC
Disp-DRB7 C...... A...A....A...... T...... AGCC..A.AA...T.ATA..CT...C...... GAG..TG..AC....
Scab-DRB ...... ATG...... C..G...... T...... CC...... GGA....GG.T.....
DLA-DRB1 C.T...... G...... C..G...... T...G.....C.CG.....C...... G....TG..TC....
Caja-DRB1 C.T....A...... ATG...... C..G...... G...... CG...... TGA...GG..TC....
HLA-DRB1 ..T....A...... C.G...... C..G...... T...G...... CG...... TGA...TG..T.....
280 290 300 310 320 330 340 350 360
....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|
Disp-DRB1 AACGGGCAGCAGGACCTCCTGGAGCAGAAGCGGGCGGCGGTGGACACCTACTGCAGACACAACTACGGGGTCGTGGACGGCTTCACCGTG
Disp-DRB2 ...... G...
Disp-DRB3 ...... G...
Disp-DRB4 ...... A...... GTG......
Disp-DRB5 ...A.C...... T...... T.C...... G.CA...... A...... A...G.ACA.G...... A...
Disp-DRB6 ...A.C...A.....G.G.....CA.TT.C..A..TT.A..A....GG---...... A.T.....TCCAT.A..T...CTAC..CTGTCA
Disp-DRB7 ...AAA---A...C.AG...... G...T.GC.....A...... GG.T...... A...T.C...G.C...... G...
Scab-DRB ...A.C...G...... G...... CCA...... TGTG...... T.GCC.GA...... T...
DLA-DRB1 ...... A....GA..T...... G...... AA...... GA.T..GA...... G...
Caja-DRB1 ...A.C...A.....T...... G...... A...... A.A.TTCA..GA.G...CTA...
HLA-DRB1 ...A.C...A.....A...... GC...... C...... T.....GA...... A...
370 exon3 380 390 400 410 420 430 440 450
....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|
Disp-DRB1 CAGCGCCGAGTTAAACCTATGGTGACCGTGTACCCCACAAAGACTGAaCCCCTGCAGCaCCACAACCTCCTGGTGTGCGCTGTGCATGGA
Disp-DRB2 ......
Disp-DRB3 ......
Disp-DRB4 ......
Disp-DRB5 ......
Disp-DRB6 TTA.AAG...... TG....A......
Disp-DRB7 ...... A...... G...G...... A......
Scab-DRB G....GA...... G..G.A...... T.....T...... TGC.G...... C...... AG...C
DLA-DRB1 .....G.....CG.G....CA.....T.....T..T..G...... C.GA..T...... T...... C...T.....A....T
Caja-DRB1 .C...GA....AC...... A...... T.....T..TG.....G.CC.G...... C...T..C..AG...T
HLA-DRB1 .....G.....CC...... A...... T..A..T..TT...... CC.G...... C...T.....AG...T
460 470 480 490 500 510 520 530 540
....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|
Disp-DRB1 TTCTACCCAGGCAACATTGAAGTCAGGTGGCTCCGCAATGGCCATGAGGAGAAGGCTGGGGTGGTGTCCACAGGCCTGGTCTACAATGGA
Disp-DRB2 ......
Disp-DRB3 ......
Disp-DRB4 ...... A...... G......
Disp-DRB5 ...... A......
Disp-DRB6 ...... A...... G......
Disp-DRB7 ...... A...... A...... C...... G......
Scab-DRB ...... TC...... T....G...... G...... G...... C...... A..C.G......
DLA-DRB1 .....T...... C...... G...... G..A...G.A...... T...... AA..CGT......
Caja-DRB1 .....T...... G...... T....G....AT..G...... A..C.G......
HLA-DRB1 .....T...... G...... T...TG..C.....G..A...... A...... A..C.G......
550 560 570 580 590 600 610 620 630
....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|
Disp-DRB1 GACTGGACCTTCCAGATCATGGTGATGCTGGAGATGACCCCCCAACAGGGGGACGTCTaCACCTGCCACGTGGAGCACCCCAGCCTGGAC
Disp-DRB2 ......
Disp-DRB3 ......
Disp-DRB4 ......
Disp-DRB5 ......
Disp-DRB6 ......
Disp-DRB7 ...... A......
Scab-DRB ...... G..C...... A.CAGTT..T..GAGT..A..G..T...GT...... G...... A...... ATG
DLA-DRB1 ...... C...... AGTT..T..GAGC..A..G...... A...... A..TT..ACA
Caja-DRB1 ...... C.C...... A.CACTT..T..GAGT..A..G..T...... A...... A...G..AC.
HLA-DRB1 ...... C.C...... A.CAGTT..T.G.AGT..A..G..T...... A...... A...G..ACA
640 650 exon4 660 670 680 690 700 710 720
....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|
Disp-DRB1 GGTCCTGTCACCGTGGAGTGGAAGCCCCAATCTGGATCTGCGCAGGGCAAGATGATGAGTGGAGTTGGGGGCTTTGTGCTGGGGCTGCTC
Disp-DRB2 ......
Disp-DRB3 ......
Disp-DRB4 ......
Disp-DRB5 A...... T....C.C......
Disp-DRB6 ......
Disp-DRB7 ...... C...... G......
Scab-DRB A...... A.....A....G.G.A..G...... A..AA.T...... C...... A...... T......
DLA-DRB1 A.C...... A....G.G.A..G....AT.....A...A...... C...... A.C...... C.....T......
Caja-DRB1 A.C...C....A...C.A....GAG.A..G....A...... A...A...... C...... C...... C...... C......
HLA-DRB1 A.C...C....A.....A....GAG.A.GG....A...... A...A...... C...... C...... C......
exon5 exon6 STOP 3’UTR
730 740 750 760 770 780 790 800 810
....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|
Disp-DRB1 TTCCTGGGTGCAGGGCTGTTCATCTACCACAGGAACTCAAAAGGACACTCTGGACTTCAACCAGCAGGACTCCTGAGCTGAAGTGAAGGT
Disp-DRB2 ...... T......
Disp-DRB3 ...... G.....TT...... T...T..------......
Disp-DRB4 ......
Disp-DRB5 ...... G...A......
Disp-DRB6 ......
Disp-DRB7 ...... G.....TT...... T...T..------......
Scab-DRB .....T.TGCTG...A...... T...... TCAG..G...... G...A......
DLA-DRB1 .....T.CA.TG...... TT...A..TCAG..G...... G...A......
Caja-DRB1 .....T..G...... TT...... TCAG...------......
HLA-DRB1 .....T..G..C...... TT...... TCAG...... G...A.....T......
3’UTR_ALL-R
820 830 840 850 860 870 880 890 900
....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|
Disp-DRB1 GGACAGCTGGGAAGGCAGGACCTCTGGGCCTTCCTCTCCTCATGACATCACTCCAGCTTGGCTCTAATTCTTCAGAGAGCAGTAACGCTT
Disp-DRB2 ...... ------
Disp-DRB3 ...... ****************************************************************
Disp-DRB4 ...... C...... C......
Disp-DRB5 ...... C...... G..T......
Disp-DRB6 ...... C......
Disp-DRB7 ...... ****************************************************************
910 920 930 940 950 960 970 980 990
....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|
Disp-DRB1 TCTCCGGACCTGGCTTCATCCCTGCTCAGTGCCCAGCAGACCCTGTCCTCCCTGATGGCTCCCCCAGCCCCTGTCCCTGAGCTGGAAGCC
Disp-DRB2 ------......
Disp-DRB3 ******************************************************************************************
Disp-DRB4 ...... C...... G...... T......
Disp-DRB5 ...... C....G......
Disp-DRB6 ...... G...... T...... G......
Disp-DRB7 ******************************************************************************************
1000 1010 1020 1030 1040 1050 1060 1070 1080
....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|
Disp-DRB1 CAGTGCAGACTGCAAGGTCTGCT-TGCACTCTCTCTTGGCCCTTTTGCATTCAAACCTTCTGCCACCCTCCCTGCCCCCATTCAATCCAA
Disp-DRB2 ...... -...... T......
Disp-DRB3 ******************************************************************************************
Disp-DRB4 ...... C...... TT..A......
Disp-DRB5 ...... C.A......
Disp-DRB6 ...... CC...... TT..A......
Disp-DRB7 ******************************************************************************************
1090 1100 1110 1120 1130 1140 1150 1160 1170
....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|
Disp-DRB1 TCTGGCCTGTGTCACAATACTTCATTTTATGTTTCCCCCAAATAAACATGGAGCAAAAATTTTTTTCCCTAAAAAAAAAAAAAAAAAAAA
Disp-DRB2 ...... T...... G......
Disp-DRB3 ******************************************************************************************
Disp-DRB4 ...... G...G.T...... ACG......
Disp-DRB5 ...... T...... A...... ACAGGTTTTTCTTACAGTTTTT
Disp-DRB6 ...... AG...G.T...... A.A......
Disp-DRB7 ******************************************************************************************
1180 1190 1200 1210 1220 1230 1240 1250 1260
....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|
Disp-DRB5 GTTTATCCCAAAAGAAATAAAATATGGTATTATATGTATTTTCTGATATTGAGAAGAAAGAAATTCAGACATATCAAAGTTATTCTGAAC
1270 1280 1290 1300 1310 1320 1330 1340 1350
....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|
Disp-DRB5 CAGAAGCAGATTCTGATTTGATATGTTTTTAATTTCTACTTTATTACAATATCTATCCAATCATTTTTACTACTTCTTAAACCGTGGATC
1360 1370 1380 1390 1400 1410 1420 1430 1440
....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|
Disp-DRB5 TCTATATGATGATCACTTTTTGTGCAGTTCAATTCAGAAGAAAGAAAGTATAGTTTTTTTGTATGGTAGATCCCTGTCCTTTATTTTAAT
1450 1460 1470 1480 1490 1500 1510 1520 1530
....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|
Disp-DRB5 GTGAGTGATCTACATGATACATATAACACATTTGTTATTCTAAATTTTGACTTCCACTTTGTATAGTTAATGGTCATTAGAGATATATCT
1540 1550 1560 1570 1580 1590
....|....|....|....|....|....|....|....|....|....|....|....|
Disp-DRB5 TCTATTAAATCAAAAAATAAAAAATATGGAGAGCTGAGAAAAAAAAAAAAAAAAAAAAAA