Supplemental Figure 2. Identification of conserved gene orders among human, chicken, X. tropicalis, and Ambystoma (Amby).

!"#$%# "&'( )! *+&,- ./0)12- 32-45+6 Chromosome and LinkageSPEN 0 Map LegendSPAG7 9.5PCOLCE2 11 1 2 3 4 5 6 7 8ENO3 11PSMB6 12EIF4A1 13 9 10 11 12 13 14 15 16*E16A9 14CLDN7 22 1CIRBP 40 17 18 19 20 21 22 23 24GPX4 40CNN2 40SLC39A3 40 25 26 27 28 Z*E12E2 40CDC34 45BSG 45 not mapped but marker PRTN3 46 belongs to a Xt scaffoldSFRS14 56 that suggests syntenyNDUFA13 57 with flanking markersUSE1 58UHRF1 65 unknown *E17C2 67EEF2 67NDUFA11 73MYO1F 73OAZ1 74BTBD2 74LSM7 79 1 !SAFB 79 2MAPRE1 79ATP5E 81 3MCL1 90ERO1L 99IFIH1 102KRTCAP2 102C1ORF230 111S100A11 113S100A13 113 2PRG4 113S100A4 113*E12E11 123TPM3 129RPS27 131ANP32E 136

TXNIP 142SSR2 149 " 3DYNC1LI2 156ATP6V0D1 167TPPP3 168NUTF2 170 # 4HDGF 170UFC1 170 $TMEM188 171PSMD11 180U2AF1_b 180*ETG93 180FXYD3 182*E12C7 187COX6B1 188 7POLR2L 190 %NUCB1 194FTH1_b 195FTL 195LOC733905 195 8KRTAP10-1 195CD163L1 205SACS 212GPI 232ITLN1 237GABARAPL2 238HNRNPK_b 238NQO1 241VPS4A 242APRT 247MAP1LC3B 250 &CA5B 250 5 'TEAD4 261GMDS 261MBOAT7 267*E12A2 276*E13E7 276LIG1 277 10MOCS3 286SFRS7 304 "LOC769550 305MMP2 313NUDT21 320 !!()*+,-./ '"0ETHE1 340RABAC1 345 12MC1R 351 6

MGST3 351APOE 356PRDX6 366FMO3 374NCF2 380ARPC5 380RGS2 380GLUL 384CLCA2 386RGS5 387 #COL11A1 390IFI44L 393GNG5 395SEPT10_b 396*E12G5 398*E17G11 398FPGT 404GPR177 408LEPROT 410USP1 412 !' 1PSMA4 427C8A 436TMEM59 445SLC1A7 448SCP2 450EPS15 454TXNDC12 454KIAA0494 462FAAH 464*E17G7 467PRDX1 ! 473 !" 2 $

DAZL 0TMLHE 2.5THRB 17STT3B 29SH3BP5 37NGLY1 41 !#C7ORF41 41*E12C2 41VWDE 51COL1A2 60 !$ 1UHRF2 63NMT2 77VIM 82 17IGF2BP3 84

TOMM7 84 !2EIF1B 84KIF15 85 !&*E54A6 92HOXA9 94HOXA4 94CBX3 102CYCS 103 %0 & 2ABI2 106KIF5B 110CREM 113 21 &WDR60 116U2AF2 119 !0HBZ 127HBA2 132 22 !!HBG1 132 !0EIF3I 151KBTBD5 161CRHR2 168 !% !!UQCRC2 169GNA12 182 !'TIMM17B 196TIMP4 199TNRC6A 204RBBP6 204DCTN5 204 !" !%NARFL 207*E17G8 210MSLNL 212SSTR5 212 23PDGFRA_b 217H3F3B_b 224UBE2I 226COQ7 227PDXDC1 228 24 !#MYL3 231ARF1_b 234 !$ABAT 239ATP6V0C 241HN1L 241MRPS34 241NME3 241C16ORF13 252STUB1 256HBA2_a 256 25 !1 !'HBD 256

LOC440335 258AURKB 2633!!)-,#! %$#45/)6.7(5'&15378! %$#CCM2 265KIF9 267 18SETD2 267 %$NGFR 267 14RAI1 269RASD1 269MED9 269MAP2K3 269DRG2 269M_NOHITS_5137_CTG1269SHMT1 269 %1PVALB 277 !&RAC1 277 !#ARPC1A 280 %2UTS2R 280ACTG1 280 %&M_NOHITS_899_CTG1280ACTB 281 20FOXK1 285 '0*E13G5 287TKTL2 287RENBP 287BGN 287SMC1A 294 '! !$TTC9C 294EEF1G 294OTUB1 299PRDX5 299RBM4 299 32 !1ACTC1_a 299ADSS 299CALM1 299TMED10 304 33 %! !$PYGM 304CAPN1 304 !2DPP3 304 34FOXA3 306*E14C12 308*E16G10 308*E23C10 309CFL1 309PLCB3 309

BANF1 309 35KCNK1 309SULT6B1 310 %%RBM4B 310UCRC 312*E16E8 312CKM 316SNRPD2 320CLPTM1 320 36*E17G3 323C22ORF32 334CYP2C19 334*E12E6 334CYP2F1 335H3F3B_a 343CAPNS1 346SNAP23 346GMFG 350NCCRP1 350 37RHOA 356 !&GNAT1 366TWF2 373 '2 %'WFDC2 373CNBP 377BTG1_a 380FLNB 387TKT 389*E12A3 398RHO 404LSM3 415SEC61A1 426RAB7A 433IP6K2 439PRKAR2A 442 %0ARPC4 453NISCH 459RPL29 459PBRM1 460SPCS1 2 471 '& %"

ZYX 0MYL6 24NANOG 38C3AR1 39GAPDH 43

ING4 46 "0 %#FKBP1A 67ASXL1 76*E16A12 76GNAS 79ADNP 97TNNC2 101UBE2V1 101 41 26 21SNAI2 101SULF2 109NCOA5 115 42 27MMP2_a 118PDLIM7 143TMED9 157 "' 22CTBP1 158RPUSD4 158*TIG_NOHITS_253 158PROD1 169VKORC1L1 170TRIM69 170FUS 170MVP 176 44NME1 176ALDOA 184*E11G12 194YPEL3 194 45SULT1C4 195BOLA2 195ATP2A1 196 46*E16E3 196*CONTIG13340 196*E50G8 199NFS1 199MAP1LC3A 201C20ORF4 206MANBAL 209 47 28 23BNIP1 218UQCRQ 228CAMLG 236SKP1 236SMAD5 239 "2SEPT10_a 241HNRNPA0 242HNRNPAB 243*E13E11 243MATR3 244 24UBE2D2 244 "& 29

PHF5A 251 POLR3H 251*E12A5 251*E14G1 251CSNK1E 257KDELR3 257TOM1 261 50 '0 %#HOXC10 271RARG 272NACA 272*E54A1 272ATP5G2 272OS9 281KRT5 281 31KRT4 281CD63 285*E50C2 287*RPS26 287WNT1 290RHEBL1 290DDX23 291 #! %$C5ORF4 294SPARC 294ATOX1 296CD74 298SQSTM1 300CCNG1 313 #% 32 %1PKM2 319MYH9 325MGP 331 ''LURP-1 331ETF1 331PRPSAP1 346SFRS2 346C17ORF28 348 28RAB37 349XYLT2 349APOH 364DDX5 364*ETG990 364PRKAR1A 369GNA13 369KCNJ16 370SOX9 371SSTR2 371RPL38 372ARHGDIA 376

THOC4 376 53 34 29CYP4F22 376ZNF248 376ZNF717 376PBX1 376*E13G1 376P4HB 379PKN2 388ASF1A 395ASF1B 395*E12C8 400PGLS 400C19ORF43 414TYK2 414JUNB 414C19ORF52 418ELOF1 418FARSA 418DNM2 418GADD45GIP1 418*E14C7 424KHSRP 430LOC28974 7 430 54

*E12A1 0*E15G10 11*E14G3 16ANAPC7 17RAB35 21SFRS9 22DYNLL1 22 55DDT 26MIF 27 #$ 78*E14A8 35FBXW8 64XBP1 71 '#SLC20A1 74PPIF 74PGAM2 75MYL7 76 #1TIA1 76OGDH 76 36*E15E3 76*E16A5 89*E12E10 94*E16C3 94

AP2M1 94EIF4G1 94 #2EIF5A 98*E13E8 101LAMP3 111 37LOC563358 112PRPF6 115PDCD10 115KPNA4 123RARRES1 128 #& '2VWA5A 138SCLY 152HDLBP 155 60 '&*E14C4 155*E14G7 155HSD17B8 177CIRBP_b 179*E54E6 186PDLIM2 198BOLA3 198SFRP1 201ENTPD4 201 $! 40*E14E1 207PHB2 212AKAP7 276EGLN1 278MAL 284MALL 285 62 "!TCP1 285BTG1_b 303CTGF 304ZUFSP 310FABP7 319KIAA0776 330 31ZNF292 331 $'CIRBP_c 334COX7A2 345COL12A1 346TMEM14A 357 $" 32PXDN 361PDIA6 366YWHAQ 367PQLC3 367ID2 367SDC1 379RHOB 379 65CTSB 391 "%PGAM2_b 402

IRGC 402GPN1 " 414

ZNF649 0LECT2 3.8CYC1 8.1EPPK1 9.5VPS28 9.5PUF60 9.5PSCA 9.5 $$ 43*E48C10 9.5PRKRIP1 21MYC 29NDUFB9 44RNF19A 62PABPC1 70 33UQCRB 76RBM12B 78CA2 82 34NBN 82MRPS28 87 $1 44*E15A2 90NUP37 109YES1 132RIOK3 132MYL12B 135CNDP1 161CYB5A 168 68CHMP5 179MYO10 179BASP1 180DAP 183 $&KDSR 194VPS4B 194 70ACOT13 203JARID2 225SERPINB6 228TXNDC5 233 35LYRM4 236 1!*E15A11 238KBTBD2 272LOC420992 272 45TMSB15A 281LOC792995 283TAF9 287FAM162A 287

*E17E10 287FHL1 292SOX3 296VMA21 297HMGB3 # 297 1% "$ 36

IDH2 0MFAP1 0IQGAP1 4.9CLPX 14GATM 38 1'MCEE 49MAPK6 55LARP6 60 1"SFTPC 62NPTN 63*CONTIG22977 64ISL2 72LIPC 75HAPLN3 87ABHD2 92RHCG 92RAB11A 99 37*MEX_NOHITS_2369_CONTIG_199TLE3 101 1# 47PHLDA2 103ATHL1 107LOC644003 113MUC5AC 114TNNI2 116CD81 117FT_AC11ORF58 134SBF2 135RRAS2 135SPON1 140PAX6 142CCND1 155 '2CD59 156 76 "2ANXA2 163LOC100091509 163SERINC2 167*E15E9 167TRNAU1AP 172 11CTSL2 174

T_ 174RCC1 174SH3BGRL3 176GRHL3 182STMN1 189ZNF593 189*E12G12 189M_NOHITS_886_CTG2189*E15A6 192RRAGC 200SF3A3 211GNL2 220 '&TRAPPC3 227 12ZNF706 231*E14C3 232*E16C8 232GJB5 235KPNA6 247KHDRBS1 247 1& "&*E13G11 247SFRS1 252YARS $ 252 "0

RAB6A 0DNAJB13 3.6 #0STARD10 3.6SPCS2 3.6LIPT2 3.6THRSP 10SYTL2 15 80UBL3 33POSTN 34*E12G3 39ITM2B 48RB1 48C13ORF31 48LCP1 48GTF2F2 48 81 #! "!RAB33B 49LMO7 54PICK1 54GPR143 77RPL24 91THOC4_a 91COL8A1 100 20

EIF1AX 117TM9SF2 128COL4A2 147ABHD13 160 82MID1IP1 161BLZF1 164DPT 166 2'TIAM1 196SOD1 196ATP5O 198RCAN1 198 84ALCAM 198CD247 208UPK1B 211FSTL1 222CCDC58 226 2# "%MAN1A2 1 232 #%

LOC643604 0TPM2 10DNAJB5 30 2$IER3IP1 47SMAD2 48 87ID3 56ZFR 67ATP8B1 67*MEX_NOHITS_2377_CONTIG_171*MEX_NOHITS_2354_CONTIG_175SEPP1 75PRKAA1 76*CONTIG95328 76GPX8 81SCAMP1 94HMGCR 101OCLN 104*MEX_NOHITS_906_CONTIG_1104VCAN 108*E11G8 146TNFAIP8 150 22*E14E6 153*E14C5 157ANXA1 172HNRNPK 195FAM108B1 2 227 2& 53 "'

HSPA8 0APLP2 11*E14E10 11NNMT 14LOC566020 24ARCN1 35PAFAH1B2 36 54FXYD2 36 90 ""MNT 48*E11G11 51*E12A11 55AATF 57ATP2A3 64 91BAZ1B 75*E16C7 75C7ORF42 79GBAS 79POR 83 &%MKS1 83MED31 86CLTC 87DOC2B 87PRR11 87 "#MED13 87 93 55*E11G4 108*E17C12 111CFLAR 113STAT1 124 94 #$TOMM20 127TRA2B 129DNAJB11 130 &# 57ZC3H15 131SUMO3 145STT3B_a 151*E54C11 151FN1 153*E12G7 154*E12G1 154NDUFA10 158UGT1A1 159 96COL6A1 160*E13E6 160ATP5G3 165HOXD8 165HOXD11 167

SCRN3 169*E13A7 169GCA 171RND3 180HNMT 186R3HDM1 188 &1SNX4 196*E14A3 206NNMT_a 209ZNF142 210ACCN4 212 98 #2 "$*E19A7 216CYP27B1 9 218

SLC37A3 0FBXO7 3.4*CARDIAC-RNA 11*E54G12 11MTPN 14IL17RA 31WNT5B 33FBXL14 33 "1*E17C9 45NTF3 55TMEM19 60 && #&UPK3B 65TWF1 71 "2HIST1H2AG 124HIST1H1E 126 !00*E12A4 128CDK2AP2 130UBE2L3 133TMX2 134CTNND1 134C11ORF31 134 101FTSJ3 134CTSK 136*E17C5 136FLJ36031 136*E17C6 136PIM3 144LUM 144PAWR 146KITLG 154 !0% "&

*TIGRINUM-UV 163LEP 166CALU 166*E15C7 166SND1 170IMPDH1 170COPG2 176 !0'TUBA1A 185RAP1B 196TMEM5 203XRCC6BP1 10 217 !0" $0

ACADSB 0EIF3A 6.7ABLIM1 24TRIM8 39COX15 53 105 #0ATP5B 62ANKRD1 71 $!HIGD1A 78DNTT 78CISD1 83SGMS1 88 106 $%*E16E2 95((!29% &1MFAP2 97UBR4 101 !01SFTPD 105VDAC2 113*E15C8 113AP3M1 113 108 $'ERRFI1 115HSPG2 115CDC42 122C1QB 125 !0& 64PCBD1 138PSAP 139C10ORF54 139H2AFY2 140MYOZ1 145KIAA0913 145DDX21 145SAR1A 150CCDC109A 150EIF4EBP2 150 110 $# #!

RPL37A 160CAMTA1 160CALM2 11 192

SLC4A5 0DCTN6 2.3PTPN9 11SFRS2 11C9ORF156 12CLTA 17 111KLHL8 17ENO3_a 25MMRN1 30C4ORF16 40 !!% $$HSDL2 40H2AFZ 41RAD23B 49KLF4 49 !!'SCOC 58LARP7 62TBCKL 63NDUFC1 77ARFIP1 87PDGFC 91 !!" $1CHDH 111TMEM165 117KIT 119 #%PDGFRA 119CNGA1 124WDR1 145SLC2A9 145 !!# $2CDC25A 161C20ORF27 161*E15C10 161KAZALD1 174*MEX_NOHITS_2379_CONTIG_1182MGC97528 !% 187

KCTD3 0PYGO2 11EPHX1 12 !!$ #'GTPBP2 33TMEM63B 34 69

HSP90AB1 38C6ORF226 42 !!1RPS6 82CCDC127 85ARRB1 90SFTPD_b 93COX7B 111SSR2_b 143*E15G1 13 163

EAPP 0AP4S1 0 118THBS1 0ACTC1 8.1 !!&ERH 17 10CHURC1 21 120 #"SFRS4 27TRMT5 39ARF6 46MAP4K5 47RPS29 58NID2 60C14ORF129 73CNIH 73FERMT2 73NPC2 73FCF1 74LGMN 81WARS 83AHSA1 113 ##UBR7 113 121CDC42BPB 120PPP1R13B 128 1!*E16C9 14 134

COL1A1 0PHB 5.1DLX3 5.1 122LSM6 5.1ARF1_a 9.5PSME3 11CCDC56 11*CONTIG81034 11

NSF 13MAPT 19*E15G4 19CRHR1 21GH1 28 123 72*E17E411 29PCK2 32TGM1 33MDP1 33SDR39U1 42 124TMEM85 42HIST2H3A 42*TCELL 47RABIF 55 !%#NDRG2 55TMEM183A 58NAV1 66CSRP1 66 !%$ 73*E15A9 66RPLP2 69TMEM167B 72SRPK1 72TAF11 74*E17C3 74RPL10A 83 !%1 74*MEX_NOHITS_2397_CONTIG_183CAPZA1 108RHOA_b 112CYP2A13 112RAB7L1 124SNRPE 130 !%2

TAF8 130 75CTGF_a !# 133

TPRG1L 0GNB1 6.9MAD2L2 14 #$TARDBP 14 !%& 76LOC100224741 14*E11E11 17NPDC1 20COBRA1 21TNC 27WDR5 34

NOTCH1 42 !'0APEX1 58LHX2 59C9ORF78 76C9ORF16 77TOR1A 16 85 !'! 77 #1

KRT24 0FKBP10 0KRT17 3.3EIF1 3.3KRT12 3.3RARA 5.5LOC100016027 5.5SNF8 9.9HOXB13 9.9NFE2L1 12 58RPL19 20MED1 29 !'% 78KEAP1 36*G2G13 39MED24 40THRA 49 !''SFRS3 67*MEX_NH_165 70TCF19 76 !'"MR1 17 80