AGRP Logo

AGRP

Asteraceae Genomic Research Platform

Gene Search

Example:
Example:

Hierarchical alignments with the Arctium lappa genome as reference

  Inter-genomic and intra-genomic comparisons can help reveal the structural complexity of Asteraceae genomes. We used Arctium lappa as a reference, and by comparing homologous gene locus maps and Ks values between Arctium lappa and other Asteraceae, we could separate orthologous and paralogous genes produced by different polyploidization in the species genomes. We constructed a 74×31,441 macro-matrices.


Select Armi_1 Sain_1 Ceso_1 Cati_1 Ccar_1 Cien_1 Cich_1 Lssa_1 Laca_1 Tako_1 Tamo_1 Pslu_1 Lomi_1 Lomi_2 Enbr_1 Ecan_1 Soca_1 Glco_1 Artr_1 Aary_1 Aary_2 Aann_1 Chma_1 Chmo_1 Chmo_2 Chmo_3 Chla_1 Chna_1 Cind_1 Pdy_1 Cobi_1 Hean_1 Bial_1 Bial_2 Dapi_1 Dapi_2 Hetu_1 Hetu_2 Hetu_3 Amtr_1 Smso_1 Smso_2 Taer_1 Fro_1 Fso_1 Ftr_1 Fra_1 Fli_1 Stre_1 Mimi_1 Cobi_2 Hean_2 Bial_3 Bial_4 Dapi_3 Dapi_4 Hetu_4 Hetu_5 Hetu_6 Amtr_2 Smso_3 Smso_4 Taer_2 Fro_2 Fso_2 Ftr_2 Fra_2 Fli_2 Stre_2 Mimi_2
. . . . Ccar2g02262 . . . . . . . . Lomi2g04141 Enbr6g01577 Ecan3g00124 Soca5g05245 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi1g00170 Sain12g00157 Ceso2g03270 Cati3g00209 . . . . . . . Pslu1g06451 . . . . . . . . . . . Chmo13g01232 Chmo14g01136 Chmo15g01081 Chla6g05402 Chna2g01051 Cind3g00393 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi1g00171 Sain12g00158 . . . . . . . . . . . . . . . . . . . . . Chmo13g01233 Chmo14g01137 Chmo15g01082 . Chna2g01052 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi1g00172 Sain12g00159 Ceso2g03272 Cati3g00211 Ccar2g02260 . . Lssa7g03721 . Tako4g03553 . Pslu1g06453 . Lomi2g04139 Enbr6g01578 Ecan3g00122 Soca5g05242 . . . . . Chma7g07556 Chmo13g01234 Chmo14g01138 Chmo15g01084 Chla6g05400 Chna2g01053 Cind3g00395 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi1g00173 Sain12g00160 . Cati3g00212 Ccar2g02259 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi1g00174 Sain12g00161 . Cati3g00213 Ccar2g02258 . . . . . . Pslu1g06454 . Lomi2g04138 Enbr6g01578 Ecan3g00121 Soca5g05241 . . . . . . Chmo13g01235 Chmo14g01139 Chmo15g01085 . Chna2g01054 Cind3g00399 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi1g00175 Sain12g00162 Ceso2g03273 Cati3g00214 Ccar2g02257 . . . . . . Pslu1g06455 . Lomi2g04137 Enbr6g01579 Ecan3g00120 . . . . . . . Chmo13g01236 Chmo14g01141 Chmo15g01086 . Chna2g01055 Cind3g00402 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi1g00177 Sain12g00163 Ceso2g03274 Cati3g00215 Ccar2g02256 . . . . . . Pslu1g06457 . Lomi2g04136 Enbr6g01576 Ecan3g00119 Soca5g05240 . . . . . Chma7g07575 Chmo13g01246 Chmo14g01147 Chmo15g01097 . Chna2g01070 Cind3g00416 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi1g00178 Sain12g00164 Ceso2g03275 Cati3g00216 Ccar2g02255 . . . . . . Pslu1g06458 . Lomi2g04135 Enbr6g01575 Ecan3g00118 Soca5g05237 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi1g00179 Sain12g00165 Ceso2g03276 Cati3g00217 Ccar2g02254 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
Gene_GFF
Select Chromosome Start End Strand Old_gene Gene Num
1 3240529 3247109 + AmiAMIRv0_Chr01g0001701 Armi1g00170 170
1 3247927 3249411 - AmiAMIRv0_Chr01g0001711 Armi1g00171 171
1 3250207 3252757 - AmiAMIRv0_Chr01g0001721 Armi1g00172 172
1 3271661 3280116 + AmiAMIRv0_Chr01g0001731 Armi1g00173 173
1 3281157 3287023 - AmiAMIRv0_Chr01g0001741 Armi1g00174 174
1 3305022 3309427 - AmiAMIRv0_Chr01g0001751 Armi1g00175 175
1 3379302 3382954 + AmiAMIRv0_Chr01g0001771 Armi1g00177 177
1 3384616 3390019 - AmiAMIRv0_Chr01g0001781 Armi1g00178 178
1 3398899 3401435 + AmiAMIRv0_Chr01g0001791 Armi1g00179 179
3 1653084 1661488 + CtAH03T0012600.1 Cati3g00209 209
3 1664549 1667295 - CtAH03T0012800.1 Cati3g00211 211
3 1672654 1680517 + CtAH03T0012900.1 Cati3g00212 212
3 1681747 1689463 - CtAH03T0013000.1 Cati3g00213 213
3 1697718 1704288 - CtAH03T0013100.1 Cati3g00214 214
3 1709473 1715078 + CtAH03T0013200.1 Cati3g00215 215
3 1716025 1722375 - CtAH03T0013300.1 Cati3g00216 216
3 1729186 1735009 + CtAH03T0013400.1 Cati3g00217 217
2 69578892 69584193 - gnl|WGS:LEKV|Ccrd_011305.mRNA.1_mrna Ccar2g02254 2254
2 69587613 69595493 + gnl|WGS:LEKV|Ccrd_011306.mRNA.1_mrna Ccar2g02255 2255
2 69594178 69599361 - gnl|WGS:LEKV|Ccrd_011307.mRNA.1_mrna Ccar2g02256 2256
2 69599106 69607528 + gnl|WGS:LEKV|Ccrd_011308.mRNA.1_mrna Ccar2g02257 2257
2 69614385 69615966 + gnl|WGS:LEKV|Ccrd_011309.mRNA.1_mrna Ccar2g02258 2258
2 69620781 69629371 - gnl|WGS:LEKV|Ccrd_011310.mRNA.1_mrna Ccar2g02259 2259
2 69631088 69633353 + gnl|WGS:LEKV|Ccrd_011311.mRNA.1_mrna Ccar2g02260 2260
2 69636893 69643964 - gnl|WGS:LEKV|Ccrd_011313.mRNA.1_mrna Ccar2g02262 2262
2 81936902 81944966 + >KAJ9562701.1 Ceso2g03270 3270
2 81962875 81971054 - >KAJ9562704.1 Ceso2g03272 3272
2 81995282 81998801 - >KAJ9562878.1 Ceso2g03273 3273
2 82006241 82009125 + >KAJ9562875.1 Ceso2g03274 3274
2 82011347 82017041 - >KAJ9562879.1 Ceso2g03275 3275
2 82026149 82029130 + >KAJ9562874.1 Ceso2g03276 3276
6 212556953 212558097 + ClaG1_Chr06g0426471 Chla6g05400 5400
6 212560766 212566266 - ClaG1_Chr06g0426491 Chla6g05402 5402
7 259581502 259582635 + CmaNakai_Chr07g0698581 Chma7g07556 7556
7 260008721 260010901 + CmaNakai_Chr07g0698771 Chma7g07575 7575
13 65019535 65025155 + evm.model.scaffold_4060.37 Chmo13g01232 1232
13 65025920 65027446 - evm.model.scaffold_4060.36 Chmo13g01233 1233
13 65027618 65030811 - evm.model.scaffold_4060.35.1 Chmo13g01234 1234
13 65033588 65038268 - evm.model.scaffold_4060.34 Chmo13g01235 1235
13 65109605 65114198 - evm.model.scaffold_4060.30 Chmo13g01236 1236
13 65728969 65734286 + evm.model.scaffold_4060.9 Chmo13g01246 1246
14 60302385 60310291 + evm.model.scaffold_948.149 Chmo14g01136 1136
14 60308689 60310215 - evm.model.scaffold_948.150 Chmo14g01137 1137
14 60310387 60313295 - evm.model.scaffold_948.151_evm.model.scaffold_948.152 Chmo14g01138 1138
14 60315684 60321697 - evm.model.scaffold_948.153 Chmo14g01139 1139
14 60381401 60386325 - evm.model.scaffold_948.158 Chmo14g01141 1141
14 60781430 60784998 + evm.model.scaffold_948.175 Chmo14g01147 1147
15 62423801 62432048 + evm.model.scaffold_1478.97 Chmo15g01081 1081
15 62430446 62431972 - evm.model.scaffold_1478.98 Chmo15g01082 1082
15 62433962 62435614 - evm.model.scaffold_1478.100 Chmo15g01084 1084
15 62458258 62462247 - evm.model.scaffold_1478.103 Chmo15g01085 1085
15 62507129 62511735 - evm.model.scaffold_1478.105 Chmo15g01086 1086
15 63028577 63031750 + evm.model.scaffold_1478.136 Chmo15g01097 1097
2 84063629 84069368 + Cn0815680 Chna2g01051 1051
2 84069888 84071414 - Cn0815690 Chna2g01052 1052
2 84071784 84074784 - Cn0815700 Chna2g01053 1053
2 84080551 84084572 - Cn0815710 Chna2g01054 1054
2 84156373 84160612 - Cn0815720 Chna2g01055 1055
2 84913756 84917529 + Cn0816040 Chna2g01070 1070
3 303630273 303635735 - D.indicum_Contig13_G00004.t1 Cind3g00393 393
3 303624902 303626008 + D.indicum_Contig13_G00006.t1 Cind3g00395 395
3 303610638 303611076 + D.indicum_Contig13_G00010.t1 Cind3g00399 399
3 303560882 303562688 + D.indicum_Contig13_G00013.t1 Cind3g00402 402
3 302363986 302365720 - D.indicum_Contig13_G00027.t1 Cind3g00416 416
3 918496 923787 + XM_043766237.1 Ecan3g00118 118
3 924148 927574 - XM_043766238.1 Ecan3g00119 119
3 944346 948761 + XM_043765630.1 Ecan3g00120 120
3 966577 970962 + XM_043762934.1 Ecan3g00121 121
3 972551 974007 + XM_043762937.1 Ecan3g00122 122
3 976010 981333 - XM_043762936.1 Ecan3g00124 124
6 54787009 54791601 + evm.model.ctg7828.2 Enbr6g01575 1575
6 54792693 54794511 - evm.model.ctg7828.3 Enbr6g01576 1576
6 54831188 54836074 + evm.model.ctg3768.1 Enbr6g01577 1577
6 54838504 54844216 - evm.model.ctg3768.3 Enbr6g01578 1578
6 54890273 54892450 - evm.model.ctg3768.4 Enbr6g01579 1579
2 46991248 46994778 + LmiAMIRv0_Chr02g0086681 Lomi2g04135 4135
2 46995687 46997085 - LmiAMIRv0_Chr02g0086691 Lomi2g04136 4136
2 47001844 47003654 + LmiAMIRv0_Chr02g0086701 Lomi2g04137 4137
2 47016988 47020160 + LmiAMIRv0_Chr02g0086711 Lomi2g04138 4138
2 47022141 47022896 + LmiAMIRv0_Chr02g0086721 Lomi2g04139 4139
2 47025441 47029235 - LmiAMIRv0_Chr02g0086741 Lomi2g04141 4141
7 196562266 196563012 - >KAJ0196378.1 Lssa7g03721 3721
1 44294926 44298592 + PluAMIRv0_Chr01g0064271 Pslu1g06451 6451
1 44301061 44301811 - PluAMIRv0_Chr01g0064291 Pslu1g06453 6453
1 44304589 44307776 - PluAMIRv0_Chr01g0064301 Pslu1g06454 6454
1 44321501 44323348 - PluAMIRv0_Chr01g0064311 Pslu1g06455 6455
1 44339681 44341143 + PluAMIRv0_Chr01g0064331 Pslu1g06457 6457
1 44342064 44345552 - PluAMIRv0_Chr01g0064341 Pslu1g06458 6458
12 2897019 2903822 + SinAMIRv0_Chr12g0357221 Sain12g00157 157
12 2905559 2907085 - SinAMIRv0_Chr12g0357231 Sain12g00158 158
12 2908380 2909765 - SinAMIRv0_Chr12g0357241 Sain12g00159 159
12 2915454 2924748 + SinAMIRv0_Chr12g0357251 Sain12g00160 160
12 2926552 2930969 - SinAMIRv0_Chr12g0357261 Sain12g00161 161
12 2943653 2948583 - SinAMIRv0_Chr12g0357271 Sain12g00162 162
12 2956840 2959049 + SinAMIRv0_Chr12g0357281 Sain12g00163 163
12 2969278 2973987 - SinAMIRv0_Chr12g0357291 Sain12g00164 164
12 2978109 2980824 + SinAMIRv0_Chr12g0357301 Sain12g00165 165
5 71109145 71113303 + augustus59618.t03 Soca5g05237 5237
5 71113867 71117258 - transfrag40178.t01 Soca5g05240 5240
5 71153018 71157477 + augustus35808.t01 Soca5g05241 5241
5 71161872 71163555 + augustus35810.t01 Soca5g05242 5242
5 71165562 71171733 - asmbl_4226.p1 Soca5g05245 5245
4 78136415 78140422 - TkA04G309720.1 Tako4g03553 3553
       
DecoBrowse