AGRP Logo

AGRP

Asteraceae Genomic Research Platform

Gene Search

Example:
Example:

Hierarchical alignments with the Vitis vinifera genome as reference

  Inter-genomic and intra-genomic comparisons can help reveal the structural complexity of Asteraceae genomes. We used Vitis vinifera as a reference, and by comparing homologous gene locus maps and Ks values between Vitis vinifera and other Asteraceae, we could separate orthologous and paralogous genes produced by different polyploidization in the species genomes. We constructed a 219×23,647 macro-matrices.
Select Vivi_1 Arla_1 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
Vivi1g00041 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00042 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00043 Arla4g01958 Armi3g04262 Sain4g00783 Ceso4g04248 Cati7g00462 Ccar13g00313 Cien3g02856 Cich2g01181 Lssa8g01699 . Tako5g02576 Tamo5g03373 Pslu5g12924 Lomi3g01867 . . Ecan1g02747 Soca1g02969 Glco1g01644 Artr1g07644 Aary9g00838 Aary17g00886 Aann5g04680 Chma8g08377 . Chmo17g03394 Chmo18g02892 Chla5g04174 Chna6g01828 Cind2g04250 Pdy1g05475 Cobi2g00622 Hean8g00403 Bial8g00363 Bial20g00128 Dapi18g02913 Dapi2g03739 Hetu23g00534 Hetu22g00459 Hetu24g00532 . Smso4g00470 Smso21g00499 Taer8g02256 Fro18g01563 Fso14g00472 Ftr1g02453 Fra1g01592 Fli5g00493 Stre8g02855 . . . . . . . . . . . . . . . . . . .
Vivi1g00044 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00045 Arla4g01959 Armi3g04263 Sain4g00785 Ceso4g04249 Cati7g00461 Ccar13g00312 Cien3g02854 Cich2g01183 Lssa8g01701 Laca8g01414 Tako5g02570 Tamo5g03372 Pslu5g12932 Lomi3g01865 . Enbr1g06002 Ecan1g02749 Soca1g02967 Glco1g01651 Artr1g07639 Aary9g02681 Aary17g00888 Aann5g04676 . Chmo16g03257 Chmo17g03399 . . Chna6g01824 Cind2g04247 Pdy1g05473 . . . . . . . . . . . . . . . . . . . . Cobi12g00188 Hean12g01061 . . Dapi8g00203 Dapi24g00159 Hetu47g03396 Hetu48g03160 Hetu46g03351 Amtr02g01412 Smso5g02212 Smso26g02839 Taer7g03570 . . Ftr13g02333 Fra14g01140 Fli15g01650
Vivi1g00046 Arla4g01960 Armi3g00282 Sain4g00786 Ceso4g04250 Cati7g00460 Ccar13g00311 Cien3g02853 . Lssa8g01702 Laca8g01416 . . Pslu5g12935 Lomi3g01864 Lomi4g01633 Enbr1g05976 Ecan1g02750 Soca1g02965 . . . . . . Chmo16g03258 Chmo17g03400 . . Chna6g01823 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00047 Arla4g01961 Armi3g04265 Sain4g00789 Ceso4g04252 Cati7g00458 Ccar13g00310 Cien3g02852 . Lssa8g01705 Laca8g01417 Tako5g02568 Tamo5g03370 Pslu5g12948 Lomi3g01863 Lomi4g01634 Enbr1g05977 Ecan1g02752 Soca1g02963 Glco1g01661 Artr1g07625 Aary9g00846 Aary17g00891 Aann5g04669 . Chmo16g03261 Chmo17g03404 Chmo18g02897 Chla5g04178 Chna6g01822 Cind2g04240 Pdy1g05471 Cobi2g00623 Hean8g00401 Bial8g00362 Bial20g00127 Dapi18g02914 Dapi2g03740 Hetu23g00535 Hetu22g00456 Hetu24g00524 Amtr09g02807 Smso4g00472 Smso21g00500 . . . . . . Stre8g02854 Mimi18g00266 . . . . . . . . . . . . . . . . . .
Vivi1g00048 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00049 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00050 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
Gene_GFF
Select Chromosome Start End Strand Old_gene Gene Num
5 146396262 146403131 + chr5g0331831 Aann5g04669 4669
5 146497237 146506169 - chr5g0331991 Aann5g04676 4676
5 146624262 146628913 + chr5g0332081 Aann5g04680 4680
8 43959689 43964069 + chr8g1064521 Aann8g00795 795
8 43967969 43971441 - chr8g1064551 Aann8g00796 796
4 194308135 194310623 + Aargg4g28880.1 Aary4g02888 2888
4 194313563 194318739 - Aargg4g28890.1 Aary4g02889 2889
9 83655789 83657045 - Aargg9g08380.1 Aary9g00838 838
9 83832762 83841228 - Aargg9g08460.1 Aary9g00846 846
9 158512654 158516069 + Aargg9g26810.1 Aary9g02681 2681
12 193791635 193794145 + Aargg12g28800.1 Aary12g02880 2880
12 193805372 193809905 - Aargg12g28810.1 Aary12g02881 2881
17 79158192 79161063 - Aargg17g08860.1 Aary17g00886 886
17 79322134 79330169 + Aargg17g08880.1 Aary17g00888 888
17 79424610 79429199 - Aargg17g08910.1 Aary17g00891 891
2 34470705 34476179 + AtrifAMIRv0_Chr02g0110081 Amtr02g01412 1412
9 74144295 74150202 - AtrifAMIRv0_Chr09g0599921 Amtr09g02807 2807
4 105349374 105352103 - evm.model.000240F.49 Arla4g01958 1958
4 105465971 105471140 + evm.model.000240F.47 Arla4g01959 1959
4 105482019 105486057 - evm.model.000240F.46 Arla4g01960 1960
4 105503620 105509780 + evm.model.000240F.45 Arla4g01961 1961
5 5394349 5399879 + evm.model.000113F.256 Arla5g00261 261
5 5415350 5420013 + evm.model.000113F.257 Arla5g00262 262
3 6154861 6159418 + AmiAMIRv0_Chr03g0092141 Armi3g00281 281
3 6187459 6191632 + AmiAMIRv0_Chr03g0092151 Armi3g00282 282
3 155048591 155051954 - AmiAMIRv0_Chr03g0131951 Armi3g04262 4262
3 155131895 155136565 + AmiAMIRv0_Chr03g0131961 Armi3g04263 4263
3 155205314 155209949 + AmiAMIRv0_Chr03g0131981 Armi3g04265 4265
1 222948839 222953430 + AtridAMIRv0_Chr01g0076251 Artr1g07625 7625
1 223400405 223405695 - AtridAMIRv0_Chr01g0076391 Artr1g07639 7639
1 223635066 223636036 + AtridAMIRv0_Chr01g0076441 Artr1g07644 7644
4 58839943 58840831 + AtridAMIRv0_Chr04g0461381 Artr4g01883 1883
4 58855597 58858133 + AtridAMIRv0_Chr04g0461411 Artr4g01886 1886
8 4016341 4019668 - g30785.t1 Bial8g00362 362
8 4023408 4030706 + g30786.t1 Bial8g00363 363
20 1442695 1445991 - g139554.t1 Bial20g00127 127
20 1454023 1457335 + g139553.t1 Bial20g00128 128
4 89478699 89481178 - CtAH04T0235800.1 Cati4g03132 3132
4 89490124 89498326 - CtAH04T0235900.1 Cati4g03133 3133
7 4269343 4275926 - CtAH07T0034100.1 Cati7g00458 458
7 4282976 4283581 + CtAH07T0034200.1 Cati7g00460 460
7 4289374 4295555 - CtAH07T0034300.1 Cati7g00461 461
7 4330798 4333853 + CtAH07T0034400.1 Cati7g00462 462
12 2227852 2234169 + gnl|WGS:LEKV|Ccrd_000183.mRNA.1_mrna Ccar12g00179 179
12 2239561 2242812 + gnl|WGS:LEKV|Ccrd_000184.mRNA.1_mrna Ccar12g00180 180
13 3715559 3721693 - gnl|WGS:LEKV|Ccrd_016191.mRNA.1_mrna Ccar13g00310 310
13 3734283 3737267 + gnl|WGS:LEKV|Ccrd_016192.mRNA.1_mrna Ccar13g00311 311
13 3738877 3744316 - gnl|WGS:LEKV|Ccrd_016193.mRNA.1_mrna Ccar13g00312 312
13 3784914 3789480 + gnl|WGS:LEKV|Ccrd_016194.mRNA.1_mrna Ccar13g00313 313
2 104855078 104857727 - >KAJ9563860.1 Ceso2g04381 4381
2 104858585 104871724 - >KAJ9563859.1 Ceso2g04382 4382
4 95651475 95655283 - >KAJ9554278.1 Ceso4g04248 4248
4 95674361 95680619 + >KAJ9554274.1 Ceso4g04249 4249
4 95682192 95686473 - >KAJ9554277.1 Ceso4g04250 4250
4 95702126 95703797 + >KAJ9554187.1 Ceso4g04252 4252
5 178986568 178990155 - ClaG1_Chr05g0338841 Chla5g04174 4174
5 179085698 179089923 - ClaG1_Chr05g0338881 Chla5g04178 4178
8 314703702 314706073 - CmaNakai_Chr08g0803511 Chma8g08377 8377
16 212773425 212789438 + evm.model.scaffold_226.54 Chmo16g03257 3257
16 212789880 212793051 - evm.model.scaffold_226.53 Chmo16g03258 3258
16 213217268 213223210 - evm.model.scaffold_226.22 Chmo16g03261 3261
17 230613027 230614592 - evm.model.scaffold_1419.91 Chmo17g03394 3394
17 230989238 231003548 + evm.model.scaffold_1419.119 Chmo17g03399 3399
17 231009939 231013238 - evm.model.scaffold_1419.120 Chmo17g03400 3400
17 231137049 231141257 - evm.model.scaffold_1419.136 Chmo17g03404 3404
18 233951179 233952202 - evm.model.scaffold_1054.83 Chmo18g02892 2892
18 234281070 234287388 - evm.model.scaffold_6071.29 Chmo18g02897 2897
6 113730153 113735765 + Cn0690580 Chna6g01822 1822
6 113981169 113984464 + Cn0690560 Chna6g01823 1823
6 113984976 113989736 - Cn0690550 Chna6g01824 1824
6 114170232 114174162 + Cn0690480 Chna6g01828 1828
2 39396903 39399434 - KAI3779129.1 Cich2g01181 1181
2 39528930 39532167 + KAI3779131.1 Cich2g01183 1183
3 6976115 6978756 + KAI3763691.1 Cich3g00251 251
3 75755364 75757688 + KAI3516592.1 Cien3g02852 2852
3 75798722 75801183 + KAI3516593.1 Cien3g02853 2853
3 75829829 75833195 - KAI3516594.1 Cien3g02854 2854
3 75914683 75918287 - KAI3516596.1 Cien3g02856 2856
8 4564964 4567745 + KAI3497801.1 Cien8g00218 218
2 117386762 117390319 + D.indicum_Contig547_G00002.t1 Cind2g04240 4240
2 117689887 117718937 - D.indicum_Contig547_G00009.t1 Cind2g04247 4247
2 118040085 118041535 + D.indicum_Contig547_G00012.t1 Cind2g04250 4250
2 7711769 7715984 - h2tg000034l_1.g20732.t1 Cobi2g00622 622
2 7730621 7734703 + h2tg000034l_1.g20731.t1 Cobi2g00623 623
12 1859901 1864529 - h2tg000030l_1.g18126.t1 Cobi12g00188 188
2 141409359 141416953 - h2tg000149l.g52070.t1 Dapi2g03739 3739
2 141422939 141428109 + h2tg000149l.g52069.t1 Dapi2g03740 3740
8 3546023 3564692 - h1tg000025l.g56604.t1 Dapi8g00203 203
18 131371565 131377427 - h1tg000021l.g26564.t1 Dapi18g02913 2913
18 131380183 131387275 + h1tg000021l.g26565.t1 Dapi18g02914 2914
24 2200964 2213334 - h1tg000067l.g106448.t1 Dapi24g00159 159
1 41772561 41775559 - XM_043781492.1 Ecan1g02747 2747
1 41818028 41823629 + XM_043757760.1 Ecan1g02749 2749
1 41824347 41827936 - XM_043784172.1 Ecan1g02750 2750
1 41841861 41847241 + XM_043757388.1 Ecan1g02752 2752
4 31356714 31360092 + XM_043770617.1 Ecan4g02022 2022
4 31371071 31374612 - XM_043770744.1 Ecan4g02025 2025
1 182172222 182175396 - evm.model.ctg228.4 Enbr1g05976 5976
1 182188101 182191988 + evm.model.ctg228.5 Enbr1g05977 5977
1 182789519 182794472 + evm.model.ctg8011.3 Enbr1g06002 6002
4 98147725 98149702 + evm.model.ctg771.8 Enbr4g02832 2832
5 8296300 8298802 - FliAMIRv0_Chr05g0125141 Fli5g00493 493
9 3198963 3203468 + FliAMIRv0_Chr09g0209201 Fli9g00153 153
15 59177066 59183489 + FliAMIRv0_Chr15g0347561 Fli15g01650 1650
1 76686925 76689465 + FraAMIRv0_Chr01g0015891 Fra1g01592 1592
14 42189934 42196057 - FraAMIRv0_Chr14g0282831 Fra14g01140 1140
13 1818387 1823008 + FroAMIRv0_Chr13g0223211 Fro13g00137 137
18 22541384 22543736 + FroAMIRv0_Chr18g0343221 Fro18g01563 1563
14 6344100 6346694 - FsoAMIRv0_Chr14g0344421 Fso14g00472 472
1 85406282 85408003 + FtrAMIRv0_Chr01g0024501 Ftr1g02453 2453
6 1368688 1373210 + FtrAMIRv0_Chr06g0162591 Ftr6g00109 109
13 76540445 76547979 + FtrAMIRv0_Chr13g0396041 Ftr13g02333 2333
1 81221949 81224318 - GcoAMIRv0_Chr01g0016441 Glco1g01644 1644
1 81687255 81715470 + GcoAMIRv0_Chr01g0016511 Glco1g01651 1651
1 82051738 82056036 - GcoAMIRv0_Chr01g0016611 Glco1g01661 1661
6 578871589 578874378 + GcoAMIRv0_Chr06g0439801 Glco6g05881 5881
6 578962673 578965495 - GcoAMIRv0_Chr06g0439821 Glco6g05883 5883
8 6830256 6836300 - gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr08g0322181 Hean8g00401 401
8 6879130 6884096 + gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr08g0322211 Hean8g00403 403
12 22856154 22857364 - gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr12g0532721 Hean12g01061 1061
17 194168465 194168960 + gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr17g0831331 Hean17g04527 4527
22 19535988 19539843 - >Htub.h1tg000131l.g523.t1 Hetu22g00456 456
22 19915100 19919309 + >Htub.h1tg000131l.g518.t1 Hetu22g00459 459
23 26987069 26989671 - >Htub.h1tg000843l.g157.t1 Hetu23g00534 534
23 27040438 27044218 + >Htub.h1tg000843l.g158.t1 Hetu23g00535 535
24 23163672 23167660 - >Htub.h1tg004074l.g253.t1 Hetu24g00524 524
24 23898460 23901743 + >Htub.h1tg004074l.g261.t1 Hetu24g00532 532
46 198391708 198398241 + >Htub.h1tg000449l.g194.t1 Hetu46g03351 3351
47 212974009 212978256 + >Htub.h1tg001680l.g385.t1 Hetu47g03396 3396
48 187484799 187496189 - >Htub.h2tg000112l.g332.t1 Hetu48g03160 3160
4 12141997 12145286 + CAI9278444.1 Laca4g00296 296
4 12151132 12153473 + CAI9278445.1 Laca4g00297 297
8 48996529 48999829 + CAI9296967.1 Laca8g01414 1414
8 49023951 49029131 - CAI9296969.1 Laca8g01416 1416
8 49199493 49202439 - CAI9296970.1 Laca8g01417 1417
3 15828338 15833324 - LmiAMIRv0_Chr03g0110511 Lomi3g01863 1863
3 15846579 15849296 + LmiAMIRv0_Chr03g0110521 Lomi3g01864 1864
3 15850861 15854984 - LmiAMIRv0_Chr03g0110531 Lomi3g01865 1865
3 15885112 15887950 + LmiAMIRv0_Chr03g0110551 Lomi3g01867 1867
4 24388557 24391166 - LmiAMIRv0_Chr04g0141031 Lomi4g01633 1633
4 24404205 24409143 + LmiAMIRv0_Chr04g0141041 Lomi4g01634 1634
8 13504791 13507259 - LmiAMIRv0_Chr08g0253861 Lomi8g01364 1364
10 12923892 12928252 + LmiAMIRv0_Chr10g0305221 Lomi10g01530 1530
10 12934116 12936569 - LmiAMIRv0_Chr10g0305231 Lomi10g01531 1531
4 20082559 20086428 + >KAJ0214564.1 Lssa4g00460 460
4 20094264 20096562 + >KAJ0214331.1 Lssa4g00461 461
8 70103956 70107239 - >KAJ0189349.1 Lssa8g01699 1699
8 70297147 70300832 + >KAJ0190823.1 Lssa8g01701 1701
8 70313957 70320376 - >KAJ0194155.1 Lssa8g01702 1702
8 70549667 70552740 - >KAJ0193539.1 Lssa8g01705 1705
18 5134256 5138609 - KAD2804160.1 Mimi18g00266 266
19 57041381 57048592 + KAD2393619.1 Mimi19g00922 922
1 115766415 115771621 - PdyAMIRv0_Chr01g0054671 Pdy1g05471 5471
1 115785279 115790287 - PdyAMIRv0_Chr01g0054691 Pdy1g05473 5473
1 115814453 115816378 + PdyAMIRv0_Chr01g0054711 Pdy1g05475 5475
2 3940152 3942477 + PdyAMIRv0_Chr02g0058241 Pdy2g00207 207
2 3953050 3957277 - PdyAMIRv0_Chr02g0058251 Pdy2g00208 208
4 21785195 21790774 + PluAMIRv0_Chr04g0612871 Pslu4g03334 3334
4 21794250 21797281 - PluAMIRv0_Chr04g0612881 Pslu4g03335 3335
5 95860449 95863922 - PluAMIRv0_Chr05g0877821 Pslu5g12924 12924
5 95917163 95921632 + PluAMIRv0_Chr05g0877901 Pslu5g12932 12932
5 95931864 95934592 - PluAMIRv0_Chr05g0877931 Pslu5g12935 12935
5 96040510 96045943 + PluAMIRv0_Chr05g0878051 Pslu5g12948 12948
4 21813951 21818097 - SinAMIRv0_Chr04g0091171 Sain4g00783 783
4 22052104 22056691 + SinAMIRv0_Chr04g0091191 Sain4g00785 785
4 22060872 22065783 - SinAMIRv0_Chr04g0091201 Sain4g00786 786
4 22090551 22094391 + SinAMIRv0_Chr04g0091231 Sain4g00789 789
9 215930839 215936211 + SinAMIRv0_Chr09g0250091 Sain9g04115 4115
9 215978899 215983669 + SinAMIRv0_Chr09g0250101 Sain9g04116 4116
4 6099818 6103043 - KAI3817323.1 Smso4g00470 470
4 6131006 6137093 + KAI3817325.1 Smso4g00472 472
5 110119248 110135362 + KAI3816632.1 Smso5g02212 2212
21 5061906 5064645 - KAI3730705.1 Smso21g00499 499
21 5073405 5080860 + KAI3730706.1 Smso21g00500 500
26 63123948 63130248 + KAI3696324.1 Smso26g02839 2839
1 33061059 33066716 - transfrag2506.t02 Soca1g02963 2963
1 33096211 33100240 + transfrag2507.t01 Soca1g02965 2965
1 33100940 33108672 - transfrag2508.t02 Soca1g02967 2967
1 33149806 33156686 + transfrag2509.t02 Soca1g02969 2969
9 21783603 21788384 + augustus02772.t04 Soca9g01931 1931
9 21802821 21806197 - transfrag2017.t02 Soca9g01937 1937
8 94794189 94799244 - Streb.8G028540.1 Stre8g02854 2854
8 94824927 94827584 + Streb.8G028550.1 Stre8g02855 2855
7 42366578 42370609 + >KAK1419889.1 Taer7g03570 3570
8 62732885 62734480 + >KAK1416013.1 Taer8g02256 2256
9 31034872 31038481 - >KAK1413728.1 Taer9g03088 3088
5 88871623 88874507 + TkA05G358130.1 Tako5g02568 2568
5 88896293 88897974 - TkA05G358170.1 Tako5g02570 2570
5 88953339 88956107 - TkA05G358380.4 Tako5g02576 2576
3 105800494 105805071 - TbA03G004380.1 Tamo3g05010 5010
5 78373409 78376118 + TbA05G097020.1 Tamo5g03370 3370
5 78384772 78390009 - TbA05G097040.1 Tamo5g03372 3372
5 78395479 78398194 - TbA05G097050.1 Tamo5g03373 3373
1 496479 498561 + GSVIVT01012217001 Vivi1g00041 41
1 498867 500438 - GSVIVT01012216001 Vivi1g00042 42
1 501310 504875 - GSVIVT01012215001 Vivi1g00043 43
1 506835 513217 - GSVIVT01012214001 Vivi1g00044 44
1 515730 520849 + GSVIVT01012213001 Vivi1g00045 45
1 523827 526024 - GSVIVT01012212001 Vivi1g00046 46
1 529830 543820 + GSVIVT01012211001 Vivi1g00047 47
1 544467 549815 - GSVIVT01012210001 Vivi1g00048 48
1 550211 556153 - GSVIVT01012209001 Vivi1g00049 49
1 558161 562819 + GSVIVT01012208001 Vivi1g00050 50
       
DecoBrowse