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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
Vivi19g00954 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g00955 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g00956 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g00957 Arla1g00420 . Sain12g00475 Ceso2g01383 Cati3g00583 Ccar2g01978 . . Lssa7g03414 Laca7g02765 . Tamo4g02929 Pslu1g21429 Lomi1g00274 Lomi2g04382 Enbr6g01732 Ecan3g02120 Soca5g02540 . . Aary5g02835 . Aann4g01177 . Chmo13g00731 Chmo14g00721 Chmo15g00604 . Chna2g00575 Cind3g03790 . . . . . . . . . . . . . . . . . . . . . Cobi4g03141 Hean11g00726 Bial4g03423 Bial16g02819 Dapi7g00278 Dapi23g00304 Hetu32g00602 Hetu31g00546 Hetu33g00693 . Smso7g00081 Smso29g00088 . . . . . .
Vivi19g00958 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g00959 Arla1g00421 Armi1g00529 Sain12g00476 Ceso2g01384 Cati3g00584 Ccar2g01977 Cien5g03175 Cich4g04445 Lssa7g03413 Laca7g02764 . Tamo4g02930 Pslu1g21430 Lomi1g00273 Lomi2g04383 Enbr6g01731 Ecan3g02119 Soca5g02541 . . Aary5g02836 . Aann4g01178 . Chmo13g00730 Chmo14g00720 Chmo15g00603 . Chna2g00574 Cind3g03791 Pdy4g00481 . Hean15g03887 Bial24g02238 Bial12g02381 . . Hetu17g02563 Hetu16g02663 . Amtr02g04051 . Smso13g00176 . . . . . . Stre9g01619 Mimi9g01450 Cobi4g03142 Hean11g00725 Bial4g03424 Bial16g02820 Dapi7g00277 Dapi23g00303 Hetu32g00600 Hetu31g00541 Hetu33g00692 . Smso7g00082 Smso29g00089 Taer1g05534 Fro12g02403 . Ftr4g03699 Fra11g02542 Fli1g00259
Vivi19g00960 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g00961 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g00962 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g00963 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
Gene_GFF
Select Chromosome Start End Strand Old_gene Gene Num
1 71668334 71675815 - chr1g0064451 Aann1g02280 2280
4 63002724 63007764 + chr4g0778051 Aann4g01177 1177
4 63007766 63014272 - chr4g0778061 Aann4g01178 1178
5 171943690 171948354 + Aargg5g28350.1 Aary5g02835 2835
5 171948511 171954242 - Aargg5g28360.1 Aary5g02836 2836
7 215054232 215061719 - Aargg7g25410.1 Aary7g02541 2541
15 197878197 197884959 - Aargg15g25690.1 Aary15g02569 2569
2 80800082 80805718 + AtrifAMIRv0_Chr02g0136471 Amtr02g04051 4051
1 10562166 10579310 + evm.model.000012F.556 Arla1g00420 420
1 10580134 10586464 - evm.model.000012F.557 Arla1g00421 421
8 8448662 8455027 + evm.model.000043F.408 Arla8g00363 363
1 11280868 11286336 - AmiAMIRv0_Chr01g0005291 Armi1g00529 529
8 91129902 91135751 - AmiAMIRv0_Chr08g0292321 Armi8g02401 2401
4 78050995 78054906 + g43262.t1 Bial4g03423 3423
4 78056260 78061719 - g43263.t1 Bial4g03424 3424
12 54157226 54163170 - g35580.t1 Bial12g02381 2381
16 72334378 72335554 + g127381.t1 Bial16g02819 2819
16 72338103 72343556 - g127380.t1 Bial16g02820 2820
24 53045004 53050943 - g67904.t1 Bial24g02238 2238
3 6047796 6059757 + CtAH03T0041000.1 Cati3g00583 583
3 6060846 6066674 - CtAH03T0041100.1 Cati3g00584 584
7 68197270 68204812 - CtAH07T0233600.1 Cati7g03159 3159
2 66523402 66529993 + gnl|WGS:LEKV|Ccrd_011024.mRNA.1_mrna Ccar2g01977 1977
2 66530503 66538720 - gnl|WGS:LEKV|Ccrd_011025.mRNA.1_mrna Ccar2g01978 1978
17 3088909 3094780 + gnl|WGS:LEKV|Ccrd_019599.mRNA.1_mrna Ccar17g00277 277
2 28263588 28269422 + >KAJ9560690.1 Ceso2g01383 1383
2 28272087 28276594 - >KAJ9560692.1 Ceso2g01384 1384
6 42477504 42484611 - CmaNakai_Chr06g0530341 Chma6g01885 1885
13 34812770 34818956 + evm.model.scaffold_597.85 Chmo13g00730 730
13 34819425 34823672 - evm.model.scaffold_597.86 Chmo13g00731 731
14 32911198 32915781 + evm.model.scaffold_489.41 Chmo14g00720 720
14 32916922 32921151 - evm.model.scaffold_489.42 Chmo14g00721 721
15 31998917 32004187 + evm.model.scaffold_1740.112 Chmo15g00603 603
15 32005621 32009476 - evm.model.scaffold_1740.113 Chmo15g00604 604
22 293655845 293663137 - evm.model.scaffold_448.430 Chmo22g04857 4857
23 286054727 286061662 - evm.model.scaffold_1107.67 Chmo23g04808 4808
24 289608385 289692856 - evm.model.scaffold_421.391 Chmo24g04818 4818
2 39819399 39825206 + Cn0172490 Chna2g00574 574
2 39825805 39838651 - Cn0172480 Chna2g00575 575
5 45798107 45804957 + Cn0367770 Chna5g00915 915
4 129953488 129958710 + KAI3753580.1 Cich4g04445 4445
5 76634197 76639596 + KAI3509695.1 Cien5g03175 3175
1 357855274 357906781 - D.indicum_Contig40_G00088.t1 Cind1g03325 3325
3 338155215 338158800 + D.indicum_Contig415_G00017.t1 Cind3g03790 3790
3 338159824 338165088 - D.indicum_Contig415_G00018.t1 Cind3g03791 3791
4 80969740 80974680 + h2tg000009l_1.g42138.t1 Cobi4g03141 3141
4 80975628 80981204 - h2tg000009l_1.g42137.t1 Cobi4g03142 3142
7 5551589 5559946 + h1tg000136l.g124387.t1 Dapi7g00277 277
7 5561300 5565109 - h1tg000136l.g124386.t1 Dapi7g00278 278
23 6167912 6174044 + h2tg000284l.g80742.t1 Dapi23g00303 303
23 6175484 6179944 - h2tg000284l.g80741.t1 Dapi23g00304 304
3 31992623 31998959 + XM_043766149.1 Ecan3g02119 2119
3 31999779 32003256 - XM_043766840.1 Ecan3g02120 2120
5 30030196 30038438 - XM_043773140.1 Ecan5g01629 1629
6 61152932 61158516 + evm.model.ctg2652.3 Enbr6g01731 1731
6 61159886 61163004 - evm.model.ctg2652.2 Enbr6g01732 1732
1 5167083 5172217 + FliAMIRv0_Chr01g0002541 Fli1g00259 259
4 82170797 82174738 - FliAMIRv0_Chr04g0109461 Fli4g01356 1356
11 79080728 79086047 - FraAMIRv0_Chr11g0225641 Fra11g02542 2542
12 31871647 31876932 - FroAMIRv0_Chr12g0219511 Fro12g02403 2403
4 120910927 120912036 - FtrAMIRv0_Chr04g0131331 Ftr4g03699 3699
8 11493173 11496853 + FtrAMIRv0_Chr08g0230021 Ftr8g00925 925
7 575559649 575568414 - GcoAMIRv0_Chr07g0516261 Glco7g06841 6841
3 122556170 122558111 - gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr03g0113691 Hean3g02220 2220
11 15515406 15524248 + gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr11g0474361 Hean11g00725 725
11 15532312 15538997 - gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr11g0474371 Hean11g00726 726
15 147609911 147616300 + gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr15g0715931 Hean15g03887 3887
7 74047140 74048819 + >Htub.h1tg004285l.g233.t1 Hetu7g01759 1759
8 69965856 69966422 + >Htub.h1tg001170l.g396.t1 Hetu8g01606 1606
16 143833864 143839379 - >Htub.h1tg002434l.g117.t1 Hetu16g02663 2663
17 136000317 136005830 - >Htub.h1tg000886l.g411.t1 Hetu17g02563 2563
31 20015212 20018933 + >Htub.h1tg001429l.g322.t1 Hetu31g00541 541
31 20109017 20110224 - >Htub.h1tg001429l.g317.t1 Hetu31g00546 546
32 24319843 24327134 + >Htub.h1tg001952l.g165.t1 Hetu32g00600 600
32 24331751 24338721 - >Htub.h1tg001952l.g163.t1 Hetu32g00602 602
33 24222642 24229968 + >Htub.h1tg000986l.g381.t1 Hetu33g00692 692
33 24269824 24275756 - >Htub.h1tg000986l.g380.t1 Hetu33g00693 693
7 132134636 132139931 + CAI9294952.1 Laca7g02764 2764
7 132139800 132143601 - CAI9294953.1 Laca7g02765 2765
9 135812375 135816581 + CAI9303897.1 Laca9g03302 3302
1 2297502 2302871 + LmiAMIRv0_Chr01g0002731 Lomi1g00273 273
1 2303853 2308194 - LmiAMIRv0_Chr01g0002741 Lomi1g00274 274
2 49195575 49199202 + LmiAMIRv0_Chr02g0089151 Lomi2g04382 4382
2 49200216 49205565 - LmiAMIRv0_Chr02g0089161 Lomi2g04383 4383
5 31952926 31955745 + LmiAMIRv0_Chr05g0177811 Lomi5g02132 2132
11 27992729 27997366 + LmiAMIRv0_Chr11g0339281 Lomi11g01957 1957
7 179333756 179339345 + >KAJ0197696.1 Lssa7g03413 3413
7 179339655 179342420 - >KAJ0195177.1 Lssa7g03414 3414
9 187312351 187316167 + >KAJ0184656.1 Lssa9g03737 3737
9 49485734 49487166 - KAD5318185.1 Mimi9g01450 1450
17 12475859 12481783 + KAD3066706.1 Mimi17g00384 384
17 12482014 12489546 - KAD3066707.1 Mimi17g00385 385
4 8929169 8934708 + PdyAMIRv0_Chr04g0152891 Pdy4g00481 481
9 41609262 41614126 - PdyAMIRv0_Chr09g0346401 Pdy9g01833 1833
1 153963750 153968692 + PluAMIRv0_Chr01g0213351 Pslu1g21429 21429
1 153969685 153974855 - PluAMIRv0_Chr01g0213361 Pslu1g21430 21430
3 117421934 117426722 + PluAMIRv0_Chr03g0562151 Pslu3g16388 16388
12 10389811 10393200 + SinAMIRv0_Chr12g0360391 Sain12g00475 475
12 10394626 10399404 - SinAMIRv0_Chr12g0360401 Sain12g00476 476
13 130975013 130979907 - SinAMIRv0_Chr13g0398791 Sain13g02323 2323
7 1685084 1690181 + KAI3809661.1 Smso7g00081 81
7 1696195 1702362 - KAI3809662.1 Smso7g00082 82
13 11176284 11182436 + KAI3786433.1 Smso13g00176 176
18 73663253 73666746 - KAI3755693.1 Smso18g01568 1568
29 1777780 1782850 + KAI3675082.1 Smso29g00088 88
29 1784133 1790950 - KAI3675083.1 Smso29g00089 89
5 27673643 27677524 + augustus16796.t01 Soca5g02540 2540
5 27677870 27684808 - transfrag11166.t01 Soca5g02541 2541
2 139181714 139184640 - Streb.2G037160.1 Stre2g03716 3716
6 9973399 9980822 + Streb.6G003740.1 Stre6g00374 374
6 9981918 9987343 - Streb.6G003750.1 Stre6g00375 375
9 28553390 28557542 - Streb.9G016190.1 Stre9g01619 1619
1 50599739 50605424 - >KAK1439714.1 Taer1g05534 5534
2 3419110 3426909 + TkA02G014930.3 Tako2g00080 80
4 55934403 55937693 + TbA04G027280.1 Tamo4g02929 2929
4 55938615 55944910 - TbA04G027270.1 Tamo4g02930 2930
19 18240229 18240658 - GSVIVT01020506001 Vivi19g00954 954
19 18279468 18280235 - GSVIVT01020504001 Vivi19g00955 955
19 18293840 18303006 + GSVIVT01020503001 Vivi19g00956 956
19 18332102 18339207 - GSVIVT01020501001 Vivi19g00957 957
19 18355036 18355749 + GSVIVT01020500001 Vivi19g00958 958
19 18431718 18445331 - GSVIVT01020495001 Vivi19g00959 959
19 18546032 18549457 - GSVIVT01020490001 Vivi19g00960 960
19 18550102 18552220 - GSVIVT01020489001 Vivi19g00961 961
19 18583209 18592268 - GSVIVT01020487001 Vivi19g00962 962
19 18593103 18595449 - GSVIVT01020486001 Vivi19g00963 963
       
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