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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
Vivi19g00904 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g00905 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g00906 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g00907 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g00908 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g00909 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g00910 Arla1g00409 Armi1g00508 Sain12g00461 Ceso2g01377 Cati3g00569 Ccar2g01986 . Cich4g04457 Lssa7g03429 Laca7g02776 . Tamo4g02910 Pslu1g21413 Lomi1g00283 Lomi2g04374 . Ecan3g02132 Soca5g02527 Glco3g01082 . Aary5g02819 Aary13g03292 Aann4g01161 Chma7g08157 Chmo13g00752 . Chmo15g00627 . Chna2g00606 . Pdy4g00489 . Hean15g03897 Bial24g02234 Bial12g02377 . . . Hetu16g02659 . Amtr02g04059 . . . . . . . . . . Cobi4g03133 Hean11g00740 Bial4g03417 Bial16g02813 Dapi7g00286 Dapi23g00314 Hetu32g00609 Hetu31g00561 Hetu33g00707 . Smso7g00071 Smso29g00079 Taer1g05525 Fro12g02396 Fso2g00236 Ftr4g03693 Fra11g02534 Fli1g00269
Vivi19g00911 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g00912 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g00913 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
Gene_GFF
Select Chromosome Start End Strand Old_gene Gene Num
4 61811986 61816947 - chr4g0777071 Aann4g01161 1161
5 169493816 169497992 - Aargg5g28190.1 Aary5g02819 2819
13 196359109 196364159 - Aargg13g32920.1 Aary13g03292 3292
2 80952954 80956800 + AtrifAMIRv0_Chr02g0136551 Amtr02g04059 4059
1 9694410 9701455 - evm.model.000012F.535 Arla1g00409 409
8 8225823 8230031 - evm.model.000043F.420 Arla8g00358 358
1 10479132 10486059 - AmiAMIRv0_Chr01g0005081 Armi1g00508 508
8 91564521 91569465 + AmiAMIRv0_Chr08g0292431 Armi8g02412 2412
4 77908760 77913012 - g43256.t1 Bial4g03417 3417
12 54107587 54111660 - g35576.t1 Bial12g02377 2377
16 72200217 72204034 - g127387.t1 Bial16g02813 2813
24 52991689 52992794 - g67900.t1 Bial24g02234 2234
3 5760394 5772918 - CtAH03T0039800.1 Cati3g00569 569
2 66676744 66685083 + gnl|WGS:LEKV|Ccrd_011033.mRNA.1_mrna Ccar2g01986 1986
17 3006963 3011422 - gnl|WGS:LEKV|Ccrd_019594.mRNA.1_mrna Ccar17g00272 272
2 28025527 28033977 - >KAJ9560685.1 Ceso2g01377 1377
2 39915043 39923956 - ClaG1_Chr02g0089841 Chla2g01282 1282
6 42549770 42552954 + CmaNakai_Chr06g0530401 Chma6g01891 1891
7 278518533 278522371 - CmaNakai_Chr07g0704591 Chma7g08157 8157
13 36193191 36197123 + evm.model.scaffold_461.11 Chmo13g00752 752
15 33427554 33432238 + evm.model.scaffold_126.170 Chmo15g00627 627
22 293822933 293831631 + evm.model.scaffold_448.446 Chmo22g04863 4863
2 41651582 41656080 + Cn0067540 Chna2g00606 606
5 45467476 45484829 - Cn0367660 Chna5g00910 910
4 130329616 130332745 + KAI3753592.1 Cich4g04457 4457
1 358002643 358016034 + D.indicum_Contig40_G00083.t1 Cind1g03320 3320
4 80827740 80831672 - h2tg000009l_1.g42146.t1 Cobi4g03133 3133
7 5826085 5828986 + h1tg000030l.g76876.t1 Dapi7g00286 286
23 6471340 6474463 + h2tg000284l.g80731.t1 Dapi23g00314 314
3 32145044 32149725 + XM_043763590.1 Ecan3g02132 2132
1 5467859 5471412 + FliAMIRv0_Chr01g0002641 Fli1g00269 269
11 78956443 78959967 - FraAMIRv0_Chr11g0225561 Fra11g02534 2534
12 31730401 31733781 - FroAMIRv0_Chr12g0219441 Fro12g02396 2396
2 3293235 3296671 + FsoAMIRv0_Chr02g0030551 Fso2g00236 236
4 120768886 120771200 - FtrAMIRv0_Chr04g0131271 Ftr4g03693 3693
3 64977377 64981387 + GcoAMIRv0_Chr03g0167111 Glco3g01082 1082
11 16196630 16201962 + gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr11g0474521 Hean11g00740 740
15 148262798 148269017 + gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr15g0716041 Hean15g03897 3897
16 142899891 142905304 - >Htub.h1tg002434l.g121.t1 Hetu16g02659 2659
31 20870748 20874310 + >Htub.h1tg001429l.g302.t1 Hetu31g00561 561
32 25017608 25021460 + >Htub.h1tg002251l.g283.t1 Hetu32g00609 609
33 25715798 25719658 + >Htub.h1tg001292l.g295.t1 Hetu33g00707 707
7 133396153 133398696 - CAI9294964.1 Laca7g02776 2776
1 2404502 2407668 + LmiAMIRv0_Chr01g0002831 Lomi1g00283 283
2 49092290 49095595 - LmiAMIRv0_Chr02g0089071 Lomi2g04374 4374
7 180983489 180987058 + >KAJ0196638.1 Lssa7g03429 3429
17 13115387 13122488 + KAD3066716.1 Mimi17g00394 394
4 9132788 9137861 + PdyAMIRv0_Chr04g0152971 Pdy4g00489 489
1 153797410 153801002 - PluAMIRv0_Chr01g0213191 Pslu1g21413 21413
12 10004266 10007786 - SinAMIRv0_Chr12g0360251 Sain12g00461 461
7 1446450 1450930 - KAI3809651.1 Smso7g00071 71
29 1581111 1586828 - KAI3675073.1 Smso29g00079 79
5 27414765 27419489 - transfrag11155.t01 Soca5g02527 2527
6 10236663 10240316 + Streb.6G003820.1 Stre6g00382 382
1 50473541 50476576 - >KAK1439705.1 Taer1g05525 5525
4 55436911 55440201 - TbA04G027920.1 Tamo4g02910 2910
19 15949808 15951051 + GSVIVT01000707001 Vivi19g00904 904
19 16043352 16044854 - GSVIVT01001953001 Vivi19g00905 905
19 16083440 16094232 + GSVIVT01001955001 Vivi19g00906 906
19 16094252 16095562 + GSVIVT01001956001 Vivi19g00907 907
19 16133519 16143123 - GSVIVT01001958001 Vivi19g00908 908
19 16143331 16146668 + GSVIVT01001959001 Vivi19g00909 909
19 16295964 16310858 + GSVIVT01001961001 Vivi19g00910 910
19 16323933 16326346 + GSVIVT01001963001 Vivi19g00911 911
19 16375070 16380407 + GSVIVT01038019001 Vivi19g00912 912
19 16398332 16399024 + GSVIVT01038021001 Vivi19g00913 913
       
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