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
Vivi19g01114 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01115 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01116 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01117 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01118 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01119 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01120 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01121 Arla1g00092 Armi1g00107 Sain12g00105 . Cati3g00143 Ccar2g02309 Cien5g03547 Cich4g04856 Lssa7g03790 . Tako4g03067 . Pslu1g20712 . Lomi2g04181 Enbr6g03568 Ecan3g00187 Soca5g05354 . Artr3g10745 . Aary13g03116 Aann4g00714 . . . . . Chna2g00998 Cind3g02021 Pdy4g00862 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01122 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01123 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
Gene_GFF
Select Chromosome Start End Strand Old_gene Gene Num
4 47850730 47852748 - chr4g0764631 Aann4g00714 714
13 183963643 183967477 - Aargg13g31160.1 Aary13g03116 3116
1 1657789 1661284 + evm.model.000012F.115 Arla1g00092 92
8 781630 796167 + evm.model.000077F.406 Arla8g00014 14
1 1618274 1621596 + AmiAMIRv0_Chr01g0001071 Armi1g00107 107
8 99767168 99784174 - AmiAMIRv0_Chr08g0297201 Armi8g02889 2889
3 362643756 362647726 - AtridAMIRv0_Chr03g0414811 Artr3g10745 10745
3 793266 809220 + CtAH03T0007900.2 Cati3g00143 143
7 72816177 72826615 + CtAH07T0262300.2 Cati7g03586 3586
2 70265400 70268225 - gnl|WGS:LEKV|Ccrd_011360.mRNA.1_mrna Ccar2g02309 2309
17 45667 60184 + gnl|WGS:LEKV|Ccrd_019324.mRNA.1_mrna Ccar17g00007 7
6 14720476 14720670 + CmaNakai_Chr06g0517531 Chma6g00604 604
24 326551487 326558006 - evm.model.scaffold_857.32 Chmo24g05749 5749
2 77803123 77806990 + Cn0814790 Chna2g00998 998
5 1965254 1971899 + Cn0259270 Chna5g00050 50
4 137410472 137411414 + KAI3753991.1 Cich4g04856 4856
5 81331527 81332539 + KAI3510067.1 Cien5g03547 3547
3 310267192 310270763 - D.indicum_Contig21_G00065.t1 Cind3g02021 2021
3 1978986 1983199 - XM_043765919.1 Ecan3g00187 187
5 33606884 33613553 - XM_043772113.1 Ecan5g02021 2021
6 132008204 132012396 + evm.model.ctg1703.2 Enbr6g03568 3568
8 109366950 109373445 + evm.model.ctg51.21 Enbr8g03408 3408
2 47393992 47396197 - LmiAMIRv0_Chr02g0087141 Lomi2g04181 4181
11 26334261 26339986 + LmiAMIRv0_Chr11g0337721 Lomi11g01801 1801
7 199069394 199070508 + >KAJ0196064.1 Lssa7g03790 3790
4 15684101 15691785 + PdyAMIRv0_Chr04g0156691 Pdy4g00862 862
1 149459844 149462413 - PluAMIRv0_Chr01g0206211 Pslu1g20712 20712
3 114408411 114414291 + PluAMIRv0_Chr03g0557301 Pslu3g15903 15903
12 1384417 1387148 + SinAMIRv0_Chr12g0356701 Sain12g00105 105
13 139362173 139370875 - SinAMIRv0_Chr13g0402621 Sain13g02706 2706
2 91341791 91348224 - augustus42321.t02 Soca2g04666 4666
5 73678625 73683624 - transfrag23898.t01 Soca5g05354 5354
4 59511430 59512886 + TkA04G234400.1 Tako4g03067 3067
19 22386461 22391612 - GSVIVT01036800001 Vivi19g01114 1114
19 22400680 22412010 + GSVIVT01036799001 Vivi19g01115 1115
19 22420569 22445496 + GSVIVT01036797001 Vivi19g01116 1116
19 22472388 22474179 - GSVIVT01036794001 Vivi19g01117 1117
19 22499713 22500162 - GSVIVT01036793001 Vivi19g01118 1118
19 22500178 22502622 - GSVIVT01036792001 Vivi19g01119 1119
19 22505327 22505756 + GSVIVT01036791001 Vivi19g01120 1120
19 22522288 22530061 + GSVIVT01036789001 Vivi19g01121 1121
19 22530547 22543278 + GSVIVT01036788001 Vivi19g01122 1122
19 22546264 22547496 + GSVIVT01036787001 Vivi19g01123 1123
       
DecoBrowse