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AGRP

Asteraceae Genomic Research Platform

Gene Search

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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
Vivi19g01134 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01135 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01136 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01137 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01138 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01139 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01140 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01141 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01142 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01143 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
Gene_GFF
Select Chromosome Start End Strand Old_gene Gene Num
8 733123 735241 + evm.model.000077F.412 Arla8g00010 10
8 735240 744503 - evm.model.000077F.411 Arla8g00011 11
8 99849989 99858672 + AmiAMIRv0_Chr08g0297241 Armi8g02893 2893
8 99859182 99860952 - AmiAMIRv0_Chr08g0297251 Armi8g02894 2894
7 72777348 72791169 + CtAH07T0262000.1 Cati7g03578 3578
7 72791263 72799149 - CtAH07T0262100.1 Cati7g03582 3582
17 19598 22191 + gnl|WGS:LEKV|Ccrd_019320.mRNA.1_mrna Ccar17g00003 3
17 21778 32036 - gnl|WGS:LEKV|Ccrd_019321.mRNA.1_mrna Ccar17g00004 4
24 326677706 326681589 + evm.model.scaffold_857.24 Chmo24g05753 5753
24 326681929 326683678 - evm.model.scaffold_857.23 Chmo24g05754 5754
5 1855799 1859416 + Cn0259160 Chna5g00044 44
5 1859563 1866450 - Cn0259170 Chna5g00045 45
5 33631484 33637753 + XM_043773775.1 Ecan5g02024 2024
5 33637739 33640957 - XM_043773776.1 Ecan5g02025 2025
8 109309080 109312585 + evm.model.ctg51.16 Enbr8g03403 3403
8 109312829 109319749 - evm.model.ctg51.17 Enbr8g03404 3404
5 30031480 30033296 + LmiAMIRv0_Chr05g0175081 Lomi5g01859 1859
5 30036515 30037723 - LmiAMIRv0_Chr05g0175101 Lomi5g01861 1861
11 26310691 26312505 + LmiAMIRv0_Chr11g0337691 Lomi11g01798 1798
3 114379732 114381483 + PluAMIRv0_Chr03g0557251 Pslu3g15898 15898
3 114383289 114389099 - PluAMIRv0_Chr03g0557261 Pslu3g15899 15899
13 139414314 139423575 + SinAMIRv0_Chr13g0402671 Sain13g02711 2711
13 139424124 139425748 - SinAMIRv0_Chr13g0402681 Sain13g02712 2712
2 91394685 91401337 + transfrag28210.t01 Soca2g04670 4670
19 22763855 22769558 + GSVIVT01036771001 Vivi19g01134 1134
19 22805628 22810184 + GSVIVT01036767001 Vivi19g01135 1135
19 22830808 22834737 + GSVIVT01036765001 Vivi19g01136 1136
19 22835275 22848066 + GSVIVT01036764001 Vivi19g01137 1137
19 22854358 22885790 + GSVIVT01036763001 Vivi19g01138 1138
19 22886899 22896623 - GSVIVT01036762001 Vivi19g01139 1139
19 22897111 22905063 + GSVIVT01036761001 Vivi19g01140 1140
19 22905487 22906558 - GSVIVT01036760001 Vivi19g01141 1141
19 22906565 22924143 - GSVIVT01036759001 Vivi19g01142 1142
19 22924599 22935504 - GSVIVT01036758001 Vivi19g01143 1143
       
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