Hierarchical alignments with the <em>Euptelea pleiosperma</em> genome as reference

Gene Search

Species

Gene ID

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Or, Query Sequence

Example:

Hierarchical alignments with the Euptelea pleiosperma genome as reference

Inter-genomic and intra-genomic comparisons can help reveal the structural complexity of Asteraceae genomes. We used Euptelea pleiosperma as a reference, and by comparing homologous gene locus maps and Ks values between Euptelea pleiosperma and other Asteraceae, we could separate orthologous and paralogous genes produced by different polyploidization in the species genomes.
The relevant gene ids can be obtained from the Asteraceae blast and match under the Tools module. This link is Asteraceae blast and match.

Query Sequence

Or, Gene ID

Species

Eupl_1	Eupl_2	Nenu_1	Nenu_2	Tesi_1	Tesi_2	Tesi_3	Tesi_4	Busi_1	Busi_2	Vivi_1	Vivi_2	Vivi_3	Nin_1	Nin_2	Nin_3	Arla_1	Arla_2	Arla_3	Arla_4	Arla_5	Arla_6	Arla_7	Arla_8	Arla_9
Eupl1g00041	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Eupl1g00042	.	Nenu2g04022	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Eupl1g00043	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Eupl1g00044	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Eupl1g00045	.	Nenu2g04018	.	.	.	.	.	.	.	.	.	Vivi13g00847	.	.	.	.	.	.	.	.	.	.	.	.
Eupl1g00046	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Eupl1g00047	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Eupl1g00048	Eupl5g00083	Nenu2g04016	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Eupl1g00049	Eupl5g00084	.	Nenu7g01090	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Eupl1g00050	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.

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Gene_GFF

Chromosome	Start	End	Strand	Old_gene	Gene	Num
1	1360442	1361208	+	evm.model.CTG_111.46	Eupl1g00041	41
1	1384667	1398755	-	evm.model.CTG_111.47	Eupl1g00042	42
1	1417178	1419233	-	evm.model.CTG_111.48	Eupl1g00043	43
1	1426440	1446490	-	evm.model.CTG_111.49	Eupl1g00044	44
1	1461952	1469358	+	evm.model.CTG_111.50	Eupl1g00045	45
1	1471080	1529675	-	evm.model.CTG_111.51.1	Eupl1g00046	46
1	1565793	1567771	+	evm.model.CTG_111.52	Eupl1g00047	47
1	1599095	1602010	-	evm.model.CTG_111.54	Eupl1g00048	48
1	1634033	1640026	+	evm.model.CTG_111.56	Eupl1g00049	49
1	1653890	1655358	+	evm.model.CTG_111.57	Eupl1g00050	50
5	1792869	1795088	+	evm.model.CTG_219.121	Eupl5g00083	83
5	1822027	1826266	+	evm.model.CTG_219.120	Eupl5g00084	84
2	108410276	108413055	+	OF23199.mRNA1	Nenu2g04016	4016
2	108511281	108578508	-	OF23197.mRNA1	Nenu2g04018	4018
2	108594826	108595626	+	OF23193.mRNA1	Nenu2g04022	4022
7	24147097	24169035	-	OF21080.mRNA1	Nenu7g01090	1090
13	15578271	15597859	+	GSVIVT01027370001	Vivi13g00847	847

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