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
Eupl1g00051	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Eupl1g00052	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Eupl1g00053	Eupl5g00089	Nenu2g04012	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Eupl1g00054	Eupl5g00090	Nenu2g04011	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Eupl1g00055	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Eupl1g00056	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Eupl1g00057	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Eupl1g00058	Eupl5g00093	Nenu2g04010	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Eupl1g00059	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Eupl1g00060	.	Nenu2g04007	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.

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Gene_GFF

Chromosome	Start	End	Strand	Old_gene	Gene	Num
1	1673360	1675225	+	evm.model.CTG_111.59	Eupl1g00051	51
1	1675570	1677243	+	evm.model.CTG_111.60	Eupl1g00052	52
1	1708996	1711054	+	evm.model.CTG_111.61	Eupl1g00053	53
1	1725383	1735089	-	evm.model.CTG_111.62	Eupl1g00054	54
1	1742361	1744513	+	evm.model.CTG_111.63	Eupl1g00055	55
1	1752930	1858713	-	evm.model.CTG_111.67	Eupl1g00056	56
1	1874958	1878036	-	evm.model.CTG_111.68	Eupl1g00057	57
1	1885043	1900993	-	evm.model.CTG_111.69	Eupl1g00058	58
1	1950126	2050129	+	evm.model.CTG_111.71	Eupl1g00059	59
1	2059447	2060500	+	evm.model.CTG_111.72	Eupl1g00060	60
5	1926317	1928733	+	evm.model.CTG_219.114	Eupl5g00089	89
5	1954292	1964608	-	evm.model.CTG_219.113	Eupl5g00090	90
5	2049146	2088791	-	evm.model.CTG_219.108	Eupl5g00093	93
2	108170413	108171315	-	OF23208.mRNA1	Nenu2g04007	4007
2	108214516	108225446	+	OF23205.mRNA1	Nenu2g04010	4010
2	108233996	108240953	+	OF23204.mRNA1	Nenu2g04011	4011
2	108267300	108269196	-	OF23203.mRNA1	Nenu2g04012	4012

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