Extract the mRNA sequences of all the orthologs of a eukaryotic gene

Question

[khorms]

I want to build a multiple sequence alignment of the 3'UTR of a single gene across all the eukaryotes. However, I am struggling to find a way to extract mRNA sequences of all the orthologs of the gene. Any recommendations?

[manaswwm]

If I understand your question correctly - you have a reference gene (mRNA sequence) and you want to perform alignments of this gene across species that are closely related to generate a multiple sequence alignment?

If you have access to all the gene sequences for all the species then have you considered performing a reciprocal ortholog search? For example, as described in the Methods section of this paper.