Export list of full length DNA gene sequences

Question

[David]

Hi all,

I'm trying to export a list of genes of multiple species from genome browser using the table browser tool.

I want to export the full DNA sequences (including exons, introns etc.) for each gene. The issue that I'm having is that I have to go through the NCBI RefSeq accession numbers and provide transcript accession numbers. Since I want the full gene length, this means that I have to identify which transcript is the longest etc. - I'm trying to avoid this as I have 50 genes from 30 species, meaning I'd have to probe 150 accession numbers for length. Is there a way to export these with the gene name alone or something like that?

Please let me know where my assumptions are wrong, open to suggestions.

Thanks

David

Answer 1

[Rafael Soler]

Hello,

For example, in the UCSC Genome Browser, you can search for a region of the genome by entering the coordinates.

Once you have the genes you want to download, you hit "Tools" in the navigation panel above, to "Table browser". In this you select in the term "table" the option "RefSeq Curated" and give get output.

You select it to be genomic information, and you can download the parts of the genes you want, clicking on the "One fasta record per gene" button.

I hope this has been helpful and is what you are looking for.

Best,

Rafa

[GenoMax]

Couple of potential issues. You may not be get the longest transcript (if you choose one record per gene unless you know otherwise). OP also needs to do this for 30 species which may not be all covered by UCSC browser.

[Rafael Soler]

Yes, that is correct. We need more information to answer the question. What species are you looking for? Do you need the longer or canonical isoforms?

Best

[David]

Hi both, sorry for the slow reply. The above is helpful, thanks! In terms of the 30 species, I've now reduced this to 10 which are in UCSC genome browser.