<div dir="ltr"><div><div><div><div>Hi Kashi,<br><br></div>Working/filtered gene sets were not created for RefGen_v3. The corresponding filtered gene set in v3 would be "protein-coding" genes including ~39K. For this, we have gff files at <a href="ftp://ftp.maizesequence.org/pub/maize/release-5b+/">ftp://ftp.maizesequence.org/pub/maize/release-5b+/</a> <br>
</div>You could get fasta sequence for all the protein coding genes using the Gramene Mart at <a href="http://ensembl.gramene.org/biomart/martview">http://ensembl.gramene.org/biomart/martview</a>. Under "Filters", select "protein_coding" gene type and "Sequence" under "Attributes".<br>
<br></div>I will see to upload a file with the sequence for the cds of all protein-coding genes in FASTA format.<br><br></div>Marcela<br><div><br></div><div class="gmail_extra"><br>
<br><br><div class="gmail_quote">On Wed, Feb 26, 2014 at 12:35 PM, <a href="mailto:kashi.revanna@unt.edu">kashi.revanna@unt.edu</a> <span dir="ltr"><<a href="mailto:kashi.revanna@unt.edu" target="_blank">kashi.revanna@unt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Kashi (<a href="mailto:kashi.revanna@unt.edu">kashi.revanna@unt.edu</a>) sent a message using the contact form at<br>
<a href="http://gramene.org/contact" target="_blank">http://gramene.org/contact</a>.<br>
<br>
Hi,<br>
<br>
I like to access the gene dna sequences of Zea mays v3.21.<br>
At the following URL,<br>
<a href="ftp://ftp.ensemblgenomes.org/pub/plants/release-21/fasta/zea_mays/" target="_blank">ftp://ftp.ensemblgenomes.org/pub/plants/release-21/fasta/zea_mays/</a><br>
I only get chromosome dna sequences, cdna, ncrna and pep sequences.<br>
<br>
Can you please direct me to the place where I can get gene dna sequences,<br>
similar to what we have for Zea Maize v2. The file called<br>
ZmB73_5a_WGS_genes.fasta.gz at this URL<br>
<a href="ftp://ftp.maizesequence.org/pub/maize/release-5b/working-set/" target="_blank">ftp://ftp.maizesequence.org/pub/maize/release-5b/working-set/</a><br>
<br>
Thank you,<br>
Kashi<br>
<br>
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