[Feedback] [Website feedback] Zea Mays version 3 gene sequences

[Marcela K. Monaco]

Hi Kashi,

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
ftp://ftp.maizesequence.org/pub/maize/release-5b+/
You could get fasta sequence for all the protein coding genes using the
Gramene Mart at http://ensembl.gramene.org/biomart/martview.  Under
"Filters", select "protein_coding" gene type and "Sequence" under
"Attributes".

I will see to upload a file with the sequence for the cds of all
protein-coding genes in FASTA format.

Marcela




On Wed, Feb 26, 2014 at 12:35 PM, kashi.revanna at unt.edu <
kashi.revanna at unt.edu> wrote:

> Kashi (kashi.revanna at unt.edu) sent a message using the contact form at
> http://gramene.org/contact.
>
> Hi,
>
> I like to access the gene dna sequences of Zea mays v3.21.
> At the following URL,
> ftp://ftp.ensemblgenomes.org/pub/plants/release-21/fasta/zea_mays/
> I only get chromosome dna sequences, cdna, ncrna and pep sequences.
>
> Can you please direct me to the place where I can get gene dna sequences,
> similar to what we have for Zea Maize v2. The file called
> ZmB73_5a_WGS_genes.fasta.gz at this URL
> ftp://ftp.maizesequence.org/pub/maize/release-5b/working-set/
>
> Thank you,
> Kashi
>
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