Yeast 3'UTR sequence fasta file

Question

[gopal2706]

I need the sequences of 3'UTRs of yeast genes. To my surprise Biomart does not have the information and spits out a "Sequence unavailable" statement for all the genes. In the SGD database,their repository has termed the utr_fasta files as obsolete (http://downloads.yeastgenome.org/sequence/S288C_reference/orf_dna/orf_dna.README) Has anyone else faced this issue - does any one have an updated and recently annotated sequence file for 3'utrs in yeast. Kindly let me know.

[GenoMax]

While it does say "Sequence unavailable" for majority of entries it is not the case for all genes. You may want to report this to Ensembl's helpdesk.

[Denise CS]

If you choose exon sewuences instead of 3' UTR, it works fine. Are you sure the UTRs have been annotated in S. cerevisiae?

Answer 1

[dyollluap]

In 2013 there was a huge volume of yeast UTR data published https://www.ncbi.nlm.nih.gov/pubmed/23615609

It reveals a huge amount of variation but you can filter by supporting reads and windowing as appropriate for your purposes.