Question: Yeast 3'UTR sequence fasta file
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gravatar for gopal2706
2.5 years ago by
gopal270610
gopal270610 wrote:

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.

ADD COMMENTlink modified 2.5 years ago by dyollluap300 • written 2.5 years ago by gopal270610

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.

ADD REPLYlink written 2.5 years ago by genomax69k

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

ADD REPLYlink written 2.5 years ago by Denise - Open Targets5.0k
0
gravatar for dyollluap
2.5 years ago by
dyollluap300
USA, California, Bay Area
dyollluap300 wrote:

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.

ADD COMMENTlink written 2.5 years ago by dyollluap300
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