Why are UTRs ommitted in yeast sequence databases?
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7.2 years ago

There have been many studies reporting and annotating UTRs in S. cerevisiae. However, the standard databases such as SGD and ENSEMBL do not provide the complete transcript sequence; they just provide the ORF.

I also checked the folder called cDNA, in ENSEMBL. All the sequences start with ATG and end with one of the stop codons (TAA 47%, TAG 23%, TGA 30%).

Is there a good reason for not reporting the complete sequence when that information is already available?

genome annotation • 1.6k views
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7.2 years ago
dyollluap ▴ 310

SGD is resource limited and has traditionally focused on manual curation of published small scale experiment results. They do not yet have the data structure setup for annotation of non canonical genomic features.

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That was true for the pre-genomics era. Now it is so easy to upload transcriptomics data and it would only be an additional work to find ORFs and just upload them. ENSEMBL is supposed to have all the necessary setup for annotation, right? Yet they haven't included these features.

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