Yeasts references SGD and Ensembl

Question

[agata88]

Hi all!

I was using SGD database to download references of Saccharomyces S228C and EC1118. I have a multipleks and NGS results of ADR1 gene for which starters were design (on S228C). So I've mapped reads to both references separately. For first S228C I see all reads mapped in ADR1 gene, but for EC1118 I see only part. Other part is mapped in intron location near ADR1 gene. So I see it as shifted amplicon where part is included in ADR1 gene, and I have no idea why ... The DNA used for multiplex (the starting material) are unknown yeasts.

I've checked Ensembl Fungi database to see whether ADR1 is differently located for EC1118 than in SGD. I was surprised when I didn't find this gene in Ensembl at all ...

Any help would be much appreciated,

Thanks,

Agata

Answer 1

[Denise CS]

ADR1 seems to have been annotated in Ensembl Fungi indeed.

[agata88]

Yes, but it is for Saccharomyces R64 strain, not EC1118...

[agata88]

I assume that this is wrong annotation in SGD database and the location of these gene is in regions where amplicon is mapped. Especially when I have confirmed the ADR1 amplicon on S228C strain. I don't see any other explanation. I wanted to compare the location between databases (SGD and Ensembl) but as I say there is no information about ADR1 gene for EC1118 strain (online and locally in gff file).