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Even the annotation files hosted on the Ensembl site have systematic names (starting with Y..) instead of ENSEMBL ids (starting with EN..).

I bet there would be a place where I can get an annotation file (GFF3 preferably). Please let me know if you know such.

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With a further search for the answer, I realised that unconventionally, ENSEMBL ids for yeast start with Y. That is strange. I guess this is because the yeast annotations are primarily maintained by SGD (yeast genome database) and ENSEMBL just hosts a copy of that.

Also these ids are called Stable Gene IDs.

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