Saccharomyces cerevisiae assembly and gene annotation


Saccharomyces cerevisiae is a unicellular fungus. It is commonly known as baker's, brewer's or budding yeast. It is used in the production of a number of human foodstuffs, including alcoholic beverages and in the baking industry, and is widely used as a model species in the study of eukaryotic biology. In 1996, the genome of S. cerevisiae was the first eukaryotic genome to be completely deciphered.

The data on this site is a direct import of the Saccharomyces Genome Database (SGD) dataset for the Saccharomyces cerevisiae S288C genome, imported in February 2011, supplemented with additional cross-references and annotations. We have also included the variation data from the Saccharomyces Genome Resequencing Project (SGRP) and functional genomics data from Yeast Genome 2.0 Array and Yeast Genome S98 Array.


  • Genetic and physical maps of Saccharomyces cerevisiae.

    Cherry JM, Ball C, Weng S, Juvik G, Schmidt R, Adler C, Dunn B, Dwight S, Riles L, Mortimer RK, Botstein D

    Nature 1997 387(6632 Suppl):67-73.


  • Population genomics of domestic and wild yeasts.

    Liti G, Carter DM, Moses AM, Warringer J, Parts L, James SA, Davey RP, Roberts IN, Burt A, Koufopanou V, Tsai IJ, Bergman CM, Bensasson D, O'Kelly MJ, van Oudenaarden A, Barton DB, Bailes E, Nguyen AN, Jones M, Quail MA, Goodhead I, Sims S, Smith F, Blomberg A, Durbin R, Louis EJ.

    Nature. 2009 Mar 19;458(7236):337-41. Epub 2009 Feb 11.


  • A large-scale full-length cDNA analysis to explore the budding yeast transcriptome.

    Miura F., Kawaguchi N., Sese J., Toyoda A., Hattori M., Morishita S., Ito T.

    Proc. Natl. Acad. Sci. U.S.A. 103(47): 17846-51 (2006)


The genome assembly represented here corresponds to GCA_000146045.2

Other assemblies

Gene annotation

This species and other fungi are also available from our sister site, Ensembl Fungi

More information

General information about this species can be found in Wikipedia.



AssemblyR64-1-1 (Saccharomyces cerevisiae S288c assembly from Saccharomyces Genome Database), INSDC Assembly GCA_000146045.2, Sep 2011
Database version80.4
Base Pairs12,157,105
Golden Path Length

The golden path is the length of the reference assembly. It consists of the sum of all top-level sequences in the seq_region table, omitting any redundant regions such as haplotypes and PARs (pseudoautosomal regions).

Genebuild bySGD
Genebuild methodImport
Genebuild startedSep 2011
Genebuild releasedNov 2011
Genebuild last updated/patchedDec 2011

Gene counts

Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

Non coding genes413
Small non coding genes

Small non coding genes are usually fewer than 200 bases long. They may be transcribed but are not translated. In Ensembl, genes with the following biotypes are classed as small non coding genes: miRNA, miscRNA, rRNA, scRNA, snlRNA, snoRNA, snRNA, and also the pseudogenic form of these biotypes. The majority of the small non coding genes in Ensembl are annotated automatically by our ncRNA pipeline. Please note that tRNAs are annotated separately using tRNAscan. tRNAs are included as 'simple fetaures', not genes, because they are not annotated using aligned sequence evidence.


A pseudogene shares an evolutionary history with a functional protein-coding gene but it has been mutated through evolution to contain frameshift and/or stop codon(s) that disrupt the open reading frame.

Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.7,126


Short Variants263,537