A comprehensive knowledge of the location, structure, and expression of genes in the human genome is central to the understanding of human biology and the mechanisms of disease. Similarly for mouse, a comprehensive high quality gene set will aid in the design of experiments, and the interpretation of the effects of gene knockouts and resulting phenotypes, and as a model for human disease will help inform human gene function. The GENCODE consortium has assembled a team of world experts in a variety of fields related to gene annotation to create and distribute this gold standard. GENCODE's wide expertise covers gene and transcript isoform identification, pseudogene evolution, sequence conservation, gene expression, proteomics and post-translational modifications, gene regulatory elements, development and maintenance of the infrastructure required to create genome annotation at scale, and demonstrated community engagement and leadership. The complete and accurate annotation of the human and mouse genomes is necessary as many of the protein-coding genes are still incomplete or misannotated. GENCODE also aims to include all non-protein-coding genes which remain poorly understood with many loci still missing. Beyond the coding and non-coding genes, GENCODE creates reference pseudogene annotation as recent studies indicate that pseudogenes can play key regulatory roles. The completion of the full first-pass manual annotation of the reference mouse genome assembly will therefore be one of the main objectives of GENCODE. Efforts are underway in the Genome Reference Consortium (GRC) to expand the definition of the reference human genome to include genomic sequence for all haplotypes and gene alleles. GRC have already committed to supporting the genomes of a collection of 16 representative mice strains, thus effectively replacing the linear genome with a ?graph-like? structure of 16 separate haplotypes. GENCODE already annotate the full reference genome for human and mouse, including all available alternate sequences. GENCODE will continue to provide annotation appropriate to these new genomic sequences. In addition to genomic mutations that impair gene product function, many phenotypes are caused or moderated by the regulation of gene products. Therefore, GENCODE's complete annotation of all transcript isoforms logically includes key regulatory regions that are fundamentally a part of each gene and GENCODE will pilot the annotation of these tissue-specific regions.
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