GENCODE

GENCODE is a valuable resource for researchers and scientists who are deeply involved in the study of the human and mouse genomes. It serves as a comprehensive database that offers a detailed catalog of gene features, providing a high level of accuracy based on biological evidence. The website is a product of the collaborative efforts between EMBL-EBI and other research institutions, aiming to facilitate biomedical research and genome interpretation. Navigating through GENCODE, you'll find an extensive collection of genomic data, including annotations for human and mouse genomes. The human genome annotations are updated regularly, with the latest version being GENCODE 49, released in September 2025. Similarly, the mouse genome annotations are also updated, with the most recent version being GENCODE M38, also from September 2025. One of the standout features of GENCODE is its human promoter windows catalog. This catalog provides a first look at the promoter regions of human genes, which are crucial for understanding gene regulation and expression. Additionally, the website is continuously expanding its long non-coding RNA (lncRNA) annotations, integrating models from the Capture Long-read Sequencing project. This integration has significantly enhanced the accuracy and depth of the annotations available. The GENCODE Primary transcript set is another essential tool for researchers. It captures a minimal set of transcripts at protein-coding genes, which is particularly useful for those studying gene expression and regulation. Moreover, GENCODE is also supporting the annotation of non-canonical human open reading frames (ORFs) predicted by Ribo-seq data. This includes the integration of peptidomics and immunopeptidomics data, providing a more comprehensive view of gene expre