NCBI RefSeq Functional Elements, a growing resource for human and mouse genomic functional discovery beyond genes

Authors

• CM Farrell
• OD Ermolaeva
• CL Wallin
• TD Murphy

Abstract

To facilitate genomic functional discovery, NCBI provides RefSeq Functional Elements (RefSeqFEs; www.ncbi.nlm.nih.gov/refseq/functionalelements/) for diverse and functionally important non-genic elements in human and mouse, including gene regulatory regions and other regions that have been experimentally validated in the literature. The dataset includes richly annotated sequence records, descriptive records in the Gene database, genomic feature annotation, and interactions between regulatory regions, target genes and each other. We have tremendously scaled up content following our initial publication describing the resource (PMID:34876495). The dataset currently has over 150K features for human and 6K features for mouse (July 2023), with significant at scale growth expected over the coming year. Recent improvements include the addition of thousands of new records, extractable cell type activity data for annotated features, additional fields for data mining in download files, and new CRISPRi-validated target gene linkages. We increased accessibility by providing annotation on the T2T-CHM13v2.0 genome assembly, with periodic updates of GRCh38, GRCm39 and T2T-CHM13v2.0 annotations and the RefSeqFE track hub. Moreover, we improved clinically relevant content by adding features for functionally validated regulatory variants, and we curated regulatory elements for genes associated with coronavirus biology and marked up biological regions that overlap known COVID-19-associated variants. Our freely available resource enables discovery of non-coding function beyond genes, and directly links it to the experimental literature. Further details on RefSeqFE data access, improvements and uses will be presented. We welcome feedback from the NIH research community, with an aim to optimize RefSeqFEs as a reference resource for experimentally validated non-genic regions.

Scientific Focus Area: Research Support Services

This page was last updated on Monday, September 25, 2023