RefSeq Functional Elements now public


NCBI is pleased to announce the initial data release of RefSeq Functional Elements, a resource that provides RefSeq and Gene records for experimentally validated human and mouse non-genic functional elements. Data can be accessed via GeneNucleotideBLASTBioProjectGraphical Displays and FTP.

These records include known gene regulatory elements (e.g., enhancers, promoters, protein binding sites), known structural elements (e.g., DNase I hypersensitive sites, matrix/scaffold-associated regions), well-characterized replication origins, and clinically-significant sites of DNA recombination and genomic instability. Further information, including a feature annotation glossary, is available on the RefSeq Functional Elements page.

Note that this is a phased release of an initial dataset (2,281 RefSeqs included in RefSeq release 82), and the dataset is currently incomplete. Curation is ongoing and additional records will be made available in the future, along with genome annotation of these elements.

Currently, the human elements are included in an interim annotation of the human genome (May 3 2017 interim annotation on GRCh38.p10), with data available in GFF3 format via FTP. This interim annotation can also be viewed by configuring the ‘NCBI Homo sapiens Interim Annotation May 3 2017 on GRCh38.p10’ track in NCBI’s Gene graphical display or in the Genome Data Viewer, with selection of ‘Biological regions’ in the ‘NCBI Other Features’ category. Similarly, interim annotation of the mouse elements can be viewed by loading the ‘NCBI Mus musculus Interim Annotation May 19 2017 on GRCm38.p5’ and ‘Biological regions’ tracks, with GFF3 data available via FTP.

Examples:

Gene record for OPSIN-LCR, a functional element.

Figure 1. An example of an NCBI Gene record for a functional element (only the Summary section is shown here). Note that the Gene type is ‘biological region’ and Feature type(s) are listed.

Gene record for OPSIN-LCR: GeneID:107604627
RefSeq record for OPSIN-LCR: NG_046887.1
Interim feature annotation for OPSIN-LCR: Graphical view

Stay tuned to NCBI Insights for future announcements about RefSeq Functional Elements.

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