Description
NCBI recently announced a new release of
functional regulatory elements.
NCBI is now providing
RefSeq and
Gene
records for non-genic functional elements that have been described in the literature and are
experimentally validated. Elements in scope include experimentally-verified gene regulatory
regions (e.g., enhancers, silencers, locus control regions), known structural elements
(e.g., insulators, DNase I hypersensitive sites, matrix/scaffold-associated regions),
well-characterized DNA replication origins, and clinically-significant sites of DNA recombination
and genomic instability. Priority is given to genomic regions that are implicated in human disease
or are otherwise of significant interest to the research community. Currently, the scope of this
project is restricted to human and mouse. The current scope does not include functional elements
predicted from large-scale epigenomic mapping studies, nor elements based on disease-associated
variation.
Display Conventions and Configuration
Functional elements are colored by Sequence Ontology (SO) term
using the same scheme as NCBI's Genome Data Viewer:
- Regulatory elements
(items labeled by INSDC regulatory class)
- Protein binding sites
(items labeled by bound moiety)
- Mobile elements
- Recombination features
- Sequence features
- Other
Methods
NCBI manually curated features in accordance with International Nucleotide
Sequence Database Collaboration (INSDC) standards. Features that are supported by direct
experimental evidence include at least one experiment qualifier with an evidence code (ECO ID)
from the Evidence and Conclusion Ontology, and at least one citation from PubMed. Currently
971 distinct PubMed citations are included in this track.
Contact
This track was made with assistance from
Terence Murphy at NCBI.
Data access
The raw data can be explored interactively with the Table Browser, or the Data Integrator. For automated analysis, the data may be
queried from our REST API,
and the genome annotations are stored in files that can be downloaded from our
download server, with more information available on
our blog.
New Version Available
Several new enhancements to the RefSeq Functional Elements dataset are available as a Public Hub.
The hub can be found on the Public Hub page.
The track hub was prepared by Dr. Catherine M. Farrell, NCBI/NLM/NIH with further insights discussed
in a related NCBI blog post.
References
Pruitt KD, Brown GR, Hiatt SM, Thibaud-Nissen F, Astashyn A, Ermolaeva O, Farrell CM, Hart J,
Landrum MJ, McGarvey KM et al.
RefSeq: an update on mammalian reference sequences.
Nucleic Acids Res. 2014 Jan;42(Database issue):D756-63.
PMID: 24259432; PMC: PMC3965018
Pruitt KD, Tatusova T, Maglott DR.
NCBI Reference Sequence (RefSeq): a curated non-redundant
sequence database of genomes, transcripts and proteins.
Nucleic Acids Res. 2005 Jan 1;33(Database issue):D501-4.
PMID: 15608248; PMC: PMC539979
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