Note that the GRCh37/hg19 assembly is not the current reference genome assembly for human. More recent NCBI annotation data may be available in the equivalent track on the GRCh38/hg38 assembly.
This track displays experimentally validated RefSeq Functional Element (RefSeqFE) non-genic functional features that are annotated on biological regions from NCBI's Gene database. A variety of gene regulatory, recombination type, structural type and other miscellaneous features are found within this track. Descriptive information, functional details, a RefSeq accession link, database cross-references, experimental evidence types and publications supporting each feature are also included in this track.
Metadata can viewed in the details page table, or by hovering the mouse over individual features in the browser window. The parental biological region from which each feature is derived can be viewed in the RefSeq Functional Elements biological regions (FE_biol_regions) track in this track hub. A link to the relevant biological region record is also included in the details page for each feature.
The feature types represented in this track are listed in the feature table on the RefSeq Functional Elements website. They are named according to the 'GFF3 column 3 SO_type' column in that table, where relevant Sequence Ontology (SO) IDs are also indicated. Features in this track are colored by general feature category as follows:
Most feature types are labeled in the format <SO_type>_<GeneID>. For biological regions with multiple underlying features, annotation order identifiers are appended to the GeneID, where the order is annotation release- and/or genome assembly-specific. Protein binding site features are labeled in the format <SO_type>_<bound_moiety>_<GeneID>, where the bound moiety name is from the HUGO Gene Nomenclature Committee (HGNC) official full name for the encoding gene
Annotated features and associated metadata were extracted from GFF3 files from a relevant NCBI annotation release, as indicated in the 'Data version' field in the top section of this track details page or in the file download path in the table schema page. These were converted to bigBed format with field customization according to the table schema.
Each represented feature is supported by experimental data in the literature. Supporting publications are available in the 'Supporting publication(s)' field and in the 'experiment=' attribute in the 'Functional and descriptive attributes' row of the details page table. They may also be viewed by hovering the mouse over individual features in the browser window. Additionally, relevant PMIDs in PubMed can be directly accessed for each feature via the RefSeq accession link in the details table. Publication data and other information can also be obtained from the bigBed download file as indicated in the table schema, by using the Table Browser or Data Integrator data explorers, or from NCBI upon request. Please visit this link for information on how to extract data from bigBed files. To take maximum advantage of experimental evidence and functional data for RefSeq Functional Elements, please explore NCBI's various data access options at this link.
All data were mined and the track hub was prepared by Dr. Catherine M. Farrell, NCBI/NLM/NIH.
Email: farrelca@ncbi.nlm.nih.gov
Further information is available on the NCBI RefSeq Functional Elements webpage.
Farrell CM, Goldfarb T, Rangwala SH, Astashyn A, Ermolaeva OD, Hem V, Katz KS, Kodali VK, Ludwig F, Wallin CL, Pruitt KD, Murphy TD. RefSeq Functional Elements as experimentally assayed nongenic reference standards and functional interactions in human and mouse. Genome Res. 2022 Jan;32(1):175-188. doi: 10.1101/gr.275819.121. Epub 2021 Dec 7. PMID: 34876495.