NCBI RefSeq Functional Elements biological regions

This track displays NCBI RefSeq Functional Element (RefSeqFE) biological regions, where each biological region represents one or more experimentally validated non-genic functional feature(s). Each region has a record in NCBI's Gene database, and is represented by a RefSeq sequence record with an NG_ accession prefix. Detailed metadata, including nomenclature, a region summary and a RefSeq accession link, can be found within this track and the associated details pages. Where applicable, the details page for each biological region also displays a pipe-separated list of loci having known functional interactions with the biological region, where these loci may be target genes or other biological regions.

This track is an overview track and can be displayed while evaluating data found in these related tracks from this track hub:

• RefSeq Functional Element features (FE_features): Underlying experimentally validated functional features that are annotated on each biological region. A variety of gene regulatory, recombination type, structural type and other miscellaneous features may be found within this track, as detailed in the feature table on the RefSeq Functional Elements website. Descriptive information, functional details, experimental evidence types and publications supporting each feature can be found within this track.
  
  
• RefSeq Functional Element recombination partners (Recomb_partners): Pairwise experimentally validated recombination interactions between RefSeq Functional Element recombination features, represented in bigInteract format. Interactions in this track are at the biological region level, not per individual feature, and thus this track is best viewed in combination with the biological regions track.
  
  
• RefSeq Functional Element regulatory interactions (Reg_interactions): Pairwise experimentally validated regulatory interactions between RefSeq Functional Element gene regulatory elements and target genes, or known interactions between regulatory elements, represented in bigInteract format. Interactions in this track are at the biological region level, not per individual feature, and thus this track is best viewed in combination with the biological regions track, also alongside a RefSeq gene annotation track, as found elsewhere in the genome browser track options.

Methods

Biological regions and associated metadata were extracted from the NCBI Gene database along with annotation locations from a relevant NCBI annotation release, as indicated in the 'Data version' field in the track details page or in the file download path. These were converted to bigBed format with field customization according to the table schema.

Verification

Each represented biological region has underlying feature annotation that is supported by experimental data in the literature. Supporting publications can be obtained from the Gene database record that is linked to in the details page for each biological region. Additionally, publications supporting underlying features or functional interactions may be obtained from the RefSeq Functional Elements features (FE_features), regulatory interactions (Reg_interactions) or recombination partners (Recomb_partners) tracks.

Data represented in this biological regions track can be downloaded in bigBed format as indicated in the file download path in the table schema page, or may also be obtained 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.

Credits

All data were mined and the track hub was prepared by Dr. Catherine M. Farrell, NCBI/NLM/NIH.
Email: farrelca@ncbi.nlm.nih.gov

Additional information

Further information is available on the NCBI RefSeq Functional Elements webpage.

References

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.