Schema for RefSeq Func Elems - NCBI RefSeq Functional Elements
  Database: hg38    Primary Table: refSeqFuncElems Data last updated: 2017-11-30
Big Bed File Download: /gbdb/hg38/ncbiRefSeq/
Item Count: 5,756
The data is stored in the binary BigBed format.

Format description: Bed 9+ representation of RefSeq functional elements.
chromchr1Reference sequence chromosome or scaffold
chromStart167327716Start position in chromosome
chromEnd167329809End position in chromosome
nameenhancertype of element
score0unused; placeholder for BED format
strand++ for forward strand, - for reverse strand
thickStart167327716Start position in chromosome
thickEnd167329809End position in chromosome
reserved0,128,128Used as itemRgb: color based on type of element
soTermenhancerSequence ontology (SO) term
noteVISTA enhancer hs1331A note describing the element
geneIds110121063|GeneID:110121063,5451|GeneID:5451Entrez Gene ID of element and/or associated gene(s)
pubMedIds17130149|PMID:17130149PubMed ID of associated publication(s)
experimentEXISTENCE:transgenic organism evidence [ECO:0001131][PMID:17130149]Experimental evidence
functionenhancer in: neural tube[4/7] | hindbrain (rhombencephalon)[4/7] | midbrain (mesencephalon)[5/7] | forebrain[7/7]Predicted function
_mouseOverVISTA enhancer hs1331 | enhancer in: neural tube[4/7] | hindbrain (rhombencephalon)[4/7] | midbrain (mesencephalon)[5/7] | forebrain[7/7]Mouse over label

Sample Rows
chr1167327716167329809enhancer0+1673277161673298090,128,128enhancerVISTA enhancer hs1331110121063|GeneID:110121063,5451|GeneID:545117130149|PMID:17130149EXISTENCE:transgenic organism evidence [ECO:0001131][PMID:17130149]enhancer in: neural tube[4/7] | hindbrain (rhombencephalon)[4/7] | midbrain (mesencephalon)[5/7] | forebrain[7/7]VISTA enhancer hs1331 | enhancer in: neural tube[4/7] | hindbrain (rhombencephalon)[4/7] | midbrain (mesencephalon)[5/7] | foreb ...
chr1169941254169943938enhancer0+1699412541699439380,128,128enhancerVISTA enhancer hs1442110121105|GeneID:11012110517130149|PMID:17130149EXISTENCE:transgenic organism evidence [ECO:0001131][PMID:17130149]enhancer in: limb[10/11] | genital tubercle[9/11]VISTA enhancer hs1442 | enhancer in: limb[10/11] | genital tubercle[9/11]
chr1181151912181154518enhancer0+1811519121811545180,128,128enhancerVISTA enhancer hs1862110121215|GeneID:11012121517130149|PMID:17130149EXISTENCE:transgenic organism evidence [ECO:0001131][PMID:17130149]enhancer in: heart[6/6]VISTA enhancer hs1862 | enhancer in: heart[6/6]
chr1183611756183612264enhancer0+1836117561836122640,128,128enhanceramplified fragment containing the chr1:183581059-183581217 (GRCh37) region with regulatory potential108318669|GeneID:10831866924670763|PMID:24670763EXISTENCE:reporter gene assay evidence [ECO:0000049][PMID:24670763]nontranscribed enhancer in HeLa cellsamplified fragment containing the chr1:183581059-183581217 (GRCh37) region with regulatory potential | nontranscribed enhancer i ...
chr1183611923183612082epigenetically_modified_region0+1836119231836120820,128,128regionco-occurring H3K27ac and H3K4me1 histone modifications and no CAGE data in HeLa cells108318669|GeneID:10831866922955616|PMID:22955616EXISTENCE:chromatin immunoprecipitation-seq evidence [ECO:0000229][PMID:22955616]co-occurring H3K27ac and H3K4me1 histone modifications and no CAGE data in HeLa cells
chr1188668051188668618DNase_I_hypersensitive_site0+1886680511886686180,128,128regionregion containing the chr1.11400 DHS; the nucleotide coordinates are approximate for this feature108281185|GeneID:10828118522955617|PMID:22955617EXISTENCE:in vivo cleavage assay evidence [ECO:0001075][PMID:22955617]region containing the chr1.11400 DHS; the nucleotide coordinates are approximate for this feature
chr1188668051188668618enhancer0+1886680511886686180,128,128enhanceramplified fragment containing the chr1.11400 DHS108281185|GeneID:10828118524670763|PMID:24670763EXISTENCE:reporter gene assay evidence [ECO:0000049][PMID:24670763]nontranscribed enhancer in HeLa cellsamplified fragment containing the chr1.11400 DHS | nontranscribed enhancer in HeLa cells
chr1198294431198296612enhancer0+1982944311982966120,128,128enhancerVISTA enhancer hs1322110121056|GeneID:110121056,140609|GeneID:14060917130149|PMID:17130149EXISTENCE:transgenic organism evidence [ECO:0001131][PMID:17130149]enhancer in: hindbrain (rhombencephalon)[9/9] | midbrain (mesencephalon)[6/9] | dorsal root ganglion[6/9] | forebrain[5/9] | bra ...VISTA enhancer hs1322 | enhancer in: hindbrain (rhombencephalon)[9/9] | midbrain (mesencephalon)[6/9] | dorsal root ganglion[6/9 ...
chr1198681669198682240enhancer0+1986816691986822400,128,128enhanceramplified fragment containing most of the chr1:198650930-198651643 (GRCh37) CAGE region108281163|GeneID:108281163,5788|GeneID:578824670763|PMID:24670763EXISTENCE:reporter gene assay evidence [ECO:0000049][PMID:24670763]mid-level expression transcribed enhancer in HeLa cellsamplified fragment containing most of the chr1:198650930-198651643 (GRCh37) CAGE region | mid-level expression transcribed enhan ...
chr1198681800198682514CAGE_cluster0+198681800198682514192,0,192sequence_featureCAGE cluster; bidirectional CAGE region108281163|GeneID:108281163,5788|GeneID:578824670763|PMID:24670763EXISTENCE:cap analysis of gene expression evidence [ECO:0000309][PMID:24670763]CAGE cluster; bidirectional CAGE region

RefSeq Func Elems (refSeqFuncElems) Track 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


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.


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.


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