Schema for RefSeq Func Elems - NCBI RefSeq Functional Elements
  Database: mm10    Primary Table: refSeqFuncElems Data last updated: 2017-11-29
Big Bed File: /gbdb/mm10/ncbiRefSeq/refSeqFuncElems.bb
Item Count: 1,968
Format description: Bed 9+ representation of RefSeq functional elements.
fieldexampledescription
chromchr1Reference sequence chromosome or scaffold
chromStart132332669Start position in chromosome
chromEnd132334462End position in chromosome
nameenhancertype of element
score0unused; placeholder for BED format
strand++ for forward strand, - for reverse strand
thickStart132332669Start position in chromosome
thickEnd132334462End position in chromosome
reserved0,128,128Used as itemRgb: color based on type of element
soTermenhancerSequence ontology (SO) term
noteVISTA enhancer mm505A note describing the element
geneIds110120368|GeneID:110120368Entrez 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: hindbrain (rhombencephalon)[9/9] | forebrain[8/9]Predicted function
_mouseOverVISTA enhancer mm505 | enhancer in: hindbrain (rhombencephalon)[9/9] | forebrain[8/9]Mouse over label

Sample Rows
 
chromchromStartchromEndnamescorestrandthickStartthickEndreservedsoTermnotegeneIdspubMedIdsexperimentfunction_mouseOver
chr1132332669132334462enhancer0+1323326691323344620,128,128enhancerVISTA enhancer mm505110120368|GeneID:11012036817130149|PMID:17130149EXISTENCE:transgenic organism evidence [ECO:0001131][PMID:17130149]enhancer in: hindbrain (rhombencephalon)[9/9] | forebrain[8/9]VISTA enhancer mm505 | enhancer in: hindbrain (rhombencephalon)[9/9] | forebrain[8/9]
chr1133180667133184217enhancer0+1331806671331842170,128,128enhancerVISTA enhancer mm971110120372|GeneID:110120372,240753|GeneID:24075317130149|PMID:17130149EXISTENCE:transgenic organism evidence [ECO:0001131][PMID:17130149]enhancer in: neural tube[3/4] | hindbrain (rhombencephalon)[3/4] | forebrain[4/4]VISTA enhancer mm971 | enhancer in: neural tube[3/4] | hindbrain (rhombencephalon)[3/4] | forebrain[4/4]
chr1133185979133189493enhancer0+1331859791331894930,128,128enhancerVISTA enhancer mm1460110120426|GeneID:110120426,240753|GeneID:24075317130149|PMID:17130149EXISTENCE:transgenic organism evidence [ECO:0001131][PMID:17130149]enhancer in: neural tube[4/5] | hindbrain (rhombencephalon)[5/5] | midbrain (mesencephalon)[5/5] | forebrain[5/5] | eye[5/5]VISTA enhancer mm1460 | enhancer in: neural tube[4/5] | hindbrain (rhombencephalon)[5/5] | midbrain (mesencephalon)[5/5] | foreb ...
chr1133345986133348046enhancer0+1333459861333480460,128,128enhancerMEL107604629|GeneID:1076046298798416|PMID:8798416,9314837|PMID:9314837EXISTENCE:reporter gene assay evidence [ECO:0000049][PMID:8798416, PMID:9314837]MEL
chr1133345986133350681promoter0+1333459861333506810,128,128promoter4.1 kb fragment (-4100 to +6)107604629|GeneID:1076046298798416|PMID:8798416EXISTENCE:reporter gene assay evidence [ECO:0000049][PMID:8798416]promotes expression in juxtaglomerular (JG) kidney cells, granular convoluted tubular cells of the submandibular gland, renal va ...4.1 kb fragment (-4100 to +6) | promotes expression in juxtaglomerular (JG) kidney cells, granular convoluted tubular cells of t ...
chr1133347802133348023conserved_region0+133347802133348023192,0,192sequence_featureconserved region; MEMM; 77% identity to human107604629|GeneID:1076046299314837|PMID:9314837COORDINATES:sequence alignment evidence [ECO:0000200][PMID:9314837]conserved region; MEMM; 77% identity to human
chr1133347802133348046enhancer0+1333478021333480460,128,128enhancerMEM or 240 bp mdE; SphI/AccI fragment (-2866 to -2625)107604629|GeneID:10760462916895910|PMID:16895910EXISTENCE:knockout evidence [ECO:0001091][PMID:16895910]important for baseline expression levels of renin in kidney and normal arterial blood pressureMEM or 240 bp mdE; SphI/AccI fragment (-2866 to -2625) | important for baseline expression levels of renin in kidney and normal ...
chr1133347815133347841protein_bind: nuclear factor I C0+133347815133347841192,0,0protein_binding_siteE0107604629|GeneID:10760462912591615|PMID:12591615EXISTENCE:protein binding evidence [ECO:0000024][PMID:12591615]E0 | nuclear factor I C
chr1133347840133347866protein_bind: nuclear factor I C0+133347840133347866192,0,0protein_binding_siteE1107604629|GeneID:10760462912591615|PMID:12591615EXISTENCE:protein binding evidence [ECO:0000024][PMID:12591615]E1 | nuclear factor I C
chr1133347912133347934protein_bind: nuclear factor I C0+133347912133347934192,0,0protein_binding_siteE5, half-binding site for Nfic107604629|GeneID:10760462912591615|PMID:12591615EXISTENCE:protein binding evidence [ECO:0000024][PMID:12591615]E5, half-binding site for Nfic | nuclear factor I C

RefSeq Func Elems (refSeqFuncElems) Track Description
 

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