Schema for RefSeq Func Elems - NCBI RefSeq Functional Elements |
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Database: mm10 Primary Table: refSeqFuncElems Data last updated: 2017-11-29
Big Bed File Download: /gbdb/mm10/ncbiRefSeq/refSeqFuncElems.bb
Item Count: 1,968
The data is stored in the binary BigBed format.
Format description: Bed 9+ representation of RefSeq functional elements.
| field | example | description |
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| chrom | chr1 | Reference sequence chromosome or scaffold | | chromStart | 132332669 | Start position in chromosome | | chromEnd | 132334462 | End position in chromosome | | name | enhancer | type of element | | score | 0 | unused; placeholder for BED format | | strand | + | + for forward strand, - for reverse strand | | thickStart | 132332669 | Start position in chromosome | | thickEnd | 132334462 | End position in chromosome | | reserved | 0,128,128 | Used as itemRgb: color based on type of element | | soTerm | enhancer | Sequence ontology (SO) term | | note | VISTA enhancer mm505 | A note describing the element | | geneIds | 110120368|GeneID:110120368 | Entrez Gene ID of element and/or associated gene(s) | | pubMedIds | 17130149|PMID:17130149 | PubMed ID of associated publication(s) | | experiment | EXISTENCE:transgenic organism evidence [ECO:0001131][PMID:17130149] | Experimental evidence | | function | enhancer in: hindbrain (rhombencephalon)[9/9] | forebrain[8/9] | Predicted function | | _mouseOver | VISTA enhancer mm505 | enhancer in: hindbrain (rhombencephalon)[9/9] | forebrain[8/9] | Mouse over label |
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Sample Rows
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| chrom | chromStart | chromEnd | name | score | strand | thickStart | thickEnd | reserved | soTerm | note | geneIds | pubMedIds | experiment | function | _mouseOver |
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| chr1 | 132332669 | 132334462 | enhancer | 0 | + | 132332669 | 132334462 | 0,128,128 | enhancer | VISTA enhancer mm505 | 110120368|GeneID:110120368 | 17130149|PMID:17130149 | EXISTENCE: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] |
| chr1 | 133180667 | 133184217 | enhancer | 0 | + | 133180667 | 133184217 | 0,128,128 | enhancer | VISTA enhancer mm971 | 110120372|GeneID:110120372,240753|GeneID:240753 | 17130149|PMID:17130149 | EXISTENCE: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] |
| chr1 | 133185979 | 133189493 | enhancer | 0 | + | 133185979 | 133189493 | 0,128,128 | enhancer | VISTA enhancer mm1460 | 110120426|GeneID:110120426,240753|GeneID:240753 | 17130149|PMID:17130149 | EXISTENCE: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 ... |
| chr1 | 133345986 | 133348046 | enhancer | 0 | + | 133345986 | 133348046 | 0,128,128 | enhancer | MEL | 107604629|GeneID:107604629 | 8798416|PMID:8798416,9314837|PMID:9314837 | EXISTENCE:reporter gene assay evidence [ECO:0000049][PMID:8798416, PMID:9314837] | | MEL |
| chr1 | 133345986 | 133350681 | promoter | 0 | + | 133345986 | 133350681 | 0,128,128 | promoter | 4.1 kb fragment (-4100 to +6) | 107604629|GeneID:107604629 | 8798416|PMID:8798416 | EXISTENCE: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 ... |
| chr1 | 133347802 | 133348023 | conserved_region | 0 | + | 133347802 | 133348023 | 192,0,192 | sequence_feature | conserved region; MEMM; 77% identity to human | 107604629|GeneID:107604629 | 9314837|PMID:9314837 | COORDINATES:sequence alignment evidence [ECO:0000200][PMID:9314837] | | conserved region; MEMM; 77% identity to human |
| chr1 | 133347802 | 133348046 | enhancer | 0 | + | 133347802 | 133348046 | 0,128,128 | enhancer | MEM or 240 bp mdE; SphI/AccI fragment (-2866 to -2625) | 107604629|GeneID:107604629 | 16895910|PMID:16895910 | EXISTENCE:knockout evidence [ECO:0001091][PMID:16895910] | important for baseline expression levels of renin in kidney and normal arterial blood pressure | MEM or 240 bp mdE; SphI/AccI fragment (-2866 to -2625) | important for baseline expression levels of renin in kidney and normal ... |
| chr1 | 133347815 | 133347841 | protein_bind: nuclear factor I C | 0 | + | 133347815 | 133347841 | 192,0,0 | protein_binding_site | E0 | 107604629|GeneID:107604629 | 12591615|PMID:12591615 | EXISTENCE:protein binding evidence [ECO:0000024][PMID:12591615] | | E0 | nuclear factor I C |
| chr1 | 133347840 | 133347866 | protein_bind: nuclear factor I C | 0 | + | 133347840 | 133347866 | 192,0,0 | protein_binding_site | E1 | 107604629|GeneID:107604629 | 12591615|PMID:12591615 | EXISTENCE:protein binding evidence [ECO:0000024][PMID:12591615] | | E1 | nuclear factor I C |
| chr1 | 133347912 | 133347934 | protein_bind: nuclear factor I C | 0 | + | 133347912 | 133347934 | 192,0,0 | protein_binding_site | E5, half-binding site for Nfic | 107604629|GeneID:107604629 | 12591615|PMID:12591615 | EXISTENCE:protein binding evidence [ECO:0000024][PMID:12591615] | | E5, half-binding site for Nfic | nuclear factor I C |
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RefSeq Func Elems (refSeqFuncElems) Track Description
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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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