| The NCBI RefSeqGene Project |
RefSeqGene, a subset of NCBI's Reference Sequence (RefSeq) project, defines genomic sequences of well-characterized genes to be used as reference standards. These sequences, labeled with the keyword RefSeqGene, can serve as a stable foundation for reporting mutations, for establishing conventions for numbering exons and introns, and for defining the coordinates of other biologically significant variation. RefSeq mRNA and protein sequences already support these functions, but have the obvious weakness of not providing explicit coordinates for flanking or intronic sequence. RefSeq chromosome sequences also support these functions, but have awkwardly large coordinate values that will change when the sequence is updated with a new genome build. Sequences of the RefSeqGene project will counter both of these drawbacks by providing gene-specific genomic sequence for each gene, as well as including upstream and downstream flanking regions. If modifications must be made to any RefSeqGene sequence, it will be versioned and tools will be provided to facilitate conversion of coordinates. The RefSeqGene sequences will also be placed on the reference chromosome, and current chromosome coordinates will be available because of that re-alignment.
The RefSeqGene project gratefully acknowledges the leadership and interest of Dr. M.L. Gulley and the Molecular Pathology Resource Committee of the College of American Pathologists.
See also M.L. Gulley et al., Clinical laboratory reports in molecular pathology.
Sequence Selection
Sequences in the RefSeqGene set will be well-supported, exist in nature, and, to the extent
for which this is possible, represent a prevalent, 'normal' allele.
Criterion 1. Well-supported
Criterion 2. Exists in nature
Criterion 3. Standard allele
The default implementation of 'well-supported genomic sequence' will be the sequence from the public reference assembly. The rationale for this definition is the quality of the genomic product. If the current public reference assembly is not well supported, then an alternate sequence will be selected, in consultation with gene-specific experts as available.
The default implementation of 'exists in nature' will be the selection, when feasible, of sequence from a single clone, based on the assumption that no sequence errors were introduced in cloning, and that a single insert represents an example of a naturally occurring haplotype.
The default implementation of 'standard allele' will be the sequence from the public reference assembly. If, however, there is published evidence, evidence from locus-specific databases, or evidence from clinical testers, that the sequence in the Reference assembly is not correct, the RefSeqGene sequence will be constructed from an alternate source sequence, or locally modified.
Search Records
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Click here to browse a list of genes (alphabetized by symbol) for which RefSeqGene records are available. From this page you can link to Entrez Gene (GeneID), our new (beta) sequence viewer (Viewer), Entrez (Core Nucleotide) and OMIM.
RefSeqGene records can be retrieved from NCBI's core nucleotide database by a single query because all are identified by the RefSeqGene keyword (RefSeqGene[keyword]). To review RefSeqGene records released in the last 30 days, click here.
To retrieve all RefSeqGene records, click here.
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Downloads
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RefSeqGene records can be retrieved from NCBI's FTP download site at:
ftp://ftp.ncbi.nih.gov/refseq/H_sapiens/RefSeqGene/
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Related Sites
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Databases
Entrez Gene is a searchable database of genes, from RefSeq genomes, and defined by sequence and/or represented in the NCBI Map Viewer.
The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products.
NCBI's Variation database (dbSNP) maintains records of submitted sequence variants, including SNPs, insertions, deletions, and rare variation.
OMIM or Online Mendelian Inheritance in Man, is a catalog of human genes and genetic disorders maintained by staff at Johns Hopkins and elsewhere.
Tools
The Genome Workbench is an integrated application for viewing and analyzing sequence data.
The Map Viewer provides a wide variety of genome mapping and sequencing data.
NCBI's new (beta) Sequence Viewer facilitates review of sequence and annotated variants.
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Contact Us
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If you have any questions or suggestions, please mail them to:
rsgene@ncbi.nlm.nih.gov