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The NCBI Reference Sequence project provides sequence data and related information for numerous organisms and provides a baseline for medical, functional, and comparative studies. Whereas GenBank is an archival repository of all sequences, the RefSeq database is a non-redundant set of reference standards that includes chromosomes, complete genomic molecules (organelle genomes, viruses, plasmids), intermediate assembled genomic contigs, curated genomic regions, mRNAs, RNAs, and proteins. RefSeq records are provided using several processes:
Curated RefSeq records are made available in several status levels [see Status Key]]. Reviewed records represent a compilation of our current knowledge of a gene and its transcripts.
The GenBank archival sequence database includes publicly available DNA sequences submitted from individual laboratories and large-scale sequencing projects. GenBank accession numbers are assigned to these submitted sequences. Submitted sequence data is exchanged between NCBIs GenBank, EMBL Data Library (EMBL) and the DNA Data Bank of Japan (DDBJ) to achieve comprehensive worldwide coverage. As an archival database, GenBank can be very redundant for some loci. GenBank sequence records are owned by the original submitter and can not be altered by a third party. RefSeq sequences are derived from GenBank and provide non-redundant curated data representing our current knowledge of known genes. Some records include additional sequence information that was never submitted to an archival database but is available in the literature. Some sequence records are provided through collaboration; the underlying primary sequence data is available in GenBank, but may not be available in any one GenBank record. RefSeq sequences are not submitted primary sequences. RefSeq records are owned by NCBI and therefore can be updated as needed to maintain current annotation or to incorporate additional sequence information.
It is appropriate to cite the RefSeq accession number and the RefSeq Handbook chapter. Ideally any accession cited should indicate both the accession and version number. For example: NCBI Accession NM_000001.1 Please cite the NCBI Handbook as follows:
For your reference, one web site that lists a number of Citation Guides for
Electronic Documents is:
http://www.ifla.org/I/training/citation/citing.htm.
RefSeq records can be accessed through several NCBI resources including:
RefSeq records are distinguished from other GenBank records by:
Please see the description of RefSeq accession prefixes.
The RefSeq accession prefix indicates the molecule type and method used to supply the record. Please see the description of RefSeq accession prefixes. NCBI Accession numbers that begin with the prefix XM_ (mRNA), XR_ (non-coding transcript), and XP_ (protein) are model reference sequences produced by NCBI's Genome Annotation project. These records represent the transcripts and proteins that are annotated on the NCBI Contigs and they may be different from GenBank submissions for mRNAs and/or the curated RefSeq records (with NM,NR,NP accession prefixes). These differences may reflect real sequence variation (polymorphism), or errors (or gaps) in the available genomic sequence. These model RefSeq records should be used with caution, after comparing them to other available sequence information (Check the evidence viewer, BLink, Gene, or sequence neighbors). [more...]
Entrez and BLAST results both present the following formatted text as part of the returned result: gi|4557284|ref|NM_000646.1|[4557284]
Identifying NM_ and NP_ RefSeq records in BLAST results: The distinct format of RefSeq accession numbers (they include an underscore) provides a quick indication that a BLAST result includes a RefSeq record.
Score E
Sequences producing significant alignments: (bits) Value
gi|6226959|ref|NM_000014.3| Homo sapiens alpha-2-macroglobu... 9073 0.0
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| RefSeq accession numbers have a distinct format
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"ref" indicates RefSeq database
RefSeq records are made available in several status levels. Reviewed records represent a compilation of our current knowledge of a gene and its transcripts. These records have been reviewed by experts, either NCBI staff or collaborating groups, to create a sequence record that is analagous to a 'review article'. Some enhancements to the reviewed record might include:
When a record is reviewed, sequence data from more than one record may be merged together, as deemed
appropriate, to construct a more complete mRNA record. The review process includes reading the primary
literature to cross-check accuracy and determine if additional data is available concerning the extent of
the UTR, alternate splicing, or function. Transcript variant records are only made when there is information
available on the full-length nature of the product; in other words, should multiple alternate exons be found
through-out the length of the gene, no assumption is made about what combinations of alternate exons exist
in vivo. Therefore, the RefSeq collection does under-represent alternate splice products.
For the NCBI curation-supported RefSeq pipeline, the review process includes analysis of all sequences that represent the gene at hand (at that time). This analysis results in expanding the list of accessions that represent the gene under investigation, identifying (and correcting) errors in the accession-to-gene associations, and identifying accessions with significant errors (i.e. chimeric). The curated list of accessions that represent a gene is available in Entrez Gene; this list is not intended to be fully comprehensive; additional 'related' sequence information will always be available in the Entrez 'related sequences' and BLink reports, and BLAST search results. For examples of reviewed RefSeq records, see the following entries:
There are several factors used in selecting the source GenBank sequence that is first used to generate the PROVISIONAL mRNA RefSeq record, but quite often the record used is selected primarily because it includes more complete UTR sequence data. Reference sequence records are not intended to represent the historical 'first sequenced' record (although for genes with very limited available sequence data they may at times do so). PROVISIONAL records may be updated before being fully reviewed to use a longer GenBank source sequence that becomes available. While the PROVISIONAL RefSeq records do represent a single GenBank source sequence, the REVIEWED RefSeq records are intended to represent the current state of knowledge as provided by the whole research community rather than by any one laboratory.
No, both records will continue to be available. RefSeq and GenBank are separate databases, and both databases are available in the Entrez nucleotides data set. Provisional RefSeq records are usually quite similar to the source GenBank records from which they were drawn. However, when RefSeq records are reviewed by experts, additional sequence data, biological annotations, and references are often added. At that time, the original source GenBank record(s) and the corresponding RefSeq entry can be quite different -- the RefSeq entry can represent a combination of information from various labs, which are credited in the Comments and/or References field of the record. The RefSeq database is designed to reduce duplication by selecting one representative sequence for each human locus, whereas GenBank is a repository of sequences that might contain numerous records for any given gene. The only duplicates in the RefSeq database will represent naturally occurring paralogs and splice variants.
RefSeq records are provided for identified complete genomes and for identified genome sequencing projects as collaborations are established or as the sequence data becomes available. For the NCBI curation-supported pipeline they are made under the following conditions:
RefSeq records are not made for loci where only partial coding region sequence data is available (as annotated on the GenBank source record). In addition, there are some loci for which we have not yet identified an appropriate representative GenBank accession number.
We welcome comments from the research community that provide as yet unidentified representative accession numbers for loci lacking RefSeq data. We also welcome corrections to errors, or additional biological information. Please send comments using the RefSeq and Gene update form, or contact the NCBI Service Desk; be
as specific as possible, and cite the RefSeq accession, GeneID, and any relevant published citations.
RefSeq records use the terminology defined by the original GenBank submission, collaborating group, or by an official nomenclature group for the organism. For example, for the human RefSeq collection uses gene symbols and names supplied by the Human Gene Nomenclature Committee; records may also include alternate symbols and names, when available. GenBank is an archive of publicly available sequence records that were submitted by the originators of the data. Submitters of GenBank records maintain editorial control over their records and decide which gene symbol to use. Some authors consult with the nomenclature committees associated with the organism from which they sequenced a gene to obtain an official gene symbol for that organism. Other authors might not do that, or might not update their submitted records if the official name changes. Therefore, it is possible that GenBank records for a given gene will use different gene symbols. |
