RefSeq Definitions

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• Accession Format
• Status Key
• Entrez Query Hints

Accession Format

RefSeq accession numbers can be distinguished from GenBank accessions by their distinct prefix format of 2 characters followed by an underscore character ('_'). For example, a RefSeq protein accession is NP_015325.

@ Method:   
Mixed: indicates the process flow includes both automated processing and expert review for some of the records; curation analysis may be provided either by NCBI staff or collaborators.
Automated: indicates records that are not individually reviewed; updates are released in bulk for a genome.

STATUS Key

The RefSeq COMMENT block indicates the Status of the record and the GenBank sequence data that was used to provide the record. In addition, the COMMENT may identify a collaboration that supplied the defining sequence information for the genome, gene, or protein. The level of curation may differ between different collaborating groups.

Retrieving RefSeq records with Entrez queries:

You can restrict your Entrez query to the RefSeq collection by using:

• Entrez Limits settings
• Entrez Property term restrictions

Using Entrez Limits:
You can use Entrez Limits settings to restrict your query to the RefSeq database. To use Entrez Limits you must first go to either the Nucleotide or Protein database; one way to do this is to query against all databases and follow links to the results in the desired database. [From the NCBI homepage, query against 'All Databases' or follow the link along the top bar to 'All Databases' and proceed from there.] Once you have navigated to Protein or Nucleotide results, note the Limits Tab located directly beneath the text area where a search term is entered.

Limits Setting		Description
select "RefSeq" from the "Only from" menu		this restricts the query to the RefSeq collection
select "Genomic DNA/RNA" from the "Molecule" menu		this restricts the query to genomic RefSeq records
select "mRNA" from the "Molecule" menu		this restricts the query to mRNA RefSeq records

Refining a query using Entrez Properties restrictions:
More refined queries can be carried out to retrieve specific types of RefSeq records, such as those with a particular status (reviewed, etc.) or those from the genome annotation pipeline. The format for these queries is "term[prop]". You can review what terms are defined using the Entrez Preview/Index Tab located to the right of the Limits Tab.

Find all of the property restriction terms that are defined for the RefSeq collection:

• navigate to the Preview/Index Tab
• select "Properties" from the menu
• enter 'refseq' or 'srcdb refseq' in the text field (without the quotes; 'srcdb' is an abbreviation of 'source database')
• click on the 'Index' button
• scroll through the resulting list to find the term(s) of interest (in this example, those beginning with 'srcdb refseq')
• add the restrictions to your query

To add a restriction to your query, select the term of interest (for example, 'srcdb refseq known') and click the appropriate Boolean button to configure the query as AND, OR, or NOT.

If you already know the property term, you can enter it directly into the search box as part of your query. The property terms defined for the RefSeq database and the accession prefixes that may be retrieved (per term) are listed below:

Query Restriction		Accession Prefix Retrieved		Description
srcdb_refseq[prop]		NC_, AC_, NG_, NT_, NW_, NZ_, NM_, NR_, XM_, XR_, NP_, AP_, XP_, ZP_		All NCBI RefSeq records Try It: Nucleotide  Protein
srcdb_refseq_reviewed[prop]		NC_, NT_, NW_, NG_, NM_, NR_, NP_, YP_		reviewed records (curated) Try It: Nucleotide  Protein
srcdb_refseq_provisional[prop]		AC_, NC_, NT_, NW_, NG_, NM_, NP_, AP_, XM_, XP_		provisional records (not curated) Try It: Nucleotide  Protein
srcdb_refseq_predicted[prop]		NG_, NM_, NR_, NP_, ZP_		predicted records (not curated) Try It: Nucleotide  Protein
srcdb_refseq_validated[prop]		NC_, NG_, NM_, NR_, NP_, YP_		validated records (curated) Try It: Nucleotide  Protein
srcdb_refseq_inferred[prop]		AC_, NG_, NM_, NP_		inferred records (not curated); annotation inferred based on alignments from other genes or organisms Try It: Nucleotide  Protein
srcdb_refseq_known[prop]		NC_, NT_, NW_, NG_, NM_, NP_, AP_, YP_, ZP_		reviewed, validated, provisional, predicted, inferred nucleotide or protein; excludes RefSeq records that are provided by the NCBI genome annotation pipeline (some NT_, NW_, and all XM_, XR_, XP_ accessions). Try It: Nucleotide  Protein
srcdb_refseq_model[prop]		NT_, NW_, XM_, XR_, XP_		RefSeq records generated by the NCBI genome annotation pipeline (not curated); model records Try It: Nucleotide  Protein

Examples:
The following examples illustrate how different information can be retrieved by querying against the NCBI Nucleotide or Protein databases. Note that queries can be restricted by using the Limits page, by adding the restriction using the Preview/Index Tab, or by typing a formatted query. To provide the links below, the Limit restrictions are translated into the equivalent property restriction in the URL; for example, the Limit of 'Molecule=Genomic' is converted in the URL into 'AND biomol_genomic[prop]'.

Sample Query	Result
CoreNucleotide database, Limits Molecule=Genomic, Query= mitochondrial AND srcdb_refseq_reviewed[prop]	returns genomic mitochondrial RefSeq records that have a status of 'reviewed'
CoreNucleotide database, Limits Fields=Gene Name, Query=CFTR	returns GenBank and RefSeq nucleotide records that use the gene name of CFTR; Note a page tab is provided to review the RefSeq subset
CoreNucleotide database, Limits Molecule=Genomic, Query=human[organism] AND srcdb_refseq[prop] AND NC_000000:NC_999999[pacc]	by restricting to a specific accession series, this query returns the set of RefSeq human chromosome records corresponding to the reference genome
Protein database, Limits Fields=Gene Name, Query= CFTR AND srcdb_refseq[prop]	returns protein RefSeq records with a CDS feature annotated with gene=CFTR
Protein database, Query=srcdb_refseq[prop] AND "saccharomyces cerevisiae"[organism]	returns the set of S. cerevisiae RefSeq proteins